title: P15_antiH3_ChIP

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
processed data file:
F2.DHR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP and ChIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs and DHRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than 10-6 were considered DMRs or DHRs. The DMR/DHR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR/DHR.
CpG density and other information was then calculated for the DMR/DHR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control or vinclozolin were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with vinclozolin. The control and vinclozolin lineage rats were housed in the same room with lighting, food and water.

extract_protocol: The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1x PBS solution for up to 24 hours at 4°C.  The epididymal tissue was minced and the released sperm was centrifuged at 6,000 x g, then the supernant removed, and the pellet resuspended in NIM buffer, to be stored at -80O C until further use. One hundred µl of sperm suspension was sonicated, spun down at 6,000 g, the pellet washed with 1x PBS once, and then combined with 820 µL DNA extraction buffer and 80 µl 0.1M DTT. The sample was incubated at 65ºC for 15 minutes. Following this incubation 80 µl proteinase K (20 mg/ml) was added and the sample incubated at 55ºC for at least 2 hours under constant rotation. Then 300 µl of protein precipitation solution (Promega, A7953) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 14,000 rpm for 30 minutes at 4ºC. One ml of the supernatant was transferred to a 2 ml tube and 2 µl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20ºC freezer for at least one hour. After precipitation the sample was centrifuged at 14,000 rpm for 20 min at 4ºC. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500 µl of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4ºC at 14,000 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 µl of nuclease free water. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat sperm DNA pools were generated using the appropriate amount of genomic DNA from each individual for 3 pools each of control and vinclozolin lineage animals. Genomic DNA was sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95˚C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ C and then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight.  The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).Histone chromatin immunoprecipitation with genomic DNA was performed as follows: rat sperm pools were generated using a total of 8 million sperm per pool for 3 pools of control and vinclozolin lineage animals. The control pools contained equal amounts of sperm for each of 3-4 individuals for a total of n=11 rats and the vinclozolin pools contained equal amounts of sperm for each of 3 individuals for a total of n=9 rats per exposure group. To remove any somatic cell contamination sperm samples from each animal were sonicated 10 seconds using a Sonic Dismembrator Model 300 (Thermo Scientific Fisher, USA) then centrifuged 4,000xg for 5 min at 4°C. The supernatant was discarded and the pellet resuspended and counted individually on a Neubauer counting chamber (Propper Manufacturing Co., Inc., New York, USA) prior to pooling. The sperm pools were reconstituted up to 1 ml with 1X PBS. To reduce disulfide bonds, 50 μl of 1M DTT was added to each pool and the pools were then incubated for 2 hours at room temperature under constant rotation. To quench any residual DTT in the reaction, 120 μl of fresh 1M NEM (N-Ethylmaleimide, Thermo Scientific, Rockford, USA) was then added and the samples incubated for 30 min at room temperature under constant rotation. The sperm cells were pelleted at 2,000g for 5 min at room temperature and the supernatant discarded. Pellets were resuspended in 1X PBS and then spun again at 2,000g for 5 min at room temperature. The supernatant was discarded. The sperm cells were then resuspended in “buffer 1” (final concentration: 15 mM Tris-HCl (pH 7.5), 60 mM KCl, 5 mM MgCl2, 0.1 mM EGTA; all filtered through a 0.22 μm filter and stored at room temperature) in a ratio of 2 million sperm cells per 50 μl. “Complete buffer” was “buffer 1” supplemented with 0.5% tergitol (vol/vol) and 1% DOC (wt/vol) (sodium deoxycholate, Sigma Aldrich 30970). 50 μl of this supplemented buffer was added to each aliquot. The samples were mixed and incubated for 20 min on ice. Sperm cell DNA was divided into aliquots of 4 μg of DNA. These aliquots were sonicated using the Covaris M220 the following way: 4 μg of genomic DNA was resuspended in 130 μl of complete buffer supplemented with tergitol 0.5% and DOC 1%. Covaris was set to a 10 min “Chromatin shearing” program and the program was run for each tube in the experiment.  For each sample 10 μl was run on a 1.5% agarose gel to verify fragment size.

treatment_protocol: On days 8 through 14 of gestation, the females were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (DMSO). DDT (dichlorodiphenyltrichloroethane) was obtained from Chem Service Inc. (West Chester, PA). Vinclozolin was obtained from Chem Service Inc. (West Chester, PA) and was injected in a 20 microliter DMSO vehicle.

value: Sprague Dawley SR

value: Sperm

tag: treatment

value: Vinclozolin lineage

tag: generation

tag: measurement

value: ChIP-seq

tag: ip antibody

value: monoclonal rabbit antihistone H3, Millipore 05-928


title: Colorectal adenocarcinoma tumor 182

status: Public on Jun 05 2018

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).
Sample182

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

organism: Homo sapiens

source_name: Colorectal adenocarcinoma

extract_protocol: AllPrep DNA/RNA Mini Kit (QUAGEN)

tag: gender

value: F

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: A

tag: site

value: Right

tag: estimated macrod2 status

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: Liver_control_rep2

type: RNA

city: Cordoba

first: Nieves

last: Abril

state: Not Applicable

address: Campus Rabanales, edificio C6, 2ª planta

country: Spain

institute: University of Córdoba

description: Gene expression after 30 days of normal diet

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

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

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

molecule: total RNA

organism: Mus spretus

source_name: Liver, control, replicate 2

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

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

value: Liver

value: Male

tag: strain

value: inbred SPRET/EiJ


title: MC1-CD44+/CD24-

type: SRA

city: Ann Arbor

first: Ming

last: Luo

state: MI

address: 2800 Plymouth Rd

department: Internal Medicine

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software was used for bcl to fastq conversion.
Sequencing reads were classified to either host (mouse) or graft (human) using Xenome 1.0.1. Resulting human fastq files were aligned to GRCh37 using STAR 2.3.1 using default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: normalized counts

