title: TOV112D ectopically expressing T372A-EZH2 vector for 72 hours, S7

city: Bloomington

first: Kenneth

last: Nephew

state: IN

country: USA

institute: Indiana University

description:
T372A-EZH2
GFP_tagged_EZH2_T372A_overexpression_S7
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372A_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372A_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_T372A_overexpression.DESeq2_Results.xlsx

data_processing:
CASAVA VERSION 1.8.2.
Sequenced reads were trimmed for adaptor sequence and low-quality using Trimmomatic version 0.32.
Trimmed reads were mapped to hg19 using Tophat2 version 2.0.10 with the parameters -p 8 --b2-very-sensitive --read-edit-dist 2 --max-multihits 100 --library-type fr-secondstrand
Custom perl scripts were used to count mapped reads using Gencode v19 as the reference annotation.
Differential expression analysis was performed using the DESeq2 package (version 1.10.0) in R/Bioconductor (R version 3.2.1) to produce the following comparisons: tagged_EZH2_T372A_overexpression vs. tagged_EZH2_overexpression, tagged_EZH2_T372A_overexpression vs. overexpressing_cells, tagged_EZH2_overexpression vs. overexpressing_cells, tagged_EZH2_T372E_overexpression vs. tagged_EZH2_T372A_overexpression, tagged_EZH2_T372E_overexpression vs. tagged_EZH2_overexpression, and tagged_EZH2_T372E_overexpression vs. overexpressing_cells.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ezh2_experiment.rpkm.txt: Tab-delimited text file includes RPKM values for each Sample.
Supplementary_files_format_and_content: *.DESeq2_Results.xlsx: Excel files include DESeq2 results.

source_name: Human Cell line TOV112D

extract_protocol:
The total RNA was extracted using Qiagen RNA extraction kit and purified RNA was given to Indiana University CGB department for library preparation and sequencing using the Illumina protocol.
CGB Illumina library prep protocol.

treatment_protocol: TOV112D cells were maintained in their appropriate growth media. Once 80% confluent, cells were transfected transiently with expression vectors for Wt-EZh2 and T372E-EZH2 mutant. 72 hours post transfection cells were lysed and RNA was extracted.

tag: transfection

value: T372A-EZH2 vector


title: genomic DNA from peripheral white blood cells [200078650024_R01C01]

status: Public on Jun 05 2018

type: genomic

city: Pamplona

first: Ana

last: Arpón

address: Irunlarrea 1

country: Spain

institute: University of Navarra

hyb_protocol: Bisulphite converted DNA from 474 samples from different cohorts were hybridised to the Illumina Infinium 450k Human Methylation Beadchip (DiOGenes-UNAV, EPALIP, Food4Me-UNAV, GEDYMET, ICTUS, NUGENOB-UNAV, PREDIMED-UNAV, RESMENA, NormoP) or Infinium MethylationEPIC Beadchip (OBEKIT).

scan_protocol: Arrays were imaged using Illumina hiScanSQ platform

data_processing:
After obtaining intensity data from minfi R package, filtering probes is performed in probes with a detection p-value above 0.01 in one or more samples, probes with a beadcount <3 in at least 5% of samples,probes non-cpg, probes with SNPs as identified in Nordlund et al, probes that align to multiple locations as identified in Nordlund et al and probes on the X or Y by champ.filter function of ChAMP version 1.11.0.  After filtering probes, intra-cell type normalization is done using Subset-quantile Within Array Normalization (SWAN) method.  After SWAN normalization, magnitude of batch effects are assessed and corrected using the ComBat normalization method.  To correct for the differences in methylation resulting from differences in cellular heterogeneity, the Houseman correction was used (Houseman et al. 2012).
Matrix_processed.txt: Normalized Average Beta using SWAN (Subset-quantile Within Array Normalization) normalization of ChAMP R package
Matrix_signal_intensities.txt: Unmethylated and methylated signal intensities by getMeth and getUnmet function of minfi R package.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral white blood cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from samples using MasterPure™DNA Purification Kit for Blood according to standard instructions

tag: Sex

value: Male

tag: age

tag: study

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: C12A_ASCL1_SOX2_DORSO_1_d14

type: SRA

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
C12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

library_source: transcriptomic

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) or mouse genome (mm10 from UCSC) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

molecule: total RNA

growth_protocol: Differentiation medium plus dorsomorphin

extract_protocol:
Single cell isolation by FACS and cDNA generation following SmartSeq2 protocol. (Nat Protoc. 2014 Jan;9(1):171-81. doi: 10.1038/nprot.2014.006. Epub 2014 Jan 2.)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

tag: donor id

value: Donor 1

tag: tissue source

value: brain

tag: cell type

tag: genotype/variation

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: B6A_ASCL1_SOX2_DORSO_1_d14

description:
B6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: TOV112D ectopically expressing T372A-EZH2 vector for 72 hours, S3

description:
T372A-EZH2
GFP_tagged_EZH2_T372A_overexpression_S3
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372A_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372A_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_T372A_overexpression.DESeq2_Results.xlsx

growth_protocol: TOV112D cells were maintained in their appropriate growth media.

tag: cell line


title: TOV112D ectopically expressing T372E-EZH2 vector for 72 hours, S8

description:
T372E-EZH2
GFP_tagged_EZH2_T372E_overexpression_S8
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_T372A_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx

value: T372E-EZH2 vector


title: Input vector #2

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Beatson CRUK

description:
input RNA
read_count_table.csv
WT_vs_2LA_Input_edgeR_analysis.csv
WT_vs_Vec_Input_edgeR_analysis.csv
2LA_vs_Vec_Input_edgeR_analysis.csv

data_processing:
Sequencing was performed using NextSeq Series High Output Kit 2 × 75 bp (Illumina).
An index of the (GRCh38/hg38) assembly of human genome was generated using the gencode comprehensive gene annotation version 25 in STAR2.5.2b (Dobin et al., 2013). Options: --runMode genomeGenerate --sjdbOverhang 74.  Reads were then aligned and reads per gene quantified using STAR 2.5.2b. Options: --quantMode GeneCounts --readFilesCommand zcat .
Read counts were coverted to counts per million and differentially expressed genes were identified using edgeR package (Robinson et al., 2010). Genes with at least 1 count per million (CPM) in all samples were analysed for differential expression. Pairwise comparisons were made between input RNA and between polysomal RNA for samples transfected with pcDNA5, pcDNA 5 HA-CMTR1 WT or HA-CMTR1 2L/A.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: read_count_table.csv contains the raw read counts per gene calculated by STAR during read alignment.  The six edgeR_analysis.csv files contain the fully analysed data including the log2 fold changes, p values and false discovery rates (FDR) for the pairwise comparisons of gene expression generated by edgeR along with gene descriptions and normalised reads counts from the samples (counts per million).  The comparison described in each file is indicated in the filename.

