title: R20_D1LG268

status: Public on Sep 06 2018

data_processing: Microarray data processing and analyses were performed in R software (version 3.3.1). Affymetrix CEL files were processed using the Bioconductor package oligo, with the function read.celfiles. Gene expression was normalized using the package rma, which performs background correction and quantile normalization. Bioconductor annotation packages mogene20sttranscriptcluster.db and pd.mogene.2.0.st were used to annotate at the transcript (probeset) level. Data filtering consisted of removal of probesets without mapping to gene symbols, which ultimately led to 24,996 probesets retained for differential expression analysis.

growth_protocol: Primary bone marrow cultures were prepared from 8-weeks old, C57BL/6J female mice (RRID:IMSR_JAX:000664,Jackson Laboratories, Bar Harbor, ME). The bone marrow was flushed from the femur, tibia and humerus, and then strained through a 70 μm cell strainer. The flushed cells were diluted in MSC media (α-MEM containing 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.25 μg/ml amphotericin B), and cells from 2–4 animals were pooled and plated so that each pool represented “n” experiment. Cells were seeded at 6×10^6/ml in 2 ml per well in 6-well plates. Medium was replaced 5 days after plating, and differentiation was induced at day 7. Prior to the day 7 medium change, undifferentiated cells were harvested as a control for gene expression analysis.

extract_protocol: Total RNA was extracted and genomic DNA was removed using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA). Microarray analyses were performed by the Boston University Microarray and Sequencing Resource using GeneChip® Mouse Gene 2.0ST arrays (Affymetrix, Santa Clara, CA).

treatment_protocol: For microarray experiments, the medium was replaced with osteoinductive medium consisting of α-MEM, 12.5 µg/ml l-ascorbate, 8 mM β-glycerol phosphate, 0.5 µg/ml insulin, 10 nM dexamethasone, 100 U/ml penicillin, 100 μg/ml streptomycin. Upon addition of differentiation medium, cells received no treatment (naïve) or were dosed with vehicle (DMSO, 0.1% final concentration), rosiglitazone (Rosi, 100 nM), LG100268 (LG268, 100 nM) or TBT (80 nM).

tag: strain

value: 8-weeks old

value: female

value: Primary mouse bone marrow mesenchymal stromal cells differentiated for osteogenesis

tag: cell status

value: Differentiated and exposed to chemical for 1 day


title: R20_D4TPhP

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

tag: age

tag: gender

tag: cell type

value: Differentiated and exposed to chemical for 4 days


title: R20_D4TBT


title: R20_D4Vh


title: R20_D1MEHP


title: R20_D4LG268


title: R20_DONaive

value: Undifferentiated cells


title: R20_D1TPhP


title: R19_D4LG268


title: R19_D4TBT


title: R19_D4Vh


title: R20_D4Rosi


title: R20_D1TBT


title: R20_D4MEHP


title: R19_D4MEHP


title: R19_D4TPhP


title: R20_D1Vh


title: R19_D4Rosi


title: R19_D1MEHP


title: R12_D4TPhP


title: R19_D1TPhP


title: R15_D1Vh


title: R19_D1Rosi


title: R19_D1LG268


title: R15_D4Rosi


title: R12_D4Vh


title: R15_D4TPhP


title: R15_D1MEHP


title: R15_DONaive


title: R15_D1TBT


title: R19_D1Vh


title: R15_D4MEHP


title: R12_D4TBT


title: R15_D4Vh


title: R12_D4MEHP


title: R15_D1TPhP


title: R15_D4LG268


title: R12_D1TPhP


title: R12_D1TBT


title: R15_D1Rosi


title: R12_D1MEHP


title: R12_D4Rosi


title: R15_D4TBT


title: R19_DONaive


title: R19_D1TBT


title: R15_D1LG268


title: R12_D4LG268


title: R20_D1Rosi


title: R12_D1Rosi


title: Sample 2, estrus phase, uninfected

status: Public on Aug 27 2018

description: Gene expression data from upper genital tract tissue of estrus-phase animal treated with PBS.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor R package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezg R package (version 17.0.0).  Expression levels were adjusted using the ComBat algorithm in the sva R package (version 3.4.0), with estrous phase, treatment, and phase:treatment interaction as covariates.

source_name: upper genital tract tissue

growth_protocol: A single strain culture of Neisseria gonorrhoeae was grown overnight on a chocolate agar plate to produce a lawn of bacterial colonies. A full plate was collected into 1mL of PBS supplemented with 0.9mM CaCl2 and 0.5mM MgCl2 (PBS++, Life Technologies, Burlington, Canada). The OD550 absorbance of the bacterial suspension was measured and used to calculate the concentration of gonococci. This initial suspension was then diluted with PBS++ to produce a 5x10^8 gonococci per milliliter suspension.

extract_protocol: Tissue was placed in TRIzol and homogenized using QIAshredder tissue homogenizer kits (Qiagen Cat #79654). RNA was extracted from the tissue homogenate using an RNeasy Mini kit (Qiagen Cat #74104).

treatment_protocol: Mice of known estrous cycle phase were anesthetized via inhalation of isoflurane. Anesthetized mice were laid prone at a 45-degree angle and, using a blunted 25-gauge needle, 20ul of the infection suspension (10^7 gonococci) was delivered directly into the uterine horns. Six hours after infection, the mice were sacrificed by CO2 asphyxiation.

tag: tissue

value: upper genital tract

tag: phase

value: estrus

tag: treatment

value: PBS

tag: batch

value: batch 2


title: Sample 12, diestrus phase, uninfected

description: Gene expression data from upper genital tract tissue of diestrus-phase animal treated with PBS.

value: diestrus

value: batch 1


title: R12_D1Vh


title: Sample 19, diestrus phase, infected

description: Gene expression data from upper genital tract tissue of diestrus-phase animal treated with Neisseria gonorrhoeae.

value: Neisseria gonorrhoeae


title: R12_D1LG268


title: P+7, replicate 24L

status: Public on Aug 22 2018

description: Gene expression data from an osteocyte cell line expressing low levels of sclerostin (SOST)

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezg R package (version 17.0.0).

source_name: low sclerostin osteocyte cell line

growth_protocol: Single cell clones from Ocy454 were grown in aMEM+10%FBS+1%AA

extract_protocol: The total RNA was extracted using Qiagen Rneasy Mini kit

treatment_protocol: There was no treatment. Single-cell sorted osteocytic cell line was screened for high- and low-Sost/sclerostin expression and were cultured for 7 days at 37C.

tag: sclerostin expression

value: low SOST


title: Sample 15, diestrus phase, uninfected


title: Sample 7, estrus phase, infected

description: Gene expression data from upper genital tract tissue of estrus-phase animal treated with Neisseria gonorrhoeae.


title: Sample 5, estrus phase, infected


title: P+7, replicate 4L


title: Sample 6, estrus phase, infected


title: Sample 13, diestrus phase, uninfected


title: P+7, replicate 15H

description: Gene expression data from an osteocyte cell line expressing high levels of sclerostin (SOST)

source_name: high sclerostin osteocyte cell line

value: high SOST


title: Sample 4, estrus phase, infected


title: Sample 18, diestrus phase, infected


title: Sample 1, estrus phase, uninfected


title: P+7, replicate 12H


title: Sample 3, estrus phase, uninfected


title: Sample 16, diestrus phase, infected


title: Sample 14, diestrus phase, uninfected


title: R12_DONaive


title: Sample 17, diestrus phase, infected


title: U87-IDH1-R132H , rep1

status: Public on Jul 12 2018

description: Gene expression data from U-87 MG cells with an IDH1-R132H mutation

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).

organism: Homo sapiens

source_name: U-87 MG glioblastoma cells

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: DMEM, High glucose, Pyruvate, Glutamax, 10% FBS

extract_protocol: RNA was isolated by using the Rneasy maxi kit by Qiagen.

treatment_protocol: Cells were grown in full media.

value: U87 glioblastoma cells

tag: genotype

value: IDH1-R132H mutant


title: P+7, replicate 9L


title: U87-IDH1-WT, rep1

description: Gene expression data from U-87 MG cells with wild-type IDH1

value: IDH1 wild type


title: HSC-3 Control siRNA replicate 3

status: Public on Jul 03 2018

description: Gene expression data from HSC-3 cells treated with control siRNA.

source_name: HSC-3 OSCC cell line

growth_protocol: Cells were grown at 37oC under 5% CO2 to 70% confluence in DMEM (Invitrogen) supplemented with 10% fetal bovine serum, penicillin, and streptomycin

extract_protocol: After 48-64 hours, the cells were trypsinized and harvested for RNA purification using miRNeasy Micro Kit (QIAGEN #217084)

treatment_protocol: Three separate wells (triplicate) from 6 well plates were seeded by HSC-3 and CAL27 cells (around 5x104/ well). After 12-24 hours (i.e. approximately 50% confluency), the cells were treated with either 0.1% DMSO or 10 µM ICG-001. For CTNNB1, Three separate wells (triplicate) from 6 well plates were seeded by HSC-3 cells (around 5x104/ well). After 48 hours, cells were transfected with 25 nM SMART pool ON-TARGET plus CTNNB1 siRNA (L-003482-00-0005, Dharmacon) by reverse transfection. ON-TARGET plus non-targeting Pool 25nM (D-001810-10-05, Dharmacon) was used for negative control

tag: cell line

value: Control siRNA


title: HSC-3 Control siRNA replicate 2


title: HSC-3 CTNNB1 siRNA replicate 1

description: Gene expression data from HSC-3 cells treated with siRNA targeting CTNNB1.

value: CTNNB1 siRNA


title: HSC-3 DMSO replicate 2

description: Gene expression data from HSC-3 cells treated with DMSO.

value: DMSO


title: HSC-3 CTNNB1 siRNA replicate 2


title: HSC-3 10 uM ICG-001 replicate 2

description: Gene expression data from HSC-3 cells treated with 10 uM ICG-001 in DMSO.


title: HSC-3 10 uM ICG-001 replicate 1


title: CAL27 DMSO replicate 3

description: Gene expression data from CAL27 cells treated with DMSO.

source_name: CAL27 OSCC cell line


title: CAL27 10 uM ICG-001 replicate 2

description: Gene expression data from CAL27 cells treated with 10 uM ICG-001 in DMSO.


title: CAL27 10 uM ICG-001 replicate 1


title: HSC-3 DMSO replicate 3


title: HSC-3 Control siRNA replicate 1


title: CAL27 DMSO replicate 2


title: HSC-3 CTNNB1 siRNA replicate 3


title: CAL27 10 uM ICG-001 replicate 3


title: HSC-3 10 uM ICG-001 replicate 3


title: B6-sst1S untreated 3

status: Public on May 30 2018

description: Gene expression data from macrophages of B6-sst1S untreated mice.

source_name: Macrophages from B6-sst1S mice

growth_protocol: BMDM macrophages from C57BL/6(B6) and B6-sst1S mice were grown at 37C in complete media containing 10% LCCM in TC treated 6 well plates for 4 days with media change every 2 days.

extract_protocol: Total RNA was isolated using the RNeasy plus Mini Kit  according to the manufacturer's instructions.

treatment_protocol: BMDM were treated with 10ng/ml TNFα for 18hrs. After that cells were harvested in RLT plus lysis buffer.

