title: Cancer_7599

source_name: Cancer sample from prostate cancer patient 7599


title: MR 766

status: Public on Jun 06 2018

type: SRA

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using tophat-2.0.11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Germ Cells

extract_protocol:
Cells were lysed using the RNAeasy mini kit from Qiagen and purified
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Primary Testicular Germ Cells

tag: strain


title: RGCs overexpressing mCherry-1

type: RNA

city: Palo Alto

first: Jeffrey

middle: L

last: Goldberg

address: 2452 Watson Ct

institute: Stanford University

hyb_protocol: not provided

scan_protocol: Scanning was performed on a GeneChip® Scanner

data_processing: .CEL files were normalized using Genespring GX 12 software

label: biotin

organism: Rattus norvegicus

source_name: RGCs overexpressing mCherry-1

label_protocol: Biotin

growth_protocol: P4 retinal ganglion cells were purified and transduced with lentivirus.

extract_protocol: Total RNA was extracted using RNEase (Qiagen), following the manufacturer's standard protocol.

treatment_protocol: For microarray analysis of RGCs, the open reading flames of KLF9, -16, -7 and -11 were cloned from plasmids obtained from Open Biosystems. All 4 KLFs and FLAG-tagged mCherry were cloned into pLenti-MP2 expression vector.

tag: cell type

value: retinal ganglion cells (RGC)


title: Cancer_8326

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Copy number values are estimated total copy number (e.g. 2~wild-type). Additional analysis details are as follows: "We fit a linear model to the normalized intensities stratified by the diallic genotype call. The intercept and slope from the linear model are both SNP- and batch-specific. Raw total copy number were estimated using crlmm package in Bioconductor (R 3.0., Bioconductor 2.12), using the default settings. At allele k, marker i, sample j, and batch p, the estimate of allelespecific copy number is computed by subtracting the estimated background from the normalized intensity and scaling by the slope coefficient.

molecule: genomic DNA

organism: Homo sapiens

source_name: Cancer sample from prostate cancer patient 8326

label_protocol: According to Affymetix protocol.

growth_protocol: Tissue samples were obtained from the Human Tissue Acquisition and Pathology Core of the Dan L. Duncan Cancer Center and were collected from fresh radical prostatectomy specimens after obtaining informed consent under an Institutional Review Board approved protocol. Cancer tissues include at least 70% tumor tissue and benign tissues were free of cancer on pathological examination.

extract_protocol: DNAs extracted using a Qiagen DNA/RNA mini kit following the manufacturer’s protocol.

tag: subject status

value: prostate cancer patient

tag: subject id

value: patient 8326

tag: ethnic background

value: African American (AA)

tag: tissue type

value: highly tumor-enriched primary prostate cancer (PCa)


title: Cancer_6760

source_name: Cancer sample from prostate cancer patient 6760

value: patient 6760


title: Normal_8220

source_name: Normal sample from prostate cancer patient 8220

value: patient 8220

value: normal; matched benign prostate tissue


title: Normal_7653

source_name: Normal sample from prostate cancer patient 7653

value: patient 7653


title: Mock 3


title: RGCs overexpressing mCherry-2

source_name: RGCs overexpressing mCherry-2


title: Normal_6544

source_name: Normal sample from prostate cancer patient 6544

value: patient 6544


title: Cancer_6544

source_name: Cancer sample from prostate cancer patient 6544


title: Normal_6543

source_name: Normal sample from prostate cancer patient 6543

value: patient 6543


title: Normal_6760

source_name: Normal sample from prostate cancer patient 6760


title: Normal_7546

source_name: Normal sample from prostate cancer patient 7546

value: patient 7546


title: Cancer_6543

source_name: Cancer sample from prostate cancer patient 6543


title: Mock 1


title: Mock 2


title: MDM Donor 3 24h Mtb

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

description: processed data file: FeatureCounts.txt

data_processing:
Torrent Suite Software v 5.2 was used for basecalling, alignment, and mapping validated reads to HG19 transcriptome and AmpliSeq specific bed files.
TMAP: The Torrent Mapping Alignment Program for Ion Torrent Data provides a fast and accurate aligner through the integration of a novel alignment algorithm and three popular algorithms: BWA-short (Li and Durbin, 2009), BWA-long (Li and Durbin, 2010), SSAHA (Ning et al., 2001).
BaseCaller steps include: Remove low-quality reads. From the signal values, create the sequence of bases. Estimate the base quality value for each base. Assign each read to a barcode. Trim the barcode sequence away. Trim extra bases at the 5' end. Filter out reads that are too short. Filter out reads that do not have the correct library key. Trim the P1 adapter (at the 3' end). Perform quality trimming.
The Torrent Suite software generates counts per transcript as well as normalized reads per million (RPM).
Additional processing using EdgeR and Qiagen Integrated Pathway Analysis (IPA).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FeatureCounts.txt: Tab-delimited text file includes abundance measurements; Super-maximal Exact Matching (Li 2012).

source_name: Human blood monocyte-derived macrophages

growth_protocol: Human blood PBMCs were cultured in RPMI medium with 20% autologous serum in Teflon wells for 5 days to allow for differentiation of monocytes into MDM. PBMCs were harvested and adhered to 24-well tissue culture plates (1.5x10^6 PBMCs/well of which ~1.5x10^5 were MDMs) for 2 h in RPMI with 10% autologous serum to achieve a purified MDM monolayer culture which was cultured for an additional 24 h in the same medium before infection with M.tb. For HAM, cells were isolated freshly from human BAL (within 6 h) and cultured in 24-well plates (1.5x10^5 cells/well) in RPMI containing 10% human AB serum and Penicillin G (10,000 U/ml) for 2 h before infection with M.tb.

extract_protocol:
Cells were lysed in Trizol. Ethanol was added to the Trizol lysate and the mix was applied to Directzol columns (Zymo Research). Columns were washed and RNA eluted per manufacturer instructions.
The AmpliSeq human transcriptome gene expression kit was used to prepare libraries covering 20,803 human transcripts, including coding and non-coding RNA. cDNA was synthesized from 10 ng of total RNA. Targeted amplification, digestion, adapter ligation and cleanup was per protocol. Libraries were quantified with qPCR.

treatment_protocol: MDM and HAM monolayer cultures in tissue culture plate were treated by infecting with single cell suspensions of live M.tb H37Rv s at a 2:1 multiplicity of infection (MOI) for 2 h. Extracellular bacteria were washed away and incubation of the infected cell monolayer was continued for 24-72 h before lysing monolayers for RNA extraction.

value: Blood monocyte-derived macrophages

tag: treatment

value: Mtb-infected cells

tag: time point

tag: donor


title: RGCs overexpressing KLF16-6

source_name: RGCs overexpressing KLF16-6


title: RGCs overexpressing KLF16-3

source_name: RGCs overexpressing KLF16-3


title: MDM Donor 3 72h Mtb

description: processed data file: FeatureCounts.txt


title: MDM Donor 3 24h Control

description: processed data file: FeatureCounts.txt

value: Control


title: MDM Donor 3 2h Mtb

description: processed data file: FeatureCounts.txt


title: Dengue


title: RGCs overexpressing KLF16-4

source_name: RGCs overexpressing KLF16-4


title: Cancer_6539

source_name: Cancer sample from prostate cancer patient 6539

value: patient 6539


title: MDM Donor 3 2h Control

description: processed data file: FeatureCounts.txt


title: Cancer_6454

source_name: Cancer sample from prostate cancer patient 6454

value: patient 6454


title: Normal_4958

source_name: Normal sample from prostate cancer patient 4958

value: patient 4958


title: Normal_6454

source_name: Normal sample from prostate cancer patient 6454

value: prostate cancer patient


title: Normal_6005

source_name: Normal sample from prostate cancer patient 6005

value: patient 6005


title: Cancer_4958

source_name: Cancer sample from prostate cancer patient 4958

value: African American (AA)


title: MDM Donor 2 72h Mtb

description: processed data file: FeatureCounts.txt


title: MDM Donor 2 72h Control

description: processed data file: FeatureCounts.txt


title: Normal_4837

source_name: Normal sample from prostate cancer patient 4837

value: patient 4837


title: MDM Donor 2 24h Mtb

description: processed data file: FeatureCounts.txt


title: Cancer_6005

source_name: Cancer sample from prostate cancer patient 6005

value: highly tumor-enriched primary prostate cancer (PCa)


title: RGCs overexpressing KLF16-2

source_name: RGCs overexpressing KLF16-2

value: retinal ganglion cells (RGC)