extract_protocol:
FACS sorted cells were pelleted and flash frozen in 50ul PBS.  Total RNA from the frozen cell pellets were extracted using Norgen Single Cell RNA Purification Kit (catalog number 51800) as per manufacturer protocol. Quality of RNA was determined using Agilent BioAnalyzer with the Eukaryote total RNA Pico assay kit.  RNA libraries were prepared with 10ng total RNA as input using the Nugen Ovation RNASeq V2 library kit (cat# 7102-08) along with Kapa LTP library kit cat# KK8230).
RNA libraries were prepared as per standard manufacturer protocol

tag: rna integrity number

value: PDX


title: VARI068-ALDH+


title: VARI068-CD44+/CD24-


title: genomic DNA from peripheral white blood cells [10003885067_R03C01]

city: Pamplona

first: Ana

last: Arpón

address: Irunlarrea 1

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

tag: age

tag: study

value: PREDIMED

tag: array

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [10003885067_R04C01]

value: Female


title: VARI068-Bulk


title: MC1-ALDH+


title: Colorectal adenocarcinoma tumor 176

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample176

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

value: Left


title: F2B_ASCL1_SOX2_DORSO_2_d14

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
F2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

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.

growth_protocol: Differentiation medium plus dorsomorphin

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

tag: donor id

value: Donor 1

tag: tissue source

value: brain

tag: cell type

tag: genotype/variation

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: P14_antiH3_ChIP

library_source: genomic

value: Sprague Dawley SR

value: Sperm

tag: treatment

value: Vinclozolin lineage

tag: generation

tag: measurement

value: ChIP-seq

tag: ip antibody

value: monoclonal rabbit antihistone H3, Millipore 05-928


title: Colorectal adenocarcinoma tumor 175

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample175

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

tag: gender

value: M

tag: tissue

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: C

tag: site

tag: estimated macrod2 status

tag: estimated chromosome segment number (ecsn)


title: MC1-Bulk

tag: rna integrity number


title: P13_antiH3_ChIP

tag: strain


title: P12_antiH3_ChIP

description:
processed data file:
F1.DHR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.


title: F4B_ASCL1_SOX2_DORSO_2_d14

description:
F4B_Ascl1Sox2Dorso2d14
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 174

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample174

value: B

value: Wild-type


title: Colorectal adenocarcinoma tumor 173

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample173

value: F

value: A

value: Rectum

value: Homozygous deletion


title: F5B_ASCL1_SOX2_DORSO_2_d14

description:
F5B_Ascl1Sox2Dorso2d14
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

tag: genotype/variation


title: P11_antiH3_ChIP

value: Sprague Dawley SR

tag: treatment


title: MM at diagnosis, sample 29

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

data_processing:
Reads were aligned to the human genome using STAR under default conditions and Gencode v25 GTF file. STAR aligner was based on splice junctions from the Ensembl database version 87.
Transcript abundance was estimated using featureCounts (default parameters)
FPKM (Fragments Per Kilobase Million) quantification was performed on sorted BAM files using cufflinks
Differentially expressed genes were identified using DeSeq at FDR<0.01, provided that expression across the whole dataset was not null.
Genome_build: GRCh38
Supplementary_files_format_and_content: files including FPKM and tab-delimited text file with unnormalized readcounts for each sample

source_name: Highly purified PCs from MM patient

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
400 ng of total RNA were used to prepare paired-end (PE) cDNA libraries using the TruSeq® RNA Sample Preparation kit for total RNA (Illumina)

value: MM

value: Bone marrow plasma cells

tag: molecular alteration


title: F6B_ASCL1_SOX2_DORSO_2_d14

description:
F6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: MM at diagnosis, sample 30


title: MM at diagnosis, sample 28

value: hyperdiploid karyotype


title: Colorectal adenocarcinoma tumor 172

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample172

value: Right


title: Colorectal adenocarcinoma tumor 170

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample170

value: M

value: Colorectal adenocarcinoma


title: F7B_ASCL1_SOX2_DORSO_2_d14

description:
F7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F8B_ASCL1_SOX2_DORSO_2_d14

description:
F8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MM at diagnosis, sample 26

value: MAF translocation


title: P10_antiH3_ChIP

value: Sperm

value: Vinclozolin lineage

tag: generation

tag: measurement

value: ChIP-seq

tag: ip antibody

value: monoclonal rabbit antihistone H3, Millipore 05-928


title: F9B_ASCL1_SOX2_DORSO_2_d14

description:
F9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: P4_antiH3_ChIP

description:
processed data file:
F2.DHR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

value: Control


title: F3B_ASCL1_SOX2_DORSO_2_d14

description:
F3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: P3_antiH3_ChIP


title: MM at diagnosis, sample 25

tag: disease state


title: P5_antiH3_ChIP


title: Colorectal adenocarcinoma tumor 168

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample168

tag: gender

tag: tissue

value: Adenocarcinoma

tag: Stage

value: A

value: Rectum

value: Heterozygous deletion


title: MM at diagnosis, sample 24

value: MM


title: MM at diagnosis, sample 27

value: Bone marrow plasma cells


title: Colorectal adenocarcinoma tumor 167

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample167

value: C

tag: site

value: Left

tag: estimated macrod2 status

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 171

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample171

value: M

value: B


title: MM at diagnosis, sample 23

value: hyperdiploid karyotype


title: G12B_ASCL1_SOX2_DORSO_2_d14

description:
G12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1

value: brain

value: Ascl1 and Sox2 transduced


title: G11B_ASCL1_SOX2_DORSO_2_d14

description:
G11B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: MM at diagnosis, sample 22

tag: cell type

value: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: Colorectal adenocarcinoma tumor 166

