title: Colorectal adenocarcinoma tumor 429

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample429


title: D6A_Ascl1_Sox2_d21

status: Public on Jun 05 2018

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:
D6A_Ascl1Sox2d21
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

organism: Homo sapiens

growth_protocol: Differentiation medium

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: D7A_Ascl1_Sox2_d21

description:
D7A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D9A_Ascl1_Sox2_d21

description:
D9A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 427

type: genomic

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).
Sample427

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

molecule: genomic DNA

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: Left

tag: estimated macrod2 status

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: E10A_Ascl1_Sox2_d21

description:
E10A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C11A_Ascl1_Sox2_d21

description:
C11A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E1A_Ascl1_Sox2_d21

description:
E1A_Ascl1Sox2d21
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 [3999356071_R03C01]

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

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: E2A_Ascl1_Sox2_d21

description:
E2A_Ascl1Sox2d21
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 [3999356071_R02C02]

value: Female


title: Colorectal adenocarcinoma tumor 426

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample426

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

value: Right


title: E3A_Ascl1_Sox2_d21

description:
E3A_Ascl1Sox2d21
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 [3999356071_R01C01]


title: Colorectal adenocarcinoma tumor 425

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample425

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

value: Rectum


title: E5A_Ascl1_Sox2_d21

description:
E5A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 430

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample430

value: B

value: Heterozygous deletion


title: E8A_Ascl1_Sox2_d21

description:
E8A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 424

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample424


title: genomic DNA from peripheral white blood cells [3999356066_R04C01]


title: C9A_Ascl1_Sox2_d21

description:
C9A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: E7A_Ascl1_Sox2_d21

description:
E7A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D1A_Ascl1_Sox2_d21

description:
D1A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D12A_Ascl1_Sox2_d21

description:
D12A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E9A_Ascl1_Sox2_d21

description:
E9A_Ascl1Sox2d21
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 [3999356066_R03C02]


title: genomic DNA from peripheral white blood cells [3999356066_R02C02]


title: Colorectal adenocarcinoma tumor 423

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample423

tag: gender


title: Colorectal adenocarcinoma tumor 422

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample422

value: F

tag: tissue


title: F11A_Ascl1_Sox2_d21

description:
F11A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: F10A_Ascl1_Sox2_d21

description:
F10A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: F1A_Ascl1_Sox2_d21

description:
F1A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: F12A_Ascl1_Sox2_d21

description:
F12A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 421

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample421

value: M

tag: disease state


title: genomic DNA from peripheral white blood cells [200308800045_R06C02]

value: DIOGENES

tag: homa-ir


title: Colorectal adenocarcinoma tumor 420

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample420

value: Colorectal adenocarcinoma

value: Adenocarcinoma

tag: Stage

tag: site


title: F8A_Ascl1_Sox2_d21

description:
F8A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F6A_Ascl1_Sox2_d21

description:
F6A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F9A_Ascl1_Sox2_d21

description:
F9A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 419

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample419

value: D

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200308800045_R06C01]

tag: Sex

tag: age


title: G10A_Ascl1_Sox2_d21

description:
G10A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G11A_Ascl1_Sox2_d21

description:
G11A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G2A_Ascl1_Sox2_d21

description:
G2A_Ascl1Sox2d21
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 [200308800045_R05C02]

tag: study

tag: array


title: Colorectal adenocarcinoma tumor 418

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample418

value: A


title: genomic DNA from peripheral white blood cells [200308800045_R05C01]

tag: waist circumference (cm)


title: G5A_Ascl1_Sox2_d21

description:
G5A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: genomic DNA from peripheral white blood cells [200308800045_R04C02]


title: G4A_Ascl1_Sox2_d21

description:
G4A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 417

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample417

tag: gender

value: C

value: Wild-type


title: G7A_Ascl1_Sox2_d21

description:
G7A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: G8A_Ascl1_Sox2_d21

description:
G8A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 416

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample416

tag: tissue

tag: disease state


title: genomic DNA from peripheral white blood cells [3999356066_R01C01]

value: Female

value: PREDIMED


title: H2A_Ascl1_Sox2_d21

description:
H2A_Ascl1Sox2d21
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 [200308800045_R04C01]


title: H4A_Ascl1_Sox2_d21

description:
H4A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 415

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample415

tag: Stage

value: Right


title: H5A_Ascl1_Sox2_d21

description:
H5A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H6A_Ascl1_Sox2_d21

description:
H6A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 413

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample413

tag: site

value: Rectum


title: H7A_Ascl1_Sox2_d21

description:
H7A_Ascl1Sox2d21
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 [200308800045_R03C01]

value: GEDYMET

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200308800045_R03C02]


title: H9A_Ascl1_Sox2_d21

description:
H9A_Ascl1Sox2d21
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 [200308800045_R02C02]


title: Colorectal adenocarcinoma tumor 412

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample412

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200308800045_R02C01]

tag: Sex

tag: age


title: A4A_Ascl1_Sox2_d22

description:
A4A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 411

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample411

value: F

value: Left


title: A3A_Ascl1_Sox2_d22

description:
A3A_Ascl1Sox2d22
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 [200308800045_R01C02]

value: Male

tag: study

tag: array


title: A6A_Ascl1_Sox2_d22

description:
A6A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Ascl1 and Sox2 transduced


title: H1A_Ascl1_Sox2_d21

description:
H1A_Ascl1Sox2d21
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 410