title: Normal_6539

source_name: Normal sample from prostate cancer patient 6539

value: normal; matched benign prostate tissue


title: MDM Donor 3 72h Control

description: processed data file: FeatureCounts.txt


title: MDM Donor 2 24h Control

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF11-6

source_name: RGCs overexpressing KLF11-6


title: MDM Donor 2 2h Control

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF16-1

source_name: RGCs overexpressing KLF16-1


title: RGCs overexpressing KLF16-5

source_name: RGCs overexpressing KLF16-5


title: MDM Donor 2 2h Mtb

description: processed data file: FeatureCounts.txt

source_name: Human blood monocyte-derived macrophages


title: MDM Donor 1 72h Mtb

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF11-5

source_name: RGCs overexpressing KLF11-5


title: RGCs overexpressing KLF11-4

source_name: RGCs overexpressing KLF11-4


title: MDM Donor 1 72h Control

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF11-3

source_name: RGCs overexpressing KLF11-3


title: MDM Donor 1 24h Mtb

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF11-1

source_name: RGCs overexpressing KLF11-1


title: Cancer_4733

source_name: Cancer sample from prostate cancer patient 4733

value: patient 4733


title: RGCs overexpressing KLF11-2

source_name: RGCs overexpressing KLF11-2


title: MDM Donor 1 24h Control

description: processed data file: FeatureCounts.txt


title: Normal_4733

source_name: Normal sample from prostate cancer patient 4733


title: Cancer_4837

source_name: Cancer sample from prostate cancer patient 4837


title: RGCs overexpressing KLF9-6

source_name: RGCs overexpressing KLF9-6


title: MDM Donor 1 2h Mtb

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF9-4

source_name: RGCs overexpressing KLF9-4


title: MDM Donor 1 2h Control

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF9-2

source_name: RGCs overexpressing KLF9-2


title: HAM Donor 9 72h Mtb

description: processed data file: FeatureCounts.txt

source_name: Human alveolar macrophages

value: Alveolar macrophages


title: RGCs overexpressing KLF9-3

source_name: RGCs overexpressing KLF9-3


title: RGCs overexpressing KLF7-5

source_name: RGCs overexpressing KLF7-5


title: Normal_4533

source_name: Normal sample from prostate cancer patient 4533

value: patient 4533


title: HAM Donor 9 24h Mtb

description: processed data file: FeatureCounts.txt


title: RGCs overexpressing KLF9-1

source_name: RGCs overexpressing KLF9-1


title: RGCs overexpressing KLF7-6

source_name: RGCs overexpressing KLF7-6


title: HAM Donor 9 24h Control

description: processed data file: FeatureCounts.txt


title: HAM Donor 9 2h Mtb

description: processed data file: FeatureCounts.txt


title: Cancer_4271

source_name: Cancer sample from prostate cancer patient 4271

value: patient 4271


title: RGCs overexpressing KLF9-5

source_name: RGCs overexpressing KLF9-5


title: HAM Donor 9 72h Control

description: processed data file: FeatureCounts.txt


title: Normal_4271

source_name: Normal sample from prostate cancer patient 4271


title: Normal_3533

source_name: Normal sample from prostate cancer patient 3533

value: patient 3533


title: RGCs overexpressing KLF7-2

source_name: RGCs overexpressing KLF7-2


title: RGCs overexpressing KLF7-1

source_name: RGCs overexpressing KLF7-1


title: RGCs overexpressing KLF7-4

source_name: RGCs overexpressing KLF7-4


title: Cancer_4533

source_name: Cancer sample from prostate cancer patient 4533


title: HAM Donor 9 2h Control

description: processed data file: FeatureCounts.txt


title: HAM Donor 8 72h Mtb

description: processed data file: FeatureCounts.txt

value: Mtb-infected cells


title: HAM Donor 8 72h Control

description: processed data file: FeatureCounts.txt

value: Control


title: ddm1a/1b smRNA-seq

city: Wuhan

first: Feng

last: Tan

state: Hubei

address: No.1 Shizishan street

country: China

institute: National Key Lab of Crop Genetic Improvement

data_processing:
Trimmomatic (version 0.32) was used to filter out low-quality reads.
For MNase-seq, clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.2.5), allowing up to two mismatches. Samtools (version 0.1.19) was used to remove potential PCR duplicates.
Nucleosome positions were identified using the TEMPLATE FILTER software (http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering/Home.html)
For smRNA-seq,  Small RNA sequence raw data were cleaned by removing adaptor contamination and low-quality reads by Trimmomatic (version 0.33). MicroRNA (http://www.mirbase.org/ftp.shtml), transfer RNA (http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), and ribosomal RNA (Rice Genome AnnotationMSU7.0) also were removed. Clean reads were aligned to the rice MSU7.0 reference genome by Bowtie (Langmead et al., 2009), allowing zero mismatches.
For BS-seq, clean data were mapped to rice genome (MSU 7.0) by Bismark (v0.16.3) (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)
Genome_build: MSU7.0
Supplementary_files_format_and_content: *.bw files contain data visualization of DNA methylation in CG, CHG, and CHH contexts and 24nt smRNA abundance

organism: Oryza sativa Japonica Group

source_name: DongJin

growth_protocol: rice seeds were germinated and grown on the hormone-free, half-strength Murashige & Skoog (MS) medium under 16/8 hrs light/dark at 30/25°C,Twelve-day-old seedling leaves from each genotype were harvested for chromatin, genomic DNA or total RNA extraction

extract_protocol:
Rice seedling total RNA samples were isolated using TRIzol reagent (Invitrogen). For genomic BS-seq, total genomic DNA of callus culture-regenerated wild-type and mutant plants was extracted from 12-d-old seedling leaves using the DNeasy plant mini kit (Qiagen). For nuclear extraction, seedling leaf of plant on 1/2MS mediun for 12-day were ground into powder in liquid nitrogen, The resulting powder was suspended in nuclear isolation buffer (NIB; 20 mM Tris-HCl, 50 mM EDTA, 5mM Spermidine, 0.15 mM Spermine, 0.1% mercaptoethanol,40% Glycerol at pH 7.5) and followed the standard protocol for nuclei isolation.
libraries were constructed following standard procedure of TruSeq Sample Preparation Kit from Illumina

tag: tissue

value: 12 day seedling

tag: genotype/variation


title: wt smRNA-seq

value: wild type


title: Cancer_2658

source_name: Cancer sample from prostate cancer patient 2658

value: patient 2658


title: HAM Donor 8 24h Mtb

description: processed data file: FeatureCounts.txt


title: ddm1a/1b/drm2 BS-seq

library_source: genomic


title: Normal_2658

source_name: Normal sample from prostate cancer patient 2658

value: prostate cancer patient


title: MDCK_CTAR1-/2+_LMP1_rep3

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data from MDCK cell line expressing CTAR1-/2+_LMP1

hyb_protocol: Fragmented cRNA was hybridized to Canine Genome 2.0 array using Affymetrix standard protocol

scan_protocol: Affymetrix Standard protocol  Affymetrix Standard protocol

data_processing: Probe level quantile normalisation and robust multi-array analysis on the raw CEL files were performed using the affy package of the Bioconductor project.

organism: Canis lupus familiaris

source_name: kidney normal epithelial cell line MDCK, expressing CTAR1-/2+_LMP1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

growth_protocol: All cell lines were cultured in high glucose DMEM (Sigma) supplemented with 5% fetal calf serum (FCS), 1% L-glutamine, and G418 (Invitrogen; 400ug/mL) to select for cells containing the neomycin resistance cassette.

extract_protocol: RNA was extracted using Trizol Reagent ((Invitrogen, UK) and purified using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen)

tag: lmp1 status


title: Cancer_3533

source_name: Cancer sample from prostate cancer patient 3533


title: HAM Donor 8 24h Control

description: processed data file: FeatureCounts.txt

source_name: Human alveolar macrophages


title: MDCK_CTAR1-/2+_LMP1_rep2


title: MDCK_CTAR1-/2-_LMP1_rep2

description: Gene expression data from MDCK cell line expressing CTAR1-/2-_LMP1

source_name: kidney normal epithelial cell line MDCK, expressing CTAR1-/2-_LMP1


title: HAM Donor 8 2h Mtb

description: processed data file: FeatureCounts.txt


title: Piggybac(PB)