source_name: HCC1806 cell line

growth_protocol: Cultured in RPMI with 10% (v/v) Foetal Bovine Serum, 100U/ml penicillin, 0.1mg/ml streptomycin and 2mM L-glutamine.

extract_protocol:
Cells were incubated in 100 μg/ml cycloheximide for 10 min, washed in ice cold PBS supplemented with 100 μg/ml cycloheximide and extracts collected in polysome lysis buffer (15mM Tris (pH7.5), 15mM MgCl2, 0.3 M NaCl, 1 mM DTT, 1% Triton X-100, 100 mg/ml cycloheximide, 100 U/ml RNasin). 10% of the extracts were retained as input and 90% resolved by centrifugation through a 10 ml 10%–50% sucrose gradient at 18 000 x g for 2 hr at 4oC. Fractions were collected on FoxyR1 fractionator (Teledyne ISCO) with OD259 nm monitoring.  Polysomal fractions 16-20 were purified by Phenol:Chloroform:Isoamyl Alcohol (25:24:1). RNA was precipitated overnight with 2M of LiCl, 20mM Tris pH 7.5, EDTA 10mM. Input RNA was purified using Trizol Reagent. RNA was quality checked using a TapeStation (Agilent Technologies).
TruSeq Stranded Total RNA with Ribo-Zero-Gold kit (Illumina).  Sequencing was performed using NextSeq Series High Output Kit 2 × 75 bp (Illumina).

treatment_protocol: Cells in 10 cm dishes were transfected with either pcDNA5 (vector control), pcDNA 5 HA-CMTR1 WT (wildtype CMTR1) or pcDNA 5 HA-CMTR1 2L/A mutant (mutant CMTR1 that does not interact with DHX15) using polyethylenimine (Polysciences). Cells were cultured for 36 hours before harvesting.

tag: cell harvest date

tag: transfected with

value: Empty vector

value: Breast carcinoma


title: genomic DNA from peripheral white blood cells [200078650016_R06C01]

value: Female

value: GEDYMET

tag: homa-ir


title: C2A_ASCL1_SOX2_DORSO_1_d14

description:
C2A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: TOV112D ectopically expressing T372E-EZH2 vector for 72 hours, S4

description:
T372E-EZH2
GFP_tagged_EZH2_T372E_overexpression_S4
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_T372A_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx


title: Colorectal adenocarcinoma tumor 304

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample304

hyb_protocol: Standard Illumina protocols for Human 610w-Quad chip

data_processing:
Log R ratio and B allele frequency were generated using using GenomeStudio (Illumina)
matrix_processed.txt is linked as a supplementary file on the Series record.  The file reports Genotype: AA,AB,BB,or NC (no call), GC_SCORE, Theta, R, B_Allele_Freq, Log_R_Ratio.
signal_intensities.txt is linked as a supplementary file on the Series record.

label: C-Bio and A-DNP

source_name: Colorectal adenocarcinoma

extract_protocol: AllPrep DNA/RNA Mini Kit (QUAGEN)

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: C

tag: site

value: Rectum

tag: estimated macrod2 status

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 308

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample308

scan_protocol: Standard Illumina protocols for Human 610w-Quad chip

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650016_R06C02]

tag: Sex

tag: age

tag: study

tag: array

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 303

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample303

label_protocol: Standard Illumina protocols for Human 610w-Quad chip

value: Right


title: C3A_ASCL1_SOX2_DORSO_1_d14

description:
C3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

tag: cell type

tag: genotype/variation

tag: timepoint (days post infection)


title: B9A_ASCL1_SOX2_DORSO_1_d14

description:
B9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 302

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample302

tag: gender

value: F


title: C4A_ASCL1_SOX2_DORSO_1_d14

description:
C4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: genomic DNA from peripheral white blood cells [200078650016_R05C02]

value: PREDIMED


title: genomic DNA from peripheral white blood cells [200078650016_R05C01]

value: Male


title: Colorectal adenocarcinoma tumor 301

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample301

tag: tissue


title: TOV112D ectopically expressing Wt-EZH2 vector for 72 hours, S2

description:
Wt-EZH2
GFP_tagged_EZH2_overexpression_S2
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372A_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx

tag: cell line

tag: transfection

value: Wt-EZH2 vector


title: TOV112D ectopically expressing Wt-EZH2 vector for 72 hours, S6

description:
Wt-EZH2
GFP_tagged_EZH2_overexpression_S6
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_T372A_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx
processed data file: tagged_EZH2_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_tagged_EZH2_overexpression.DESeq2_Results.xlsx


title: C5A_ASCL1_SOX2_DORSO_1_d14

description:
C5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain

value: Ascl1 and Sox2 transduced


title: Colorectal adenocarcinoma tumor 305

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample305

tag: disease state

tag: Stage

value: B

tag: site

value: Left

value: Homozygous deletion


title: C6A_ASCL1_SOX2_DORSO_1_d14

description:
C6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200078650016_R04C02]

tag: Sex

value: DIOGENES

tag: homa-ir


title: Colorectal adenocarcinoma tumor 299

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample299

value: M

value: Colorectal adenocarcinoma

value: Adenocarcinoma

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200078650016_R04C01]

value: Female

tag: age

tag: study

tag: array

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 300

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample300

value: C

value: Rectum

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650016_R03C02]


title: C7A_ASCL1_SOX2_DORSO_1_d14

description:
C7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1

tag: tissue source

tag: cell type

tag: genotype/variation


title: FL plus DL1 DC2 rep2

city: New York

first: Margaret

middle: E

last: Kirkling

state: NY

institute: Columbia University

description:
Sample 8
mRNA

data_processing:
Basecalls performed using CASAVA version 1.8.4.
Calculating insert size and standard deviation performed using Picard v.1.126.
Reads were mapped to mm10 using STAR guided by GTF version.
Read counting performed using HT-seq v0.6.0.
Normalization and Differential expression analysis performed using DEseq2.
BAM to bedgraph performed using bedtools v2.17.0.
bedgraph to bigwig performed using bedGraphToBigWig v4.
Statistics and plotting performed in R v3.1.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig: Coverage for mapped reads.
Supplementary_files_format_and_content: *_ct_genes.txt: Tab-separated text files include read counts for genomic features.