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample410

value: M

value: Colorectal adenocarcinoma

value: B


title: B11A_Ascl1_Sox2_d22

description:
B11A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 409

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample409

value: Adenocarcinoma

value: Homozygous deletion


title: A9A_Ascl1_Sox2_d22

description:
A9A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 408

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample408

tag: gender

value: D

value: Wild-type


title: B12A_Ascl1_Sox2_d22

description:
B12A_Ascl1Sox2d22
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 [200308800045_R01C01]

value: PREDIMED

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200308800038_R06C02]


title: B3A_Ascl1_Sox2_d22

description:
B3A_Ascl1Sox2d22
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 [200308800038_R06C01]


title: Colorectal adenocarcinoma tumor 414

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample414

tag: tissue

tag: disease state

value: A


title: B1A_Ascl1_Sox2_d22

description:
B1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 407

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample407

tag: Stage

tag: site

value: Rectum

value: Heterozygous deletion


title: A1A_Ascl1_Sox2_d22

description:
A1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B4A_Ascl1_Sox2_d22

description:
B4A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 406

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample406

value: C

tag: estimated macrod2 status


title: A10A_Ascl1_Sox2_d22

description:
A10A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B5A_Ascl1_Sox2_d22

description:
B5A_Ascl1Sox2d22
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 [200308800038_R05C02]

value: Female

value: GEDYMET

tag: homa-ir


title: B7A_Ascl1_Sox2_d22

description:
B7A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: C10A_Ascl1_Sox2_d22

description:
C10A_Ascl1Sox2d22
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 405

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample405

value: M

value: Left

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200308800038_R05C01]

tag: Sex

tag: age


title: B6A_Ascl1_Sox2_d22

description:
B6A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C12A_Ascl1_Sox2_d22

description:
C12A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 404

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample404

value: Colorectal adenocarcinoma


title: genomic DNA from peripheral white blood cells [200308800038_R04C01]

tag: study

value: DIOGENES

tag: array


title: genomic DNA from peripheral white blood cells [200308800038_R04C02]

value: Male


title: C1A_Ascl1_Sox2_d22

description:
C1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: C3A_Ascl1_Sox2_d22

description:
C3A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation


title: C4A_Ascl1_Sox2_d22

description:
C4A_Ascl1Sox2d22
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 402

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample402

tag: gender

value: F

value: Adenocarcinoma


title: C5A_Ascl1_Sox2_d22

description:
C5A_Ascl1Sox2d22
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 [200308800038_R03C01]

tag: waist circumference (cm)


title: C8A_Ascl1_Sox2_d22

description:
C8A_Ascl1Sox2d22
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 [200308800038_R03C02]


title: C6A_Ascl1_Sox2_d22

description:
C6A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C9A_Ascl1_Sox2_d22

description:
C9A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A8A_Ascl1_Sox2_d22

description:
A8A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 401

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample401

tag: tissue

tag: disease state

value: B

value: Right

value: Wild-type


title: genomic DNA from peripheral white blood cells [200308800038_R02C02]

value: PREDIMED


title: D1A_Ascl1_Sox2_d22

description:
D1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D12A_Ascl1_Sox2_d22

description:
D12A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 400

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample400

tag: Stage

value: D

tag: site


title: D2A_Ascl1_Sox2_d22

description:
D2A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D11A_Ascl1_Sox2_d22

description:
D11A_Ascl1Sox2d22
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 [200308800038_R02C01]

value: Female


title: Colorectal adenocarcinoma tumor 399

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample399

value: A

tag: estimated macrod2 status

value: Heterozygous deletion


title: D5A_Ascl1_Sox2_d22

description:
D5A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: Colorectal adenocarcinoma tumor 398

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample398

value: M

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200308800038_R01C01]

tag: Sex

value: GEDYMET

tag: homa-ir


title: D4A_Ascl1_Sox2_d22

description:
D4A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: D3A_Ascl1_Sox2_d22

description:
D3A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D6A_Ascl1_Sox2_d22

description:
D6A_Ascl1Sox2d22
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 [200308800038_R01C02]

tag: age

tag: study


title: Colorectal adenocarcinoma tumor 397

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample397

value: Colorectal adenocarcinoma


title: D7A_Ascl1_Sox2_d22

description:
D7A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id


title: Colorectal adenocarcinoma tumor 396

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample396

value: C


title: Colorectal adenocarcinoma tumor 403

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample403

value: Rectum


title: D8A_Ascl1_Sox2_d22

description:
D8A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: Colorectal adenocarcinoma tumor 395

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample395

value: F

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [200078650096_R06C01]

tag: array


title: D9A_Ascl1_Sox2_d22

description:
D9A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation


title: E10A_Ascl1_Sox2_d22

description:
E10A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: E11A_Ascl1_Sox2_d22

description:
E11A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E12A_Ascl1_Sox2_d22

description:
E12A_Ascl1Sox2d22
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 [200078650096_R05C02]

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 393

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample393

tag: gender

tag: tissue

value: B

value: Right

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [200078650096_R05C01]

value: Male

value: PREDIMED


title: Colorectal adenocarcinoma tumor 394

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample394

tag: disease state

tag: Stage

value: Wild-type


title: E5A_Ascl1_Sox2_d22

description:
E5A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E3A_Ascl1_Sox2_d22

description:
E3A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E6A_Ascl1_Sox2_d22

description:
E6A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E4A_Ascl1_Sox2_d22

description:
E4A_Ascl1Sox2d22
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 [200078650096_R04C02]

value: Female

value: DIOGENES


title: E8A_Ascl1_Sox2_d22

description:
E8A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: F10A_Ascl1_Sox2_d22

description:
F10A_Ascl1Sox2d22
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 [200078650096_R03C02]


title: Colorectal adenocarcinoma tumor 392

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample392

tag: site

tag: estimated macrod2 status

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 390

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample390

value: Left

tag: estimated chromosome segment number (ecsn)


title: F11A_Ascl1_Sox2_d22

description:
F11A_Ascl1Sox2d22
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 391