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from BGI company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of BGI.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HES2 human embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: transfection

value: PB


title: pCREB1 FI Chip-seq replicate2

city: Genéve

first: Didier

last: Picard

address: Quai Ernest-Anserment, 30

department: Cell Biology- Science 3

country: Switzerland

institute: University of Genéve

data_processing:
Basecalling was performed using the software bcl2fastq2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.3.2.2
peaks were called using MACS2 callpeak version 2.1 with the following settings: ChIP threshold (0.05), Enrichment Fold (minimum 5)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated with the bedgraph files obtained from peak-calling

source_name: pCREB1 FI Chip-seq

growth_protocol: MDA-MB-134 cells were maintained in phenol red-free DMEM Glutamax medium supplemented with  10% fetal bovine serum and 1% penicillin-streptomycin; to prepare cells for treatments, they were cultured for 3 days in phenol red-free DMEM supplemented with  5% charcoal-stripped fetal bovine serum, 1% penicillin-streptomycin, and 1% L-glutamine.

extract_protocol:
Cells were processed for ChIP after crosslinking with 1% formaldehyde according to the protocols of Schmidt et al. (2009) Methods 48, 240-248. The following antibodies were used: the rabbit monoclonal antibody 87G3 against phospho-CREB from Cell Signaling Technology and the rabbit polyclonal A300-498A against ERα from Bethyl Laboratories.
ChIP samples were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatments were for 1 hour with 100 nM estradiol (E2) or a cocktail of 10 µM forskolin plus 100 µM 3-isobutyl-1-methylxanthine (FI) to increase intracellular cAMP levels.

value: Epithelial ERalpha positive breast cancer cell line

tag: passage

value: between 10 and 12

tag: treated with

value: a cocktail of 10 µM forskolin plus 100 µM 3-isobutyl-1-methylxanthine (FI) for 1hr

tag: chip antibodies

value: pCREB1 (Cell Signalling Technology, 87G3, lot 14)


title: Normal_2328

source_name: Normal sample from prostate cancer patient 2328

value: patient 2328

value: African American (AA)

value: normal; matched benign prostate tissue


title: Cancer_2621

source_name: Cancer sample from prostate cancer patient 2621

value: patient 2621

value: highly tumor-enriched primary prostate cancer (PCa)


title: MDCK_CTAR1-/2-_LMP1_rep3


title: Cancer_2328

source_name: Cancer sample from prostate cancer patient 2328


title: Normal_1883

source_name: Normal sample from prostate cancer patient 1883

value: patient 1883


title: HAM Donor 8 2h Control

description: processed data file: FeatureCounts.txt

value: Alveolar macrophages

value: Control


title: 20180130.B-bean_nodule_rpoNmt_4_R1

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism: Paraburkholderia phymatum STM815

source_name: STM815 wt in symbiosis with bean

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . For RNA extracted from nodules, first nodules were disrupted with TissueLyzer and then rRNA of plants was removed using Ribo-zero kit (Epicentre). The cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Encore Complete Prokaryotic RNA-Seq DR Muliplex System

tag: genotype

value: rpoN mutant

value: bacteroid cells

tag: growth

value: nodules harvested 21 days post infection

tag: medium

value: inside bean nodules


title: pCREB1 FI Chip-seq replicate1

tag: cell line

tag: cell type


title: MDCK_CTAR1-/2+_LMP1_rep1


title: 20171213.B-bean_nodule_rpoNmt_3_R1

tag: strain


title: MDCK_CTAR1+/2-_LMP1_rep3

description: Gene expression data from MDCK cell line expressing CTAR1+/2-_LMP1

source_name: kidney normal epithelial cell line MDCK, expressing CTAR1+/2-_LMP1


title: pCREB1 E2 ChIP-seq replicate 2

source_name: pCREB1 E2 ChIP-seq

value: 100 nM estradiol (E2) for 1hr


title: Normal_2621

source_name: Normal sample from prostate cancer patient 2621

tag: subject status

value: prostate cancer patient

tag: subject id

tag: ethnic background

tag: tissue type


title: 20150521.A-201505_Bp_nod_o_R1

value: wt

tag: tissue


title: pCREB1 E2 ChIP-seq replicate 1

value: Epithelial ERalpha positive breast cancer cell line

value: between 10 and 12


title: Cancer_1810

source_name: Cancer sample from prostate cancer patient 1810

value: patient 1810


title: PB-Tfcp2l1

value: embryo


title: MDCK_CTAR1-/2-_LMP1_rep1


title: HAM Donor 7 72h Control

description: processed data file: FeatureCounts.txt

tag: treatment

tag: time point

tag: donor


title: MDCK_CTAR1+/2-_LMP1_rep2

tag: lmp1 status


title: HAM Donor 7 24h Control

description: processed data file: FeatureCounts.txt


title: MDCK_wt-LMP1_rep3

description: Gene expression data from MDCK cell line expressing wt-LMP1

source_name: kidney normal epithelial cell line MDCK, expressing wt-LMP1


title: pCREB1 DMSO ChIP-seq replicate 1

source_name: pCREB1 DMSO ChIP-seq

tag: passage

tag: treated with

value: DMSO

value: pCREB1 (Cell Signalling Technology, 87G3, lot 14)


title: Cancer_1883

source_name: Cancer sample from prostate cancer patient 1883

value: African American (AA)

value: highly tumor-enriched primary prostate cancer (PCa)


title: HAM Donor 7 2h Mtb

description: processed data file: FeatureCounts.txt

value: Alveolar macrophages

value: Mtb-infected cells


title: HAM Donor 7 72h Mtb

description: processed data file: FeatureCounts.txt


title: HAM Donor 7 24h Mtb

description: processed data file: FeatureCounts.txt


title: Normal_1810

source_name: Normal sample from prostate cancer patient 1810

value: normal; matched benign prostate tissue


title: ERα FI ChIP-seq replicate 2

source_name: ERα FI ChIP-seq

value: a cocktail of 10 µM forskolin plus 100 µM 3-isobutyl-1-methylxanthine (FI) for 1hr

tag: chip antibodies

value: ERα  (Bethyl Laboratories, A300-498A )


title: MDCK_wt-LMP1_rep2


title: Normal_1793

source_name: Normal sample from prostate cancer patient 1793

value: patient 1793


title: HAM Donor 7 2h Control

description: processed data file: FeatureCounts.txt

source_name: Human alveolar macrophages

value: Control


title: Cancer_1793

source_name: Cancer sample from prostate cancer patient 1793

value: prostate cancer patient


title: ERα FI ChIP-seq replicate 1


title: pCREB1 DMSO ChIP-seq replicate 2


title: ERα E2 ChIP-seq replicate 1

source_name: ERα E2 ChIP-seq

value: 100 nM estradiol (E2) for 1hr


title: Normal_1298

source_name: Normal sample from prostate cancer patient 1298

value: patient 1298


title: Cancer_1298

source_name: Cancer sample from prostate cancer patient 1298


title: Normal_1356

source_name: Normal sample from prostate cancer patient 1356

value: patient 1356


title: MCF7-FOXO3.A3  doxycyclin 16 hrs, biological replicate 2

city: Eindhoven

first: Henk

last: van Ooijen

address: High Tech Campus 11

department: Precision & Decentralized Diagnostics

country: Netherlands

institute: Philips Research

hyb_protocol: Done by service lab (AROS, ServiceXS) per default Affymetrix HT HG-U133+ PM Array Plate protocol

data_processing: fRMA (McCall, Biostatistics. 2010 Apr;11(2):242-53)

growth_protocol: MCF7 and MDA-MB-231 breast cancer cell lines were cultured in DMEM-F12 containing 10% FBS (Lonza) 100U/ml penicillin and 100 g/ml streptomycin (Lonza)

extract_protocol: RNeasy kit (Qiagen)

treatment_protocol: Cells were treated with 20% FBS or 10 µM PI3K inhibitor LY294002 (Selleckchem) for 16 hours to activate and inactivate the endogenous PI3K pathway, respectively. FOXO3.A3 expression was induced by 16 hours treatment with 10 ng/ml doxycycline


title: MDCK_CTAR1+/2-_LMP1_rep1


title: MDCK_wt-LMP1_rep1


title: MCF7-FOXO3.A3  doxycyclin 16 hrs, biological replicate 3

scan_protocol: Done by service lab (AROS, ServiceXS) per default Affymetrix HT HG-U133+ PM Array Plate protocol


title: MDCK_control_rep3

description: Gene expression data from MDCK cell line, control

source_name: kidney normal epithelial cell line MDCK, control

growth_protocol: All cell lines were cultured in high glucose DMEM (Sigma) supplemented with 5% fetal calf serum (FCS), 1% L-glutamine, and G418 (Invitrogen; 400 ug/mL) to select for cells containing the neomycin resistance cassette.