organism: Mus musculus

source_name: primary bone marrow

growth_protocol: Bone marrow cells were cultured in medium supplemented with Flt3L. On day 3 of culture, cells were cocultured with OP9-DL1 cells and allowed to differentiate for an additional 4 days.

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the PicoPure kit (KIT0204).
RNASeq libraries were prepared using the Clontech Ultra low RNA kit, starting with 3 ng, with 10 cycles of PCR for cDNA amplification, and the Clontech Low Input Kit for library prep, with 7 cycles of PCR amplification, following the manufacturer’s protocol. The amplified library was purified using AMPure beads, quantified by Qubit and QPCR, and visualized in an Agilent Bioanalyzer. The libraries were pooled equimolarly, and run on a HiSeq 2500, as 50 nucleotide in length.

tag: strain/background

value: WT

value: 8-16 weeks

value: culture-derived dendritic cells

tag: harvest time

value: day 7 of culture

tag: treatment

value: Flt3L and OP9-DL1


title: C8A_ASCL1_SOX2_DORSO_1_d14

description:
C8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 298

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample298

tag: gender

tag: tissue

tag: disease state

tag: Stage

tag: site

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 297

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample297

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 296

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample296

value: Left


title: genomic DNA from peripheral white blood cells [200078650016_R02C01]

tag: Sex

value: Male

tag: age

tag: study

value: PREDIMED

tag: array


title: genomic DNA from peripheral white blood cells [200078650016_R02C02]

tag: waist circumference (cm)


title: D10A_ASCL1_SOX2_DORSO_1_d14

description:
D10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

tag: cell type

tag: genotype/variation


title: FL DC2 rep2

description:
Sample 6
mRNA

growth_protocol: Bone marrow cells were cultured in medium supplemented with Flt3L for 7 days.

tag: strain/background

tag: harvest time

tag: treatment


title: Colorectal adenocarcinoma tumor 295

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample295

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

value: Right


title: FL plus DL1 DC2 rep1

description:
Sample 7
mRNA


title: C9A_ASCL1_SOX2_DORSO_1_d14

description:
C9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200078650033_R01C02]

value: Female


title: TOV112D ectopically expressing empty vector for 72 hours, S5

description:
Control (Empty vector control)
GFP_overexpressing_cells_S5
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372A_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx

tag: cell line

tag: transfection

value: empty vector


title: FL plus DL1 DC1 rep2

description:
Sample 4
mRNA

value: WT

tag: age


title: D12A_ASCL1_SOX2_DORSO_1_d14

description:
D12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: D11A_ASCL1_SOX2_DORSO_1_d14

description:
D11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: FL DC2 rep1

description:
Sample 5
mRNA

value: 8-16 weeks

value: culture-derived dendritic cells


title: TOV112D ectopically expressing empty vector for 72 hours, S1

description:
Control (Empty vector control)
GFP_overexpressing_cells_S1
processed data file: ezh2_experiment.rpkm.txt
processed data file: tagged_EZH2_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372A_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx
processed data file: tagged_EZH2_T372E_overexpression_vs_overexpressing_cells.DESeq2_Results.xlsx


title: genomic DNA from peripheral white blood cells [200078650016_R01C01]

tag: Sex

tag: study


title: FL plus DL1 DC1 rep1

description:
Sample 3
mRNA

value: day 7 of culture

value: Flt3L and OP9-DL1


title: genomic DNA from peripheral white blood cells [200053740229_R06C02]

tag: array

tag: waist circumference (cm)


title: D1A_ASCL1_SOX2_DORSO_1_d14

description:
D1A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

value: brain

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [200078650016_R01C02]


title: Colorectal adenocarcinoma tumor 293

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample293

tag: Stage

value: C

tag: site

value: Rectum

tag: estimated macrod2 status

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200053740229_R06C01]

value: PREDIMED


title: Colorectal adenocarcinoma tumor 292

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample292

tag: gender

value: M

value: Colorectal adenocarcinoma


title: FL DC1 rep2

description:
Sample 2
mRNA

tag: strain/background

tag: genotype/variation

tag: cell type

tag: harvest time

tag: treatment


title: genomic DNA from peripheral white blood cells [200053740229_R05C02]

tag: age


title: FL DC1 rep1

description:
Sample 1
mRNA


title: D4A_ASCL1_SOX2_DORSO_1_d14

description:
D4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 291

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample291

tag: tissue

tag: disease state

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [200053740229_R05C01]

tag: Sex

value: Male

tag: study

tag: array

tag: waist circumference (cm)


title: D5A_ASCL1_SOX2_DORSO_1_d14

description:
D5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: Colorectal adenocarcinoma tumor 290

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample290

tag: Stage

tag: site

value: Right

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 294

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample294

tag: gender

value: B

value: Left


title: genomic DNA from peripheral white blood cells [200053740229_R04C01]


title: Colorectal adenocarcinoma tumor 288

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample288

value: F


title: genomic DNA from peripheral white blood cells [200053740229_R03C02]

value: Female

value: GEDYMET

tag: homa-ir


title: D6A_ASCL1_SOX2_DORSO_1_d14

description:
D6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: cell type

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200053740229_R03C01]

tag: age


title: Colorectal adenocarcinoma tumor 289

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample289

tag: tissue


title: Colorectal adenocarcinoma tumor 287

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample287

tag: disease state


title: genomic DNA from peripheral white blood cells [200053740229_R02C02]

tag: Sex

value: DIOGENES


title: D3A_ASCL1_SOX2_DORSO_1_d14

description:
D3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200053740229_R02C01]

tag: study

tag: array


title: D7A_ASCL1_SOX2_DORSO_1_d14

description:
D7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: Colorectal adenocarcinoma tumor 286