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample166

value: Colorectal adenocarcinoma

value: D


title: Colorectal adenocarcinoma tumor 169

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample169

value: Adenocarcinoma

value: Right


title: Colorectal adenocarcinoma tumor 165

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample165

value: F

value: Heterozygous deletion


title: P1_antiH3_ChIP

description:
processed data file:
F1.DHR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

tag: strain

value: Sprague Dawley SR

value: Sperm

value: Control

value: ChIP-seq

value: monoclonal rabbit antihistone H3, Millipore 05-928


title: P6_antiH3_ChIP

tag: treatment


title: VF3P17_MeDIP

description:
processed data file:
F3.DMR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

value: Vinclozolin lineage

value: MeDIP-seq

value: monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006


title: MM at diagnosis, sample 21

value: MM

value: Bone marrow plasma cells

tag: molecular alteration

value: hyperdiploid karyotype


title: MM at diagnosis, sample 20


title: Colorectal adenocarcinoma tumor 164

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample164

value: M

value: Colorectal adenocarcinoma

value: A

value: Rectum

value: Wild-type


title: Colorectal adenocarcinoma tumor 163

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample163

value: F

value: Adenocarcinoma

value: B


title: G2B_ASCL1_SOX2_DORSO_2_d14

description:
G2B_Ascl1Sox2Dorso2d14
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

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: VF3P18_MeDIP

value: Sprague Dawley SR

value: Sperm

value: Vinclozolin lineage

tag: generation

tag: measurement


title: G3B_ASCL1_SOX2_DORSO_2_d14

description:
G3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G10B_ASCL1_SOX2_DORSO_2_d14

description:
G10B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MM at diagnosis, sample 19

tag: disease state

value: MM


title: Colorectal adenocarcinoma tumor 162

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample162

tag: gender

value: Left

value: Heterozygous deletion


title: P2_antiH3_ChIP

value: Control

value: ChIP-seq

tag: ip antibody

value: monoclonal rabbit antihistone H3, Millipore 05-928


title: CF3P9_MeDIP

value: MeDIP-seq

value: monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006


title: G5B_ASCL1_SOX2_DORSO_2_d14

description:
G5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G4B_ASCL1_SOX2_DORSO_2_d14

description:
G4B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: CF3P8_MeDIP


title: Colorectal adenocarcinoma tumor 161

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample161

value: F

tag: tissue

value: Colorectal adenocarcinoma

tag: Stage

value: C

value: Right

value: Wild-type


title: Colorectal adenocarcinoma tumor 160

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample160

value: M

value: Adenocarcinoma

tag: site

tag: estimated macrod2 status


title: MM at diagnosis, sample 17

value: Bone marrow plasma cells


title: G6B_ASCL1_SOX2_DORSO_2_d14

description:
G6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1

value: brain

value: Ascl1 and Sox2 transduced


title: CF3P7_MeDIP

value: Sprague Dawley SR

value: Sperm


title: G1B_ASCL1_SOX2_DORSO_2_d14

description:
G1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: G7B_ASCL1_SOX2_DORSO_2_d14

description:
G7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: VF2P15_MeDIP

description:
processed data file:
F2.DMR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

tag: strain

value: Vinclozolin lineage


title: Colorectal adenocarcinoma tumor 159

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample159

value: B

value: Homozygous deletion

tag: estimated chromosome segment number (ecsn)


title: MM at diagnosis, sample 16

value: MM

tag: molecular alteration


title: MM at diagnosis, sample 15

value: MAF translocation


title: VF3P16_MeDIP

tag: treatment

value: MeDIP-seq

value: monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006


title: G8B_ASCL1_SOX2_DORSO_2_d14

description:
G8B_Ascl1Sox2Dorso2d14
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: MM at diagnosis, sample 14


title: MM at diagnosis, sample 13


title: G9B_ASCL1_SOX2_DORSO_2_d14

description:
G9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: VF2P14_MeDIP

tag: generation

tag: measurement


title: Colorectal adenocarcinoma tumor 156

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample156

tag: gender

value: Colorectal adenocarcinoma

tag: disease state

value: C

value: Rectum

value: Heterozygous deletion


title: VF2P13_MeDIP

tag: ip antibody


title: MM at diagnosis, sample 18

value: Bone marrow plasma cells


title: MM at diagnosis, sample 12


title: CF2P6_MeDIP

value: Control


title: H11B_ASCL1_SOX2_DORSO_2_d14

description:
H11B_Ascl1Sox2Dorso2d14
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 155

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample155

value: F

tag: tissue

value: Adenocarcinoma

tag: Stage

value: Right

value: Wild-type


title: H12B_ASCL1_SOX2_DORSO_2_d14

description:
H12B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 and Sox2 transduced


title: CF2P4_MeDIP

value: Sprague Dawley SR

value: Sperm


title: MM at diagnosis, sample 11

value: MM

value: hyperdiploid karyotype


title: Colorectal adenocarcinoma tumor 154

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample154

value: Colorectal adenocarcinoma

tag: site

value: Left

tag: estimated macrod2 status


title: H1B_ASCL1_SOX2_DORSO_2_d14

description:
H1B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: H2B_ASCL1_SOX2_DORSO_2_d14

description:
H2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 158

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample158

value: M

value: B

tag: estimated chromosome segment number (ecsn)


title: VF1P12_MeDIP

description:
processed data file:
F1.DMR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

tag: strain

value: Vinclozolin lineage

value: MeDIP-seq

value: monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006


title: MM at diagnosis, sample 10

value: Bone marrow plasma cells

tag: molecular alteration

value: MAF translocation


title: Colorectal adenocarcinoma tumor 157

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample157

value: Adenocarcinoma

value: C

value: Homozygous deletion


title: MM at diagnosis, sample 9

value: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: Colorectal adenocarcinoma tumor 153

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample153

value: Rectum

value: Wild-type


title: VF1P11_MeDIP

value: Sprague Dawley SR

value: Sperm

tag: treatment


title: Colorectal adenocarcinoma tumor 152

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample152

value: Colorectal adenocarcinoma


title: MM at diagnosis, sample 8

value: MM


title: VF1P10_MeDIP


title: Colorectal adenocarcinoma tumor 151

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample151

value: F

value: A

value: Left


title: H4B_ASCL1_SOX2_DORSO_2_d14

description:
H4B_Ascl1Sox2Dorso2d14
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

value: Ascl1 and Sox2 transduced

tag: timepoint (days post infection)


title: H5B_ASCL1_SOX2_DORSO_2_d14

description:
H5B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 150

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample150

value: Right


title: MM at diagnosis, sample 6

value: Bone marrow plasma cells

value: hyperdiploid karyotype


title: CF2P5_MeDIP

description:
processed data file:
F2.DMR.vin.csv.gz
The complete extraction protocol is available in a pdf on the series record.

value: Control

tag: generation

tag: measurement

value: MeDIP-seq

value: monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006


title: H6B_ASCL1_SOX2_DORSO_2_d14

description:
H6B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: CF1P2_MeDIP


title: Colorectal adenocarcinoma tumor 149

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample149

tag: gender

value: M

tag: disease state

value: Adenocarcinoma

value: C

value: Rectum

value: Wild-type


title: CF1P1_MeDIP

value: Sprague Dawley SR

value: Sperm

tag: ip antibody


title: MM at diagnosis, sample 7

value: MM


title: MM at diagnosis, sample 5


title: CF1P3_MeDIP


title: Colorectal adenocarcinoma tumor 148

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample148

value: F

tag: tissue

value: Colorectal adenocarcinoma

tag: Stage

value: B


title: H7B_ASCL1_SOX2_DORSO_2_d14

description:
H7B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain

value: Ascl1 and Sox2 transduced


title: H3B_ASCL1_SOX2_DORSO_2_d14

description:
H3B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 147

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample147

tag: site

value: Right

tag: estimated macrod2 status


title: H8B_ASCL1_SOX2_DORSO_2_d14

description:
H8B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: H9B_ASCL1_SOX2_DORSO_2_d14

description:
H9B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: Colorectal adenocarcinoma tumor 146

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample146

value: Left

tag: estimated chromosome segment number (ecsn)


title: MM at diagnosis, sample 2

value: Bone marrow plasma cells

tag: molecular alteration

value: MAF translocation


title: MM at diagnosis, sample 3

value: hyperdiploid karyotype


title: A1A_ASCL1_SOX2_NGN2_2_d14

description:
A1A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

growth_protocol: Differentiation medium

value: Ascl1, Sox2, Ngn2 transduced


title: MM at diagnosis, sample 1


title: Colorectal adenocarcinoma tumor 144

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample144

value: Adenocarcinoma

value: D


title: Colorectal adenocarcinoma tumor 143

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample143

value: C

value: Rectum

value: Heterozygous deletion


title: B1A_ASCL1_SOX2_NGN2_2_d14

description:
B1A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A2A_ASCL1_SOX2_NGN2_2_d14

description:
A2A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 141

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample141

value: F

value: Wild-type


title: B5A_ASCL1_SOX2_NGN2_2_d14

description:
B5A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B8A_ASCL1_SOX2_NGN2_2_d14

description:
B8A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B2A_ASCL1_SOX2_NGN2_2_d14

description:
B2A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 139

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample139

value: M

value: Colorectal adenocarcinoma

value: B


title: Colorectal adenocarcinoma tumor 140

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample140


title: C12A_ASCL1_SOX2_NGN2_2_d14

description:
C12A_Ascl1Sox2Ngn2d14
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 138

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample138

value: Right


title: Colorectal adenocarcinoma tumor 137

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample137


title: C4A_ASCL1_SOX2_NGN2_2_d14

description:
C4A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: MM at diagnosis, sample 4

value: MM

value: Bone marrow plasma cells

value: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: Colorectal adenocarcinoma tumor 136

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample136

value: A


title: Colorectal adenocarcinoma tumor 135

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample135

value: Adenocarcinoma


title: D1A_ASCL1_SOX2_NGN2_2_d14

description:
D1A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1, Sox2, Ngn2 transduced


title: Colorectal adenocarcinoma tumor 145

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample145

value: D


title: D7A_ASCL1_SOX2_NGN2_2_d14

description:
D7A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 134

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample134

value: Left


title: D9A_ASCL1_SOX2_NGN2_2_d14

description:
D9A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 133

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample133


title: F12A_ASCL1_SOX2_NGN2_2_d14

description:
F12A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F3A_ASCL1_SOX2_NGN2_2_d14

description:
F3A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F4A_ASCL1_SOX2_NGN2_2_d14

description:
F4A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 142

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample142

value: C

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 131

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample131

value: F

value: Rectum


title: Colorectal adenocarcinoma tumor 132

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample132

value: M

value: Colorectal adenocarcinoma


title: Colorectal adenocarcinoma tumor 130

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample130

value: Wild-type


title: F5A_ASCL1_SOX2_NGN2_2_d14

description:
F5A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: G3A_ASCL1_SOX2_NGN2_2_d14

description:
G3A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 129

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample129

value: B

value: Right


title: H1A_ASCL1_SOX2_NGN2_2_d14

description:
H1A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 128

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample128


title: G6A_ASCL1_SOX2_NGN2_2_d14

description:
G6A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C3A_ASCL1_SOX2_NGN2_2_d14

description:
C3A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 127

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample127


title: H9A_ASCL1_SOX2_NGN2_2_d14

description:
H9A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H7A_ASCL1_SOX2_NGN2_2_d14

description:
H7A_Ascl1Sox2Ngn2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 124

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample124


title: Colorectal adenocarcinoma tumor 126

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample126


title: A10B_ctrl_d2

description:
A10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: control vector transduced


title: Colorectal adenocarcinoma tumor 125

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample125

value: Homozygous deletion


title: A11B_ctrl_d2

description:
A11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 123

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample123

value: Adenocarcinoma


title: Colorectal adenocarcinoma tumor 122

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample122


title: A12B_ctrl_d2

description:
A12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 121

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample121

value: A


title: A2B_ctrl_d2

description:
A2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 120

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample120


title: A3B_ctrl_d2

description:
A3B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A1B_ctrl_d2

description:
A1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 119

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample119


title: Colorectal adenocarcinoma tumor 118

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample118


title: A5B_ctrl_d2

description:
A5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A4B_ctrl_d2

description:
A4B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A7B_ctrl_d2

description:
A7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 116

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample116


title: Colorectal adenocarcinoma tumor 117

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample117

value: D


title: Colorectal adenocarcinoma tumor 115

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample115


title: A8B_ctrl_d2

description:
A8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 113

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample113


title: Colorectal adenocarcinoma tumor 114

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample114


title: B11B_ctrl_d2

description:
B11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B12B_ctrl_d2

description:
B12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B1B_ctrl_d2

description:
B1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Liver_control_rep1

description: Gene expression after 30 days of normal diet

source_name: Liver, control, replicate 1

value: Liver

value: Male

tag: strain

value: inbred SPRET/EiJ


title: Colorectal adenocarcinoma tumor 112

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample112

value: F

value: C


title: B2B_ctrl_d2

description:
B2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: Colorectal adenocarcinoma tumor 111

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample111

value: Left


title: B3B_ctrl_d2

description:
B3B_ctrld2
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 109

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample109

value: M

value: Colorectal adenocarcinoma


title: Colorectal adenocarcinoma tumor 110

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample110

value: Wild-type


title: B4B_ctrl_d2

description:
B4B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

value: brain


title: B5B_ctrl_d2

description:
B5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B6B_ctrl_d2

description:
B6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 108

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample108

value: B


title: Colorectal adenocarcinoma tumor 106

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample106


title: Colorectal adenocarcinoma tumor 105

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample105

value: Right


title: Colorectal adenocarcinoma tumor 104

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample104


title: B9B_ctrl_d2

description:
B9B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: control vector transduced


title: B8B_ctrl_d2

description:
B8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B7B_ctrl_d2

description:
B7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 101

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample101

value: Adenocarcinoma


title: C4B_ctrl_d2

description:
C4B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C10B_ctrl_d2

description:
C10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C1B_ctrl_d2

description:
C1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C11B_ctrl_d2

description:
C11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 100

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample100

value: Rectum

value: Heterozygous deletion


title: C6B_ctrl_d2

description:
C6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 102

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample102


title: Colorectal adenocarcinoma tumor 98

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample98


title: C8B_ctrl_d2

description:
C8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 97

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample97


title: D10B_ctrl_d2

description:
D10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 107

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample107


title: Colorectal adenocarcinoma tumor 94

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample94


title: Colorectal adenocarcinoma tumor 96

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample96

value: Homozygous deletion


title: D11B_ctrl_d2

description:
D11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 99

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample99


title: D12B_ctrl_d2

description:
D12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 92

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample92


title: C7B_ctrl_d2

description:
C7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 103

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample103


title: D1B_ctrl_d2

description:
D1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D3B_ctrl_d2

description:
D3B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 95

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample95


title: D2B_ctrl_d2

description:
D2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D5B_ctrl_d2

description:
D5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D7B_ctrl_d2

description:
D7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 91

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample91


title: Colorectal adenocarcinoma tumor 89

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample89


title: Colorectal adenocarcinoma tumor 90

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample90


title: Colorectal adenocarcinoma tumor 86

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample86

value: A


title: Colorectal adenocarcinoma tumor 88

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample88


title: Colorectal adenocarcinoma tumor 85

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample85


title: D8B_ctrl_d2

description:
D8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E10B_ctrl_d2

description:
E10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E11B_ctrl_d2

description:
E11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 84

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample84


title: Colorectal adenocarcinoma tumor 87

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample87


title: Colorectal adenocarcinoma tumor 83

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample83


title: E2B_ctrl_d2

description:
E2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 93

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample93


title: Colorectal adenocarcinoma tumor 82

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample82


title: Colorectal adenocarcinoma tumor 81

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample81


title: E3B_ctrl_d2

description:
E3B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 78

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample78

value: D


title: Colorectal adenocarcinoma tumor 80

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample80

value: F


title: E8B_ctrl_d2

description:
E8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E9B_ctrl_d2

description:
E9B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 79

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample79


title: Colorectal adenocarcinoma tumor 77

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample77

value: C


title: E5B_ctrl_d2

description:
E5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E7B_ctrl_d2

description:
E7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F11B_ctrl_d2

description:
F11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F12B_ctrl_d2

description:
F12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F10B_ctrl_d2

description:
F10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 75

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample75


title: Colorectal adenocarcinoma tumor 76

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample76


title: Colorectal adenocarcinoma tumor 74

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample74

value: Left


title: E12B_ctrl_d2

description:
E12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E1B_ctrl_d2

description:
E1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F1B_ctrl_d2

description:
F1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 70

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample70


title: Colorectal adenocarcinoma tumor 72

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample72


title: F6B_ctrl_d2

description:
F6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F5B_ctrl_d2

description:
F5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 69

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample69


title: F7B_ctrl_d2

description:
F7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F8B_ctrl_d2

description:
F8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E6B_ctrl_d2

description:
E6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 68

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample68


title: Colorectal adenocarcinoma tumor 67

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample67


title: G11B_ctrl_d2

description:
G11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 66

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample66


title: Colorectal adenocarcinoma tumor 65

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample65

value: M


title: G12B_ctrl_d2

description:
G12B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G2B_ctrl_d2

description:
G2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 64

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample64

value: Colorectal adenocarcinoma


title: G3B_ctrl_d2

description:
G3B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 62

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample62

value: Wild-type


title: Colorectal adenocarcinoma tumor 60

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample60


title: Colorectal adenocarcinoma tumor 59

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample59


title: Colorectal adenocarcinoma tumor 73

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample73


title: G7B_ctrl_d2

description:
G7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: G1B_ctrl_d2

description:
G1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: G9B_ctrl_d2

description:
G9B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H10B_ctrl_d2

description:
H10B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 58

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample58


title: Colorectal adenocarcinoma tumor 57

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample57


title: Colorectal adenocarcinoma tumor 71

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample71


title: Colorectal adenocarcinoma tumor 56

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample56


title: Colorectal adenocarcinoma tumor 63

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample63


title: G6B_ctrl_d2

description:
G6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 55

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample55


title: H1B_ctrl_d2

description:
H1B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H3B_ctrl_d2

description:
H3B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 54

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample54


title: F2B_ctrl_d2

description:
F2B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 52

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample52


title: H6B_ctrl_d2

description:
H6B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G5B_ctrl_d2

description:
G5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 53

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample53


title: Colorectal adenocarcinoma tumor 51

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample51


title: H7B_ctrl_d2

description:
H7B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 50

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample50


title: Colorectal adenocarcinoma tumor 49

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample49


title: H9B_ctrl_d2

description:
H9B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 48

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample48


title: H8B_ctrl_d2

description:
H8B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: H11B_ctrl_d2

description:
H11B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 47

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample47


title: Colorectal adenocarcinoma tumor 45

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample45


title: Colorectal adenocarcinoma tumor 43

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample43


title: WT3 LPS d2

city: London

first: Carlson

last: Tsui

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
TSU687A15WT1_non-stim_d2_S37_L004
WT3 LPS d2

data_processing:
Read trimming and adapter removal were performed using Trim Galore! (version 0.4.2)
The RSEM package (version 1.2.31), and Bowtie2 (version 2.2.9) were used to align reads to the mouse genome (Ensembl GRCm38 release 85) and to obtain gene level counts.  For RSEM, all parameters were run as default except “--forward-prob” that was set to “0”.
Differential expression analysis was carried out with DESeq2 package (version 1.14.1) within R version 3.3.2
TPM values were obtained from RSEM (genes.results files)
Genome_build: Ensembl GRCm38 release 85
Supplementary_files_format_and_content: Tab-delimited text include TPM values for each gene on each sample

organism: Mus musculus

source_name: WT3 LPS d2

growth_protocol: Murine B cells were grown in RPMI 1640 supplemeted with 10 % FCS and 1x Glutamax. Non-stim samples are cells cultured for 1 day in complete RPMI supplemented with IL-4. Stimulated samples were cultured for 2 days in complete RPMI supplemented with LPS + IL-4 + IL-5.

extract_protocol:
Ambion MagMAX-96 Total RNA Isolation kit was used and manufacturer's protocol was followed
KAPA Stranded RNA-Seq Kit with RiboErase (HMR) from KAPA Biosystems

treatment_protocol: Cells were harvested and resuspend in RNAlater (Qiagen)

tag: genotype

value: WT


title: H4B_ctrl_d2

description:
H4B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: KO1 LPS d2

description:
TSU687A16WT1_non-stim_d2_S38_L004
KO1 LPS d2

source_name: KO1 LPS d2

value: KO


title: WT2 LPS d2

description:
TSU687A14WT1_non-stim_d2_S36_L004
WT2 LPS d2

source_name: WT2 LPS d2


title: WT1 LPS d2

description:
TSU687A13WT1_non-stim_d2_S35_L004
WT1 LPS d2

source_name: WT1 LPS d2


title: KO2 LPS d2

description:
TSU687A17WT1_non-stim_d2_S39_L005
KO2 LPS d2

source_name: KO2 LPS d2


title: Colorectal adenocarcinoma tumor 46

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample46

value: Right


title: KO2 non-stim d1

description:
TSU687A5WT1_non-stim_d2_S27_L003
KO2 non-stim d1

source_name: KO2 non-stim d1


title: KO1 non-stim d1

description:
TSU687A4_WT1_non-stim_d2_S26_L003
KO1 non-stim d1

source_name: KO1 non-stim d1


title: Colorectal adenocarcinoma tumor 44

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample44

value: Adenocarcinoma


title: WT3 non-stim d1

description:
TSU687A3_WT1_non-stim_d2_S25_L003
WT3 non-stim d1

source_name: WT3 non-stim d1


title: H5B_ctrl_d2

description:
H5B_ctrld2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: control vector transduced


title: Colorectal adenocarcinoma tumor 42

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample42

value: Rectum


title: Colorectal adenocarcinoma tumor 41

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample41

value: Heterozygous deletion


title: Colorectal adenocarcinoma tumor 40

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample40


title: WT2 non-stim d1

description:
TSU687A2_WT1_non-stim_d2_S24_L003
WT2 non-stim d1

source_name: WT2 non-stim d1


title: Colorectal adenocarcinoma tumor 39

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample39


title: WT1 non-stim d1

description:
TSU687A1_WT1_non-stim_d1_S23_L003
WT1 non-stim d1

source_name: WT1 non-stim d1


title: Colorectal adenocarcinoma tumor 37

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample37


title: Colorectal adenocarcinoma tumor 38

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample38


title: Colorectal adenocarcinoma tumor 36

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample36


title: Colorectal adenocarcinoma tumor 35

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample35


title: Colorectal adenocarcinoma tumor 61

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample61


title: Colorectal adenocarcinoma tumor 34

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample34


title: Colorectal adenocarcinoma tumor 33

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample33


title: Colorectal adenocarcinoma tumor 27

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample27


title: Colorectal adenocarcinoma tumor 29

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample29


title: Colorectal adenocarcinoma tumor 26

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample26


title: Colorectal adenocarcinoma tumor 28

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample28


title: Colorectal adenocarcinoma tumor 23

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample23


title: D_5

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
The dataset were normalized using NanoStringNorm function in the R NanoStringNorm package
genome build: UCSC hg19
Tab-deliminted raw counts for each gene across all the 24 samples

source_name: Mix of A and B (1:3)

extract_protocol: Universal Human Reference RNA purchased as total RNA from Agilent Technologies; Human Brain Reference RNA purchased as total RNA from Thermo Fisher

tag: seqc sample

tag: sample type

value: Mixed human cancer cell lines and human brain tissue at a ratio of 1:3


title: D_6

value: D


title: Colorectal adenocarcinoma tumor 32

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample32

tag: gender

tag: disease state


title: Colorectal adenocarcinoma tumor 22

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample22

tag: tissue


title: KO_HZ8079

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the nCounter experiments, sample preparation and quality analysis was done using an nCounter Prep Station 5s and an nCounter Digital Analyzer 5s. Expression of 784 genes (750 endogenous genes with 34 housekeeping genes and positive and negative controls) was assessed using the nCounter Mouse PanCancer Pathways Panel. We used NanoStringNorm function (Waggott et al., 2012) in the R NanoStringNorm package to normalize the dataset and DESeq2 for differential expression analysis .

label: Nanostring

source_name: Cellebellum

label_protocol: Not provided

growth_protocol: All mice used in this study were FVB.129 F1-hybrids. They were group-housed with up to five mice per cage. They were maintained on a 14h light:10h dark cycle (light on at 06:00) with standard mouse chow and water ad libitum in our AAALAS-accredited facility. All research and animal care procedures were approved by the Baylor College of Medicine Institutional Animal Care and Use Committee.

extract_protocol: We performed RNA extraction and purification from the cerebellum of male mice 8 to 9 weeks of age (three biological replicates of wild type and Mecp2-null) using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad 7326830) per the manufacturer’s instructions. Genomic DNA was eliminated using an on-column DNase digestion step. RNA quality was assessed using the Agilent 2100 Bioanalyzer system prior to library preparation for deep sequencing or use of the total RNA for Nanostring nCounter quantification.

value: FVB.129 F1-hybrids

tag: age

value: 8-9 weeks

tag: genotypes

value: Mecp2 KO


title: WT_HZ8081


title: WT_HZ8075


title: KO_HZ8082


title: WT_HZ8078


title: KO_HZ8085


title: Colorectal adenocarcinoma tumor 31

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample31

source_name: Colorectal adenocarcinoma

value: F

tag: Stage

value: C

tag: site

tag: estimated macrod2 status


title: siZNF281_rep4

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

institute: University of Rome "Tor Vergata"

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarrays (039494)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then allowed to dry.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human neuroblastoma cells BE2(M17)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the LowInput QuickAmp Labelling kit One colour (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human neuroblastoma cell line BE2(M17) was purchased from ATCC. Cells were cultured in DMEM-F12 (Lonza) supplemented with 10% FBS, 100 U penicillin, and 100 μg/mL streptomycin (Gibco) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit 50 (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer. The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 300 thousand cells were transfected with 400 pmol of either siSCR siRNA (Dharmacon, cat. no. D-001810-10) or siZNF281 siRNA (Dharmacon, cat. no. L-006958-00) using Lipofectamine RNAiMAX transfection reagent (Invitrogen). After 72 h cells were harvested for the further RNA extraction.

value: human neuroblastoma cells BE2(M17)

tag: transfection

value: siZNF281 siRNA


title: siZNF281_rep2


title: siSCR_rep4

value: control siRNA


title: siZNF281_rep3


title: D_4


title: siSCR_rep1


title: siSCR_rep3


title: siSCR_rep2


title: Colorectal adenocarcinoma tumor 30

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample30

value: M

value: Colorectal adenocarcinoma

value: Left

tag: estimated chromosome segment number (ecsn)


title: siZNF281_rep1


title: Colorectal adenocarcinoma tumor 25

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample25

value: Adenocarcinoma

value: Right

value: Wild-type


title: Colorectal adenocarcinoma tumor 24

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample24

value: Rectum


title: Colorectal adenocarcinoma tumor 21

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample21


title: Colorectal adenocarcinoma tumor 20

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample20

value: Heterozygous deletion


title: C_6

source_name: Mix of A and B (3:1)

value: Mixed human cancer cell lines and human brain tissue at a ratio of 3:1


title: C_5


title: Colorectal adenocarcinoma tumor 19

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample19


title: Colorectal adenocarcinoma tumor 16

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample16


title: C_4


title: Differentiated small proliferative adipocytes

city: Gifu city

first: Shigeo

last: Takashima

state: Gifu

address: 1-1 Yanagido

department: Life Science Research Center

country: Japan

institute: Gifu University

description: Gene expression in SPA

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome ver.2.0 Microarrays (G2519F #26655) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then lightly dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_sep09 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 30 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoView spectrophotometer (General Electric).

extract_protocol: RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Fitchburg, WI) following the manufacturer's instructions.  The quality of RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The concentration of the RNA solution was determined by NanoView spectrophotometer (General Electric, Boston, MA).

treatment_protocol: Epididymal fat from male C57/BL mice were digested with collagenase, and then centrifuged at 9 ×g for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 ×g for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were incubated with differentiation medium containing insulin/dexamethasone/IBMX for 3 day followed by subsequent incubation with DMEM for 2 day. The cells were collected and RNA was extracted.

tag: Sex

value: male

value: Adipose tissue


title: 5A18-NP1 rep1

city: Grand Forks

first: Tim

last: Casselli

state: ND

address: UND School of Medicine & HS 1301 N Columbia Road Stop 9037

department: Basic Sciences

institute: University of North Dakota

description: countTable.csv

data_processing:
SMRT sequencing: Basecalls and IPD values were generated using PacBio's PulseToBase pipeline.
SMRT sequencing: Alignment of sequences to the B. burgdorferi B31 genome,  modified base calling, and clustering of motifs were all determined using the RS_Modification_and_Motif_analysis tool from the SMRT analysis package 2.3.0 (http://www.pacb.com/devnet/).
Genome_build: SMRT sequencing: B. burgdorferi B31 consensus genome (NCBI)
Supplementary_files_format_and_content: SMRT sequencing: BigWig files for each sample of IPD for all bases (*.bw). Tab-delimited text files (*.gff) for called modified bases and sequence context for each sample.
RNA seq: Illumina Casava1.8 software used for basecalling.
RNA seq: Adapter sequences removed using Trimmomatic (Bolger et al., 2014) with parameters ILLUMINACLIP:2:30:10 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25
RNA seq: Sequences aligned to B. burgdorferi reference transcriptome and counted using Salmon 0.81 with parameters quant -i  -1 A  --seqBias --gcBias
Genome_build: RNA seq: B. burgdorferi B31 consensus genome (NCBI) and ncRNAs (Arnold et al, 2016).
Supplementary_files_format_and_content: RNA seq: Comma delimited file of raw read counts for each sample.

organism: Borreliella burgdorferi

source_name: Log-phase in vitro bacterial culture

growth_protocol: All Borrelia burgdorferi clones were grown at 35°C under 5% CO2 in modified Barbour-Stoenner-Kelly medium (BSK) supplemented with 6% rabbit serum. Mutant strains were grown with kanamycin (200 µg/ml). Cell densities and growth phase were monitored by visualization under dark-field microscopy and counting using a Petroff-Hausser counting chamber. Cells were harvested for nucleic acid isolation during mid-late log phase (~3X107 cells / ml).

extract_protocol:
Three independent cultures of each of WT and MTase mutant strains were grown to mid-late log phase (3 X 107 cells / ml) for RNA isolation. RNA was isolated by first adding 20 ml RNAprotect (Qiagen) to 10 ml culture to stabilize transcripts during processing. Cells were collected by centrifugation, resuspended in 1 ml of pre-warmed (65°C) Trizol reagent (Invitrogen), and frozen at -80°C overnight. Cell suspensions were thawed at room temperature, and RNA was isolated using the Direct-zol RNA mini kit (Zymo Research) following the manufacturer’s instructions. RNA concentration was determined using using a Qubit® 2.0 Fluorometer (Life Technologies), and RNA integrity was verified using microfluidic-based capillary electrophoresis with an Agilent 2100 Bioanalyzer (RIN ≥ 9.8 for all samples).
Directional cDNA libraries were prepared from 5 μg of purified RNA using the ScriptSeq complete bacteria kit and SciptSeq index PCR primers (Illumina)  following the manufacturer’s instructions.

tag: isolate

tag: strain

value: lp56-; {delta}bbe02


title: A3 rep3

description:
Other plasmids missing: lp5, cp9, lp38
countTable.csv

value: wild-type


title: 5A18-NP1 rep2

description: countTable.csv