value: Control without LMP1


title: MCF7-FOXO3.A3  doxycyclin 16 hrs, biological replicate 1

label_protocol: Done by service lab (AROS, ServiceXS) per default Affymetrix HT HG-U133+ PM Array Plate protocol


title: ERα DMSO ChIP-seq replicate 1

source_name: ERα DMSO ChIP-seq

value: Epithelial ERalpha positive breast cancer cell line

value: between 10 and 12


title: 20150521.A-201505_Bp_nod_n_R1

source_name: STM815 wt in symbiosis with bean

tag: genotype

value: wt

value: bacteroid cells

tag: growth

value: nodules harvested 21 days post infection

value: inside bean nodules


title: MDCK_control_rep2


title: ERα DMSO ChIP-seq replicate 2

tag: cell line

value: DMSO


title: Cancer_1356

source_name: Cancer sample from prostate cancer patient 1356

value: African American (AA)

value: highly tumor-enriched primary prostate cancer (PCa)


title: MCF7-FOXO3.A3 control, biological replicate 3


title: MDCK_control_rep1


title: MCF7-FOXO3.A3 contro, biological replicate 2


title: spleen_d5_MTC26

city: Easter Bush Campus

first: Laura

last: McCulloch

state: Midlothian

address: The Roslin Institute

department: Neuropathology Division

institute: The Roslin Institute, University of Edinburgh

description: gene expression data from mouse spleen 5d post stroke

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized to the Affymetrix MoGene 1.0 ST array plate using Gene Titan was and stain kit for WT array plates using affymetrix standard protocols . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene chips were scanned by edinburgh genomics

data_processing: The resulting CEL files were used for analysis in Partek Genomics Suite (Partek Incorporated, St. Louis, Missoiri, USA) by ANOVA, raw data was also analysed for specific genes of interest.

source_name: spleen 5 d after experimental stroke

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) and labelled using affymetrix Genechip WT terminal labelling kit .

growth_protocol: 40 minute occlusion of the middle cerebral artery was performed on male 8-10 week old C57BL/6J mice.   Sham-surgery was performed on age and sex matched controls animals.  Animals were allowed to recover for 5 d before perfusion with saline + 0.01% DEPC and harvesting of spleens.

extract_protocol: Extraction of RNA was carried out using the Qiagen Rneasy mini kit according to the manufacturers instructions

treatment_protocol: 1/4 of the spleen was manually homogenised in 350 ml RLT buffer from Qiagen Rneasy mini kit (Qiagen, Manchester, UK) with 3.5 ml b-mercaptoethanol

value: spleen

value: stroke + 5d


title: spleen_d5_MTC16


title: MCF7-FOXO3.A3 control, biological replicate 1


title: MDA-MB-231-FOXO3.A3  doxycyclin 16 hrs, biological replicate 3


title: spleen_d5_MTC9


title: spleen_d5_MTC11


title: spleen_d2_MTC23

description: gene expression data from mouse spleen 2d post stroke

source_name: spleen 2 d after experimental stroke

value: stroke + 2d


title: MDA-MB-231-FOXO3.A3  doxycyclin 16 hrs, biological replicate 2


title: MDA-MB-231-FOXO3.A3 control, biological replicate 3


title: Cancer_1199

source_name: Cancer sample from prostate cancer patient 1199

value: prostate cancer patient

value: patient 1199


title: spleen_d2_MTC20


title: spleen_d1_MTC25

description: gene expression data from mouse spleen 1d post stroke

source_name: spleen 1 d after experimental stroke

value: stroke + 1d


title: spleen_d2_MTC21


title: MDA-MB-231-FOXO3.A3 control, biological replicate 1


title: MDA-MB-231-FOXO3.A3  doxycyclin 16 hrs, biological replicate 1


title: MCF7-FOXO3.A3 +LY294002 + doxycyclin rep 3


title: MDA-MB-231-FOXO3.A3 control, biological replicate 2


title: nse4a-2_zeb

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

data_processing:
Read trimming and quality filtering with FAST-X tools (http://hannonlab.cshl.edu/fastx_toolkit/).
Read mapping to the TAIR10 Arabidopsis reference genome using Tophat2 with default settings.
Calculating the coverage of individual genes with Qualimap from the set of uniquely mapped reads.
Calculating FPKM values and significant chnages (threshold set at adjusted P value < 0.05) with Cuffdiff package (Trapnell et al., 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: CSV file containing raw read counts, normalized FPKM counts produced with Cuffdiff and calculated log2 fold changes.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 10 days old plants

growth_protocol: Seeds were germinated on drug free ½ MS solid media and grown for 9 days at long day 16h light : 8 h dark at 21°C.

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
The libraries were prepared from 1 mg total RNA with RNA integrity number >7.8 (Bioanalyzer; Agilent) using TruSeq type RNA kit (Illumina) at the Cologne Genome Centre and sequenced as 100-bp single-end reads on HiSeq2500 (Illumina) instrument.

treatment_protocol: Nine days old plants were carefully transferred to liquid ½ MS media with or without 20 μM zebularine. After 24 h, plants were washed with drug free liquid ½ MS media, their leaves, hypocotyl and roots were removed and shoot apices were flash-frozen in liquid nitrogen for later use.

value: dissected shoot apices

value: nse4a-2 mutant

value: zebularine

tag: ecotype


title: nse4a-2_ctrl

value: control


title: spleen_d1_MTC10


title: Normal_1199

source_name: Normal sample from prostate cancer patient 1199

value: normal; matched benign prostate tissue


title: WT_ctrl

value: wild-type


title: hda1-3

first: Shannon

last: Esher

state: NC

address: 337 Sands Building, 303 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

description:
FS6-clr3-3
hda1∆

data_processing:
Base-calling and demultiplexing were done using bcl2fastq
Data was processed using 2 separate analysis pipelines described in detail below
(1) TopHat2/Cufflinks
Reads were aligned to the C. neoformans genome using TopHat2 with default parameters
Transcriptomes were assembled for each sample using Cufflinks with default parameters. The accepted_hits.bam files from each sample were used as input.
Cuffmerge was used to merge the assembled transcriptomes with the reference transcriptome
Reads for each transcript were quantified using Cuffquant with default parameters and the accepted_hits.bam files as inputs
Cuffdiff was used to quantify differential expression between the samples with parameters -u -o cuffdiff_out/ -L hda1,H99 -FDR 0.1
Genome_build: The C. neoformans H99 reference genome used for this analysis was obtained from the Sequencing Project at the Broad Institute of MIT and Harvard (accessed 03/31/2015). The genome was indexed using Bowtie2 with default parameters.
Supplementary_files_format_and_content: *_abundances.cxb files were generated from Cuffquant for each individual sample. FS1-3 are H99 1-3, FS4-6 are hda1 1-3.
Supplementary_files_format_and_content: cuffdiff_101817_gene_exp.csv is the "gene_exp.diff" output file from Cuffdiff, which tests differences in the summed FPKM of transcripts sharing each gene_id for each strain, replicates included. This comma separated file includes FPKM, log2(fold change), and significance values for each locus by strain.
STAR/DeSeq2
Reads were aligned to the C. neoformans genome using STAR alignment software with default parameters
Differential expression analysis was performed in R with DESeq2 following an RNA-Seq Bioconductor workflow (Love, M. I., Anders, S., Kim, V. & Huber, W. RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res 4, 1070, doi:10.12688/f1000research.7035.1 (2015).)
Genome_build: The C. neoformans H99 reference genome used for this analysis was obtained from NCBI (assembly CNA3, accessed 07/2017)
Supplementary_files_format_and_content: H99_v_hda1_counts.csv is a comma separated file with read counts for each strain/biological replicate
Supplementary_files_format_and_content: DESeq_results.csv is a comma separated file with log2(fold change) and significance values for each gene

organism: Cryptococcus neoformans H99

source_name: fungal cells

growth_protocol: Three biological replicates of WT and hda1∆ mutant cells were incubated in YPD medium to mid-log phase and transferred to minimal medium for 2 hrs at 30˚C

extract_protocol:
Cells were flash frozen, lyophilized, and lysed by vortexing with glass beads. RNA was extracted using the Qiagen RNeasy Plant Mini Kit with optional on-column DNase digestion.
Libraries were prepared by the Duke Sequencing and Genomic Technologies Shared Resource using the Kapa Stranded mRNA-Seq library prep kit (Catalog # KK8421). A single 6 bp index strategy was used, followed by pooling all 6 libraries.