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample391

value: Colorectal adenocarcinoma

value: A


title: F12A_Ascl1_Sox2_d22

description:
F12A_Ascl1Sox2d22
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 [200078650096_R06C02]

tag: Sex

value: GEDYMET

tag: homa-ir


title: Colorectal adenocarcinoma tumor 389

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample389

value: F

value: Adenocarcinoma

value: D


title: F4A_Ascl1_Sox2_d22

description:
F4A_Ascl1Sox2d22
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 [200078650096_R03C01]

tag: age

tag: study


title: F1A_Ascl1_Sox2_d22

description:
F1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: genomic DNA from peripheral white blood cells [200078650096_R02C02]

tag: array


title: F5A_Ascl1_Sox2_d22

description:
F5A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 388

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample388

value: M

value: Right


title: genomic DNA from peripheral white blood cells [200078650096_R02C01]

value: Male

value: PREDIMED

tag: waist circumference (cm)


title: F6A_Ascl1_Sox2_d22

description:
F6A_Ascl1Sox2d22
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 387

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample387

tag: gender

tag: tissue


title: F8A_Ascl1_Sox2_d22

description:
F8A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 386

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample386

tag: disease state

tag: Stage

value: C

value: Rectum

value: Wild-type


title: G10A_Ascl1_Sox2_d22

description:
G10A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: G11A_Ascl1_Sox2_d22

description:
G11A_Ascl1Sox2d22
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 [200078650096_R04C01]

value: DIOGENES


title: G12A_Ascl1_Sox2_d22

description:
G12A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: E9A_Ascl1_Sox2_d22

description:
E9A_Ascl1Sox2d22
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 [200078650096_R01C02]

value: Female


title: Colorectal adenocarcinoma tumor 385

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample385

value: Colorectal adenocarcinoma

value: B

tag: site

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 384

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample384

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200078650080_R05C02]

tag: Sex

value: EPALIP

tag: homa-ir


title: G2A_Ascl1_Sox2_d22

description:
G2A_Ascl1Sox2d22
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 [200078650083_R06C02]

tag: age

tag: study


title: G3A_Ascl1_Sox2_d22

description:
G3A_Ascl1Sox2d22
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 383

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample383

value: Adenocarcinoma


title: G5A_Ascl1_Sox2_d22

description:
G5A_Ascl1Sox2d22
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 [200078650080_R03C01]

tag: array


title: G6A_Ascl1_Sox2_d22

description:
G6A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 382

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample382

value: M


title: G7A_Ascl1_Sox2_d22

description:
G7A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: G9A_Ascl1_Sox2_d22

description:
G9A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H12A_Ascl1_Sox2_d22

description:
H12A_Ascl1Sox2d22
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 [200078650069_R05C02]

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650069_R04C01]

value: GEDYMET


title: Colorectal adenocarcinoma tumor 381

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample381

tag: gender

value: F

tag: tissue


title: H1A_Ascl1_Sox2_d22

description:
H1A_Ascl1Sox2d22
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 [200078650096_R01C01]


title: G1A_Ascl1_Sox2_d22

description:
G1A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H3A_Ascl1_Sox2_d22

description:
H3A_Ascl1Sox2d22
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 [200078650069_R03C01]


title: Colorectal adenocarcinoma tumor 380

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample380

tag: disease state

tag: Stage

value: Left

value: Homozygous deletion


title: Colorectal adenocarcinoma tumor 379

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample379

value: C

tag: site

value: Right

tag: estimated macrod2 status


title: H5A_Ascl1_Sox2_d22

description:
H5A_Ascl1Sox2d22
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 [200078650069_R02C01]

tag: Sex


title: Colorectal adenocarcinoma tumor 378

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample378

tag: estimated chromosome segment number (ecsn)


title: G4A_Ascl1_Sox2_d22

description:
G4A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: genomic DNA from peripheral white blood cells [200078650069_R01C01]

tag: age

tag: homa-ir


title: Colorectal adenocarcinoma tumor 377

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample377

value: A

value: Wild-type


title: H8A_Ascl1_Sox2_d22

description:
H8A_Ascl1Sox2d22
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Ascl1 and Sox2 transduced


title: genomic DNA from peripheral white blood cells [200078650067_R06C02]

value: Female

tag: study


title: A11A_Ascl1_Sox2_d7

description:
A11A_Ascl1Sox2d7
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 [200078650067_R06C01]

tag: array


title: Colorectal adenocarcinoma tumor 375

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample375

value: Colorectal adenocarcinoma

value: D


title: A12A_Ascl1_Sox2_d7

description:
A12A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation

tag: timepoint (days post infection)


title: MSC_RelA_TNFa_rep1

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: RelA knockout upon TNFa stimuli

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: vascular mesenchymal stem cells

growth_protocol: Human VECs were cultured in EC culture medium containing EGM-2 (Lonza) medium with 50 ng/mL VEGF (HumanZyme), 10 mM SB431542 (Selleck) and FGF2 (Joint Protein Central, JPC). Human VSMCs were cultured in N2B27 medium (500 mL DMEM/F12 medium (Gibco), 500 mL Neurobasal medium (Gibco), 20 mL B27 (Gibco), 10 mL N2 (Gibco), 1 mL β-Mercaptoethanol (Gibco) and 10 ng/mL PDGF-BB (Peprotech)). Human MSCs were cultured in -MEM medium (Gibco) supplemented with 10% fetal bovine serum (Ausbian, VS500T), 1% penicillin/streptomycin (Gibco), and 1 ng/mL FGF2 (JPC).