value: untreated


title: CAL27 DMSO replicate 1


title: B6-sst1S untreated 1


title: HSC-3 DMSO replicate 1


title: B6-sst1S TNFa 1

description: Gene expression data from macrophages of B6-sst1S mice treated with TNF-alpha.

value: TNFa


title: B6-sst1S untreated 2


title: LuCaP_189.3_Organoid_Rep2

status: Public on May 10 2018

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove reads from mouse RNA using tophat/bowtie2 and aligning to either hg19 or mm10.
Bowtie-mapped reads were compared with Disambiguate and human-reads were converted back to FASTQ files.
Paired-end human-only FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, 75th percentile-normalized TPM estimate of expression

source_name: LuCaP 189.3 Organoid

growth_protocol: LuCaP tumors were grown in mice and then as organoids.

extract_protocol:
Total RNA was extracted from fresh organoids using the Qiagen AllPrep DNA/RNA mini kit
rRNA-depleted RNA was converted into cDNA and assembled into libraries using Illumina TruSeq v2 kit with standard protocols

treatment_protocol: Organoids were passaged.

tag: subject id

value: LuCaP 189.3

value: male

tag: replicate

value: PDX-derived organoid


title: LuCaP_189.3_Organoid_Rep1


title: LuCaP_23.1_Organoid_Rep2

source_name: LuCaP 23.1 Organoid

value: LuCaP 23.1


title: LuCaP_23.1_Organoid_Rep1


title: LuCaP_170.2_Organoid_Rep2

source_name: LuCaP 170.2 Organoid

value: LuCaP 170.2


title: B6 TNFa 2

description: Gene expression data from macrophages of B6 mice treated with TNF-alpha.

source_name: Macrophages from C57/BL6(B6) mice


title: LuCaP_167_Organoid_Rep2

source_name: LuCaP 167 Organoid

value: LuCaP 167


title: LuCaP_170.2_Organoid_Rep1


title: B6 TNFa 1


title: B6-sst1S TNFa 3


title: B6-sst1S TNFa 2


title: B6 TNFa 3


title: B6 untreated 2

description: Gene expression data from macrophages of B6 untreated mice.


title: B6 untreated 1


title: LuCaP_167_Organoid_Rep1


title: B6 untreated 3


title: ES_E4_Mtf2_Rep2

status: Public on Apr 09 2018

city: Nijmegen

first: Gert

middle: Jan

last: Veenstra

state: Not US or Canada

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: ChIP seq for Mtf2 in E4 mESC.

library_source: genomic

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads were aligned to the mouse genome (mm10) using bwa 0.7.10-r789 with default settings.
Peaks were called with macs2-2.7 using the --no-model and manual shift provided with the –extsize parameter. The extent of shifting was calculated with spp R library (https://github.com/hms-dbmi/spp). A q value threshold of 0.001 was applied in all cases and either the --call-summits (Mtf2 and Ezh2) or the --broad (H3K27me3 and H3K4me3) parameters was used.
Reproducible peaks among ChIPseq replicates were identified using MAnorm.
Coverage files in bigWig format were created using bam2bw (https://bitbucket.org/simonvh/bam2bw/) with the -e auto and -c parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Common peaks identified with Manorm in BED format.
Supplementary_files_format_and_content: Coverage files in bigWig format.

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: mESC were grown in serum+LIF medium as described in Marks, H. et al. (doi:10.1016/j.cell.2012.03.026).

extract_protocol:
Chromatin extraction and ChIP were performed as described in Kloet, S. L. et al. (doi:10.1038/nsmb.3248).
Five ng/sample of ChIP were prepared for sequencing with the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using E-gel (Invitrogen) and sequenced on an Illumina NextSeq machine to obtain 75bp reads.

value: Jarid2 KO

tag: antibody

tag: antibody vendor/catalog#

value: Aviva System Biology ARP34292, lot QC49692-42166


title: ES_Mtf2GT_Jarid2_Rep2

description: ChIP seq for Jarid2 in Mtf2 GT/GT mESC.

value: Mtf2 GT/GT

value: Gene trapping cassette disrupting Mtf CDS

value: Novus Biologicals NB100-2214, Lot E2


title: day 36-SC- C

status: Public on Apr 12 2018

description: Gene expression data from SCGB3A2- RUES2 cells at day 36.

source_name: RUES2 cells

growth_protocol: Directed differentiation via definitive endoderm to anterior foregut endoderm and lung progenitors. Lung progenitors were sorted on CD47 expression and differentiated in low-Wnt media to promote airway epithelial differentiation, at which point SCGB3A2+ and SCGB3A2- cells were sorted. Cells were harvested at defined timepoints between day 0 and day 36.

extract_protocol: RNA was extracted with QIAzol and the Qiagen RNeasy kit according to the manufacturer's protocol.

tag: group

value: day 36 SCGB3A2-


title: ES_Mtf2GT_H3K27me3_Rep2

description:
ChIP seq for H3K27me3 in E14 mESC
ES_Mtf2GT_H3K27me3_MAnorm_unbiased.bed


title: ES_E4_Mtf2_Rep1

description: ChIP seq for Mtf2 in E4 mESC.


title: EEDKO_Mtf2

description: ChIP seq for Mtf2 in Eed -/- mESC.

value: EED -/-

value: EED KO


title: ES_Mtf2GT_Jarid2_Rep1

description: ChIP seq for Jarid2 in Mtf2 GT/GT mESC.


title: day 36-SC+ B

description: Gene expression data from SCGB3A2+ RUES2 cells at day 36.

value: day 36 SCGB3A2+


title: day 36-SC- B


title: day 36-SC+ C


title: day 36-SC+ A


title: E14_Input

description: input DNA

value: WT


title: E14_Jarid2_Rep1

description: ChIP seq for Jarid2 in E14 mESC.


title: day 36-SC- A


title: day 22 A

description: Gene expression data from RUES2 cells at day 22.

value: day 22


title: ES_Mtf2GT_H3K27me3_Rep1


title: day 22 C


title: day 15-47hi B

description: Gene expression data from CD47hi RUES2 cells at day 15.

value: day 15 CD47hi


title: day 0 C

description: Gene expression data from RUES2 cells at day 0.

value: day 0


title: day 15-47hi C


title: ES_Mtf2GT_Ezh2_Rep2

description:
ChIP seq for Ezh2 in E14 mESC
ES_Mtf2GT_Ezh2_MAnorm_unbiased.bed

value: Diagenode C15410039, lot 003


title: day 0 A


title: E14_Jarid2_Rep2

description: ChIP seq for Jarid2 in E14 mESC.


title: ES_Mtf2GT_Ezh2_Rep1


title: E14_Mtf2_Rep2

description:
ChIP seq for Mtf2 in E14 mESC
E14_Mtf2_MAnorm_unbiased.bed


title: E14_Mtf2_Rep1


title: E14_H3K4me3_Rep2

description:
ChIP seq for H3K4me3 in E14 mESC
E14_H3K4me3_MAnorm_unbiased.bed

value: Abicam Ab858, lot GR240214-4


title: E14_H3K27me3_Rep2

description:
ChIP seq for H3K27me3 in E14 mESC
E14_H3K27me3_MAnorm_unbiased.bed


title: E14_H3K27me3_Rep1


title: E14_H3K4me3_Rep1


title: E14_Ezh2_Rep1

description:
ChIP seq for Ezh2 in E14 mESC
E14_Ezh2_MAnorm_unbiased.bed


title: E14_Ezh2_Rep2


title: Ezh2rescue_H3K27me1_ChIP_cor

status: Public on Jan 12 2018

city: Copenhagen N

first: Jonas

middle: Westergaard

last: Hojfeldt

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Trimmed with Trimmomatic: SLIDINGWINDOW across 4 bases, average quality required 2
Alligned with STAR 2.4.0, built-in index mm10, default parameters
htseq-count, union mode, non-stranded, minimum alignment quality 10
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-Seq] tabular files contain gene counts
[ChIP-Seq]  No processed data.  Aligned BAM-files have been imported and analyzed/visualized within a software called Easeq (Easeq.net<http://Easeq.net>,  Nature Structural & Molecular Biology Volume 23 No 4 (April 2016), 349-357)).

source_name: Embryonic stem cells

growth_protocol: Cells grown on gelatin in 2i media

extract_protocol: NEBNext Ultra protocol (NEB, E7370S)

tag: strain

tag: chip antibody

value: H3K27me1 (Takara, mouse mAb, MABI0321)

value: EZH2 rescue


title: P2_Non-Mes_Igf2-KO-rep3

status: Public on Dec 31 2017

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC07

data_processing:
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameters
FPKM values and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Fastq files for raw data and raw count values in tab-delimted txt format

source_name: pancreas

extract_protocol:
P2 pancreata were dissected and dissociated into single cells using trypsin-EDTA. Cells were then isolated by FACS into mesenchymal cells (YFP+) and non-mesenchymal cells (YFP-). Total RNA was extracted using RNEasy Micro kit (Qiagen-74004)
2ng total RNA was whole-transcriptome amplified using the Ovation RNA–seq System V2 (NuGEN). 2 ?g amplified cDNA was then used to prepare the RNA–seq libraries using the Ovation Rapid DR Library System (NuGEN).
RNA-seq using Illumina HiSeq 2500 system for single-end 50-bp sequencing

value: non-mesenchymal cells

tag: age

value: post natal day 2

value: Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)


title: P2_Non-Mes_Igf2-KO-rep1

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC05


title: P2_Non-Mes_Igf2-KO-rep2

description:
Mus musculus post natal day 2 non-mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC06


title: P2_Non-Mes_Igf2-C-rep4

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC16

value: Controls 1 (Igf2+/+; Nkx3.2Cre/+)


title: C021-EPZ-5676-A

status: Public on Feb 14 2018

description: Gene expression data from C021 cells treated with EPZ-5676.

source_name: C021 melanoma cell line

growth_protocol: Cells were grown in Medium 254 (Thermo Fisher M-254-500) with the addition of Human Melanocyte Growth Supplement (HMGS).

extract_protocol: RNA was extracted using the QIAgen RNeasy Mini Kit according to the manufacturer's protocol.

treatment_protocol: C021 cells (DOT1L wild type) were treated with DMSO or the DOT1L inhibitor EPZ-5676 (5 µM), and C025 melanoma cells (DOT1L mutant) were treated with DMSO. After 48 hours of treatment the cells were exposed to UVB (100J/m2), and 3 hours later RNA was extracted from the cells.

value: melanoma

tag: dot1l genotype

value: wildtype


title: P2_Non-Mes_Igf2-C-rep3

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC15

tag: cell type


title: C025-C

description: Gene expression data from C025 cells treated with DMSO vehicle.

source_name: C025 melanoma cell line

value: mutant

value: DMSO vehicle


title: C021-C

description: Gene expression data from C021 cells treated with DMSO vehicle.


title: C021-B


title: C025-B


title: C021 shDOT1L 1

description: Gene expression data from C021 cells treated with a shRNA targeting DOT1L.

treatment_protocol: C021 melanoma cells treated with shRNA against DOT1L or scrambled control were exposed to UVB (100J/m2), and 3 hours later RNA was extracted from the cells.

tag: shRNA


title: C021 scrambled 2

description: Gene expression data from C021 cells treated with scrambled control shRNA.