tag: genotype/variation


title: MCF7-FOXO3.A3 20% FBS rep 3

source_name: MCF7-FOXO3.A3 20% FBS rep 3


title: hda1-2

description:
FS5-clr3-2
hda1∆


title: MCF7-FOXO3.A3 +LY294002 + doxycyclin rep 2


title: MCF7-FOXO3.A3 + doxycyclin rep 3

source_name: MCF7-FOXO3.A3 + doxycyclin rep 3


title: spleen_sham_MTC45

description: control gene expression data from sham-operated mouse spleen

source_name: spleen5 d after sham surgery

value: sham


title: MCF7-FOXO3.A3 +LY294002 (PI3K inhibitor) rep 3


title: spleen_sham_MTC44

source_name: spleen 5 d after sham surgery


title: MSC-OBs

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 100μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
HuGene-1_0-st-v1.r3.pgf
HuGene-1_0-st-v1.r3.mps

source_name: Mesenchymal stem cells derived osteoblasts

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Each cells were cultured at 37℃ in a humid atmosphere with 5% CO2.

extract_protocol: Total RNA were extracted using ISOGENII

tag: cell type


title: MCF7-FOXO3.A3 control rep 3

source_name: MCF7-FOXO3.A3 control rep 3


title: WT_zeb


title: pOBs

source_name: primary osteoblasts

value: primary osteoblasts


title: CiOBs

source_name: CiOB

value: CiOB


title: hda1-1

description:
FS4-clr3-1
hda1∆


title: HDF OBM

source_name: Human dermal fibrobalsts cultured in OBM


title: MCF7-FOXO3.A3 20% FBS rep 2

source_name: MCF7-FOXO3.A3 20% FBS rep 2


title: WT-3

value: wildtype


title: MCF7-FOXO3.A3 +LY294002 (PI3K inhibitor) rep 2


title: MCF7-FOXO3.A3 control rep 2

source_name: MCF7-FOXO3.A3 control rep 2


title: MCF7-FOXO3.A3 +LY294002 (PI3K inhibitor) rep 1


title: WT-2


title: MCF7-FOXO3.A3 +LY294002 + doxycyclin rep 1


title: WT-1


title: HDF

source_name: Human dermal fibroblasts

value: Human dermal fibroblasts


title: Osfuct mutant_leaf_4weeks_rep3

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.probe file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

source_name: Leaf at the tillering stage_transgenic

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Rice seeds were sterilized and germinated on 2N6 media in a growth chamber with a 16 hr light (28°C), 8 hr dark (26°C) photoperiod for 7 dats. The seedling were transferred to individual pots and grown in a greenhouse under the controlled conditions

extract_protocol: Total RNA from frozen wild-type and mutant leaves was prepared as previously described [Davis, KR & Ausubel, FM (1989) Mol. Plant-Microbe Interact 2: 363-368). Genomic DNA contamination was removed by DNase I at 37°C for 30 min and cDNA was generated by commercial cDNA synthesis kit according to the manufacturer's guidelines.

treatment_protocol: No treatment

tag: cultivar

value: Oryza sativa japonica Dongjin

value: alpha1,3-fucosyltransferase mutant

tag: age

value: 4 weeks; tillering stage

value: leaf


title: MCF7-FOXO3.A3 + doxycyclin rep 2

source_name: MCF7-FOXO3.A3 + doxycyclin rep 2


title: Osfuct mutant_leaf_4weeks_rep2


title: 9904796153_R03C02

status: Public on Jun 05 2018

type: genomic

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: RnBeads v0.99

label: Cy5 and Cy3

source_name: human ovarian cancer tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and and purified from ovarian cancer tissues or ascites from ovarian cancer patients using Qiagen AllPrep DNA/RNA/protein mini kit

tag: patient id

tag: organ

value: ovary

value: human ovarian cancer tissue

value: pre-guadecitabine


title: 9904796153_R04C02

tag: tissue

tag: treatment


title: 9904796153_R03C01

value: post-guadecitabine


title: 9904796153_R06C02


title: 9904796153_R05C02


title: MCF7-FOXO3.A3 20% FBS rep 1

source_name: MCF7-FOXO3.A3 20% FBS rep 1


title: 9904796153_R04C01


title: Dongjin_leaf_4weeks_rep3

source_name: Leaf at the tillering stage_non-transgenic

value: wild type; non-transgenic


title: 9904796153_R06C01


title: 9904796153_R05C01


title: Osfuct mutant_leaf_4weeks_rep1


title: ERα E2 ChIP-seq replicate 2

source_name: ERα E2 ChIP-seq

value: Epithelial ERalpha positive breast cancer cell line

value: between 10 and 12

value: 100 nM estradiol (E2) for 1hr

value: ERα  (Bethyl Laboratories, A300-498A )


title: Dongjin_leaf_4weeks_rep2


title: Dongjin_leaf_4weeks_rep1


title: MCF7TAMR_NS2

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

description: control

hyb_protocol: Microarray hybridization was performed on the Affymetrix PrimeView™ Human Gene Expression Array following the manufacturer's protocol.

scan_protocol: Not provided

data_processing: CEL files were further processed in the R software (v 3.4.3) environment using affy (Gautier et al., 2004) and limma (Ritchie et al., 2015) packages from Bioconductor.

source_name: MCF7, nonsense (NS) control

label_protocol: Not provided

growth_protocol: Cells were grown in RPMI1604 media (Thermofisher) supplemented with 10% FBS (GE Healthcare),  20 mM Hepes (ThermoFisher), 0.28 IU/ml insulin (Novo Nordisk) & 5 uM tamoxifen (Sigma)

extract_protocol: RNA was extracted using RNeasy (Qiagen)

treatment_protocol: Cells were transfected with either 10 nM nonsense (NS) siRNA (Thermo Fisher Silencer® Select Negative Control no.1 siRNA # 4390843) or AR siRNA (Thermo Fisher  Silencer® Select Pre-Designed siRNA #4390824)