extract_protocol:
Cells were harvested in TRIzol reagent (Invitrogen) and RNA was extracted according to the manufacturers’ instruction.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: ES-derived mesenchymal stem cells

tag: genotype

value: RelA Knockout

tag: passage


title: MSC_RelA_basal_rep1

description: RelA knockout under basal condition


title: MSC_RelA_IL1b_rep1

description: RelA knockout upon IL1b stimuli


title: A1A_Ascl1_Sox2_d7

description:
A1A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 376

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample376

tag: gender

value: M

tag: tissue

tag: disease state

value: Adenocarcinoma

value: B


title: MSC_RelA_basal_rep2

description: RelA knockout under basal condition


title: MSC_RelA_IL1b_rep2

description: RelA knockout upon IL1b stimuli


title: Colorectal adenocarcinoma tumor 374

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample374

tag: Stage

tag: site

tag: estimated macrod2 status


title: MSC_IkBa_TNFa_rep2

description: IB knockout upon TNFa stimuli

value: IkBa Knockout


title: A4A_Ascl1_Sox2_d7

description:
A4A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MSC_RelA_TNFa_rep2

description: RelA knockout upon TNFa stimuli


title: genomic DNA from peripheral white blood cells [200078650061_R06C01]

tag: Sex

tag: age

value: GEDYMET

tag: waist circumference (cm)


title: H6A_Ascl1_Sox2_d22

description:
H6A_Ascl1Sox2d22
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 [200078650061_R06C02]

tag: study

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200078650061_R05C02]

tag: array


title: genomic DNA from peripheral white blood cells [200078650061_R05C01]


title: MSC_IkBa_TNFa_rep1

description: IB knockout upon TNFa stimuli

tag: cell type


title: A6A_Ascl1_Sox2_d7

description:
A6A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: genotype/variation

tag: timepoint (days post infection)


title: A7A_Ascl1_Sox2_d7

description:
A7A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MSC_IkBa_IL1b_rep2

description: IB knockout upon IL1b stimuli

tag: genotype

tag: passage


title: Colorectal adenocarcinoma tumor 372

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample372

tag: gender

tag: tissue

tag: disease state

value: Rectum

tag: estimated chromosome segment number (ecsn)


title: MSC_IkBa_IL1b_rep1

description: IB knockout upon IL1b stimuli


title: Colorectal adenocarcinoma tumor 373

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample373

tag: Stage

tag: site

tag: estimated macrod2 status


title: genomic DNA from peripheral white blood cells [200078650061_R04C02]

tag: Sex

value: Male

tag: age

value: DIOGENES

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 370

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample370

value: F

value: Right


title: genomic DNA from peripheral white blood cells [200078650061_R04C01]

tag: study

tag: array


title: A8A_Ascl1_Sox2_d7

description:
A8A_Ascl1Sox2d7
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

value: brain

tag: cell type


title: MSC_IkBa_basal_rep2

description: IB knockout under basal condition

tag: genotype


title: Colorectal adenocarcinoma tumor 369

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample369

value: A

value: Left

value: Wild-type


title: Colorectal adenocarcinoma tumor 368

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample368

value: Colorectal adenocarcinoma

value: D


title: B10A_Ascl1_Sox2_d7

description:
B10A_Ascl1Sox2d7
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

tag: timepoint (days post infection)


title: A9A_Ascl1_Sox2_d7

description:
A9A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MSC_IkBa_basal_rep1

description: IB knockout under basal condition

value: ES-derived mesenchymal stem cells

tag: passage


title: genomic DNA from peripheral white blood cells [200078650061_R03C01]

value: Female

tag: homa-ir


title: B11A_Ascl1_Sox2_d7

description:
B11A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MSC_WT_TNFa_rep2

description: WT upon TNFa stimuli

value: WT


title: genomic DNA from peripheral white blood cells [200078650061_R02C02]

value: GEDYMET


title: MSC_WT_TNFa_rep1

description: WT upon TNFa stimuli


title: Colorectal adenocarcinoma tumor 366

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample366

tag: gender

tag: tissue

tag: disease state

value: Adenocarcinoma

value: C

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 367

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample367

tag: Stage

tag: site

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 365

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample365

value: M

value: Rectum

value: Homozygous deletion


title: B12A_Ascl1_Sox2_d7

description:
B12A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: Colorectal adenocarcinoma tumor 371

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample371

value: B


title: B2A_Ascl1_Sox2_d7

description:
B2A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: MSC_WT_IL1b_rep2

description: WT upon IL1b stimuli


title: genomic DNA from peripheral white blood cells [200078650061_R01C02]

tag: Sex

tag: age

tag: study

tag: waist circumference (cm)


title: Colorectal adenocarcinoma tumor 364

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample364

value: F

value: Left


title: MSC_WT_IL1b_rep1

description: WT upon IL1b stimuli

tag: cell type


title: genomic DNA from peripheral white blood cells [200078650061_R01C01]

tag: array


title: MSC_WT_basal_rep2

description: WT under basal condition

tag: genotype


title: B3A_Ascl1_Sox2_d7

description:
B3A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

tag: genotype/variation

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200078650061_R03C02]

tag: homa-ir


title: Colorectal adenocarcinoma tumor 362

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample362

tag: gender

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Right

value: Wild-type


title: MSC_WT_basal_rep1

description: WT under basal condition

value: ES-derived mesenchymal stem cells

tag: passage


title: genomic DNA from peripheral white blood cells [200078650060_R06C02]

value: Female

value: PREDIMED


title: Colorectal adenocarcinoma tumor 361

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample361

tag: Stage

value: A

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: VSMC_RelA_basal_rep2

description: RelA knockout under basal condition

source_name: vascular smooth muscle cells

value: ES-derived vascular smooth muscle cells

value: RelA Knockout


title: B6A_Ascl1_Sox2_d7

description:
B6A_Ascl1Sox2d7
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 [200078650060_R05C02]

tag: Sex

tag: age

tag: study

value: GEDYMET

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650061_R02C01]

tag: array


title: Colorectal adenocarcinoma tumor 360

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample360

value: M

value: Adenocarcinoma

value: D

value: Heterozygous deletion


title: B7A_Ascl1_Sox2_d7

description:
B7A_Ascl1Sox2d7
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

value: brain

tag: cell type


title: Colorectal adenocarcinoma tumor 359

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample359

value: F

value: Colorectal adenocarcinoma

value: C

value: Rectum


title: genomic DNA from peripheral white blood cells [200078650060_R05C01]

value: Female

tag: homa-ir


title: VSMC_RelA_basal_rep1

description: RelA knockout under basal condition

tag: genotype


title: genomic DNA from peripheral white blood cells [200078650060_R04C02]

value: Male

value: PREDIMED


title: VSMC_RelA_TNFa_rep1

description: RelA knockout upon TNFa stimuli

value: ES-derived vascular smooth muscle cells


title: Colorectal adenocarcinoma tumor 358

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample358

tag: gender

tag: tissue

value: Left


title: VSMC_RelA_TNFa_rep2

description: RelA knockout upon TNFa stimuli

value: RelA Knockout

tag: passage


title: B4A_Ascl1_Sox2_d7

description:
B4A_Ascl1Sox2d7
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