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample286

value: C


title: Colorectal adenocarcinoma tumor 285

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample285

value: Rectum

value: Wild-type


title: D8A_ASCL1_SOX2_DORSO_1_d14

description:
D8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 284

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample284

value: M

tag: Stage


title: Colorectal adenocarcinoma tumor 283

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample283

value: Colorectal adenocarcinoma

tag: site

value: Homozygous deletion


title: E12A_ASCL1_SOX2_DORSO_1_d14

description:
E12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740208_R06C02]

value: Male

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200053740208_R06C01]


title: Colorectal adenocarcinoma tumor 282

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample282

value: Adenocarcinoma

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: E10A_ASCL1_SOX2_DORSO_1_d14

description:
E10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740229_R01C01]

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200053740229_R01C02]


title: E1A_ASCL1_SOX2_DORSO_1_d14

description:
E1A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: E2A_ASCL1_SOX2_DORSO_1_d14

description:
E2A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200053740208_R05C02]

tag: age


title: E3A_ASCL1_SOX2_DORSO_1_d14

description:
E3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 280

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample280

tag: gender

tag: tissue


title: genomic DNA from peripheral white blood cells [200053740208_R05C01]

tag: Sex


title: Colorectal adenocarcinoma tumor 279

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample279

tag: disease state


title: D9A_ASCL1_SOX2_DORSO_1_d14

description:
D9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200053740208_R04C02]

tag: study

tag: array


title: E11A_ASCL1_SOX2_DORSO_1_d14

description:
E11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: E5A_ASCL1_SOX2_DORSO_1_d14

description:
E5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 278

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample278

tag: Stage

tag: site


title: Colorectal adenocarcinoma tumor 277

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample277

tag: estimated macrod2 status


title: E6A_ASCL1_SOX2_DORSO_1_d14

description:
E6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740208_R03C02]

value: PREDIMED

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 276

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample276

value: Left

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200053740208_R03C01]


title: E7A_ASCL1_SOX2_DORSO_1_d14

description:
E7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: E8A_ASCL1_SOX2_DORSO_1_d14

description:
E8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200053740208_R04C01]

tag: age

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200053740208_R02C02]


title: Colorectal adenocarcinoma tumor 275

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample275

tag: gender

tag: tissue


title: Colorectal adenocarcinoma tumor 281

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample281

tag: disease state

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 274

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample274

value: B

value: Right


title: genomic DNA from peripheral white blood cells [200053740208_R02C01]

tag: Sex

value: Female


title: Colorectal adenocarcinoma tumor 272

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample272

value: F


title: Colorectal adenocarcinoma tumor 271

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample271

value: D


title: genomic DNA from peripheral white blood cells [200053740208_R01C01]

tag: study


title: F12A_ASCL1_SOX2_DORSO_1_d14

description:
F12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: F10A_ASCL1_SOX2_DORSO_1_d14

description:
F10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: E9A_ASCL1_SOX2_DORSO_1_d14

description:
E9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 270

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample270

tag: Stage

value: C

value: Wild-type


title: F3A_ASCL1_SOX2_DORSO_1_d14

description:
F3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E4A_ASCL1_SOX2_DORSO_1_d14

description:
E4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740194_R05C01]

tag: array


title: Colorectal adenocarcinoma tumor 268

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample268

value: M

value: Colorectal adenocarcinoma

tag: site

value: Rectum

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [200053740194_R05C02]

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200053740194_R06C02]

value: Male


title: genomic DNA from peripheral white blood cells [200053740194_R04C02]

value: DIOGENES


title: Colorectal adenocarcinoma tumor 267

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample267

value: Adenocarcinoma

tag: estimated chromosome segment number (ecsn)


title: F2A_ASCL1_SOX2_DORSO_1_d14

description:
F2A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200053740194_R04C01]

tag: age

tag: homa-ir


title: F5A_ASCL1_SOX2_DORSO_1_d14

description:
F5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 266

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample266

tag: gender

tag: tissue

value: Left


title: F6A_ASCL1_SOX2_DORSO_1_d14

description:
F6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740208_R01C02]

tag: Sex

value: PREDIMED


title: Colorectal adenocarcinoma tumor 273

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample273

tag: disease state

value: B


title: genomic DNA from peripheral white blood cells [200053740194_R03C02]

tag: study


title: F11A_ASCL1_SOX2_DORSO_1_d14

description:
F11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: timepoint (days post infection)


title: TAC-Yap1ChIPSeq

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

library_source: genomic

data_processing:
Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to the genome using the BWA algorithm with default settings. Alignment  information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are  removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This  information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be  visualized in genome browsers. bigWig files also provide the peak metrics in the  Active Motif analysis program described below.
“Peak Finding”: MACS v.1.4.2 was used to identify the binding sites of Yap1
Normalization: The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample. This normalization method works well for most assays and can detect site-specific as well as most global differences in target enrichments between samples.
Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping  Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most  upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping  Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines  the Merged Region. The use of Merged Regions is necessary because the locations and lengths of  Intervals are rarely exactly the same when comparing different samples.  6. Annotations: After defining the Intervals and Merged Regions, their genomic locations along with  their proximities to gene annotations and other genomic features are determined and presented in  Excel spreadsheets. In addition, average and peak (i.e. at “summit”) fragment densities within  Intervals and Merged Regions are compiled.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files show peak shapes in the form of a signal histogram and cand be visualized in the UCSC browser
Supplementary_files_format_and_content: Excel file of Active Regions (Merged Regions), which are genomic regions containing 1 or multiple overlapping Intervals

source_name: heart tissue

extract_protocol:
Heart were surgically removed and snap frozen and shipped to Active Motif for ChIP-Seq
Library was constructed by Active Motif (https://www.activemotif.com/)

treatment_protocol: Wild type C57BL/6J male mice were subjected to a sham or a transverse aortic constriction surgery. Hearts were removed 7 days post-surgery