value: MCF7 tamoxifen resistant cell line

value: breast cancer


title: MCF7-FOXO3.A3 + doxycyclin rep 1

source_name: MCF7-FOXO3.A3 + doxycyclin rep 1


title: 9904796153_R01C02


title: 9904796153_R02C01


title: 9904796153_R01C01


title: 9904796151_R06C02

source_name: human ovarian cancer ascites fluid

value: human ovarian cancer ascites fluid


title: MCF7TAMR_AR3

description: knockdown

source_name: MCF7, AR siRNA


title: MCF7TAMR_NS3

description: control


title: MCF7TAMR_AR1

description: knockdown


title: MCF7TAMR_AR2

description: knockdown


title: MCF7TAMR_NS1

description: control


title: MCF7-FOXO3.A3 control rep 1

source_name: MCF7-FOXO3.A3 control rep 1


title: 9904796151_R06C01


title: 9904796153_R02C02


title: 9904796151_R05C02


title: 9904796151_R05C01


title: 9904796151_R02C02


title: 9904796151_R04C01


title: 9904796151_R03C02


title: 9904796151_R03C01


title: 9904796151_R02C01


title: 9904796151_R01C02


title: 9904796151_R01C01


title: 9904796062_R06C02


title: 9904796062_R06C01


title: 9904796062_R05C01


title: 9904796062_R03C02


title: 9904796062_R04C01


title: 9904796062_R04C02


title: 9904796062_R02C01


title: 9904796062_R03C01


title: 9904796062_R01C02


title: 9904796151_R04C02


title: 9904796062_R02C02


title: 9904796043_R06C01


title: 9904796043_R05C02


title: 9904796043_R04C02


title: 9904796043_R05C01


title: 9904796062_R01C01


title: 9904796043_R03C02


title: 9904796043_R04C01


title: 9904796040_R06C02


title: 9904796043_R03C01


title: 9904796033_R06C02


title: 9904796043_R01C01


title: 9904796043_R01C02


title: 9904796062_R05C02


title: 9904796033_R06C01


title: 9904796033_R05C01


title: 9904796033_R04C02


title: 9904796033_R05C02


title: 9904796033_R04C01


title: 9904796033_R02C02


title: 9904796033_R03C02


title: 9904796032_R06C02


title: 9904796033_R01C02


title: 9904796033_R01C01


title: spleen_d1_MTC24

source_name: spleen 1 d after experimental stroke

value: spleen

value: stroke + 1d


title: 9904796033_R02C01


title: 9904796032_R05C01


title: 9904796032_R05C02


title: 9904796032_R03C01


title: 9904796032_R03C02


title: 9904796032_R04C02


title: 9904796043_R02C01


title: 9904796032_R02C02


title: 9904796032_R04C01


title: 9904796043_R02C02


title: 9904796032_R02C01


title: 9904796032_R01C02


title: 9904796031_R05C02


title: 9904796031_R06C01


title: 9904796032_R01C01


title: 9904796031_R05C01


title: 9904796031_R03C02


title: 9904796031_R04C02


title: 9904796031_R04C01


title: 9904796033_R03C01


title: 9904796032_R06C01


title: 9904796031_R03C01


title: 9904796031_R02C01


title: 9904796031_R02C02


title: 9904796031_R01C01


title: 9904796030_R06C02


title: 9904796030_R06C01


title: 9904796031_R01C02


title: 9904796030_R05C02


title: 9904796030_R03C02


title: 9904796030_R04C01


title: 9904796030_R03C01


title: 9904796030_R05C01


title: 9904796030_R02C01


title: 9904796030_R02C02


title: 9904796030_R01C02


title: 9904796029_R06C02


title: 9904796030_R04C02


title: 9904796029_R05C02


title: 9904796029_R04C02


title: 9904796029_R05C01


title: 9904796029_R04C01


title: 9904796031_R06C02


title: 9904796029_R03C02


title: 9904796029_R03C01


title: 9904796029_R02C02


title: 9904796030_R01C01


title: 9904796029_R02C01


title: 9904796029_R01C02


title: 3998609071_R05C02


title: 3998609071_R06C02


title: 3998609071_R04C02


title: 9904796029_R01C01


title: 3998609071_R03C02


title: 3998609065_R06C01


title: 3998609065_R06C02


title: 3998609065_R04C02


title: 3998609065_R05C02


title: 3998609065_R05C01


title: 3998609065_R04C01


title: 3998609065_R03C02


title: 3998609065_R03C01


title: 3998609065_R02C02


title: 9904796029_R06C01


title: 3998609065_R02C01


title: 3998609065_R01C02


title: 3998609065_R01C01


title: 3998590054_R06C01


title: 3998590054_R04C01


title: 3998590054_R03C02


title: 3998590054_R02C02


title: 3998590054_R05C01


title: 3998590054_R03C01


title: 3998590054_R02C01


title: 3998590054_R01C02


title: 3998590020_R05C01


title: 3998590020_R04C02


title: 3998590020_R04C01


title: 3998590020_R03C02


title: 3998590020_R03C01


title: 3998590020_R02C02


title: 3998590020_R02C01


title: neuro 20C, rep 1

city: Leeds

first: Patricija

last: van Oosten-Hawle

state: Please Select

address: Garstang Building 8.53c

department: Faculty of Biological Sciences, School of Molecular and Cell Biology, Garstang 8.53c

institute: UNIVERSITY OF LEEDS

data_processing:
Read quality on the raw sequencing data was performed with FastQC
Reference sequences were indexed using Bowtie2 (version 2.0.0-beta7) and the raw reads were mapped using Tophat (version 2.0.4).
Cufflinks (version 2.0.2) was used for read quantification and differential expression analysis between wild type and the C. elegans strain overexpressing HSP-90::GFP in the neurons
Genome_build: C. elegans genome WS220
Supplementary_files_format_and_content: diff

organism: Caenorhabditis elegans

source_name: Whole organism C. elegans

growth_protocol: Eggs were synchronized to L1 larvae overnight in M9 and 1000 larvae were grown to L4 on NGM seeded with OP50.

extract_protocol:
RNA was extracted using TriZol and then purified using the RNeasy mini kit (QIAGEN). RNA quality was measured using an Agilent Technologies 2100 Bioanalyzer. All samples had an RNA integrity number of > 9.5.
cDNA libraries were prepared from 5 μgs of total RNA using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Wild type and AM778 were grown at 20C on NGM seeded with OP50 bacteria. Animals were collected and washed three times with M9 media to remove bacteria. Worms were then snap frozen in liquid nitrogen.

tag: strain


title: 3998590020_R01C02


title: WT 20C, rep 3

value: N2 Bristol

value: wild type


title: neuro 20C, rep 2


title: neuro 20C, rep 3


title: WT 20C, rep 2


title: 3998590020_R01C01


title: WT 20C, rep 1


title: 3998590054_R01C01


title: 3998590020_R06C01


title: 3998590020_R06C02


title: 3998590020_R05C02


title: H292_2_mycoplasma

city: Novosibirsk

first: Mariya

middle: Alexandrovna

last: Smetanina

address: 8 Lavrentiev Avenue

country: Russia

institute: Institute of Chemical Biology and Fundamental Medicine SB RAS

description: SAMPLE 4

hyb_protocol: Standard Illumina protocol for Direct Hybridization Gene Expression Assay.

scan_protocol: Standard Illumina scanning protocol, iScan System, iScan Control Software.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio, Gene Expression Module.

source_name: H292 lung adenocarcinoma cell line, Mycoplasma infected

label_protocol: Biotinylated cRNA was prepared using Illumina TotalPrep RNA Amplification kit according to manufacturer's instructions.

growth_protocol: All stages of cultivation were carried out in a DMEM/F12 medium containing 10% FBS and 0.03% Glutamine at 37˚С in an atmosphere of 5% СО2.

extract_protocol: Total RNA was extracted with TRIzol according to the manufacturer's protocol. Quality control was performed with electrophoresis of RNA in 1% agarose gel, and its quantity was assessed spectrophotometrically.

treatment_protocol: The cells of H292 line infected with M. hyorhinis (further - Н292Myc.h) were presented by Dr. Timofeeva O. (Georgetown University Medical Center). The cells uninfected with mycoplasma (further - Н292) were obtained after Н292Myc.h incubation in a ciprofloxacin-containing medium (10 mg/ml) within two weeks. Later on, the cells Н292 and Н292Myc.h were cultivated within four weeks (12 passages). Cell contamination with mycoplasma was tested at each cultivation passage using PCR with mycoplasma-specific primers.

value: non-small cell lung cancer cell line

tag: infection

value: Mycoplasma hyorhinis


title: genomic DNA from peripheral white blood cells [201105900063_R08C01]

city: Pamplona

first: Ana

last: Arpón

address: Irunlarrea 1

country: Spain

institute: University of Navarra

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

scan_protocol: Arrays were imaged using Illumina hiScanSQ platform

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

source_name: peripheral white blood cells

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

tag: Sex

value: Female

tag: study

value: OBEKIT

tag: array

value: EPIC

tag: homa-ir

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [201105900063_R06C01]


title: genomic DNA from peripheral white blood cells [201105900063_R05C01]


title: genomic DNA from peripheral white blood cells [201105900063_R07C01]

value: Male


title: Colorectal adenocarcinoma tumor 651

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

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).
Sample651

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

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

label: C-Bio and A-DNP

source_name: Colorectal adenocarcinoma

extract_protocol: AllPrep DNA/RNA Mini Kit (QUAGEN)

tag: gender

value: M

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

value: D

tag: site

value: Left

tag: estimated macrod2 status

value: Wt

tag: estimated chromosome segment number (ecsn)


title: Colorectal adenocarcinoma tumor 650

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample650

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

value: F

value: B

value: Homozygous deletion


title: H292_1_control

description: SAMPLE 1

source_name: H292 lung adenocarcinoma cell line, uninfected

tag: cell line

tag: cell type


title: Colorectal adenocarcinoma tumor 649

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample649

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

tag: tissue

value: C

value: Wild-type


title: Colorectal adenocarcinoma tumor 648

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample648

value: Rectum


title: Colorectal adenocarcinoma tumor 647

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample647

value: Right


title: genomic DNA from peripheral white blood cells [201105900063_R04C01]

value: Female

tag: age


title: H292_2_control

description: SAMPLE 2

value: non-small cell lung cancer cell line


title: H292_1_mycoplasma

description: SAMPLE 3

value: Mycoplasma hyorhinis


title: Colorectal adenocarcinoma tumor 646

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample646


title: genomic DNA from peripheral white blood cells [201105900063_R02C01]

value: Male

value: OBEKIT

value: EPIC


title: Colorectal adenocarcinoma tumor 645

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample645

value: M

value: Colorectal adenocarcinoma

value: Adenocarcinoma


title: Colorectal adenocarcinoma tumor 644

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample644

value: A


title: Colorectal adenocarcinoma tumor 643

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample643

value: F

value: Left


title: genomic DNA from peripheral white blood cells [201105900062_R08C01]


title: genomic DNA from peripheral white blood cells [201105900063_R01C01]


title: Colorectal adenocarcinoma tumor 642

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample642

value: Heterozygous deletion


title: genomic DNA from peripheral white blood cells [201105900062_R07C01]


title: genomic DNA from peripheral white blood cells [201105900062_R06C01]


title: Colorectal adenocarcinoma tumor 640

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample640

value: C


title: Colorectal adenocarcinoma tumor 641

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample641

value: D

value: Wild-type


title: genomic DNA from peripheral white blood cells [201105900062_R05C01]