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200078650060_R04C01]


title: Colorectal adenocarcinoma tumor 357

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample357

tag: disease state

tag: Stage

tag: site

value: Right

tag: estimated macrod2 status

value: Wild-type


title: C10A_Ascl1_Sox2_d7

description:
C10A_Ascl1Sox2d7
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 [200078650060_R03C02]

tag: Sex

tag: age

tag: study

value: GEDYMET


title: Colorectal adenocarcinoma tumor 363

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample363

value: Adenocarcinoma

value: B

tag: estimated chromosome segment number (ecsn)


title: VSMC_IkBa_basal_rep2

description: IB knockout under basal condition

value: IkBa Knockout


title: B5A_Ascl1_Sox2_d7

description:
B5A_Ascl1Sox2d7
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

value: brain


title: Colorectal adenocarcinoma tumor 356

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample356

value: F

value: Colorectal adenocarcinoma

value: D

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [200078650060_R06C01]

value: Female

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: C12A_Ascl1_Sox2_d7

description:
C12A_Ascl1Sox2d7
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 [200078650060_R03C01]

tag: homa-ir


title: VSMC_IkBa_TNFa_rep2

description: IB knockout upon TNFa stimuli

value: ES-derived vascular smooth muscle cells

tag: genotype

tag: passage


title: VSMC_IkBa_TNFa_rep1

description: IB knockout upon TNFa stimuli


title: Colorectal adenocarcinoma tumor 355

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample355

tag: gender

value: M

tag: tissue

value: Rectum


title: B8A_Ascl1_Sox2_d7

description:
B8A_Ascl1Sox2d7
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

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 354

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample354

tag: disease state

tag: Stage

tag: site

value: Left

tag: estimated macrod2 status

value: Heterozygous deletion


title: B9A_Ascl1_Sox2_d7

description:
B9A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C2A_Ascl1_Sox2_d7

description:
C2A_Ascl1Sox2d7
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 [200078650060_R02C01]

tag: Sex

tag: age

tag: study

value: DIOGENES


title: genomic DNA from peripheral white blood cells [200078650060_R02C02]

value: Male

tag: array


title: VSMC_WT_basal_rep2

description: WT under basal condition

value: WT


title: Colorectal adenocarcinoma tumor 353

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample353

value: Adenocarcinoma

value: B

tag: estimated chromosome segment number (ecsn)


title: VSMC_IkBa_basal_rep1

description: IB knockout under basal condition

tag: cell type

value: IkBa Knockout


title: Colorectal adenocarcinoma tumor 351

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample351

value: F

value: Colorectal adenocarcinoma

value: C

value: Right


title: genomic DNA from peripheral white blood cells [200078650060_R01C02]

value: PREDIMED

tag: waist circumference (cm)


title: C5A_Ascl1_Sox2_d7

description:
C5A_Ascl1Sox2d7
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

value: brain


title: VSMC_WT_TNFa_rep2

description: WT upon TNFa stimuli

value: ES-derived vascular smooth muscle cells

tag: genotype

tag: passage


title: genomic DNA from peripheral white blood cells [200078650054_R06C02]

value: Female


title: VSMC_WT_TNFa_rep1

description: WT upon TNFa stimuli


title: Colorectal adenocarcinoma tumor 352

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample352

tag: gender

value: M

tag: tissue

value: Rectum

value: Wild-type


title: Colorectal adenocarcinoma tumor 350

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample350

tag: disease state


title: genomic DNA from peripheral white blood cells [200078650054_R05C02]

value: GEDYMET

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200078650060_R01C01]


title: VEC_RelA_KO_basal_rep2

description: RelA knockout under basal condition

source_name: vascular endothelial cells

value: ES-derived vascular endothelial cells

value: RelA Knockout


title: C7A_Ascl1_Sox2_d7

description:
C7A_Ascl1Sox2d7
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

tag: timepoint (days post infection)


title: C8A_Ascl1_Sox2_d7

description:
C8A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C1A_Ascl1_Sox2_d7

description:
C1A_Ascl1Sox2d7
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 [200078650054_R05C01]

tag: Sex


title: C9A_Ascl1_Sox2_d7

description:
C9A_Ascl1Sox2d7
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 [200078650054_R04C02]

tag: age


title: Colorectal adenocarcinoma tumor 348

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample348

value: Adenocarcinoma

tag: Stage

value: D

tag: site

tag: estimated macrod2 status


title: C4A_Ascl1_Sox2_d7

description:
C4A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: D10A_Ascl1_Sox2_d7

description:
D10A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 347

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample347

value: Colorectal adenocarcinoma

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200078650054_R04C01]

value: Male

tag: study

tag: array

tag: waist circumference (cm)


title: VEC_RelA_KO_TNFa_rep2

description: RelA knockout upon TNFa stimuli

tag: genotype

tag: passage


title: D2A_Ascl1_Sox2_d7

description:
D2A_Ascl1Sox2d7
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 346