tag: phenotype

value: wild-type

tag: surgical procedure

value: transverse aortic constriction

tag: days post-surgery

tag: antibody

value: anti-YAP1 (US Biological; Y1200-01D)


title: input

value: a pool of both sham and transverse aortic constriction


title: F7A_ASCL1_SOX2_DORSO_1_d14

description:
F7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: tissue source

value: brain


title: Colorectal adenocarcinoma tumor 264

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample264

tag: Stage

value: C

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: Sham-Yap1ChIPSeq

value: sham


title: F8A_ASCL1_SOX2_DORSO_1_d14

description:
F8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [200053740194_R02C02]

value: Female

tag: age

value: GEDYMET

tag: array

tag: homa-ir

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 263

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample263

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Homozygous deletion


title: F9A_ASCL1_SOX2_DORSO_1_d14

description:
F9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: timepoint (days post infection)


title: F4A_ASCL1_SOX2_DORSO_1_d14

description:
F4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740194_R02C01]

tag: Sex

tag: study


title: genomic DNA from peripheral white blood cells [200053740194_R01C02]


title: Colorectal adenocarcinoma tumor 261

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample261

value: F

value: Adenocarcinoma

tag: Stage

value: Rectum

value: Wild-type


title: Colorectal adenocarcinoma tumor 259

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample259

value: B

tag: site


title: Colorectal adenocarcinoma tumor 269

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample269

value: Right

tag: estimated macrod2 status


title: G11A_ASCL1_SOX2_DORSO_1_d14

description:
G11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: G1A_ASCL1_SOX2_DORSO_1_d14

description:
G1A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: G10A_ASCL1_SOX2_DORSO_1_d14

description:
G10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200053740193_R06C02]

tag: age


title: genomic DNA from peripheral white blood cells [200053740193_R06C01]

tag: array


title: Colorectal adenocarcinoma tumor 258

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample258

value: A

value: Left

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 265

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample265


title: G12A_ASCL1_SOX2_DORSO_1_d14

description:
G12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: genomic DNA from peripheral white blood cells [200053740193_R05C02]

value: PREDIMED

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200053740194_R03C01]

value: DIOGENES


title: G2A_ASCL1_SOX2_DORSO_1_d14

description:
G2A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: Colorectal adenocarcinoma tumor 257

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample257

tag: gender


title: G3A_ASCL1_SOX2_DORSO_1_d14

description:
G3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 256

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample256

tag: tissue


title: genomic DNA from peripheral white blood cells [200053740193_R05C01]

value: Female


title: genomic DNA from peripheral white blood cells [200053740193_R04C02]

value: Male


title: G4A_ASCL1_SOX2_DORSO_1_d14

description:
G4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 255

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample255

value: Colorectal adenocarcinoma

tag: disease state

value: D


title: G5A_ASCL1_SOX2_DORSO_1_d14

description:
G5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: genomic DNA from peripheral white blood cells [200053740193_R04C01]


title: Colorectal adenocarcinoma tumor 262

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample262

value: M


title: Colorectal adenocarcinoma tumor 254

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample254

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [200053740194_R01C01]


title: Colorectal adenocarcinoma tumor 260

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample260

value: C


title: G6A_ASCL1_SOX2_DORSO_1_d14

description:
G6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: G7A_ASCL1_SOX2_DORSO_1_d14

description:
G7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740193_R03C02]

tag: Sex


title: Colorectal adenocarcinoma tumor 252

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample252

value: Wild-type


title: Colorectal adenocarcinoma tumor 253

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample253

value: F

value: B


title: genomic DNA from peripheral white blood cells [200053740193_R02C02]

tag: study

tag: homa-ir


title: G8A_ASCL1_SOX2_DORSO_1_d14

description:
G8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200053740193_R03C01]


title: G9A_ASCL1_SOX2_DORSO_1_d14

description:
G9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 251

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample251

tag: Stage

tag: site

value: Right


title: Colorectal adenocarcinoma tumor 250

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample250

value: Rectum

tag: estimated macrod2 status


title: H10A_ASCL1_SOX2_DORSO_1_d14

description:
H10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: tissue source

tag: cell type


title: genomic DNA from peripheral white blood cells [200053740193_R01C01]

tag: age


title: H11A_ASCL1_SOX2_DORSO_1_d14

description:
H11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 249

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample249

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 248

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample248


title: genomic DNA from peripheral white blood cells [10003886138_R06C01]

tag: array

tag: waist circumference (cm)


title: H1A_ASCL1_SOX2_DORSO_1_d14

description:
H1A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 247

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample247

tag: gender

tag: tissue


title: genomic DNA from peripheral white blood cells [10003886138_R05C01]


title: Colorectal adenocarcinoma tumor 245

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample245

tag: disease state

value: Homozygous deletion


title: H4A_ASCL1_SOX2_DORSO_1_d14

description:
H4A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: timepoint (days post infection)


title: H3A_ASCL1_SOX2_DORSO_1_d14

description:
H3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886138_R03C01]

tag: Sex

tag: study


title: Colorectal adenocarcinoma tumor 244

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample244

tag: Stage

value: Heterozygous deletion


title: H5A_ASCL1_SOX2_DORSO_1_d14

description:
H5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [10003886138_R04C01]

value: Female

tag: homa-ir


title: genomic DNA from peripheral white blood cells [10003886138_R01C01]


title: H6A_ASCL1_SOX2_DORSO_1_d14

description:
H6A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 243

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample243

tag: site

tag: estimated macrod2 status


title: H7A_ASCL1_SOX2_DORSO_1_d14

description:
H7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: cell type


title: genomic DNA from peripheral white blood cells [200053740193_R02C01]

tag: age

value: DIOGENES


title: genomic DNA from peripheral white blood cells [10003886138_R02C01]

value: Male


title: H8A_ASCL1_SOX2_DORSO_1_d14

description:
H8A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [10003886097_R06C02]

tag: array


title: genomic DNA from peripheral white blood cells [200053740193_R01C02]

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 241

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample241

tag: gender

value: Colorectal adenocarcinoma

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 242

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample242

value: M

tag: tissue

tag: disease state


title: genomic DNA from peripheral white blood cells [10003886097_R06C01]


title: H12A_ASCL1_SOX2_DORSO_1_d14

description:
H12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: timepoint (days post infection)


title: H9A_ASCL1_SOX2_DORSO_1_d14

description:
H9A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886097_R05C02]

tag: Sex

tag: study


title: Colorectal adenocarcinoma tumor 239

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample239

value: Adenocarcinoma

tag: Stage

value: Left


title: A10B_ASCL1_SOX2_DORSO_2_d14

description:
A10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 246

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample246

value: C

tag: site

value: Wild-type


title: Colorectal adenocarcinoma tumor 240

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample240

value: F

value: B

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [10003886097_R05C01]

tag: homa-ir


title: Colorectal adenocarcinoma tumor 238

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample238


title: A11B_ASCL1_SOX2_DORSO_2_d14

description:
A11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: cell type


title: genomic DNA from peripheral white blood cells [10003886097_R03C02]

tag: age


title: genomic DNA from peripheral white blood cells [10003886097_R03C01]

tag: array


title: genomic DNA from peripheral white blood cells [10003886097_R02C02]

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 236

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample236

tag: gender

value: Right


title: Colorectal adenocarcinoma tumor 237

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample237

tag: estimated chromosome segment number (ecsn)


title: A2B_ASCL1_SOX2_DORSO_2_d14

description:
A2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 235

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample235

tag: tissue

tag: disease state


title: genomic DNA from peripheral white blood cells [10003886097_R02C01]


title: A3B_ASCL1_SOX2_DORSO_2_d14

description:
A3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: brain

tag: timepoint (days post infection)


title: A12B_ASCL1_SOX2_DORSO_2_d14

description:
A12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886097_R01C02]

tag: Sex

tag: study


title: A4B_ASCL1_SOX2_DORSO_2_d14

description:
A4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 233

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample233

tag: Stage

tag: site


title: A1B_ASCL1_SOX2_DORSO_2_d14

description:
A1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 232

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample232

tag: estimated macrod2 status

value: Homozygous deletion


title: A5B_ASCL1_SOX2_DORSO_2_d14

description:
A5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: A6B_ASCL1_SOX2_DORSO_2_d14

description:
A6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: genomic DNA from peripheral white blood cells [10003886088_R06C01]

tag: age

tag: homa-ir


title: Colorectal adenocarcinoma tumor 231

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample231


title: genomic DNA from peripheral white blood cells [10003886088_R06C02]

tag: array

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 230

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample230

tag: gender

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: A7B_ASCL1_SOX2_DORSO_2_d14

description:
A7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [10003886088_R05C02]


title: genomic DNA from peripheral white blood cells [10003886088_R05C01]

value: Female


title: Colorectal adenocarcinoma tumor 229

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample229

tag: tissue

tag: disease state


title: A8B_ASCL1_SOX2_DORSO_2_d14

description:
A8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 227

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample227

value: A


title: Colorectal adenocarcinoma tumor 234

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample234


title: B10B_ASCL1_SOX2_DORSO_2_d14

description:
B10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 226

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample226


title: A9B_ASCL1_SOX2_DORSO_2_d14

description:
A9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886088_R03C01]

tag: Sex

value: Male

tag: study


title: genomic DNA from peripheral white blood cells [10003886097_R01C01]


title: B12B_ASCL1_SOX2_DORSO_2_d14

description:
B12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886088_R04C02]


title: genomic DNA from peripheral white blood cells [10003886088_R02C02]


title: B1B_ASCL1_SOX2_DORSO_2_d14

description:
B1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B11B_ASCL1_SOX2_DORSO_2_d14

description:
B11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 223

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample223

value: Colorectal adenocarcinoma

tag: Stage

value: D

tag: site


title: Colorectal adenocarcinoma tumor 225

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample225

value: M

value: Adenocarcinoma

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 224

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample224


title: B3B_ASCL1_SOX2_DORSO_2_d14

description:
B3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: cell type


title: genomic DNA from peripheral white blood cells [10003886088_R04C01]

tag: age

tag: homa-ir


title: B2B_ASCL1_SOX2_DORSO_2_d14

description:
B2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886088_R02C01]

tag: array

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 222

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample222

tag: gender

value: Left

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [10003886088_R01C02]


title: genomic DNA from peripheral white blood cells [10003886088_R01C01]


title: Colorectal adenocarcinoma tumor 221

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample221

tag: tissue


title: B5B_ASCL1_SOX2_DORSO_2_d14

description:
B5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: B4B_ASCL1_SOX2_DORSO_2_d14

description:
B4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: Colorectal adenocarcinoma tumor 220

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample220

tag: disease state


title: genomic DNA from peripheral white blood cells [10003886080_R06C02]

tag: Sex


title: B6B_ASCL1_SOX2_DORSO_2_d14

description:
B6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 219

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample219

tag: Stage

value: C

value: Wild-type


title: Colorectal adenocarcinoma tumor 218

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample218

value: F

tag: site


title: genomic DNA from peripheral white blood cells [10003886080_R06C01]

tag: study


title: genomic DNA from peripheral white blood cells [10003886080_R05C02]


title: genomic DNA from peripheral white blood cells [10003886088_R03C02]


title: Colorectal adenocarcinoma tumor 217

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample217

value: B

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [10003886080_R05C01]


title: B9B_ASCL1_SOX2_DORSO_2_d14

description:
B9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: tissue source

tag: cell type


title: Colorectal adenocarcinoma tumor 216

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample216

value: Right


title: genomic DNA from peripheral white blood cells [10003886080_R04C02]

tag: age

tag: homa-ir


title: C10B_ASCL1_SOX2_DORSO_2_d14

description:
C10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: B8B_ASCL1_SOX2_DORSO_2_d14

description:
B8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886080_R04C01]

tag: array

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 228

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample228

tag: gender

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [10003886080_R03C02]


title: Colorectal adenocarcinoma tumor 214

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample214

tag: tissue


title: C11B_ASCL1_SOX2_DORSO_2_d14

description:
C11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 213

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample213

tag: disease state


title: genomic DNA from peripheral white blood cells [10003886080_R03C01]

tag: Sex


title: C1B_ASCL1_SOX2_DORSO_2_d14

description:
C1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: C12B_ASCL1_SOX2_DORSO_2_d14

description:
C12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 212

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample212

tag: Stage

tag: site


title: genomic DNA from peripheral white blood cells [10003886080_R02C02]

tag: study


title: C2B_ASCL1_SOX2_DORSO_2_d14

description:
C2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 211

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample211

value: Rectum

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [10003886080_R01C02]

tag: age


title: C3B_ASCL1_SOX2_DORSO_2_d14

description:
C3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

value: Ascl1 and Sox2 transduced


title: Colorectal adenocarcinoma tumor 209

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample209


title: C4B_ASCL1_SOX2_DORSO_2_d14

description:
C4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003886080_R01C01]

value: Female

tag: array

tag: homa-ir


title: Colorectal adenocarcinoma tumor 210

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample210

tag: gender


title: C5B_ASCL1_SOX2_DORSO_2_d14

description:
C5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 208

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample208

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 207

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample207

tag: tissue


title: genomic DNA from peripheral white blood cells [10003885087_R05C01]

value: PREDIMED

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [10003885087_R04C02]

value: Male


title: Colorectal adenocarcinoma tumor 206

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample206

value: Colorectal adenocarcinoma

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 215

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample215

value: M


title: C7B_ASCL1_SOX2_DORSO_2_d14

description:
C7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [10003885087_R04C01]

tag: Sex


title: C8B_ASCL1_SOX2_DORSO_2_d14

description:
C8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: C9B_ASCL1_SOX2_DORSO_2_d14

description:
C9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885087_R03C02]


title: Colorectal adenocarcinoma tumor 204

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample204

tag: disease state

value: Adenocarcinoma

tag: Stage


title: genomic DNA from peripheral white blood cells [10003885087_R03C01]

tag: study


title: D10B_ASCL1_SOX2_DORSO_2_d14

description:
D10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 203

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample203

tag: site

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 202

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample202


title: genomic DNA from peripheral white blood cells [10003885087_R02C02]

tag: age


title: D11B_ASCL1_SOX2_DORSO_2_d14

description:
D11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 201

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample201

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [10003885087_R02C01]

tag: array


title: genomic DNA from peripheral white blood cells [10003885087_R06C01]


title: D12B_ASCL1_SOX2_DORSO_2_d14

description:
D12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885087_R01C01]


title: D1B_ASCL1_SOX2_DORSO_2_d14

description:
D1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D3B_ASCL1_SOX2_DORSO_2_d14

description:
D3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885087_R01C02]


title: Colorectal adenocarcinoma tumor 200

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample200

tag: gender


title: Colorectal adenocarcinoma tumor 199

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample199

value: C

tag: estimated chromosome segment number (ecsn)


title: B7B_ASCL1_SOX2_DORSO_2_d14

description:
B7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 198

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample198

tag: tissue

value: Wild-type


title: C6B_ASCL1_SOX2_DORSO_2_d14

description:
C6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885075_R05C02]

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [10003885075_R06C02]


title: Colorectal adenocarcinoma tumor 197

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample197

value: Left


title: D5B_ASCL1_SOX2_DORSO_2_d14

description:
D5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: Colorectal adenocarcinoma tumor 205

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample205

value: F

value: B


title: D4B_ASCL1_SOX2_DORSO_2_d14

description:
D4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: genotype/variation


title: D6B_ASCL1_SOX2_DORSO_2_d14

description:
D6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: Colorectal adenocarcinoma tumor 195

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample195

value: Right


title: D7B_ASCL1_SOX2_DORSO_2_d14

description:
D7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [10003885075_R04C02]

tag: Sex

value: Female


title: Colorectal adenocarcinoma tumor 196

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample196


title: genomic DNA from peripheral white blood cells [10003885075_R04C01]

value: PREDIMED


title: Colorectal adenocarcinoma tumor 194

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample194


title: genomic DNA from peripheral white blood cells [10003885075_R03C02]

value: Male


title: D8B_ASCL1_SOX2_DORSO_2_d14

description:
D8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: D9B_ASCL1_SOX2_DORSO_2_d14

description:
D9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E10B_ASCL1_SOX2_DORSO_2_d14

description:
E10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885075_R03C01]


title: Colorectal adenocarcinoma tumor 193

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample193

value: Colorectal adenocarcinoma

tag: disease state


title: genomic DNA from peripheral white blood cells [10003885075_R02C02]


title: E11B_ASCL1_SOX2_DORSO_2_d14

description:
E11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 191

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample191

tag: Stage

value: A


title: Colorectal adenocarcinoma tumor 190

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample190

value: M


title: Colorectal adenocarcinoma tumor 189

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample189

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [10003885075_R05C01]

tag: study


title: E12B_ASCL1_SOX2_DORSO_2_d14

description:
E12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: genomic DNA from peripheral white blood cells [10003885075_R01C01]


title: genomic DNA from peripheral white blood cells [10003885075_R01C02]


title: E2B_ASCL1_SOX2_DORSO_2_d14

description:
E2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885075_R02C01]


title: Colorectal adenocarcinoma tumor 188

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample188

value: D

tag: site


title: E1B_ASCL1_SOX2_DORSO_2_d14

description:
E1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [10003885068_R05C01]


title: E3B_ASCL1_SOX2_DORSO_2_d14

description:
E3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 186

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample186

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [10003885068_R04C01]

tag: age


title: E4B_ASCL1_SOX2_DORSO_2_d14

description:
E4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 185

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample185


title: E5B_ASCL1_SOX2_DORSO_2_d14

description:
E5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 192

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample192


title: genomic DNA from peripheral white blood cells [10003885068_R03C02]

tag: array


title: genomic DNA from peripheral white blood cells [10003885068_R02C01]


title: Colorectal adenocarcinoma tumor 184

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample184

tag: gender


title: genomic DNA from peripheral white blood cells [10003885068_R01C02]


title: E6B_ASCL1_SOX2_DORSO_2_d14

description:
E6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: retina/RPE/choroid_nolens_pooled

type: RNA

city: Melbourne

first: Loretta

last: Giummarra

state: Victoria

address: c/o Psychological Science

department: Psychology & Counselling

institute: La Trobe University

description:
Chicks were raised normally (with no lenses) for 11 days
NL

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner GS3000.

data_processing: To determine present/absent calls, raw data was analyzed with Expression Console using MAS5 using default analysis settings. To determine expression values, raw data was analyzed with Expression Console using RMA using default analysis settings.

label: biotin

organism: Gallus gallus

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

extract_protocol: Total RNA was extracted using the SV total RNA isolation system (Promega Australia, NSW), including DNA digestion. The quality of the RNA samples was assessed via NanoDrop® ND-1000 Spectrophotometer and found to fall within the acceptable absorbance (260/280) range of 1.8-2.1.

treatment_protocol: Male chicks (Leghorn/New Hampshire) were raised from post-hatch days 0-2 under a 12-hr day/night light cycle in groups of <25.  In the middle of the light cycle on day 2, chicks were randomly assigned to a lens condition (FD or No Lens) and occluders attached to Velcro were fixed to the periocular feathers of the right eye. Following a further 10 days, tissue was collected from no lens and FDM chicks. At the same time, occluders were removed from FDMR chicks. Tissue was collected from these FDMR chicks following 6hrs or 24hrs recovery.

tag: breed

value: Leghorn/New Hampshire

value: male

tag: treatment

value: control

tag: post-treatment

value: Post-hatch day 11

tag: time-point

value: 7 days (post-occlusion)

tag: lens type

value: No Lens

value: Retina, RPE, choroid


title: retina/RPE/choroid_FD_6hr_pooled

description:
After initiation of form deprivation myopia (FDM) for 7 days, occluders were removed to allow 6 hrs of normal light and FDM recovery (FDMR)
FD_6hrs

value: 7 days form deprivation (FDM)

value: 6 hours recovery

value: FDMR (6hrs)

tag: tissue


title: retina/RPE/choroid_FD_0hr_pooled

description:
Form deprivation myopia (FDM) was initiated for 7 days
FD_0hrs

value: 0 hours recovery

value: FDM (7 days)


title: Liver_DDE_rep4

city: Cordoba

first: Nieves

last: Abril

state: Not Applicable

address: Campus Rabanales, edificio C6, 2ª planta

institute: University of Córdoba

description: Gene expression after 30 days of 450mg/kg feed DDE supplemented diet

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Fragmentation Buffer (Agilent) and 2x Gene Expression Blocking Agent (Agilent) following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µL of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent HD Mouse GE 4×44K v2 Microarrays (G2519F-026655) for 17 hours at 65°C in a rotating Agilent G2545A hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent), then dried in an ozone-free atmosphere.

scan_protocol: Microarray slides were scanned with an Axon GenePix 4100A Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Image analysis and quantification of fluorescence data were carried out with GenePix Pro 4.1 software (Molecular Devices, LLC. Sunnyvale, USA) using default parameters (Grid: 026655_D_20150604) to obtain background substracted and spatially detrended Processed Signal intensities. Features flagged as Feature Non-uniform outliers were excluded.

organism: Mus spretus

source_name: Liver, DDE, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Agilent Low-Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) following the manufacturer's recomendations. The protocol includes an on-column DNase digestion. Total RNA was quantified in a DU800 Spectrophotometer (BECKMAN COULTER) using a Hellma cuvette and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Liver

value: Male

tag: strain

value: inbred SPRET/EiJ


title: Liver_DDE_rep3

source_name: Liver, DDE, replicate 3


title: E8B_ASCL1_SOX2_DORSO_2_d14

description:
E8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1

value: brain

tag: genotype/variation

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 183

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample183

value: F

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: C

value: Left

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 187

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample187

value: D

tag: site

tag: estimated macrod2 status

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [10003885067_R03C02]

tag: Sex

tag: age

tag: study

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: E9B_ASCL1_SOX2_DORSO_2_d14

description:
E9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: cell type


title: Colorectal adenocarcinoma tumor 181

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample181

tag: gender

tag: tissue

value: Right


title: Liver_control_rep4

description: Gene expression after 30 days of normal diet

source_name: Liver, control, replicate 4

tag: strain


title: F10B_ASCL1_SOX2_DORSO_2_d14

description:
F10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: genotype/variation


title: Liver_control_rep3

source_name: Liver, control, replicate 3


title: retina/RPE/choroid_FD_24hr_pooled

description:
After initiation of form deprivation myopia (FDM) for 7 days, occluders were removed to allow 24hrs of normal light and FDM recovery (FDMR)
FD_24hrs

tag: breed

value: Leghorn/New Hampshire

value: male

tag: treatment

value: 7 days form deprivation (FDM)

tag: post-treatment

value: 24 hours recovery

value: Post-hatch day 12

tag: time-point

value: 8 days (post-occlusion)

tag: lens type

value: FDMR (24hrs)

value: Retina, RPE, choroid


title: Colorectal adenocarcinoma tumor 180

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample180

value: M

value: Colorectal adenocarcinoma

tag: disease state

tag: Stage

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: E7B_ASCL1_SOX2_DORSO_2_d14

description:
E7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: tissue source

value: brain

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: F11B_ASCL1_SOX2_DORSO_2_d14

description:
F11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 179

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample179

tag: gender

tag: tissue

value: Adenocarcinoma

value: D

value: Left

value: Wild-type


title: genomic DNA from peripheral white blood cells [10003885067_R02C02]

tag: Sex

value: Female

tag: age

tag: study

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: F12B_ASCL1_SOX2_DORSO_2_d14

description:
F12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 177

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample177

value: F

tag: disease state

value: Heterozygous deletion


title: F1B_ASCL1_SOX2_DORSO_2_d14

description:
F1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 178

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample178

tag: Stage

value: Homozygous deletion


title: Liver_DDE_rep1

description: Gene expression after 30 days of 450mg/kg feed DDE supplemented diet

source_name: Liver, DDE, replicate 1

value: Liver

value: Male

tag: strain

value: inbred SPRET/EiJ


title: genomic DNA from peripheral white blood cells [10003885067_R01C01]


title: Liver_DDE_rep2

source_name: Liver, DDE, replicate 2