title: genomic DNA from peripheral white blood cells [201105900062_R04C01]


title: Colorectal adenocarcinoma tumor 639

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample639


title: genomic DNA from peripheral white blood cells [201105900063_R03C01]


title: Colorectal adenocarcinoma tumor 637

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample637

value: Right


title: Colorectal adenocarcinoma tumor 638

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample638

value: B


title: genomic DNA from peripheral white blood cells [201105900062_R03C01]

value: Female


title: Colorectal adenocarcinoma tumor 636

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample636


title: Colorectal adenocarcinoma tumor 633

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample633


title: Colorectal adenocarcinoma tumor 634

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample634

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [201096090169_R07C01]

value: Male


title: genomic DNA from peripheral white blood cells [201105900062_R02C01]

value: OBEKIT


title: genomic DNA from peripheral white blood cells [201096090169_R06C01]

value: EPIC


title: genomic DNA from peripheral white blood cells [201096090169_R08C01]


title: Colorectal adenocarcinoma tumor 631

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample631

value: M

value: Rectum


title: Colorectal adenocarcinoma tumor 635

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample635

value: Colorectal adenocarcinoma

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [201096090169_R02C01]


title: genomic DNA from peripheral white blood cells [201096090169_R03C01]


title: genomic DNA from peripheral white blood cells [201096090169_R05C01]


title: genomic DNA from peripheral white blood cells [201096090169_R04C01]


title: Colorectal adenocarcinoma tumor 632

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample632

value: F

value: A


title: genomic DNA from peripheral white blood cells [201105900062_R01C01]


title: Colorectal adenocarcinoma tumor 629

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample629

value: Left


title: Colorectal adenocarcinoma tumor 627

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample627


title: genomic DNA from peripheral white blood cells [201096090138_R08C01]


title: genomic DNA from peripheral white blood cells [201096090138_R07C01]


title: Colorectal adenocarcinoma tumor 626

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample626

value: C


title: genomic DNA from peripheral white blood cells [201096090138_R06C01]


title: Colorectal adenocarcinoma tumor 625

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample625

value: Heterozygous deletion


title: genomic DNA from peripheral white blood cells [201096090138_R05C01]


title: genomic DNA from peripheral white blood cells [201096090138_R04C01]


title: Colorectal adenocarcinoma tumor 623

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample623


title: Colorectal adenocarcinoma tumor 622

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample622

value: Wild-type


title: genomic DNA from peripheral white blood cells [201096090138_R02C01]


title: genomic DNA from peripheral white blood cells [201096090138_R03C01]


title: Colorectal adenocarcinoma tumor 630

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample630


title: Colorectal adenocarcinoma tumor 620

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample620

value: Right


title: genomic DNA from peripheral white blood cells [200994790045_R08C01]


title: genomic DNA from peripheral white blood cells [200994790045_R07C01]


title: Colorectal adenocarcinoma tumor 617

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample617

value: B


title: genomic DNA from peripheral white blood cells [200994790045_R05C01]

value: Female


title: Colorectal adenocarcinoma tumor 628

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample628


title: Colorectal adenocarcinoma tumor 621

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample621


title: Colorectal adenocarcinoma tumor 616

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample616


title: Colorectal adenocarcinoma tumor 619

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample619


title: Colorectal adenocarcinoma tumor 618

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample618


title: genomic DNA from peripheral white blood cells [200994790045_R06C01]


title: genomic DNA from peripheral white blood cells [201096090169_R01C01]


title: genomic DNA from peripheral white blood cells [200994790045_R03C01]


title: Colorectal adenocarcinoma tumor 614

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample614


title: Colorectal adenocarcinoma tumor 613

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample613


title: Colorectal adenocarcinoma tumor 615

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample615


title: genomic DNA from peripheral white blood cells [200994790024_R07C01]


title: genomic DNA from peripheral white blood cells [200994790045_R01C01]


title: genomic DNA from peripheral white blood cells [200994790045_R02C01]


title: Colorectal adenocarcinoma tumor 612

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample612


title: genomic DNA from peripheral white blood cells [200994790024_R06C01]


title: Colorectal adenocarcinoma tumor 624

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample624


title: Colorectal adenocarcinoma tumor 611

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample611


title: genomic DNA from peripheral white blood cells [200994790024_R04C01]


title: Colorectal adenocarcinoma tumor 609

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample609


title: Colorectal adenocarcinoma tumor 610

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample610

value: D

value: Homozygous deletion


title: genomic DNA from peripheral white blood cells [200994790024_R03C01]

value: OBEKIT


title: genomic DNA from peripheral white blood cells [200994790024_R02C01]

value: EPIC


title: genomic DNA from peripheral white blood cells [200994790045_R04C01]

value: Male


title: Colorectal adenocarcinoma tumor 608

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample608

value: M


title: genomic DNA from peripheral white blood cells [200992350041_R07C01]


title: genomic DNA from peripheral white blood cells [200994790024_R01C01]


title: Colorectal adenocarcinoma tumor 606

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample606

value: Colorectal adenocarcinoma


title: Colorectal adenocarcinoma tumor 604

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample604

value: Adenocarcinoma

value: Rectum


title: Colorectal adenocarcinoma tumor 603

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample603

value: F


title: genomic DNA from peripheral white blood cells [200992350041_R06C01]


title: genomic DNA from peripheral white blood cells [200992350041_R08C01]


title: genomic DNA from peripheral white blood cells [200992350041_R04C01]


title: genomic DNA from peripheral white blood cells [200992350041_R05C01]


title: Colorectal adenocarcinoma tumor 602

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample602


title: Colorectal adenocarcinoma tumor 601

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample601


title: Colorectal adenocarcinoma tumor 599

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample599


title: genomic DNA from peripheral white blood cells [200992350041_R03C01]


title: genomic DNA from peripheral white blood cells [200992350041_R02C01]


title: Colorectal adenocarcinoma tumor 600

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample600


title: genomic DNA from peripheral white blood cells [200992350041_R01C01]


title: genomic DNA from peripheral white blood cells [200994790024_R05C01]


title: Colorectal adenocarcinoma tumor 607

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample607


title: genomic DNA from peripheral white blood cells [200992350040_R08C01]


title: Colorectal adenocarcinoma tumor 605

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample605

value: Left


title: A1B_Ascl1_d2

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
A1B_Ascl1d2
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

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: genotype/variation

value: Ascl1 only transduced

tag: timepoint (days post infection)


title: A10B_Ascl1_d2

description:
A10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: 10X_ASCL1_SOX2_DORSO_d14

description: Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells

growth_protocol: Differentiation medium plus dorsomorphin

extract_protocol:
Single cell isolation and cDNA generation was performed using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
Sequencing libraries were generated using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).

value: Donor 4

value: Ascl1 and Sox2 transduced


title: A12B_Ascl1_d2

description:
A12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 596

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample596

value: C

value: Right

value: Wild-type


title: genomic DNA from peripheral white blood cells [200992350040_R07C01]

tag: Sex

tag: study

value: NORMOPESO

tag: array


title: A3B_Ascl1_d2

description:
A3B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 597

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample597

tag: gender

value: B


title: Colorectal adenocarcinoma tumor 595

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample595

tag: disease state

value: Heterozygous deletion


title: A5B_Ascl1_d2

description:
A5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992350040_R05C01]

value: Female

value: EPIC

tag: homa-ir

tag: waist circumference (cm)


title: A7B_Ascl1_d2

description:
A7B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: A2B_Ascl1_d2

description:
A2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 594

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample594

value: M

value: Colorectal adenocarcinoma

value: Adenocarcinoma

tag: Stage

value: D

tag: site

tag: estimated macrod2 status


title: A9B_Ascl1_d2

description:
A9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: cell type


title: B10B_Ascl1_d2

description:
B10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: Colorectal adenocarcinoma tumor 593