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample346

tag: gender

value: F

tag: tissue

tag: disease state

value: B


title: Colorectal adenocarcinoma tumor 345

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample345

value: C

value: Right


title: D3A_Ascl1_Sox2_d7

description:
D3A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain

tag: genotype/variation

tag: timepoint (days post infection)


title: VEC_IkBa_KO_basal_rep2

description: IB knockout under basal condition

value: IkBa Knockout


title: Colorectal adenocarcinoma tumor 349

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample349

tag: Stage

value: Left

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650054_R03C02]

tag: Sex

value: Female

tag: age

value: PREDIMED


title: VEC_IkBa_KO_basal_rep1

description: IB knockout under basal condition

tag: cell type

value: ES-derived vascular endothelial cells


title: D6A_Ascl1_Sox2_d7

description:
D6A_Ascl1Sox2d7
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 344

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample344

value: Adenocarcinoma

value: A

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: VEC_RelA_KO_basal_rep1

description: RelA knockout under basal condition

value: RelA Knockout


title: genomic DNA from peripheral white blood cells [200078650054_R03C01]

tag: study

tag: array

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650054_R02C02]

value: GEDYMET

tag: homa-ir


title: VEC_IkBa_KO_TNFa_rep2

description: IB knockout upon TNFa stimuli

tag: genotype

tag: passage


title: Colorectal adenocarcinoma tumor 343

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample343

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma


title: genomic DNA from peripheral white blood cells [200078650054_R02C01]


title: D7A_Ascl1_Sox2_d7

description:
D7A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

tag: genotype/variation


title: D9A_Ascl1_Sox2_d7

description:
D9A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: VEC_IkBa_KO_TNFa_rep1

description: IB knockout upon TNFa stimuli


title: Colorectal adenocarcinoma tumor 342

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample342

value: F

tag: disease state

tag: Stage

value: D


title: VEC_RelA_KO_TNFa_rep1

description: RelA knockout upon TNFa stimuli

tag: cell type


title: VEC_WT_basal_rep2

description: WT under basal condition

value: WT


title: genomic DNA from peripheral white blood cells [200078650054_R01C02]

tag: Sex

tag: age

value: DIOGENES


title: Colorectal adenocarcinoma tumor 341

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample341

value: C

tag: site

value: Rectum

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: E1A_Ascl1_Sox2_d7

description:
E1A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: Colorectal adenocarcinoma tumor 340

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample340

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650054_R01C01]

value: Male

tag: study

tag: array

tag: homa-ir

tag: waist circumference (cm)


title: VEC_WT_basal_rep1

description: WT under basal condition

value: ES-derived vascular endothelial cells

tag: genotype

tag: passage


title: E6A_Ascl1_Sox2_d7

description:
E6A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source

value: Ascl1 and Sox2 transduced


title: VEC_WT_TNFa_rep2

description: WT upon TNFa stimuli


title: genomic DNA from peripheral white blood cells [200078650033_R06C02]

value: Female


title: Colorectal adenocarcinoma tumor 339

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample339

tag: gender

tag: tissue

value: Adenocarcinoma

value: B

value: Right

value: Heterozygous deletion


title: genomic DNA from peripheral white blood cells [200078650033_R06C01]


title: VEC_WT_TNFa_rep1

description: WT upon TNFa stimuli


title: F1A_Ascl1_Sox2_d7

description:
F1A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 338

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample338

value: F

value: Colorectal adenocarcinoma

tag: disease state

tag: Stage

value: A


title: genomic DNA from peripheral white blood cells [200078650033_R05C01]

tag: Sex

tag: age

value: DIOGENES


title: F2A_Ascl1_Sox2_d7

description:
F2A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: F3A_Ascl1_Sox2_d7

description:
F3A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 336

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample336

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200078650033_R05C02]

tag: study

tag: array

tag: homa-ir

tag: waist circumference (cm)


title: F8A_Ascl1_Sox2_d7

description:
F8A_Ascl1Sox2d7
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 335

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample335

tag: gender

value: M

tag: tissue

value: D


title: genomic DNA from peripheral white blood cells [200078650033_R04C02]

value: PREDIMED


title: genomic DNA from peripheral white blood cells [200078650033_R04C01]


title: Colorectal adenocarcinoma tumor 334

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample334

value: Left


title: G7A_Ascl1_Sox2_d7

description:
G7A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain

tag: genotype/variation

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 333

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample333

tag: disease state

tag: Stage

value: Rectum

value: Wild-type


title: E7A_Ascl1_Sox2_d7

description:
E7A_Ascl1Sox2d7
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 [200078650033_R03C02]

tag: Sex

value: Male

tag: age


title: genomic DNA from peripheral white blood cells [200078650033_R02C02]

value: Female

value: GEDYMET


title: G9A_Ascl1_Sox2_d7

description:
G9A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 337

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample337

value: Adenocarcinoma

value: B

tag: site

value: Right

tag: estimated macrod2 status


title: ivEPC1 biological rep 3

type: RNA

city: Mexico

first: Hector

last: Mayani

state: Mexico City

address: Cuahutemoc 330

country: Mexico

institute: Oncology Research Unit

description:
ivEPC3
Gene expression data from in vitro generated EPC from fresh HSC took from USB.

hyb_protocol: Following fragmentation, 20 µg cRNA was hybridized for 16 hrs at 45ºC to 60 RPM on GeneChip Human Transcriptome Array V2. GeneChip was washed and stained in the station Fluidics Station 450 (Affymetrix, Santa Clara, USA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensities were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

label: biotin

source_name: Fresh umbilical cord blood

label_protocol: The WT Pico Reagent Kit was used to generate the biotinylated cRNA starting from 100pg of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

extract_protocol: RNA extraction was made according to the protocol for Single cell RNA purification Kit by Norgen Biotek Cat. 51800.

treatment_protocol: Cells were labeled using CD34, CD38, CD71 and CD45RA by purification using FACS. Recovery of cells was made using PBS 1X + EDTA 2mM + 2% BFS. Before RNA extraction, cells were washed using PBS and placed in lysis solution quickly.

tag: blood fraction/population

value: fHSC population

value: ivEPC


title: genomic DNA from peripheral white blood cells [200078650033_R02C01]

tag: study

tag: array


title: H1A_Ascl1_Sox2_d7

description:
H1A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 331

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample331

value: F

value: Colorectal adenocarcinoma

value: Homozygous deletion

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 330

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample330

value: M

value: D


title: ivEPC1 biological rep 2

description:
ivEPC2
Gene expression data from in vitro generated EPC from fresh HSC took from USB.


title: H9A_Ascl1_Sox2_d7

description:
H9A_Ascl1Sox2d7
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


title: G8A_Ascl1_Sox2_d7

description:
G8A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: fEPC_biological rep 3

description:
fEPC3
Gene expression data from fresh purified EPC from UCB.

value: MNC fraction

value: fEPC


title: fEPC_biological rep 4

description:
fEPC4
Gene expression data from fresh purified EPC from UCB.


title: fEPC_biological rep 2

description:
fEPC2
Gene expression data from fresh purified EPC from UCB.


title: Colorectal adenocarcinoma tumor 329

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample329

tag: gender

value: C

value: Left

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650033_R01C01]

value: Male

value: PREDIMED

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650031_R06C02]

value: Female

value: GEDYMET

tag: homa-ir


title: fEPC_biological rep 1

description:
fEPC1
Gene expression data from fresh purified EPC from UCB.


title: ivEPC1 biological rep 1

description:
ivEPC1
Gene expression data from in vitro generated EPC from fresh HSC took from USB.

value: fHSC population

value: ivEPC


title: A10A_ASCL1_SOX2_DORSO_1_d14

description:
A10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

growth_protocol: Differentiation medium plus dorsomorphin

tag: genotype/variation

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: ivMPC_biological rep 2

description:
ivMPC2
Gene expression data from in vitro generated MPC from fresh HSC took from USB.

value: ivMPC


title: VSMC_WT_basal_rep1

description: WT under basal condition

value: ES-derived vascular smooth muscle cells

tag: genotype

value: WT

tag: passage


title: genomic DNA from peripheral white blood cells [200078650031_R06C01]

tag: Sex

tag: age


title: Colorectal adenocarcinoma tumor 328

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample328

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: D

tag: site


title: Colorectal adenocarcinoma tumor 327

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample327

value: B

tag: estimated macrod2 status


title: C3A_Ascl1_Sox2_d7

description:
C3A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain

tag: cell type


title: Colorectal adenocarcinoma tumor 326

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample326

value: C

value: Left

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: A11A_ASCL1_SOX2_DORSO_1_d14

description:
A11A_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: A12A_ASCL1_SOX2_DORSO_1_d14

description:
A12A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H3A_Ascl1_Sox2_d7

description:
H3A_Ascl1Sox2d7
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: ivMPC_biological rep 3

description:
ivMPC3
Gene expression data from in vitro generated MPC from fresh HSC took from USB.

tag: blood fraction/population


title: genomic DNA from peripheral white blood cells [200078650031_R05C02]

value: Female

tag: study

value: GEDYMET

tag: array

tag: homa-ir

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650031_R05C01]


title: Colorectal adenocarcinoma tumor 325

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample325

tag: gender

value: Right

value: Wild-type


title: A1A_ASCL1_SOX2_DORSO_1_d14

description:
A1A_Ascl1Sox2Dorso1d14
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

tag: timepoint (days post infection)


title: A2A_ASCL1_SOX2_DORSO_1_d14

description:
A2A_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 [200078650031_R04C02]

tag: Sex

tag: age

value: PREDIMED


title: genomic DNA from peripheral white blood cells [200078650031_R04C01]


title: A3A_ASCL1_SOX2_DORSO_1_d14

description:
A3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 323

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample323

value: F

tag: tissue

tag: disease state

tag: Stage


title: fMPC_biological rep 3

description:
fMPC3
Gene expression data from fresh purified MPC from UCB.

value: MNC fraction

tag: cell type

value: fMPC


title: ivMPC_biological rep 1

description:
ivMPC1
Gene expression data from in vitro generated MPC from fresh HSC took from USB.

value: fHSC population

value: ivMPC


title: fMPC_biological rep 4

description:
fMPC4
Gene expression data from fresh purified MPC from UCB.


title: fMPC_biological rep 2

description:
fMPC2
Gene expression data from fresh purified MPC from UCB.


title: Colorectal adenocarcinoma tumor 324

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample324

value: M

value: Colorectal adenocarcinoma

value: Adenocarcinoma

value: A

tag: site

value: Rectum

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: A4A_ASCL1_SOX2_DORSO_1_d14

description:
A4A_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

value: brain


title: genomic DNA from peripheral white blood cells [200078650031_R03C01]

value: Male

tag: study

tag: array


title: ivHSC_biological rep 2

description:
ivHSC2
Gene expression data from in vitro generated HSC from fresh HSC took from USB.

tag: blood fraction/population

value: ivHSC


title: Colorectal adenocarcinoma tumor 332

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample332

tag: gender

value: C

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 321

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample321

value: D

value: Right

value: Wild-type


title: Colorectal adenocarcinoma tumor 322

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample322

value: F

value: Left


title: A5A_ASCL1_SOX2_DORSO_1_d14

description:
A5A_Ascl1Sox2Dorso1d14
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: A6A_ASCL1_SOX2_DORSO_1_d14

description:
A6A_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 320

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample320

value: M


title: Colorectal adenocarcinoma tumor 319

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample319

value: Colorectal adenocarcinoma


title: A7A_ASCL1_SOX2_DORSO_1_d14

description:
A7A_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 [200078650031_R03C02]

tag: Sex

value: PREDIMED

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200078650031_R02C01]

tag: age

value: DIOGENES

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200078650031_R01C02]


title: genomic DNA from peripheral white blood cells [200078650031_R02C02]

value: Female


title: Polysome CMTR1 2/LA #2

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Beatson CRUK

description:
polysome RNA
read_count_table.csv
WT_vs_2LA_Polys_edgeR_analysis.csv
WT_vs_Vec_Polys_edgeR_analysis.csv
2LA_vs_Vec_Polys_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: HA CMTR1 2L/A

value: Breast carcinoma

tag: cell line


title: Polysome CMTR1 #2

value: HA CMTR1 WT

tag: cell type


title: fMPC_biological rep 1

description:
fMPC1
Gene expression data from fresh purified MPC from UCB.

value: MNC fraction

value: fMPC


title: Colorectal adenocarcinoma tumor 318

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample318

tag: tissue

tag: disease state

value: Adenocarcinoma

tag: Stage

value: C

tag: site

value: Rectum

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: A8A_ASCL1_SOX2_DORSO_1_d14

description:
A8A_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

value: brain


title: fHSC_ biological rep 2

description:
fHSC2
Gene expression data from fresh purified HSC from UCB.

tag: blood fraction/population

value: fHSC


title: fHSC_ biological rep 1

description:
fHSC1
Gene expression data from fresh purified HSC from UCB.


title: Colorectal adenocarcinoma tumor 317

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample317

tag: gender

value: F

value: Left

value: Wild-type


title: genomic DNA from peripheral white blood cells [200078650024_R06C02]

tag: Sex

value: Male

tag: study

tag: array

tag: waist circumference (cm)


title: Polysome vector #2

tag: cell harvest date

tag: transfected with

value: Empty vector


title: fHSC_ biological rep 3

description:
fHSC3
Gene expression data from fresh purified HSC from UCB.

tag: cell type


title: A9A_ASCL1_SOX2_DORSO_1_d14

description:
A9A_Ascl1Sox2Dorso1d14
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

tag: timepoint (days post infection)


title: B10A_ASCL1_SOX2_DORSO_1_d14

description:
B10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 316

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample316

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

tag: Stage

value: B

value: Right


title: Polysome CMTR1 2/LA #1

value: HA CMTR1 2L/A

value: Breast carcinoma

tag: cell line


title: Colorectal adenocarcinoma tumor 315

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample315

value: Adenocarcinoma

value: C

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200078650031_R01C01]

value: Female

tag: age

value: DIOGENES


title: B12A_ASCL1_SOX2_DORSO_1_d14

description:
B12A_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

value: brain


title: B3A_ASCL1_SOX2_DORSO_1_d14

description:
B3A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Polysome CMTR1 #1

value: HA CMTR1 WT


title: genomic DNA from peripheral white blood cells [200078650024_R06C01]

tag: Sex

tag: study

tag: array


title: genomic DNA from peripheral white blood cells [200078650024_R05C02]

tag: homa-ir

tag: waist circumference (cm)


title: B4A_ASCL1_SOX2_DORSO_1_d14

description:
B4A_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: Colorectal adenocarcinoma tumor 314

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample314

tag: gender

tag: tissue

value: Rectum

value: Wild-type


title: Polysome vector #1

tag: cell harvest date

tag: transfected with

value: Empty vector


title: Colorectal adenocarcinoma tumor 313

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample313

value: F

tag: disease state

tag: Stage

tag: site


title: genomic DNA from peripheral white blood cells [200078650024_R05C01]

value: Male

tag: age


title: genomic DNA from peripheral white blood cells [200078650024_R04C02]

value: GEDYMET


title: B5A_ASCL1_SOX2_DORSO_1_d14

description:
B5A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: Colorectal adenocarcinoma tumor 312

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample312

value: M

value: Colorectal adenocarcinoma

value: Right

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: Input CMTR1 2/LA #2

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

value: HA CMTR1 2L/A

value: Breast carcinoma

tag: cell line


title: genomic DNA from peripheral white blood cells [200078650024_R04C01]

tag: Sex

value: Female

tag: study

tag: array

tag: homa-ir


title: Input CMTR1 #2

tag: cell type


title: genomic DNA from peripheral white blood cells [200078650024_R03C02]

tag: waist circumference (cm)


title: B7A_ASCL1_SOX2_DORSO_1_d14

description:
B7A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 310

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample310

tag: gender

tag: tissue

tag: disease state

value: Adenocarcinoma

value: C


title: genomic DNA from peripheral white blood cells [200078650024_R03C01]

tag: age


title: Input CMTR1 2/LA #1

tag: cell harvest date

tag: transfected with


title: Colorectal adenocarcinoma tumor 311

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample311

tag: Stage

tag: site

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 309

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample309

value: Left

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: B8A_ASCL1_SOX2_DORSO_1_d14

description:
B8A_Ascl1Sox2Dorso1d14
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: timepoint (days post infection)


title: ivHSC_biological rep 1

description:
ivHSC1
Gene expression data from in vitro generated HSC from fresh HSC took from USB.

tag: blood fraction/population

value: fHSC population

value: ivHSC


title: Input CMTR1 #1

value: HA CMTR1 WT

tag: cell type

tag: cell line


title: genomic DNA from peripheral white blood cells [200078650024_R02C02]

tag: Sex

tag: study

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: Input vector #1

value: Empty vector


title: genomic DNA from peripheral white blood cells [200078650024_R02C01]

value: Male


title: genomic DNA from peripheral white blood cells [200078650024_R01C02]


title: C10A_ASCL1_SOX2_DORSO_1_d14

description:
C10A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: genotype/variation

value: Ascl1 and Sox2 transduced


title: C11A_ASCL1_SOX2_DORSO_1_d14

description:
C11A_Ascl1Sox2Dorso1d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 306

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample306

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Right

value: Wild-type


title: Colorectal adenocarcinoma tumor 307

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample307

value: F

value: Adenocarcinoma

tag: Stage

tag: site

value: Rectum