value: scrambled control


title: C021-EPZ-5676-B


title: C021 scrambled 1


title: C021 scrambled 3


title: C021-A


title: C021-EPZ-5676-C


title: Ezh2rescue_H3K27me3_ChIP_cor

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)


title: P2_Non-Mes_Igf2-C-rep2

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC14


title: JG-98 2

status: Public on Jan 11 2018

description: JG 2

growth_protocol: MCF7 cells were grown on plates in DMEM + 10%FBS till 40% density.

extract_protocol: mRNA was extracted using the Qiagen kit.

treatment_protocol: Cells were treated with 2 micromoles of JG-98 for 24 hours.

tag: treated with

value: 2 uM JG-98 for 24hrs


title: P2_Mes_Igf2-KO-rep4

description:
Mus musculus post natal day 2 mesenchymal cells-Mutants 1 (Igf2+/fl; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC04

value: mesenchymal cells


title: Untreated 2

description: Untreated 2

value: none (untreated)


title: C021 shDOT1L 3


title: Untreated 1

description: Untreated 1


title: JG-98 1

description: JG 1


title: Untreated 3

description: Untreated 3


title: JG-98 3

description: JG 3


title: C025-A

tag: treatment


title: C021 shDOT1L 2


title: P2_Non-Mes_Igf2-C-rep1

description:
Mus musculus post natal day 2 non-mesenchymal cells-Controls 1 (Igf2+/+; Nkx3.2Cre/+)
data1.tsv
SLX-8880.L2DRBC13


title: Stat5fl/fl, Nestin-Cre+EA (421)_Epi-WAT

status: Public on Sep 14 2017

city: Nanjing

first: Bing-Mei

last: Zhu

state: Jiangsu

address: 138 Xianlin Avenue

country: China

institute: Nanjing university of Chinese Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat (v2.0.6) followed by Cufflinks
Differential gene and transcript expression analysis using a protocol from Cole Trapnell et al., nature protocols, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Epi-WAT

extract_protocol:
Hypothalamus and Epi-WAT were removed, flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Stat5fl/fl, Nestin-cre

tag: tissue

value: epididymal white adipose tissue

tag: gender

value: male


title: Stat5fl/fl, Nestin-Cre (184)_Epi-WAT

tag: genotype


title: BMP4+Wnt3A mCherry+ 2

status: Public on Oct 31 2017

description: Gene expression data from Nkx2.1+ embryonic stem cells treated with BMP4+Wnt3A (directed towards a lung lineage).

growth_protocol: Mouse ESCs (carrying an mCherry reporter targeted to the Nkx2-1 3'UTR) were differentiated according to the methods detailed in our publicatin (Serra, Kotton et al, 2017. In serum-free conditions the cells were first differentiated as embryoid bodies in suspension culture into definitive endoderm with Activin A, followed by anterior foregut endoderm by day 6, and then each sample in monolayered 2D culture on gelatin-coated plates was treated on days 6-14 with the growth factor supplements to be tested for each condition (BMP4+FGF2 for thyroid; and BMP4+Wnt3a for lung.)

extract_protocol: Three biological replicates for each indicated condition were processed on day 14 of differentiation for sorting of mESC-derived cells based on expression of the Nkx2-1mCherry reporter by flow cytometry. Total RNA was extracted using miRNeasy Mini Kit (Qiagen). RNA extracts from each sample were processed for analysis of gene expression

treatment_protocol: Three independent biological replicates from each of the 2 differentiation conditions (either thyroid specification with BMP4+FGF2 or lung specification with BMP4+Wnt3a) were prepared, and cells on Day14 of differentiation were sorted: Nkx2-1mCherry+ vs. Nkx2-1mCherry-.

tag: lineage

value: lung

value: mCherry+


title: Stat5fl/fl, Nestin-Cre (200)_Epi-WAT


title: Stat5fl/fl (W4)_Epi-WAT


title: Stat5fl/fl (W1)_Epi-WAT


title: Stat5fl/fl (W3)_Epi-WAT


title: Stat5fl/fl, Nestin-Cre+EA (456)_Epi-WAT


title: Stat5fl/fl (W2)_Epi-WAT


title: Stat5fl/fl, Nestin-Cre+EA (T4)_hypothalamus

source_name: hypothalamus

value: hypothalamus


title: Stat5fl/fl, Nestin-Cre+EA (456)_hypothalamus


title: Stat5fl/fl, Nestin-Cre+EA (451)_hypothalamus


title: BMP4+Wnt3A mCherry+ 3


title: Stat5fl/fl, Nestin-Cre (182)_hypothalamus


title: BMP4+Wnt3A mCherry- 1

description: Gene expression data from Nkx2.1- embryonic stem cells treated with BMP4+Wnt3A (directed towards a lung lineage).

value: mCherry-


title: BMP4+FGF2 mCherry+ 3

description: Gene expression data from Nkx2.1+ embryonic stem cells treated with BMP4+FGF2 (directed towards a thyroid lineage).

value: thyroid


title: Wild type atria

status: Public on Oct 25 2017

description: Gene expression data from pooled atria of seven 2-month-old Mef2a+/+ mice.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor R package and the Brainarray mogene10stv1mmentrezg R package (version 13.0.0).

source_name: atria

growth_protocol: Mef2a KO and WT mice were aged normally to early adulthood under the care of the Boston University Charles River Campus Laboratory Animal Care Facility (LACF). Mice were used for this analysis at 2 months of age.

extract_protocol: Total RNA extraction was performed using Trizol following the manufacturer's recommendations. Total RNA was extracted from dissected cardiac chambers and pooled at equimolar concentrations to obtain four samples for microarray analysis: WT atria (N=7), KO atria (N=7), WT ventricles (N=7), and KO ventricles (N=7).

treatment_protocol: Adult Mef2a KO and WT mice were sacrificed following BU CRC LACF and IACUC policies and guidelines. Cardiac chambers were dissected, rinsed in phosphate-buffered saline, and prepared for total RNA extraction.

value: Mef2a wild type

value: atria


title: BMP4+Wnt3A mCherry- 3


title: Mef2a knockout ventricles

description: Gene expression data from pooled ventricles of seven 2-month-old Mef2a-/- mice.

source_name: ventricles

value: Mef2a knockout

value: ventricles


title: Stat5fl/fl (T3)_hypothalamus


title: BMP4+Wnt3A mCherry- 2


title: BMP4+FGF2 mCherry+ 1


title: Wild type ventricles

description: Gene expression data from pooled ventricles of seven 2-month-old Mef2a+/+ mice.


title: BMP4+FGF2 mCherry- 2

description: Gene expression data from Nkx2.1- embryonic stem cells treated with BMP4+FGF2 (directed towards a thyroid lineage).


title: BMP4+Wnt3A mCherry+ 1


title: BMP4+FGF2 mCherry- 1


title: BMP4+FGF2 mCherry+ 2


title: BMP4+FGF2 mCherry- 3


title: Mef2a knockout atria

description: Gene expression data from pooled atria of seven 2-month-old Mef2a-/- mice.


title: Stat5fl/fl (T2)_hypothalamus


title: Stat5fl/fl (T1)_hypothalamus


title: Stat5fl/fl, Nestin-Cre (184)_hypothalamus


title: Stat5fl/fl (262)_hypothalamus


title: Shoot after salt treatment 2

status: Public on Aug 10 2017

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
The tagged libraries were sequenced using a HiSeq 2500 (Illumina Inc.).
Trimmomatic (Bolger et al., 2014) was used to discard low-quality reads, trim adaptor sequences, trim low quality nucleotides at the beginning or end of the read (PHRED33 quality score of less than 3), and discard short reads (under 21 nt).
The retained high-quality reads were mapped to the C. sativa reference genome and transcripts available in the NCBI C. sativa release 100 (JFZQ00000000.1, Kagale et al., 2014) using STAR (Dobin et al, 2012)
For each gene, normailization for library size was performed by dividing the counts by the library size following the method described by Anders and Huber, 2010 to yield CPM
Further normalization was performed using DESeq to approximate a negative binomial distribution.
The differential expression analysis of digital gene expression data software (edgeR) was used to calculate expression changes between libraries (Chen et al., 2014).  The Biological Coefficient of Variation (BCV) value was set to 2 according to the software's instructions.  Expression changes were said to be significant if the multiple test corrected p-value and the false discovery rate (FDR) were ≤ 0.05 and the absolute value of  log 2 CPM was higher than 1.
Genome_build: C. sativa release 100 (JFZQ00000000.1)
Supplementary_files_format_and_content: MS Excel spreadsheet with the genes as rows and the samples as columns.  Each replicate is it's own column.

molecule: polyA RNA

organism: Camelina sativa

source_name: Whole Shoot

growth_protocol: Camelina sativa cv. DH55 seeds were sown in soil-less potting mixture (Stringham, 1971) in 10 x 10 x 8 cm square pots.  Plants were grown in a controlled growth chamber (16 h light/8 h dark, 20/17°C) supplemented with halogen lights.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen Inc.)
cDNA libraries were prepared using the TruSeq Stranded mRNA and Total RNA Library Prep kits with TruSeq LT indexed adaptors (Illumina Inc.).

treatment_protocol: NaCl solutions at 192 mM were prepared to obtain a solution with an electrical conductivitie (EC) of 15 dSm-1 at 20°C. 50 ml of tap water (EC 1,248 µSm-1) was applied daily to each pot and replaced with 50 ml of saline solution (EC 15 dSm-1) 7 days after sowing.  The accumulation of salt in the pots was controlled by draining and the EC of the drained water was measured weekly.  Shoot and root matter was harvested 21 days after the initial salt treatment just before the plants began to bolt.

tag: infraspecific name

tag: developmental stage

value: 28 days after planting

value: Whole Shoot


title: Shoot after salt treatment 3


title: aB_Mycflfl_CreER_GROseq

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description: Gro-Seq

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
MNaseI-Seq_density: quality and adapter trimming: fqtrim-v0.94/fqtrim -A 125 -q 20  -f adapters -p22 -P33
MNaseI-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --local --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 22
MNaseI-Seq_density: filtering and sorting(uniquely aligned reads): samtools-0.1.19/samtools view -Sb | samtools sort -@ 20 -m 1G
MNaseI-Seq_density: merging: samtools-1.1/samtools merge
MNaseI-Seq_density: raw tag density: custom program, density estimate of nucleosome dyads genome wide, wigToBigWig -fixedSummaries -keepAllChromosomes
MNaseI-Seq_density: tag ratio between input and control: ucsc-314/wiggletools ratio input.bw control.bw | wigToBigWig
MNaseI-Seq_density: aB_minus_rB density: ucsc-314/wiggletools diff aB_ratio.bw rb_ratio.bw | wigToBigWig
ATAC-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --end-to-end --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 16
ATAC-Seq_density: filtering (remove random contigs): sed '/random/d;/chrUn/d'
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19/samtools view -S -b -F4
ATAC-Seq_density: merging: samtools-0.1.19/samtools merge && samtools sort -m 10G
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: contact_matrix: 5kb contact matrix was generated from the filtered alignment
HiC-Seq: loop call: juicebox hiccups -m 500 -r 5000 -k KR -f 0.1 -p 4 -i 10 -t 0.01,1.5,1.75,2 -d 20000
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: Gro-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: MNaseI-Seq: .wig files tag density ratio difference between activated and resting B cells (ratio)
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: HiC-Seq: tab seperated loop coordinates with other information

source_name: activated B cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing.  Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).                                                                                HiC-Seq:  we used the same protocol for situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)                                                                                ATAC-Seq: we followed the protocol at Buenrostri J.D. et al. (Nat Methods, 2013 Dec; 10(12):1213-8)                 Gro-seq:  Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the  RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated  with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and  purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was  dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation.  Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz  Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis  was performed the next day as described in (Wang et al., 2011). However, for reverse  transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT  GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA  TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England  Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and  RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA  fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel  (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The  final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA  clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                MNase-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina)                                                        ATAC-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                   HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                    Gro-seq: 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).

treatment_protocol: Gro-seq: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

value: spleen

tag: activation time


title: Shoot after salt treatment 1


title: shMef2C 3

status: Public on Sep 08 2017

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting Mef2c.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Rat Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray ragene20stmmentrezg R package (version 17.0.0).

organism: Rattus norvegicus

growth_protocol: NRVMs were extracted from neonatal rat hearts, and cultured in DMEM + 10% FBS/pen+strep+L-glut for 24h. High-serum media was then replaced with DMEM + 0.5x Nutridoma SP for remainder of experiment.

extract_protocol: Total RNA from NRVMs was preparted by TRIzol© isolation (Invitrogen). A single biological replicate was used per microarray.

treatment_protocol: 24h after transition to DMEM + 0.5x ND, NRVMs were trnasduced with a single adenovirus containing an shRNA targeting a single MEF2 factor, or the negative control shLacZ.


title: shMef2A 1

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting Mef2a.


title: shMef2A 3

value: neonatal rat ventricular myocytes (NRVMs)


title: shLacZ 3

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting lacZ.

source_name: shLacZ

value: shLacZ


title: shMef2C 2


title: shMef2D 2

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting Mef2d.


title: shMef2A 2


title: shLacZ 2


title: shMef2C 1


title: shMef2D 1


title: Knockout sample 3

status: Public on Aug 17 2017

description: Gene expression data from alveolar macrophages of Zcchc6-/- mice.

source_name: Alveolar macrophages

extract_protocol: Isolated cells were centrifuged at 300 x g for 5 minutes at 4°C, then cytocentrifuged and stained with Diff-Quick (Dade-Behring) to perform cell differential analysis. Total RNA was prepared using Qiazol, and purified using an RNAeasy column (Qiagen).

treatment_protocol: Lungs were lavaged with ice-cold PBS 10 times in 1 mL increments.


title: Wildtype sample 3

description: Gene expression data from alveolar macrophages of Zcchc6+/+ mice.


title: Wildtype sample 2


title: shMef2D 3


title: Wildtype sample 1


title: Knockout sample 2


title: Donor N4, TGFb+DMF

status: Public on Jun 22 2017

description: Gene expression data from dermal fibroblasts treated with TGFb+DMF for 24h.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0) (http://mbni.org/customcdf/17.0.0/entrezg.download/hugene20st_Hs_ENTREZG_17.0.0.zip).

source_name: fibroblasts isolated from skin biopsy

growth_protocol: Human dermal skin fibroblasts were grown to confluency in DMEM+10%FBS.  Medium was changed to serum free 16h before treatment.

extract_protocol: TRIzol reagent and ethanol precipitation

treatment_protocol: 24h treatment with 50uM dimethyl fumarate (DMF,D) or DMSO(C) +/- 2.5ng/ml TGFb(T)

tag: donor

value: TGFb+DMF


title: Donor N28, TGFb

description: Gene expression data from dermal fibroblasts treated with TGFb+DMSO for 24h.

value: TGFb+DMSO


title: Donor N28, DMF

description: Gene expression data from dermal fibroblasts treated with DMF for 24h.

value: DMF


title: aB_wt_GROseq

description: Gro-Seq

value: WT


title: Donor N1, TGFb


title: Donor N4, TGFb


title: shLacZ 1


title: Donor N28, TGFb+DMF


title: MB_SubtypeStudy_55761_methylation

status: Public on Jun 13 2017

type: genomic

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

institute: The Hospital for Sick Children

hyb_protocol: Standard Illumina Protocol

scan_protocol: Samples were processed as per manufacturer’s instructions. Raw data files (.idat) generated by the Illumina iScan array scanner

data_processing: Raw data was processed in R using the minfi (v1.6.0) and IlluminaHumanMethylation450kmanifest (v0.4.0) R Bioconductor packages. We checked all samples for unexpected genotype matches by pairwise correlation of the 65 genotyping probes on the 450k arrays, allowing us to remove remaining duplicates. We ran the detectionP function from the minfi package to identify probes and samples with low quality. Samples were removed if more than 1% of their probes had a p-value above 0.01 and probes were removed if their p-value was above 0.01 in at least 5% of samples.  We removed probes on sex chromosomes as well as those located on or close to known single nucleotide polymorphisms (SNP). We retained a total of 321,174 probes for the analysis. The data was normalized using the SWAN method (Makismovic et al., Genome Biology 2012) as implemented in the minfi package.  The matrix of normalized beta values is available on the series record.

label: Cy3 and Cy5

source_name: Fresh frozen

label_protocol: Standard Illumina Protocol

extract_protocol: Snap frozen tissue was digested overnight at 55 C with Proteinase K and SDS in TE. DNA was extracted from the digest with phenol-chloroform and precipitated with ammonium acetate and ethanol. The pellet was resuspended in TE buffer. Bisulfite conversion was carried out according to the manufacturer's instructions for the Zymo EZ DNA Methylation Kit

value: medulloblastoma

tag: type

value: primary tumor

tag: subgroup


title: Knockout sample 1


title: MB_SubtypeStudy_55757_methylation


title: MB_SubtypeStudy_55763_methylation


title: MB_SubtypeStudy_55762_methylation


title: MB_SubtypeStudy_55758_methylation


title: MB_SubtypeStudy_55753_methylation


title: MB_SubtypeStudy_55751_methylation


title: Donor N4, DMF


title: Donor N1, DMF


title: MB_SubtypeStudy_55755_methylation


title: MB_SubtypeStudy_55749_methylation


title: MB_SubtypeStudy_55747_methylation


title: MB_SubtypeStudy_55746_methylation


title: MB_SubtypeStudy_55744_methylation


title: MB_SubtypeStudy_55750_methylation


title: Donor N4, control

description: Gene expression data from dermal fibroblasts treated with DMSO for 24h.

value: DMSO


title: MB_SubtypeStudy_55741_methylation


title: Donor N1, TGFb+DMF


title: MB_SubtypeStudy_55743_methylation


title: Donor N28, control


title: Donor N1, control


title: MB_SubtypeStudy_55740_methylation


title: Knockdown of ERG and FLI1

description: Gene expression data from HPAECs treated with siRNAs targeting ERG and FLI1.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0) (http://mbni.org/customcdf/16.0.0/entrezg.download/hugene20st_Hs_ENTREZG_16.0.0.zip).

source_name: cultured human pulmonary arterial endothelial cells (HPAECs)

growth_protocol: HPAECs were grown to 50% confluency in EGM (Lonza) before transfection.

extract_protocol: TRIzol extraction with ethanol precipitation

treatment_protocol: siRNA against ERG and FLI1 were transfected into cells using lipofectamine RNAiMAX according to the manufacturer's protocol.

tag: sirna targets

value: ERG and FLI1


title: MB_SubtypeStudy_55732_methylation


title: MB_SubtypeStudy_55724_methylation


title: MB_SubtypeStudy_55726_methylation


title: MB_SubtypeStudy_55725_methylation


title: MB_SubtypeStudy_55720_methylation


title: Scrambled siRNA

description: Gene expression data from HPAECs treated with scrambled siRNA control.

value: scrambled control


title: MB_SubtypeStudy_55713_methylation


title: MB_SubtypeStudy_55711_methylation


title: MB_SubtypeStudy_55716_methylation


title: MB_SubtypeStudy_55718_methylation


title: MB_SubtypeStudy_55715_methylation


title: MB_SubtypeStudy_55709_methylation


title: MB_SubtypeStudy_55714_methylation


title: MB_SubtypeStudy_55703_methylation


title: MB_SubtypeStudy_55701_methylation


title: MB_SubtypeStudy_55704_methylation


title: MB_SubtypeStudy_55696_methylation


title: MB_SubtypeStudy_55699_methylation


title: MB_SubtypeStudy_55691_methylation


title: MB_SubtypeStudy_55685_methylation


title: MB_SubtypeStudy_55688_methylation


title: MB_SubtypeStudy_55687_methylation


title: MB_SubtypeStudy_55693_methylation


title: MB_SubtypeStudy_55678_methylation


title: MB_SubtypeStudy_55671_methylation


title: MB_SubtypeStudy_55674_methylation


title: MB_SubtypeStudy_55677_methylation


title: MB_SubtypeStudy_55663_methylation


title: MB_SubtypeStudy_55692_methylation


title: MB_SubtypeStudy_55666_methylation


title: MB_SubtypeStudy_55659_methylation


title: MB_SubtypeStudy_55658_methylation


title: MB_SubtypeStudy_55655_methylation


title: MB_SubtypeStudy_55708_methylation


title: MB_SubtypeStudy_55653_methylation


title: MB_SubtypeStudy_55650_methylation


title: MB_SubtypeStudy_55651_methylation


title: MB_SubtypeStudy_55661_methylation


title: MB_SubtypeStudy_55706_methylation


title: MB_SubtypeStudy_55645_methylation


title: MB_SubtypeStudy_55643_methylation


title: MB_SubtypeStudy_55641_methylation


title: MB_SubtypeStudy_55636_methylation


title: MB_SubtypeStudy_55635_methylation


title: MB_SubtypeStudy_55637_methylation


title: MB_SubtypeStudy_55634_methylation


title: MB_SubtypeStudy_55633_methylation


title: MB_SubtypeStudy_55665_methylation


title: MB_SubtypeStudy_55627_methylation


title: MB_SubtypeStudy_55626_methylation


title: MB_SubtypeStudy_55623_methylation


title: MB_SubtypeStudy_55629_methylation


title: MB_SubtypeStudy_55614_methylation


title: MB_SubtypeStudy_55613_methylation


title: MB_SubtypeStudy_55609_methylation


title: MB_SubtypeStudy_55646_methylation


title: MB_SubtypeStudy_55611_methylation


title: MB_SubtypeStudy_55599_methylation


title: MB_SubtypeStudy_55600_methylation


title: MB_SubtypeStudy_55598_methylation


title: MB_SubtypeStudy_55594_methylation


title: MB_SubtypeStudy_55590_methylation


title: MB_SubtypeStudy_55591_methylation


title: MB_SubtypeStudy_55593_methylation


title: MB_SubtypeStudy_55584_methylation


title: MB_SubtypeStudy_55583_methylation


title: MB_SubtypeStudy_55588_methylation


title: MB_SubtypeStudy_55581_methylation


title: MB_SubtypeStudy_55579_methylation


title: MB_SubtypeStudy_55574_methylation


title: MB_SubtypeStudy_55573_methylation


title: MB_SubtypeStudy_55576_methylation


title: MB_SubtypeStudy_55568_methylation


title: MB_SubtypeStudy_55577_methylation


title: MB_SubtypeStudy_55567_methylation


title: MB_SubtypeStudy_55569_methylation


title: MB_SubtypeStudy_55572_methylation


title: MB_SubtypeStudy_55618_methylation


title: MB_SubtypeStudy_55562_methylation


title: MB_SubtypeStudy_55558_methylation


title: MB_SubtypeStudy_55560_methylation


title: MB_SubtypeStudy_55557_methylation


title: MB_SubtypeStudy_55587_methylation


title: MB_SubtypeStudy_55559_methylation


title: MB_SubtypeStudy_55555_methylation


title: MB_SubtypeStudy_55554_methylation


title: MB_SubtypeStudy_55548_methylation


title: MB_SubtypeStudy_55547_methylation


title: MB_SubtypeStudy_55542_methylation


title: MB_SubtypeStudy_55533_methylation


title: MB_SubtypeStudy_55544_methylation


title: MB_SubtypeStudy_55537_methylation


title: MB_SubtypeStudy_55541_methylation


title: MB_SubtypeStudy_55570_methylation


title: MB_SubtypeStudy_55564_methylation


title: MB_SubtypeStudy_55566_methylation


title: MB_SubtypeStudy_55529_methylation


title: MB_SubtypeStudy_55527_methylation


title: MB_SubtypeStudy_55532_methylation


title: MB_SubtypeStudy_55515_methylation


title: MB_SubtypeStudy_55552_methylation


title: MB_SubtypeStudy_55517_methylation


title: MB_SubtypeStudy_55540_methylation


title: MB_SubtypeStudy_55522_methylation


title: MB_SubtypeStudy_55514_methylation


title: MB_SubtypeStudy_55518_methylation


title: MB_SubtypeStudy_55511_methylation


title: MB_SubtypeStudy_55510_methylation


title: MB_SubtypeStudy_55509_methylation


title: MB_SubtypeStudy_55513_methylation


title: MB_SubtypeStudy_55496_methylation


title: MB_SubtypeStudy_55508_methylation


title: MB_SubtypeStudy_55501_methylation


title: MB_SubtypeStudy_55506_methylation


title: MB_SubtypeStudy_55539_methylation


title: MB_SubtypeStudy_55491_methylation


title: MB_SubtypeStudy_55486_methylation


title: MB_SubtypeStudy_55478_methylation


title: MB_SubtypeStudy_55472_methylation


title: MB_SubtypeStudy_55528_methylation


title: MB_SubtypeStudy_55470_methylation


title: MB_SubtypeStudy_55475_methylation


title: MB_SubtypeStudy_55473_methylation


title: MB_SubtypeStudy_55465_methylation


title: MB_SubtypeStudy_55464_methylation


title: MB_SubtypeStudy_55463_methylation


title: MB_SubtypeStudy_55467_methylation


title: MB_SubtypeStudy_55454_methylation


title: MB_SubtypeStudy_55499_methylation


title: MB_SubtypeStudy_55451_methylation


title: MB_SubtypeStudy_55439_methylation


title: MB_SubtypeStudy_55453_methylation


title: MB_SubtypeStudy_55430_methylation


title: MB_SubtypeStudy_55426_methylation


title: MB_SubtypeStudy_55417_methylation


title: MB_SubtypeStudy_55435_methylation


title: MB_SubtypeStudy_55446_methylation


title: MB_SubtypeStudy_55438_methylation


title: MB_SubtypeStudy_55428_methylation


title: MB_SubtypeStudy_55489_methylation


title: MB_SubtypeStudy_55488_methylation


title: MB_SubtypeStudy_55414_methylation


title: MB_SubtypeStudy_55416_methylation


title: MB_SubtypeStudy_55412_methylation


title: MB_SubtypeStudy_55466_methylation


title: MB_SubtypeStudy_55403_methylation


title: MB_SubtypeStudy_55409_methylation


title: MB_SubtypeStudy_55448_methylation


title: MB_SubtypeStudy_55407_methylation


title: MB_SubtypeStudy_55476_methylation


title: MB_SubtypeStudy_55399_methylation


title: MB_SubtypeStudy_55441_methylation


title: MB_SubtypeStudy_55391_methylation


title: MB_SubtypeStudy_55379_methylation


title: MB_SubtypeStudy_55375_methylation


title: MB_SubtypeStudy_55376_methylation


title: MB_SubtypeStudy_55396_methylation


title: MB_SubtypeStudy_55402_methylation


title: MB_SubtypeStudy_55388_methylation


title: MB_SubtypeStudy_55372_methylation


title: MB_SubtypeStudy_55367_methylation


title: MB_SubtypeStudy_55369_methylation


title: MB_SubtypeStudy_55366_methylation


title: MB_SubtypeStudy_55364_methylation


title: MB_SubtypeStudy_55365_methylation


title: MB_SubtypeStudy_55371_methylation


title: MB_SubtypeStudy_55361_methylation


title: MB_SubtypeStudy_55362_methylation


title: MB_SubtypeStudy_55360_methylation


title: MB_SubtypeStudy_55359_methylation


title: MB_SubtypeStudy_55413_methylation


title: MB_SubtypeStudy_55355_methylation


title: MB_SubtypeStudy_55350_methylation


title: MB_SubtypeStudy_55349_methylation


title: MB_SubtypeStudy_55347_methylation


title: MB_SubtypeStudy_55342_methylation


title: MB_SubtypeStudy_55341_methylation


title: MB_SubtypeStudy_55336_methylation


title: MB_SubtypeStudy_55335_methylation


title: MB_SubtypeStudy_55343_methylation


title: MB_SubtypeStudy_55334_methylation


title: MB_SubtypeStudy_55346_methylation


title: MB_SubtypeStudy_55332_methylation


title: MB_SubtypeStudy_55333_methylation


title: MB_SubtypeStudy_55373_methylation


title: MB_SubtypeStudy_55328_methylation


title: MB_SubtypeStudy_55331_methylation


title: MB_SubtypeStudy_55326_methylation


title: MB_SubtypeStudy_55320_methylation


title: MB_SubtypeStudy_55358_methylation


title: MB_SubtypeStudy_55308_methylation


title: MB_SubtypeStudy_55304_methylation


title: MB_SubtypeStudy_55310_methylation


title: MB_SubtypeStudy_55318_methylation


title: MB_SubtypeStudy_55309_methylation


title: MB_SubtypeStudy_55317_methylation


title: MB_SubtypeStudy_55299_methylation


title: MB_SubtypeStudy_55303_methylation


title: MB_SubtypeStudy_55301_methylation


title: MB_SubtypeStudy_55296_methylation


title: MB_SubtypeStudy_55298_methylation


title: MB_SubtypeStudy_55306_methylation


title: MB_SubtypeStudy_55290_methylation


title: MB_SubtypeStudy_55292_methylation


title: MB_SubtypeStudy_55288_methylation


title: MB_SubtypeStudy_55283_methylation


title: MB_SubtypeStudy_55281_methylation


title: MB_SubtypeStudy_55327_methylation


title: MB_SubtypeStudy_55282_methylation


title: MB_SubtypeStudy_55274_methylation


title: MB_SubtypeStudy_55271_methylation


title: MB_SubtypeStudy_55273_methylation


title: MB_SubtypeStudy_55267_methylation


title: MB_SubtypeStudy_55269_methylation


title: MB_SubtypeStudy_55272_methylation


title: MB_SubtypeStudy_55266_methylation


title: MB_SubtypeStudy_55258_methylation


title: MB_SubtypeStudy_55256_methylation


title: MB_SubtypeStudy_55257_methylation


title: MB_SubtypeStudy_55255_methylation


title: MB_SubtypeStudy_55249_methylation


title: MB_SubtypeStudy_55252_methylation


title: MB_SubtypeStudy_55251_methylation


title: MB_SubtypeStudy_55248_methylation


title: MB_SubtypeStudy_55247_methylation


title: MB_SubtypeStudy_55250_methylation


title: MB_SubtypeStudy_55246_methylation


title: MB_SubtypeStudy_55277_methylation


title: MB_SubtypeStudy_55244_methylation


title: MB_SubtypeStudy_55241_methylation


title: MB_SubtypeStudy_55240_methylation


title: MB_SubtypeStudy_55237_methylation


title: MB_SubtypeStudy_55232_methylation


title: MB_SubtypeStudy_55233_methylation


title: MB_SubtypeStudy_55235_methylation


title: MB_SubtypeStudy_55231_methylation


title: MB_SubtypeStudy_55230_methylation


title: MB_SubtypeStudy_55259_methylation


title: MB_SubtypeStudy_55220_methylation


title: MB_SubtypeStudy_55227_methylation


title: MB_SubtypeStudy_55221_methylation


title: MB_SubtypeStudy_55226_methylation


title: MB_SubtypeStudy_55224_methylation


title: MB_SubtypeStudy_55222_methylation


title: MB_SubtypeStudy_55219_methylation


title: MB_SubtypeStudy_55218_methylation


title: MB_SubtypeStudy_55214_methylation


title: MB_SubtypeStudy_55217_methylation


title: MB_SubtypeStudy_55253_methylation


title: MB_SubtypeStudy_55203_methylation


title: MB_SubtypeStudy_55200_methylation


title: MB_SubtypeStudy_55207_methylation


title: MB_SubtypeStudy_55212_methylation


title: MB_SubtypeStudy_55199_methylation


title: MB_SubtypeStudy_55211_methylation


title: MB_SubtypeStudy_55196_methylation


title: MB_SubtypeStudy_55195_methylation


title: MB_SubtypeStudy_55194_methylation


title: MB_SubtypeStudy_55190_methylation


title: MB_SubtypeStudy_55193_methylation


title: MB_SubtypeStudy_55186_methylation


title: MB_SubtypeStudy_55185_methylation


title: MB_SubtypeStudy_55177_methylation


title: MB_SubtypeStudy_55166_methylation


title: MB_SubtypeStudy_55162_methylation


title: MB_SubtypeStudy_55168_methylation


title: MB_SubtypeStudy_55160_methylation


title: MB_SubtypeStudy_55159_methylation


title: MB_SubtypeStudy_55156_methylation


title: MB_SubtypeStudy_55155_methylation


title: MB_SubtypeStudy_55151_methylation


title: MB_SubtypeStudy_55208_methylation


title: MB_SubtypeStudy_55153_methylation


title: MB_SubtypeStudy_55149_methylation


title: MB_SubtypeStudy_55148_methylation


title: MB_SubtypeStudy_55145_methylation


title: MB_SubtypeStudy_55146_methylation


title: MB_SubtypeStudy_55140_methylation


title: MB_SubtypeStudy_55128_methylation


title: MB_SubtypeStudy_55184_methylation


title: MB_SubtypeStudy_55133_methylation


title: MB_SubtypeStudy_55125_methylation


title: MB_SubtypeStudy_55135_methylation


title: MB_SubtypeStudy_55119_methylation


title: MB_SubtypeStudy_55132_methylation


title: MB_SubtypeStudy_55158_methylation


title: MB_SubtypeStudy_55117_methylation


title: MB_SubtypeStudy_55114_methylation


title: MB_SubtypeStudy_55095_methylation


title: MB_SubtypeStudy_55098_methylation


title: MB_SubtypeStudy_55139_methylation


title: MB_SubtypeStudy_55116_methylation


title: MB_SubtypeStudy_55094_methylation


title: MB_SubtypeStudy_55090_methylation


title: MB_SubtypeStudy_55126_methylation


title: MB_SubtypeStudy_55115_methylation


title: MB_SubtypeStudy_55091_methylation


title: MB_SubtypeStudy_55086_methylation


title: MB_SubtypeStudy_55089_methylation


title: MB_SubtypeStudy_55084_methylation


title: MB_SubtypeStudy_55081_methylation


title: MB_SubtypeStudy_55134_methylation


title: MB_SubtypeStudy_55079_methylation


title: MB_SubtypeStudy_55070_methylation


title: MB_SubtypeStudy_55074_methylation


title: MB_SubtypeStudy_55101_methylation


title: MB_SubtypeStudy_55068_methylation


title: MB_SubtypeStudy_55067_methylation


title: MB_SubtypeStudy_55064_methylation


title: MB_SubtypeStudy_55057_methylation


title: MB_SubtypeStudy_55055_methylation


title: MB_SubtypeStudy_55058_methylation


title: MB_SubtypeStudy_55056_methylation


title: MB_SubtypeStudy_55059_methylation


title: MB_SubtypeStudy_55053_methylation


title: MB_SubtypeStudy_55039_methylation


title: MB_SubtypeStudy_55035_methylation


title: MB_SubtypeStudy_55042_methylation


title: MB_SubtypeStudy_55046_methylation


title: MB_SubtypeStudy_55044_methylation


title: MB_SubtypeStudy_55045_methylation


title: MB_SubtypeStudy_55029_methylation


title: MB_SubtypeStudy_55038_methylation


title: MB_SubtypeStudy_55041_methylation


title: MB_SubtypeStudy_55088_methylation


title: MB_SubtypeStudy_55027_methylation


title: MB_SubtypeStudy_55026_methylation


title: MB_SubtypeStudy_55025_methylation


title: MB_SubtypeStudy_55028_methylation


title: MB_SubtypeStudy_55024_methylation


title: MB_SubtypeStudy_55023_methylation


title: MB_SubtypeStudy_55021_methylation


title: MB_SubtypeStudy_55020_methylation


title: MB_SubtypeStudy_55018_methylation


title: MB_SubtypeStudy_55017_methylation


title: MB_SubtypeStudy_55062_methylation


title: MB_SubtypeStudy_55009_methylation


title: MB_SubtypeStudy_55004_methylation


title: MB_SubtypeStudy_55008_methylation


title: MB_SubtypeStudy_55002_methylation


title: MB_SubtypeStudy_55003_methylation


title: genomic DNA from medulloblastoma_PNET350124

status: Public on May 29 2017

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

description: medulloblastoma 420

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Arrays were processed using the R package minfi. Beta values were reported after functional normalisation. Intensity values were calculated without background subtraction and normalized to internal controls.

label: Cy5 and Cy3

source_name: genomic DNA from medulloblastoma

extract_protocol: Extraction of DNA from tumor samples was carried out using Qiagen Allprep DNA/RNA/Protein Mini kit (Fresh Frozen) and Qiagen QIAamp DNA FFPE Tissue Kit (FFPE)

tag: sample type

tag: disease state

value: primary medulloblastoma

value: M

tag: age (yrs)

tag: pathology

value: CLA


title: genomic DNA from medulloblastoma_NMB915

description: medulloblastoma 427

label_protocol: According to the manufacturer’s instructions

value: F


title: genomic DNA from medulloblastoma_PNET350161

description: medulloblastoma 421


title: genomic DNA from medulloblastoma_PNET350015

description: medulloblastoma 415


title: genomic DNA from medulloblastoma_PNET30186

description: medulloblastoma 410


title: genomic DNA from medulloblastoma_PNET350012

description: medulloblastoma 414


title: genomic DNA from medulloblastoma_PNET350217

description: medulloblastoma 423


title: genomic DNA from medulloblastoma_PNET350198

description: medulloblastoma 422


title: genomic DNA from medulloblastoma_PNET30191

description: medulloblastoma 411

value: LCA


title: genomic DNA from medulloblastoma_NMB916

description: medulloblastoma 428


title: genomic DNA from medulloblastoma_PNET30066

description: medulloblastoma 404


title: genomic DNA from medulloblastoma_PNET30015

description: medulloblastoma 400


title: genomic DNA from medulloblastoma_PNET30106

description: medulloblastoma 406


title: genomic DNA from medulloblastoma_PNET30141

description: medulloblastoma 409


title: genomic DNA from medulloblastoma_PNET30078

description: medulloblastoma 405


title: genomic DNA from medulloblastoma_NMB92

description: medulloblastoma 396


title: genomic DNA from medulloblastoma_NMB908

description: medulloblastoma 394


title: genomic DNA from medulloblastoma_PNET30116

description: medulloblastoma 407


title: genomic DNA from medulloblastoma_PNET350292

description: medulloblastoma 425


title: Scleroderma patient 4

status: Public on Jun 12 2017

description: Gene expression from monocytes of scleroderma patient.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450.

source_name: monocytes from scleroderma patient

growth_protocol: Monocytes were isolated by negative depletion from the negative fraction of PBMCs depleted of CD19+ cells, using magnetic beads (easySep, StemCell).

extract_protocol: Total RNA from monocytes was extracted using an miRNeasy kit according to the manufacturer's protocol (QIAGEN, Valencia, CA).

tag: disease status

value: diffuse cutaneous scleroderma (dcSSc)

tag: cell type

value: monocytes


title: genomic DNA from medulloblastoma_NMB910

description: medulloblastoma 395


title: Scleroderma patient 2


title: Scleroderma patient 3


title: Scleroderma patient 1


title: genomic DNA from medulloblastoma_PNET30200

description: medulloblastoma 413


title: Normal control subject 4

description: Gene expression from monocytes of normal control subject.

source_name: monocytes from normal control subject

value: healthy


title: Normal control subject 1


title: Normal control subject 3


title: genomic DNA from medulloblastoma_NMB907

description: medulloblastoma 393


title: Normal control subject 2


title: genomic DNA from medulloblastoma_NMB898

description: medulloblastoma 390


title: genomic DNA from medulloblastoma_NMB905

description: medulloblastoma 392


title: genomic DNA from medulloblastoma_NMB892

description: medulloblastoma 387


title: genomic DNA from medulloblastoma_NMB89

description: medulloblastoma 384


title: genomic DNA from medulloblastoma_NMB894

description: medulloblastoma 388


title: genomic DNA from medulloblastoma_NMB897

description: medulloblastoma 389


title: genomic DNA from medulloblastoma_NMB889

description: medulloblastoma 383


title: genomic DNA from medulloblastoma_NMB890

description: medulloblastoma 385


title: genomic DNA from medulloblastoma_NMB899

description: medulloblastoma 391

value: NOS


title: genomic DNA from medulloblastoma_NMB868

description: medulloblastoma 377


title: genomic DNA from medulloblastoma_NMB872

description: medulloblastoma 380


title: genomic DNA from medulloblastoma_NMB859

description: medulloblastoma 374


title: genomic DNA from medulloblastoma_NMB830

description: medulloblastoma 370


title: genomic DNA from medulloblastoma_NMB832

description: medulloblastoma 372


title: genomic DNA from medulloblastoma_NMB867

description: medulloblastoma 376


title: genomic DNA from medulloblastoma_NMB825

description: medulloblastoma 369


title: genomic DNA from medulloblastoma_NMB816

description: medulloblastoma 366


title: genomic DNA from medulloblastoma_NMB807

description: medulloblastoma 361


title: genomic DNA from medulloblastoma_NMB805

description: medulloblastoma 359


title: genomic DNA from medulloblastoma_NMB801

description: medulloblastoma 356


title: genomic DNA from medulloblastoma_NMB804

description: medulloblastoma 358


title: genomic DNA from medulloblastoma_NMB80

description: medulloblastoma 354


title: genomic DNA from medulloblastoma_NMB799

description: medulloblastoma 353


title: genomic DNA from medulloblastoma_NMB800

description: medulloblastoma 355


title: genomic DNA from medulloblastoma_NMB794

description: medulloblastoma 349


title: genomic DNA from medulloblastoma_NMB797

description: medulloblastoma 351


title: genomic DNA from medulloblastoma_NMB891

description: medulloblastoma 386


title: genomic DNA from medulloblastoma_NMB787

description: medulloblastoma 344


title: genomic DNA from medulloblastoma_NMB785

description: medulloblastoma 343


title: genomic DNA from medulloblastoma_NMB793

description: medulloblastoma 348


title: genomic DNA from medulloblastoma_NMB782

description: medulloblastoma 340


title: genomic DNA from medulloblastoma_NMB78

description: medulloblastoma 339


title: genomic DNA from medulloblastoma_NMB774

description: medulloblastoma 338


title: genomic DNA from medulloblastoma_NMB82

description: medulloblastoma 367


title: genomic DNA from medulloblastoma_NMB770

description: medulloblastoma 334


title: genomic DNA from medulloblastoma_NMB772

description: medulloblastoma 336


title: genomic DNA from medulloblastoma_NMB77

description: medulloblastoma 333


title: genomic DNA from medulloblastoma_NMB768

description: medulloblastoma 331


title: genomic DNA from medulloblastoma_NMB812

description: medulloblastoma 365


title: genomic DNA from medulloblastoma_NMB769

description: medulloblastoma 332


title: genomic DNA from medulloblastoma_NMB771

description: medulloblastoma 335


title: genomic DNA from medulloblastoma_NMB766

description: medulloblastoma 329


title: genomic DNA from medulloblastoma_NMB764

description: medulloblastoma 327


title: genomic DNA from medulloblastoma_NMB762

description: medulloblastoma 325


title: genomic DNA from medulloblastoma_NMB760

description: medulloblastoma 323


title: genomic DNA from medulloblastoma_NMB758

description: medulloblastoma 321


title: genomic DNA from medulloblastoma_NMB755

description: medulloblastoma 318


title: genomic DNA from medulloblastoma_NMB749

description: medulloblastoma 316


title: genomic DNA from medulloblastoma_NMB747

description: medulloblastoma 314


title: genomic DNA from medulloblastoma_NMB754

description: medulloblastoma 317


title: genomic DNA from medulloblastoma_NMB767

description: medulloblastoma 330


title: genomic DNA from medulloblastoma_NMB742

description: medulloblastoma 311


title: genomic DNA from medulloblastoma_NMB783

description: medulloblastoma 341


title: genomic DNA from medulloblastoma_NMB784

description: medulloblastoma 342


title: genomic DNA from medulloblastoma_NMB741

description: medulloblastoma 310


title: genomic DNA from medulloblastoma_NMB773

description: medulloblastoma 337

value: DN


title: genomic DNA from medulloblastoma_NMB739

description: medulloblastoma 308


title: genomic DNA from medulloblastoma_NMB737

description: medulloblastoma 306


title: genomic DNA from medulloblastoma_NMB736

description: medulloblastoma 305


title: genomic DNA from medulloblastoma_NMB734

description: medulloblastoma 303


title: genomic DNA from medulloblastoma_NMB735

description: medulloblastoma 304


title: genomic DNA from medulloblastoma_NMB733

description: medulloblastoma 302


title: genomic DNA from medulloblastoma_NMB729

description: medulloblastoma 299


title: genomic DNA from medulloblastoma_NMB725

description: medulloblastoma 296


title: genomic DNA from medulloblastoma_NMB723

description: medulloblastoma 294


title: genomic DNA from medulloblastoma_NMB718

description: medulloblastoma 291


title: genomic DNA from medulloblastoma_NMB761

description: medulloblastoma 324


title: genomic DNA from medulloblastoma_NMB709

description: medulloblastoma 284


title: genomic DNA from medulloblastoma_NMB716

description: medulloblastoma 289


title: genomic DNA from medulloblastoma_NMB727

description: medulloblastoma 298


title: genomic DNA from medulloblastoma_NMB70

description: medulloblastoma 280


title: genomic DNA from medulloblastoma_NMB671

description: medulloblastoma 270


title: genomic DNA from medulloblastoma_NMB648

description: medulloblastoma 261


title: genomic DNA from medulloblastoma_NMB684

description: medulloblastoma 277


title: genomic DNA from medulloblastoma_NMB658

description: medulloblastoma 264


title: genomic DNA from medulloblastoma_NMB669

description: medulloblastoma 268


title: genomic DNA from medulloblastoma_NMB748

description: medulloblastoma 315


title: genomic DNA from medulloblastoma_NMB637

description: medulloblastoma 257


title: genomic DNA from medulloblastoma_NMB666

description: medulloblastoma 266


title: genomic DNA from medulloblastoma_NMB68

description: medulloblastoma 276


title: genomic DNA from medulloblastoma_NMB636

description: medulloblastoma 256


title: genomic DNA from medulloblastoma_NMB646

description: medulloblastoma 260


title: genomic DNA from medulloblastoma_NMB633

description: medulloblastoma 255


title: genomic DNA from medulloblastoma_NMB632

description: medulloblastoma 254


title: genomic DNA from medulloblastoma_NMB629

description: medulloblastoma 251


title: genomic DNA from medulloblastoma_NMB626

description: medulloblastoma 250


title: genomic DNA from medulloblastoma_NMB631

description: medulloblastoma 253


title: genomic DNA from medulloblastoma_NMB620

description: medulloblastoma 246


title: genomic DNA from medulloblastoma_NMB615

description: medulloblastoma 242


title: genomic DNA from medulloblastoma_NMB610

description: medulloblastoma 239


title: genomic DNA from medulloblastoma_NMB69

description: medulloblastoma 278


title: genomic DNA from medulloblastoma_NMB715

description: medulloblastoma 288


title: genomic DNA from medulloblastoma_NMB609

description: medulloblastoma 238


title: genomic DNA from medulloblastoma_NMB601

description: medulloblastoma 235


title: genomic DNA from medulloblastoma_NMB618

description: medulloblastoma 244


title: genomic DNA from medulloblastoma_NMB679

description: medulloblastoma 275


title: genomic DNA from medulloblastoma_NMB606

description: medulloblastoma 236


title: genomic DNA from medulloblastoma_NMB60

description: medulloblastoma 233


title: genomic DNA from medulloblastoma_NMB600

description: medulloblastoma 234


title: genomic DNA from medulloblastoma_NMB592

description: medulloblastoma 231


title: genomic DNA from medulloblastoma_NMB591

description: medulloblastoma 230


title: genomic DNA from medulloblastoma_NMB535

description: medulloblastoma 211


title: genomic DNA from medulloblastoma_NMB550

description: medulloblastoma 218


title: genomic DNA from medulloblastoma_NMB582

description: medulloblastoma 226


title: genomic DNA from medulloblastoma_NMB624

description: medulloblastoma 248


title: genomic DNA from medulloblastoma_NMB536

description: medulloblastoma 212


title: genomic DNA from medulloblastoma_NMB569

description: medulloblastoma 224


title: genomic DNA from medulloblastoma_NMB533

description: medulloblastoma 210


title: genomic DNA from medulloblastoma_NMB568

description: medulloblastoma 223


title: genomic DNA from medulloblastoma_NMB614

description: medulloblastoma 241


title: genomic DNA from medulloblastoma_NMB529

description: medulloblastoma 206


title: genomic DNA from medulloblastoma_NMB532

description: medulloblastoma 209


title: genomic DNA from medulloblastoma_NMB521

description: medulloblastoma 205


title: genomic DNA from medulloblastoma_NMB531

description: medulloblastoma 208


title: genomic DNA from medulloblastoma_NMB52

description: medulloblastoma 204


title: genomic DNA from medulloblastoma_NMB518

description: medulloblastoma 202


title: genomic DNA from medulloblastoma_NMB51

description: medulloblastoma 201


title: genomic DNA from medulloblastoma_NMB530

description: medulloblastoma 207


title: genomic DNA from medulloblastoma_NMB499

description: medulloblastoma 199


title: genomic DNA from medulloblastoma_NMB490

description: medulloblastoma 192


title: genomic DNA from medulloblastoma_NMB491

description: medulloblastoma 193


title: genomic DNA from medulloblastoma_NMB493

description: medulloblastoma 194


title: genomic DNA from medulloblastoma_NMB489

description: medulloblastoma 190


title: genomic DNA from medulloblastoma_NMB459

description: medulloblastoma 174


title: genomic DNA from medulloblastoma_NMB463

description: medulloblastoma 177


title: genomic DNA from medulloblastoma_NMB585

description: medulloblastoma 228


title: genomic DNA from medulloblastoma_NMB542

description: medulloblastoma 214


title: genomic DNA from medulloblastoma_NMB456

description: medulloblastoma 172


title: genomic DNA from medulloblastoma_NMB443

description: medulloblastoma 170


title: genomic DNA from medulloblastoma_NMB457

description: medulloblastoma 173


title: genomic DNA from medulloblastoma_NMB43

description: medulloblastoma 161


title: genomic DNA from medulloblastoma_NMB421

description: medulloblastoma 159


title: genomic DNA from medulloblastoma_NMB433

description: medulloblastoma 162


title: genomic DNA from medulloblastoma_NMB419

description: medulloblastoma 157


title: genomic DNA from medulloblastoma_NMB438

description: medulloblastoma 166


title: genomic DNA from medulloblastoma_NMB416

description: medulloblastoma 154


title: genomic DNA from medulloblastoma_NMB420

description: medulloblastoma 158


title: genomic DNA from medulloblastoma_NMB519

description: medulloblastoma 203


title: genomic DNA from medulloblastoma_NMB415

description: medulloblastoma 153


title: genomic DNA from medulloblastoma_NMB41

description: medulloblastoma 149


title: genomic DNA from medulloblastoma_NMB418

description: medulloblastoma 156


title: genomic DNA from medulloblastoma_NMB405

description: medulloblastoma 145


title: genomic DNA from medulloblastoma_NMB410

description: medulloblastoma 150


title: genomic DNA from medulloblastoma_NMB484

description: medulloblastoma 187


title: genomic DNA from medulloblastoma_NMB407

description: medulloblastoma 147


title: genomic DNA from medulloblastoma_NMB403

description: medulloblastoma 144


title: genomic DNA from medulloblastoma_NMB399

description: medulloblastoma 141


title: genomic DNA from medulloblastoma_NMB385

description: medulloblastoma 134


title: genomic DNA from medulloblastoma_NMB393

description: medulloblastoma 138


title: genomic DNA from medulloblastoma_NMB394

description: medulloblastoma 139


title: genomic DNA from medulloblastoma_NMB398

description: medulloblastoma 140


title: genomic DNA from medulloblastoma_NMB401

description: medulloblastoma 143


title: genomic DNA from medulloblastoma_NMB384

description: medulloblastoma 133


title: genomic DNA from medulloblastoma_NMB388

description: medulloblastoma 137


title: genomic DNA from medulloblastoma_NMB383

description: medulloblastoma 132


title: genomic DNA from medulloblastoma_NMB422

description: medulloblastoma 160


title: genomic DNA from medulloblastoma_NMB381

description: medulloblastoma 130


title: genomic DNA from medulloblastoma_NMB378

description: medulloblastoma 127


title: genomic DNA from medulloblastoma_NMB377

description: medulloblastoma 126


title: genomic DNA from medulloblastoma_NMB375

description: medulloblastoma 124


title: genomic DNA from medulloblastoma_NMB369

description: medulloblastoma 119


title: genomic DNA from medulloblastoma_NMB374

description: medulloblastoma 123


title: genomic DNA from medulloblastoma_NMB376

description: medulloblastoma 125


title: genomic DNA from medulloblastoma_NMB366

description: medulloblastoma 116


title: genomic DNA from medulloblastoma_NMB365

description: medulloblastoma 115


title: genomic DNA from medulloblastoma_NMB358

description: medulloblastoma 108


title: genomic DNA from medulloblastoma_NMB373

description: medulloblastoma 122


title: genomic DNA from medulloblastoma_NMB346

description: medulloblastoma 105


title: genomic DNA from medulloblastoma_NMB357

description: medulloblastoma 107


title: genomic DNA from medulloblastoma_NMB362

description: medulloblastoma 112


title: genomic DNA from medulloblastoma_NMB360

description: medulloblastoma 110


title: genomic DNA from medulloblastoma_NMB335

description: medulloblastoma 101


title: genomic DNA from medulloblastoma_NMB387

description: medulloblastoma 136


title: genomic DNA from medulloblastoma_NMB361

description: medulloblastoma 111


title: genomic DNA from medulloblastoma_NMB333

description: medulloblastoma 100


title: genomic DNA from medulloblastoma_NMB331

description: medulloblastoma 99


title: genomic DNA from medulloblastoma_NMB330

description: medulloblastoma 98


title: genomic DNA from medulloblastoma_NMB344

description: medulloblastoma 103


title: genomic DNA from medulloblastoma_NMB326

description: medulloblastoma 94


title: genomic DNA from medulloblastoma_NMB329

description: medulloblastoma 96


title: genomic DNA from medulloblastoma_NMB316

description: medulloblastoma 88


title: genomic DNA from medulloblastoma_NMB320

description: medulloblastoma 91


title: genomic DNA from medulloblastoma_NMB318

description: medulloblastoma 89


title: genomic DNA from medulloblastoma_NMB314

description: medulloblastoma 87


title: genomic DNA from medulloblastoma_NMB287

description: medulloblastoma 86


title: genomic DNA from medulloblastoma_NMB285

description: medulloblastoma 85


title: genomic DNA from medulloblastoma_NMB368

description: medulloblastoma 118


title: genomic DNA from medulloblastoma_NMB284

description: medulloblastoma 84


title: genomic DNA from medulloblastoma_NMB283

description: medulloblastoma 83


title: genomic DNA from medulloblastoma_NMB277

description: medulloblastoma 80


title: genomic DNA from medulloblastoma_NMB266

description: medulloblastoma 75


title: genomic DNA from medulloblastoma_NMB260

description: medulloblastoma 73


title: genomic DNA from medulloblastoma_NMB255

description: medulloblastoma 70


title: genomic DNA from medulloblastoma_NMB257

description: medulloblastoma 71


title: genomic DNA from medulloblastoma_NMB251

description: medulloblastoma 66


title: genomic DNA from medulloblastoma_NMB250

description: medulloblastoma 65


title: genomic DNA from medulloblastoma_NMB227

description: medulloblastoma 64


title: genomic DNA from medulloblastoma_NMB2

description: medulloblastoma 61


title: genomic DNA from medulloblastoma_NMB203

description: medulloblastoma 63


title: genomic DNA from medulloblastoma_NMB199

description: medulloblastoma 60


title: genomic DNA from medulloblastoma_NMB188

description: medulloblastoma 56


title: genomic DNA from medulloblastoma_NMB186

description: medulloblastoma 54


title: genomic DNA from medulloblastoma_NMB187

description: medulloblastoma 55


title: genomic DNA from medulloblastoma_NMB189

description: medulloblastoma 57


title: genomic DNA from medulloblastoma_NMB183

description: medulloblastoma 51


title: genomic DNA from medulloblastoma_NMB182

description: medulloblastoma 50


title: genomic DNA from medulloblastoma_NMB185

description: medulloblastoma 53


title: genomic DNA from medulloblastoma_NMB177

description: medulloblastoma 45


title: genomic DNA from medulloblastoma_NMB179

description: medulloblastoma 47


title: genomic DNA from medulloblastoma_NMB180

description: medulloblastoma 48


title: genomic DNA from medulloblastoma_NMB178

description: medulloblastoma 46


title: genomic DNA from medulloblastoma_NMB281

description: medulloblastoma 82


title: genomic DNA from medulloblastoma_NMB176

description: medulloblastoma 44


title: genomic DNA from medulloblastoma_NMB273

description: medulloblastoma 79


title: genomic DNA from medulloblastoma_NMB173

description: medulloblastoma 42


title: genomic DNA from medulloblastoma_NMB267

description: medulloblastoma 76


title: genomic DNA from medulloblastoma_NMB171

description: medulloblastoma 40


title: genomic DNA from medulloblastoma_NMB175

description: medulloblastoma 43


title: genomic DNA from medulloblastoma_NMB17

description: medulloblastoma 39


title: genomic DNA from medulloblastoma_NMB172

description: medulloblastoma 41


title: genomic DNA from medulloblastoma_NMB153

description: medulloblastoma 33


title: genomic DNA from medulloblastoma_NMB190

description: medulloblastoma 58


title: genomic DNA from medulloblastoma_NMB169

description: medulloblastoma 38


title: genomic DNA from medulloblastoma_NMB167

description: medulloblastoma 36


title: genomic DNA from medulloblastoma_NMB151

description: medulloblastoma 31


title: genomic DNA from medulloblastoma_NMB152

description: medulloblastoma 32


title: genomic DNA from medulloblastoma_NMB184

description: medulloblastoma 52


title: genomic DNA from medulloblastoma_NMB145

description: medulloblastoma 27


title: genomic DNA from medulloblastoma_NMB144

description: medulloblastoma 26


title: genomic DNA from medulloblastoma_NMB148

description: medulloblastoma 29


title: genomic DNA from medulloblastoma_NMB142

description: medulloblastoma 24


title: genomic DNA from medulloblastoma_NMB146

description: medulloblastoma 28


title: genomic DNA from medulloblastoma_NMB149

description: medulloblastoma 30


title: genomic DNA from medulloblastoma_NMB166

description: medulloblastoma 35


title: genomic DNA from medulloblastoma_NMB140

description: medulloblastoma 22


title: genomic DNA from medulloblastoma_NMB134

description: medulloblastoma 17


title: genomic DNA from medulloblastoma_NMB130

description: medulloblastoma 14


title: genomic DNA from medulloblastoma_NMB125

description: medulloblastoma 10


title: genomic DNA from medulloblastoma_NMB126

description: medulloblastoma 11


title: genomic DNA from medulloblastoma_NMB127

description: medulloblastoma 12


title: genomic DNA from medulloblastoma_NMB109

description: medulloblastoma 1


title: genomic DNA from medulloblastoma_NMB110

description: medulloblastoma 2


title: genomic DNA from medulloblastoma_NMB111

description: medulloblastoma 3


title: genomic DNA from medulloblastoma_NMB132

description: medulloblastoma 16


title: genomic DNA from medulloblastoma_NMB136

description: medulloblastoma 19


title: Yap1 wild-type 3

status: Public on May 24 2017

description: Gene expression from submandibular gland of Yap1+/+ animal.

hyb_protocol: Two micrograms of biotin labeled sscDNA probe were hybridized to a GPL11180 [HT_MG-430_PM] Affymetrix Array Plate with modifications as previously described (PMID: 23289891)

scan_protocol: The processed GeneChip plate arrays were scanned using GeneTitan scanner (Affymetrix).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray htmg430pmmmentrezg R package (version 17.0.0) (http://mbni.org/customcdf/17.0.0/entrezg.download/htmg430pm_Mm_ENTREZG_17.0.0.zip).

source_name: submandibular gland

label_protocol: Isolated RNA was normalized and then automated sample amplification and biotin labeling were carried out using the NuGEN Ovation RNA Amplification system V2, Ovation WB reagent and Encore Biotin module according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Beckman Coulter).

growth_protocol: SMGs from E15.5 litter mate embryos from three separate timed matings were collected.

extract_protocol: SMGs were lysed in RLT buffer and RNA was isolated using a Qiagen RNeasy kit.

treatment_protocol: E15.5 WT and Yap knockout SMGs were dissected and the epithelium was separated from the mesenchyme as previously described (PMID:19247608).

tag: tissue

value: submandibular gland


title: Yap1 wild-type 2


title: differentiated AT2 cells

status: Public on May 02 2017

description:
25
Gene expression data from distal fetal lung epithelium

source_name: Distal fetal lung epithelium, embryo 1

growth_protocol: iPSCs were transitioned to feeder-free conditions on Matrigel (Corning) in mTeSR1 (Stem Cell Technologies) and passaged with Gentle Cell Dissociation Reagent (Stem Cell Technologies). For the lung  differentiation we first induced definitive endoderm using STEMDiff definitive endoderm kit (STEMCELL Technologies) according to the accompanying protocol. After approximately 72 cells were plated in small clumps at approximately 150-200,000 cells/cm2  on Matrigel-coated plates in complete serum-free differentiation media (CSFDM) supplemented with 2μM Dorsomorphin (Stemgent), 10μM SB431542 (Tocris) for 72 hours. 10μM Y-27632 (Tocris) was added for the first 24 hours. The differentiation media was changed on day 6 to “CFKBRa”; CSFDM supplemented with 3μM CHIR99021 (Tocris), 10ng/ml rhFGF10, 10ng/ml rhKGF, 10ng/ml rhBMP4 (all from R&D Systems), 50-100nM Retinoic acid (Sigma). On day 15 cells were dissociated by incubating in 0.05% trypsin (ThermoFisher Scientific) at 37°C for 2-4 minutes, aspirating trypsin, washing once with DMEM (ThermoFisher Scientific)+10% FBS (ThermoFisher Scientific), resuspending as small clumps in CSFDM supplemented with 3uM CHIR99021, 10ng/ml rhFGF10 and 10ng/ml rhKGF (“CFK” media) and plated on freshly-coated Matrigel (Corning 354277) plates.  10μM Y-27632 was added to “CFK” media for the first 24 hours. On day 22 media was changed to “CFK+DCI”: “CFK” media plus 50nM dexamethasone (Sigma), 0.1mM 8-Bromoadenosine 3′,5′-cyclic monophosphate  (8-Br-cAMP) sodium salt (Sigma) and 0.1mM 3-Isobutyl-1-methylxanthine (IBMX) (Sigma). Neuroectodermal NKX2-1GFP+ cells were generated using STEMDdiff Neural Induction Medium (STEMCELL Technologies) according to the manufacturer’s protocol. On day 6 of differentiation, 2μM of purmorphamine (Stemgent) was added to the base media. NKX2-1+ cells were sorted on Day 12.

extract_protocol: RNA was extracted by first lysing cells in Qiazol (Qiagen) and subsequently using RNeasy Plus Minikit (Qiagen) according to the manufacturer’s protocol and without DNase treatment.

treatment_protocol: Not applicable

tag: group

value: fetal lung

tag: timepoint

value: week 21


title: Yap1 Shh-Cre knockout 2

description: Gene expression from submandibular gland of Shh-Cre Yap1-/- animal.

tag: genotype

value: Shh-Cre Yap1-/-


title: day 28 Nkx2-1-GFP+ 3

description:
18
Gene expression data from iPSC-derived Nkx2-1GFP+ differentiated cells

value: Day 28 GFP+

value: day 28


title: Yap1 Shh-Cre knockout 3


title: day 15 Nkx2-1-GFP+ 3

description:
12
Gene expression data from iPSC-derived Nkx2-1GFP+ primordial progenitors

value: Day 15 GFP+

value: day 15


title: day 28 Nkx2-1-GFP+ 2

description:
17
Gene expression data from iPSC-derived Nkx2-1GFP+ differentiated cells


title: uncultured naïve lung epithelium 1

description:
39
Gene expression data from distal fetal lung epithelium

source_name: Distal fetal lung epithelium, embryo 2


title: uncultured naïve lung epithelium 2

description:
40
Gene expression data from distal fetal lung epithelium


title: day 28 Nkx2-1-GFP+ 1

description:
16
Gene expression data from iPSC-derived Nkx2-1GFP+ differentiated cells


title: day 28 Nkx2-1-GFP- 3

description:
21
Gene expression data from iPSC-derived Nkx2-1GFP- differentiated cells

value: Day 28 GFP-


title: day 15 Nkx2-1-GFP- 3

description:
15
Gene expression data from iPSC-derived Nkx2-1GFP- primordial progenitors

value: Day 15 GFP-


title: Yap1 wild-type 1


title: day 28 Nkx2-1-GFP- 2

description:
20
Gene expression data from iPSC-derived Nkx2-1GFP- differentiated cells


title: day 15 Nkx2-1-GFP+ 2

description:
11
Gene expression data from iPSC-derived Nkx2-1GFP+ primordial progenitors


title: day 3 definitive endoderm 2

description:
5
Gene expression data from iPSC-derived CXCR4+ definitive endoderm

source_name: iPSC-derived CXCR4+ definitive endoderm

value: definitive endoderm

value: day 3


title: day 3 definitive endoderm 3

description:
6
Gene expression data from iPSC-derived CXCR4+ definitive endoderm


title: day 15 Nkx2-1-GFP- 1

description:
13
Gene expression data from iPSC-derived Nkx2-1GFP- primordial progenitors


title: day 6 anterior foregut endoderm 1

description:
7
Gene expression data from iPSC-derived anterior foregut-like endoderm

value: anterior foregut endoderm

value: day 6


title: Yap1 Shh-Cre knockout 1


title: day 0 undifferentiated iPSC17 2

description:
35
Gene expression data from undifferentiated iPSCs

source_name: Undifferentiated iPSCs

value: undifferentiated iPSC

value: day 0


title: day 0 undifferentiated iPSC17 3

description:
36
Gene expression data from undifferentiated iPSCs


title: day 28 Nkx2-1-GFP- 1

description:
19
Gene expression data from iPSC-derived Nkx2-1GFP- differentiated cells


title: day 15 Nkx2-1-GFP- 2

description:
14
Gene expression data from iPSC-derived Nkx2-1GFP- primordial progenitors


title: day 3 definitive endoderm 1

description:
4
Gene expression data from iPSC-derived CXCR4+ definitive endoderm


title: day 6 anterior foregut endoderm 2

description:
8
Gene expression data from iPSC-derived anterior foregut-like endoderm


title: day 15 Nkx2-1-GFP+ 1

description:
10
Gene expression data from iPSC-derived Nkx2-1GFP+ primordial progenitors


title: day 0 undifferentiated iPSC17 1

description:
34
Gene expression data from undifferentiated iPSCs


title: day 6 anterior foregut endoderm 3

description:
9
Gene expression data from iPSC-derived anterior foregut-like endoderm


title: neural GFP+ 3

description:
24
Gene expression data from iPSC-derived forebrain-like neural NKX2-1GFP+ cells

value: neural GFP+