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample593

value: F

tag: tissue

value: A

tag: estimated chromosome segment number (ecsn)


title: A4B_Ascl1_d2

description:
A4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Ascl1 only transduced


title: genomic DNA from peripheral white blood cells [200992350040_R04C01]

tag: age


title: A6B_Ascl1_d2

description:
A6B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

tag: genotype/variation


title: B12B_Ascl1_d2

description:
B12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: genomic DNA from peripheral white blood cells [200992350040_R03C01]

tag: Sex

value: Male

tag: study

value: OBEKIT


title: Colorectal adenocarcinoma tumor 598

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample598

tag: gender

value: Left

value: Wild-type


title: B1B_Ascl1_d2

description:
B1B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 592

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample592

tag: disease state


title: B2B_Ascl1_d2

description:
B2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B5B_Ascl1_d2

description:
B5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 591

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample591


title: genomic DNA from peripheral white blood cells [200992350040_R06C01]

tag: array

tag: homa-ir


title: B4B_Ascl1_d2

description:
B4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992350040_R02C01]

value: NORMOPESO

tag: waist circumference (cm)


title: genomic DNA from peripheral white blood cells [200992350040_R01C01]


title: genomic DNA from peripheral white blood cells [200992340059_R08C01]


title: B8B_Ascl1_d2

description:
B8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 589

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample589

tag: Stage

value: C

tag: site

value: Right


title: B6B_Ascl1_d2

description:
B6B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: C10B_Ascl1_d2

description:
C10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C11B_Ascl1_d2

description:
C11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340059_R06C01]

value: Female

value: EPIC


title: C12B_Ascl1_d2

description:
C12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B11B_Ascl1_d2

description:
B11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 587

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample587

tag: tissue

value: Colorectal adenocarcinoma

value: Rectum

tag: estimated macrod2 status

value: Heterozygous deletion


title: genomic DNA from peripheral white blood cells [200992340059_R05C01]


title: genomic DNA from peripheral white blood cells [200992340059_R04C01]


title: C2B_Ascl1_d2

description:
C2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1


title: C4B_Ascl1_d2

description:
C4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: Colorectal adenocarcinoma tumor 586

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample586

value: F

value: Adenocarcinoma

value: B

tag: estimated chromosome segment number (ecsn)


title: C5B_Ascl1_d2

description:
C5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source

value: Ascl1 only transduced


title: genomic DNA from peripheral white blood cells [200992340059_R03C01]

tag: age

value: OBEKIT


title: Colorectal adenocarcinoma tumor 590

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample590

value: M


title: Colorectal adenocarcinoma tumor 585

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample585

value: Wild-type


title: C6B_Ascl1_d2

description:
C6B_Ascl1d2
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: C7B_Ascl1_d2

description:
C7B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 584

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample584


title: genomic DNA from peripheral white blood cells [200992340059_R01C01]

tag: Sex

value: Male

tag: study


title: C8B_Ascl1_d2

description:
C8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: B9B_Ascl1_d2

description:
B9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: C9B_Ascl1_d2

description:
C9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 588

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample588

tag: gender

tag: disease state

value: C

value: Left


title: genomic DNA from peripheral white blood cells [200992340057_R08C01]

value: Female

tag: array

tag: homa-ir


title: genomic DNA from peripheral white blood cells [200992340057_R07C01]

value: EPIC

tag: waist circumference (cm)


title: D1B_Ascl1_d2

description:
D1B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 582

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample582

value: Colorectal adenocarcinoma

tag: Stage

tag: site

value: Homozygous deletion


title: Colorectal adenocarcinoma tumor 583

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample583

tag: tissue

value: Right


title: C3B_Ascl1_d2

description:
C3B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1

tag: cell type


title: Colorectal adenocarcinoma tumor 581

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample581

tag: estimated macrod2 status


title: D4B_Ascl1_d2

description:
D4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: brain


title: D5B_Ascl1_d2

description:
D5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: tissue source


title: D3B_Ascl1_d2

description:
D3B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340057_R06C01]

tag: age


title: Colorectal adenocarcinoma tumor 580

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample580

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: genomic DNA from peripheral white blood cells [200992340057_R05C01]


title: D6B_Ascl1_d2

description:
D6B_Ascl1d2
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: D7B_Ascl1_d2

description:
D7B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D8B_Ascl1_d2

description:
D8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340057_R04C01]

tag: Sex

tag: study


title: Colorectal adenocarcinoma tumor 579

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample579

tag: gender

value: F

tag: disease state

value: Adenocarcinoma


title: genomic DNA from peripheral white blood cells [200992340057_R03C01]

tag: array

tag: homa-ir


title: E10B_Ascl1_d2

description:
E10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 only transduced


title: D12B_Ascl1_d2

description:
D12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: D9B_Ascl1_d2

description:
D9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 577

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample577

tag: Stage

value: B


title: Colorectal adenocarcinoma tumor 578

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample578

tag: site


title: E11B_Ascl1_d2

description:
E11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340057_R01C01]

value: OBEKIT

tag: waist circumference (cm)


title: D2B_Ascl1_d2

description:
D2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: E2B_Ascl1_d2

description:
E2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340057_R02C01]


title: E1B_Ascl1_d2

description:
E1B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340048_R08C01]


title: E3B_Ascl1_d2

description:
E3B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E4B_Ascl1_d2

description:
E4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340048_R07C01]


title: Colorectal adenocarcinoma tumor 576

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample576

value: M

tag: tissue

tag: estimated macrod2 status


title: E7B_Ascl1_d2

description:
E7B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

tag: tissue source


title: E5B_Ascl1_d2

description:
E5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: E8B_Ascl1_d2

description:
E8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 574

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample574

value: Wild-type

tag: estimated chromosome segment number (ecsn)


title: E9B_Ascl1_d2

description:
E9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200992340048_R06C01]

value: Male

tag: age


title: Colorectal adenocarcinoma tumor 573

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample573

value: C


title: F11B_Ascl1_d2

description:
F11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: timepoint (days post infection)


title: F10B_Ascl1_d2

description:
F10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340048_R05C01]

tag: Sex

tag: study


title: Colorectal adenocarcinoma tumor 572

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample572

tag: gender

tag: disease state


title: F12B_Ascl1_d2

description:
F12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340048_R04C01]

value: Female

value: NORMOPESO

tag: array

tag: homa-ir


title: F1B_Ascl1_d2

description:
F1B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F2B_Ascl1_d2

description:
F2B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 571

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample571

value: Colorectal adenocarcinoma

tag: Stage

tag: site


title: Colorectal adenocarcinoma tumor 575

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample575


title: genomic DNA from peripheral white blood cells [200992340048_R03C01]

value: EPIC

tag: waist circumference (cm)


title: F3B_Ascl1_d2

description:
F3B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: cell type


title: F5B_Ascl1_d2

description:
F5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340048_R02C01]


title: F7B_Ascl1_d2

description:
F7B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 570

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample570

tag: tissue

value: Right

tag: estimated macrod2 status


title: Colorectal adenocarcinoma tumor 569

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample569

value: Left

value: Homozygous deletion


title: Colorectal adenocarcinoma tumor 568

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample568


title: G10B_Ascl1_d2

description:
G10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: donor id

value: Donor 1

tag: tissue source

value: brain


title: F9B_Ascl1_d2

description:
F9B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

tag: genotype/variation


title: genomic DNA from peripheral white blood cells [200992340046_R08C01]

tag: age


title: genomic DNA from peripheral white blood cells [200992340048_R01C01]


title: Colorectal adenocarcinoma tumor 567

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample567

value: Adenocarcinoma

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: G12B_Ascl1_d2

description:
G12B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Ascl1 only transduced

tag: timepoint (days post infection)


title: G4B_Ascl1_d2

description:
G4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F8B_Ascl1_d2

description:
F8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: Colorectal adenocarcinoma tumor 566

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample566

value: F

value: B


title: G1B_Ascl1_d2

description:
G1B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340046_R06C01]

tag: Sex

tag: study


title: G11B_Ascl1_d2

description:
G11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: G6B_Ascl1_d2

description:
G6B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: F4B_Ascl1_d2

description:
F4B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340046_R05C01]


title: genomic DNA from peripheral white blood cells [200992340046_R04C01]

value: OBEKIT


title: Colorectal adenocarcinoma tumor 565

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample565

tag: gender

value: M

tag: disease state

value: D


title: Colorectal adenocarcinoma tumor 563

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample563

value: C

value: Rectum

value: Wild-type


title: Colorectal adenocarcinoma tumor 564

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample564

value: Colorectal adenocarcinoma

value: A


title: H10B_Ascl1_d2

description:
H10B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv


title: genomic DNA from peripheral white blood cells [200992340046_R03C01]

value: Female

tag: array

value: EPIC

tag: homa-ir


title: G5B_Ascl1_d2

description:
G5B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: Donor 1


title: H11B_Ascl1_d2

description:
H11B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv

value: brain


title: genomic DNA from peripheral white blood cells [200992340046_R07C01]

value: NORMOPESO


title: G8B_Ascl1_d2

description:
G8B_Ascl1d2
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv