title: Sample BACHD old-1: BACHD at 10 months of age

type: RNA

city: Lund

first: Rana

last: Soylu-Kucharz

address: Sölvegatan 19

institute: Lund University

description: BACHD mouse (ubiquitous full-length 97Q HTT expression) at 10 months of age

hyb_protocol: Performed using the Affymetrix GeneChip hybridization kit. Hybridization cocktails were heated at 99 degrees celcius for 5 minutes, followed by cooling to 42 degrees celcius for 5 minutes and centrifuged at max speed for 1 minute. 200 ul of hybridization solution was transferred to each array. Hybridization was performed for 16 hours at 45 degrees celcius and 60 rpm. Gene chips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data analysis was performed in R v.4.1.1. Raw .CEL files were pre-processed using RMA (affy package v.1.70.0). A design matrix was created to illustrate analysis groups for the samples. Each respective control group were used as a reference level. A linear model was fitted for each gene using lmFit  and MakeContrasts was used to specify which groups to compare (79Q, 18Q vs WT), (BACHD 2 months of age vs WT 2 months of age), (BACHD 10 months of age vs WT 10 months of age) followed by contrasts.fit to perform the comparison (limma, v.3.48.3). Subsequently, empirical Bayes smoothing was applied to the standard errors (limma, v.3.48.3).
log2-RMA sample signals, compiled from the following comparisons: 1) 79Q samples and 18Q samples with Control samples as the reference level, 2) BACHD young samples with WT young samples as the reference level and 3) BACHD old samples with WT old samples as the reference level.

label: biotin

source_name: hypothalamus, BACHD, 10 months of age

label_protocol: Enzymatic fragmentation and biotinylation of samples were performed on 200 ng total RNA using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: All mice were housed in groups and maintained at a 12-hour light/dark cycle with free access to a standard chow diet and water.

extract_protocol: RNA isolation was performed using the Rneasy Lipid Tissue Mini Kit (Qiagen, US) according to the manufacturer's instructions

treatment_protocol: 18Q and 79Q mice were bilaterally injected at 8 weeks of age with a recombinant AAV vector of serotype 5 (rAAV5) carrying an 853 amino acid N-terminal HTT fragment corresponding to either wild-type HTT (18 CAG repeats; AAV-HTT853-18Q) or mHTT (79 CAG repeats; AAV-HTT853-79Q) under control by the human Synapsin (Syn-1) promoter. Wild-type mice that were untreated (uninjected) were used as controls, and all three groups (18Q, 79Q, Control) were sacrificed at 4 weeks post-injection (12 weeks of age).  BACHD mice are transgenic mice with ubiquitous full-length 97 CAG HTT. BACHD mice were sacrificed at two timepoints: 2 months of age corresponding to early disease stage and 10 months of age corresponding to late disease stage. Age-matched wild-type mice were used as control groups for BACHD.  For all mice groups, hypothalamus was collected by dissection and ice followed by snap-freezing in liquid nitrogen after a terminal dose of sodium pentobarbital.

value: Hypothalamus

tag: gender

value: female

value: BACHD

tag: genetic background

value: FVB/N

value: 10 months of age

tag: timepoint

value: 10 months of age (late disease stage)


title: CVS_71022_Female_Spontaneous

status: Public on Oct 18 2022

type: SRA

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

state: CA

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

country: USA

institute: Cedars-Sinai Medical Center

description:
Spontaneous Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

library_source: transcriptomic

data_processing:
After quality check with FastQC, transcript abundances were quantified against the human reference genome (Ensembl build GRCh38) using Kallisto. Transcript counts were combined per gene to generate gene counts.
DESeq2 differential expression analysis was performed using Kallisto raw counts rounted and converted to integers. Four DESeq2 models were run to compare different modes of conception, adjusted for fetal sex and RNA-seq dataset. The dataset adjustment corrected for batch effects from RNA isolation and/or sequencing runs and is recommended as a covariate in any models using this data.
DESeq2 results were annotated with R package annotables using Ensembl release 91.
Log2FPKM expression values were corrected for batch effects using the limma R package function removeBatchEffect() and the RNAseq dataset for each sample. Log2FPKM values were converted to FPKM and then to transcripts per million (TPM) values.
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: Counts matrix: raw Kallisto counts for each sample and each gene, not corrected for batch effects.
Supplementary files format and content: Counts matrix: batch-corrected log2FPKM and TPM expression values.
Supplementary files format and content: Datasets: DESeq2 differential expression analysis results. Columns: gene = Ensembl Gene ID, symbol = gene symbol, chr = chromosome, start and end are GRCh38 chromosome locations, biotype from Ensembl release 91, description from Ensembl, baseMean = counts normalized for sequencing depth (all samples), log2FoldChange = ratio of group1/group2 expression from DESeq2 (group1 vs group2 as in file name order), lfcSE = log2FoldChange standard error,. pvalue = Wald test, padj = Benjamini-Hochberg False Discovery Rate adjusted pvalue.

molecule: total RNA

organism: Homo sapiens

source_name: Placenta - chorionic villi

growth_protocol: Continuing human pregnancies undergoing chorionic villus sampling (a prenatal test) in late first trimester.

extract_protocol:
Chorionic villi tissue was homogenized in RLT Plus lysis buffer (QIAGEN) containing 1% beta-mercaptoethanol, physically dissociated with single use needles attached to a 1 mL syringe. Total RNA was isolated from the homogenate using the AllPrep DNA/RNA Mini Kit (QIAGEN) following the manufacturer protocol.
RNA-seq libraries of >200 nt RNA were constructed from 200 ng total RNA per sample using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina). Libraries were depleted of cytoplasmic and mitochondrial ribosomal RNAs.

treatment_protocol: Pregnancies are spontaneous (unassisted, not medically assisted) or conceived with fertility treatments (NIFT: non-IVF fertility treatments, IVF: in vitro fertilization). Chorionic villi tissue discarded after CVS was stored in RNAlater RNA Stabilization Reagent (QIAGEN) and stored at -80C until further processing.

tag: tissue

value: Placenta - chorionic villi

tag: genotype

value: WT

tag: treatment

value: Spontaneous

tag: rnaseq dataset

value: ART Set1

tag: fetal sex

value: Female

tag: fetal race

value: Caucasian

tag: fetal ethnicity

value: Hispanic

tag: gestational age_at_cvs_(days)


title: CVS_71026_Female_Spontaneous

description:
Spontaneous Female; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Sex Diff Set2

value: CaucasianAsianBiracial

value: NonHispanic


title: Sample WT old-1: wild-type control for BACHD old

country: Sweden

description: Age-matched wild-type control for BACHD 10 months of age

organism: Mus musculus

source_name: hypothalamus, wild-type, 10 months of age

value: wild-type

tag: age


title: Sample BACHD old-3: BACHD at 10 months of age

value: Hypothalamus


title: Sample BACHD old-5: BACHD at 10 months of age

value: female


title: V0829

type: genomic

city: Madrid

first: Lara

last: Fernández

state: Madrid

address: Carretera Cantoblanco 8

country: Spain

institute: IMDEA Food

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 275

data_processing: Results were analyzed using TaqMan Genotyper software.

label: VIC

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: Genotyping was performed with QuantStudio 12 K Flex Real-Time PCR System (Life Technologies Inc., Carlsbad, CA, USA) using TaqMan OpenArray plates following manufacturer’s instructions.

extract_protocol: Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen Sciences, Inc, Germantown, MD, USA)

tag: Sex

tag: bmi

tag: fat mass

tag: muscle mass

label: FAM


title: CVS_71018_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Set2


title: Sample WT old-2: wild-type control for BACHD old

value: FVB/N


title: V0826

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 273


title: Sample BACHD old-2: BACHD at 10 months of age

value: BACHD

value: 10 months of age


title: Sample WT young-3: wild-type control for BACHD young

description: Age-matched wild-type control for BACHD 2 months of age

source_name: hypothalamus, wild-type, 2 months of age

value: 2 months of age


title: Sample WT young-5: wild-type control for BACHD young


title: Sample WT old-3: wild-type control for BACHD old


title: Sample WT young-4: wild-type control for BACHD young


title: Sample WT young-7: wild-type control for BACHD young


title: Sample WT young-2: wild-type control for BACHD young


title: U87 cell,ART,Day9 [U87-ART-2]

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

country: China

institute: Institute of Chinese Medicine

hyb_protocol: The purity and concentration of DNA was estimated using Nanodrop 2000 (Thermo) / Quibt3.0. Then 500 ng DNA of each sample was used to bisulfite converted using EZ DNA Methylation Kits(Zymo Research, USA),then converted products were put into 850K BeadChips in accordance with manufacturer guide and protocol(Illumina).

scan_protocol: scan：AutoLoader 2.x, Dual-Scanner Configuration (110/220 V)

data_processing: The data were mainly analyzed using ChAMP package in R. And we used β value to represent DNA methylation level / the proportion of methylated each CpG site . First , we filtered probes with detection p-value β value matrix were normalized using BMIQ for adjusting type I and type II probe bias . Next, we used SVA (Singular Value Decomposition Analysis) to analysis the batch effect caused by BeadChip Slide and Array , then applied Combat  to correct this batch effect. We annotated all CpG sites using EPICanno.ilm10b4.hg19. Differential Methylated CpGs Position(probes) were calculated by champ.DMP() function , the adj.p values were computed using the Benjamini-Hochberg method. CpGs having |Δβ|≥0.20 / 0.10 / 0.06 and adjusted p-value≤0.05 / p-value≤0.01 were considered as DMPs. Differential Methylated Region were calculated using ProbeLasso, all CpGs were for DMR calling and minSigProbesLasso、lassoRadius、boundary were the default value . In order to evaluate the DMP and DMR biologic processes ,cellular components ,molecular and pathway , we conducted Gene Ontology(GO) and KEGG enrichment analysis respectively using R package. Finally, we use Functional Epigenetic Modules to infer differential methylated gene modules in protein to protein iinteraction network(PPI) using FEM package. Additionally , we use Conumee [11] package to analysis copy number variation.

label: ddTTPDNP, ddGTPBiotin, ddCTPBiotin, ddATPDNP, ddGTPBioT

source_name: Glioma

label_protocol: Standard Illumina Protocol

growth_protocol: DMEM medium with 10%FBS and 1%PS was added

extract_protocol: DNA was isolated from whole blood / peripheral blood / tissue by using DNeasy Blood and Tissue   Kit (Qiagen).

treatment_protocol: DMEM medium with 10%FBS,1%PS or different doses of artesunate were added

tag: cell line

tag: cell type

value: brain,grade IV

value: artesunate treated


title: Sample BACHD young-4: BACHD at 2 months of age

description: BACHD mouse (ubiquitous full-length 97Q HTT expression) at 2 months of age

source_name: hypothalamus, BACHD, 2 months of age

tag: gender

tag: genetic background

value: 2 months of age (early disease stage)


title: Sample WT young-1: wild-type control for BACHD young

tag: tissue

tag: timepoint


title: Sample BACHD young-5: BACHD at 2 months of age

tag: genotype


title: V0824

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 271

value: Female


title: CVS_70993_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

tag: treatment

value: Spontaneous

tag: rnaseq dataset

value: ART Supplemental

value: Male

value: Caucasian


title: Sample BACHD young-2: BACHD at 2 months of age

value: Hypothalamus


title: CVS_70992_Female_Spontaneous

tag: fetal sex

tag: fetal race

value: NonHispanic


title: CVS_70982_Male_Spontaneous

tag: fetal ethnicity

tag: gestational age_at_cvs_(days)


title: V0823

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 270

tag: Sex

tag: age


title: CVS_70980_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: IVF

value: ART Set1


title: Sample BACHD old-4: BACHD at 10 months of age

value: female

value: BACHD

value: FVB/N

value: 10 months of age (late disease stage)


title: V0822

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 269

tag: bmi

tag: fat mass


title: V0821

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 268

tag: muscle mass


title: CVS_70969_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Sex Diff Set2


title: V0820

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 267


title: Sample Control-5: uninjected control for 18Q and 79Q

description: uninjected wild-type mouse used as control for AAV-HTT853 overexpression in hypothalamus

source_name: hypothalamus, uninjected control, wild-type

value: wild-type

value: 12 weeks of age

value: 4 weeks post-injection


title: Sample BACHD young-3: BACHD at 2 months of age

value: 2 months of age

value: 2 months of age (early disease stage)


title: Sample Control-7: uninjected control for 18Q and 79Q


title: Sample Control-4: uninjected control for 18Q and 79Q


title: CVS_70951_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

value: Spontaneous

value: ART Set2

value: CaucasianAsianBiracial


title: V0819

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 266

value: Female


title: Sample Control-1: uninjected control for 18Q and 79Q

value: Hypothalamus


title: CVS_70927_Female_Spontaneous

value: Caucasian

value: Hispanic


title: V0818

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 265

value: Male


title: Sample Control-2: uninjected control for 18Q and 79Q

value: female

value: FVB/N


title: CVS_70971_Male_Spontaneous

value: Sex Diff Set2

value: NonHispanic


title: Sample BACHD young-1: BACHD at 2 months of age

value: BACHD


title: Sample 79Q-8: 79Q CAG overexpression in hypothalamus

description: wild-type mouse with AAV-HTT853-79Q overexpression in hypothalamus, 4 weeks post-injection

source_name: hypothalamus, AAV-HTT853-79Q, wild-type

value: wild-type

value: 12 weeks of age

value: 4 weeks post-injection


title: V0817

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 264


title: Sample 79Q-5: 79Q CAG overexpression in hypothalamus


title: CVS_70905_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

value: IVF

value: ART Set1


title: Sample 79Q-4: 79Q CAG overexpression in hypothalamus


title: Sample 79Q-6: 79Q CAG overexpression in hypothalamus


title: CVS_70909_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: NIFT


title: Sample 79Q-3: 79Q CAG overexpression in hypothalamus

value: Hypothalamus


title: Sample 79Q-1: 79Q CAG overexpression in hypothalamus


title: Sample 18Q-6: 18Q CAG overexpression in hypothalamus

description: wild-type mouse with AAV-HTT853-18Q overexpression in hypothalamus, 4 weeks post-injection

source_name: hypothalamus, AAV-HTT853-18Q, wild-type


title: Sample 79Q-2: 79Q CAG overexpression in hypothalamus


title: CVS_70904_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Female

value: Caucasian


title: Sample 79Q-7: 79Q CAG overexpression in hypothalamus


title: V0814

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 262


title: Sample 18Q-2: 18Q CAG overexpression in hypothalamus


title: CVS_70897_Female_IVF


title: V0813

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 261


title: V0812

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 260


title: CVS_70895_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Spontaneous

value: ART Set2


title: Sample 18Q-3: 18Q CAG overexpression in hypothalamus

value: female

value: FVB/N


title: Foxf2_3

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

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using Tophat (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

extract_protocol:
These libraries were prepared using Illumina TruSeq Stranded mRNA Kit. We used the regular yield mode of hiseq2000.
Total RNA samples were made into cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (using both random priming and poly d(T) priming). cDNA from the SMART kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

tag: cell line

tag: cell type

value: human prostatic stromal myofibroblast cell line

tag: infected with


title: Foxf2_4


title: Sample 18Q-4: 18Q CAG overexpression in hypothalamus

tag: tissue

tag: gender

tag: genetic background


title: Vector2

source_name: WPMY1_control vector

value: control vector


title: Vector4


title: Foxf2_2


title: Sample 18Q-1: 18Q CAG overexpression in hypothalamus

tag: genotype

value: wild-type

tag: timepoint


title: CVS_70889_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: treatment

tag: rnaseq dataset

value: ART Supplemental

tag: fetal sex

value: NonHispanic


title: V0816

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 263

value: Male


title: Vector3


title: CVS_70887_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

value: Sex Diff Set2

tag: fetal race

tag: fetal ethnicity

tag: gestational age_at_cvs_(days)


title: V0810

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 258

tag: Sex

tag: age

tag: bmi


title: V0809

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 257

tag: fat mass

tag: muscle mass


title: V0808

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 256


title: V0811

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 259


title: liver_tumor_myc_batch3_rep2

city: Stanford

first: Dean

last: Felsher

address: 269 Campus Drive

department: Medicine

institute: Stanford University

description: Date: 2010

hyb_protocol: A total of 1500 ng of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 being used for detection.

scan_protocol: Slides were scanned on an Illumina BeadArray reader and analyzed using BeadStudio (Illumina, Inc).

data_processing: The R package, lumi, computed normalized (log2-transformed, quantile-normalized) signal intensity valuees.

source_name: liver hepatocellular carcinoma

label_protocol: Each RNA sample was amplified using the Ambion Illumina RNA amplification kit with biotin UTP labeling. The Ambion Illumina RNA amplification kit uses T7 oligo(dT) primer to generate single stranded cDNA followed by a second strand synthesis to generate double-stranded cDNA, which is then column purified. In vitro transcription was done to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA was then column purified and measured.

extract_protocol: Total RNA was extracted using TRIzol reagent after tissue homogenization.

treatment_protocol: Doxycycline was added to mice's drinking water at a concentration of 100 µg/mL.

tag: strain

value: LAP-tTA/TetO-MYC

value: off doxycycline (MYC activated)


title: CVS_70844_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: tissue

value: NIFT

value: Hispanic


title: CVS_70859_Female_Spontaneous

value: Spontaneous

value: Female

value: Caucasian


title: CVS_70837_Female_Spontaneous

value: ART Set2


title: liver_normal_batch2_rep2

description: Date: 2013

source_name: normal liver tissue

value: FVB/N


title: liver_tumor_myc_batch3_rep1

description: Date: 2010


title: V0803

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 253


title: CVS_70833_Female_Spontaneous


title: liver_normal_batch3_rep1

description: Date: 2010


title: liver_normal_batch3_rep2

description: Date: 2010


title: CVS_70862_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V0807

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 255


title: V0805

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 254


title: CVS_70823_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Set1


title: V0802

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 252


title: V0801

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 251


title: V0800

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 250


title: CVS_70821_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Sex Diff Set1


title: liver_normal_batch2_rep1

description: Date: 2013


title: liver_tumor_myc_batch2_rep2

description: Date: 2013


title: kidney_preneo_myc_2wk_batch2_rep2

description: Date: 2013

source_name: kidney preneoplastic tissue

value: GGT-tTA/TetO-MYC

value: off doxycycline 2 weeks (MYC activated)


title: kidney_preneo_myc_1wk_batch2_rep1

description: Date: 2010

value: off doxycycline 1 week (MYC activated)


title: kidney_normal_batch2

description: Date: 2010

source_name: normal kidney tissue


title: kidney_preneo_myc_2wk_batch2_rep1

description: Date: 2013


title: liver_tumor_myc_batch1_rep2

description: Date: 2011


title: CVS_70818_Female_Spontaneous

description:
Spontaneous Female; sample batch=Sex Diff Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi


title: kidney_preneo_myc_1wk_batch2_rep2

description: Date: 2010


title: kidney_tumor_myc_4wk_batch1_rep2

description: Date: 2013

source_name: kidney renal cell carcinoma

value: off doxycycline 4 weeks (MYC activated)


title: kidney_tumor_myc_4wk_batch1_rep1

description: Date: 2013


title: V0797

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 248


title: kidney_preneo_myc_2wk_batch1

description: Date: 2010


title: kidney_preneo_myc_1wk_batch1

description: Date: 2013


title: liver_tumor_myc_batch2_rep1

description: Date: 2013


title: V0799

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 249


title: CVS_70819_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: WT

value: Male

value: NonHispanic


title: V0796

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 247


title: CVS_70814_Male_Spontaneous


title: CVS_70792_Female_Spontaneous


title: V0795

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 246


title: liver_tumor_myc_batch1_rep1

description: Date: 2011

value: LAP-tTA/TetO-MYC

value: off doxycycline (MYC activated)


title: kidney_tumor_myc_4wk_batch2

description: Date: 2013


title: CVS_70789_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Spontaneous

value: ART Supplemental


title: osteosarcoma_a8295_cells_myc_off_24hr

description: Date: 2013

source_name: osteosarcoma cells

extract_protocol: Total RNA was extracted using TRIzol reagent

treatment_protocol: Doxycycline was added to cell culture at a concentration of 20 ng/mL to achieve MYC inactivation.

value: Eμ-SRα-tTA/TetO-MYC

value: doxycycline for 24 hours (MYC inactivated)


title: CVS_70899_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: IVF

value: Female

value: Caucasian

value: Hispanic


title: osteosarcoma_a7106_cells_myc_off_24hr

description: Date: 2013


title: V0825

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 272


title: Sample BACHD young-7: BACHD at 2 months of age

description: BACHD mouse (ubiquitous full-length 97Q HTT expression) at 2 months of age

value: Hypothalamus

tag: gender

value: female

value: BACHD

value: FVB/N

value: 2 months of age

value: 2 months of age (early disease stage)


title: CVS_70768_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

value: NIFT

value: ART Set2

value: Male

value: NonHispanic


title: V0794

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 245


title: CVS_70772_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Set1


title: V0791

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 243


title: V0790

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 242


title: osteosarcoma_a8295_cells_myc_on

description: Date: 2013

value: Eμ-SRα-tTA/TetO-MYC

value: MYC activated


title: CVS_70747_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Spontaneous

value: Sex Diff Set2

value: Caucasian


title: CVS_70780_Male_Spontaneous


title: V0788

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 241

value: Female


title: osteosarcoma_a7106_cells_myc_on

description: Date: 2013


title: V0787

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 240


title: CVS_70739_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_70734_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Supplemental


title: lymphoma_9663_cells_bcrabl_off_24hr

description: Date: 2013

source_name: lymphoma cells

value: Eμ-SRα-tTA/TetO-BCR-ABL

value: doxycycline for 24 hours (BCR-ABL inactivated)


title: lymphoma_9659_cells_bcrabl_off_24hr

description: Date: 2013


title: lymphoma_9663_cells_bcrabl_on

description: Date: 2013

value: BCR-ABL activated


title: lymphoma_4270_cells_kras_off_24hr

description: Date: 2013

value: doxycycline for 24 hours (KRAS inactivated)


title: lymphoma_4188_cells_myc_off_48hr

description: Date: 2013

value: doxycycline for 48 hours (MYC inactivated)


title: lymphoma_9659_cells_bcrabl_on

description: Date: 2013


title: V0786

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 239


title: kidney_normal_batch1_rep1

description: Date: 2010

value: FVB/N


title: CVS_70729_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

source_name: Placenta - chorionic villi

value: Placenta - chorionic villi

value: WT

value: Hispanic


title: lymphoma_4188_cells_myc_on

description: Date: 2013


title: lymphoma_4270_cells_kras_on

description: Date: 2013

value: KRAS activated


title: lymphoma_4188_cells_myc_off_24hr

description: Date: 2013

value: Eμ-SRα-tTA/TetO-MYC

value: doxycycline for 24 hours (MYC inactivated)


title: CVS_70726_Female_Spontaneous

value: Spontaneous

value: NonHispanic


title: liver_ec4_cells_myc_off_72hr

description: Date: 2013

source_name: liver hepatocellular carcinoma cells

value: LAP-tTA/TetO-MYC

value: doxycycline for 72 hours (MYC inactivated)


title: liver_hcc4-4_cells_myc_off_72hr

description: Date: 2013


title: liver_ec4_cells_myc_off_24hr

description: Date: 2013


title: liver_ec4_cells_myc_on

description: Date: 2013

value: MYC activated


title: liver_ec4_cells_myc_off_48hr

description: Date: 2013


title: V0782

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 237

source_name: Peripheral blood

value: Female


title: CVS_70716_Male_IVF

description:
IVF Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: IVF

value: ART Set2

value: Male

value: CaucasianAsianBiracial


title: liver_hcc4-4_cells_myc_off_48hr

description: Date: 2013

value: doxycycline for 48 hours (MYC inactivated)


title: kidney_normal_batch1_rep2

description: Date: 2010

value: FVB/N


title: liver_hcc4-4_cells_myc_off_24hr

description: Date: 2013


title: V0781

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 236


title: kidney_es02_cells_myc_off_72hr

description: Date: 2013

source_name: kidney renal cell carcinoma cells

value: GGT-tTA/TetO-MYC


title: V0780

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 235


title: V0783

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 238


title: CVS_70706_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT

value: Caucasian


title: CVS_70714_Female_Spontaneous

value: ART Set1


title: CVS_70699_Male_Spontaneous

value: Spontaneous


title: SWR_d6c32PGCLCs_rep2

city: Osaka

first: Masafumi

last: Hayashi

address: 2-2 Yamada-oka, Suita

department: Department of Genome Biology

country: Japan

institute: Osaka University

data_processing:
Obtained reads were mapped to the CerSimSim1.0/cerSim1 genome using STAR. Mapped reads were counted and processed to TPM value by RSEM.
The gene ID were converted to human gene symbol using a rhinoceros-human-mouse correspondence table.
Assembly: CerSimSim1.0/cerSim1
Supplementary files format and content: Matrix table with TPM values for every gene and every sample

molecule: polyA RNA

organism: Ceratotherium simum simum

source_name: primordial germ cell like cells at expanded culture day 32 of southern white rhinoceros

growth_protocol: Embryonic stem cells of southern white rhinoceros and induced pluripotent stem cells of northern white rhinoceros were maintained in hypoxic condition(5% O2 and 5% CO2) with DMEM/F12, 20% KSR, and 10 ng/ml of bFGF with or without 20ng/ml of activin A.

extract_protocol:
Total RNAs were extracted and purified using an RNeasy Micro Kit, and mRNAs were isolated with the NEBNext poly(A) mRNA magnetic isolation module (NEB).
Purified RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

tag: cell type

value: primordial germ cell like cells

tag: parental line


title: SWR_d6c32PGCLCs_rep1

tag: genotype


title: SWR_d6c8PGCLCs_rep2

source_name: primordial germ cell like cells at expanded culture day 8 of southern white rhinoceros


title: V0778

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 233


title: SWR_d6c8PGCLCs_rep1


title: V0777

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 232


title: SWR_d6PGCLCs_rep2

source_name: primordial germ cell like cells at day 6 of southern white rhinoceros induced by advanced RPMI 1640 with 10% KSR supplemented with BMP4, LIF, SCF, EGF, Y-27632, IWR1, bpV, and forskolin


title: CVS_70632_Male_Spontaneous

tag: treatment

value: NonHispanic


title: V0779

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 234


title: kidney_es02_cells_myc_on

description: Date: 2013


title: kidney_es01_cells_myc_on

description: Date: 2013


title: V0775

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 231


title: kidney_es01_cells_myc_off_48hr

description: Date: 2013


title: kidney_es02_cells_myc_off_48hr

description: Date: 2013


title: SWR_Preinduction(Ad)_rep2

data_processing:
Obtained reads were mapped to the CerSimSim1.0/cerSim1 genome using STAR. Mapped reads were counted and processed to TPM value by RSEM.
The gene ID were converted to human gene symbol using a rhinoceros-human-mouse correspondence table.
Genome_build: CerSimSim1.0/cerSim1
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: pre-induced cells of southern white rhinoceros cultured with advanced RPMI 1640 with 10% KSR

value: pre-induced cells

tag: cell line


title: SWR_PGCLCs(aRK10+BLSEYF2i)_rep2

source_name: primordial germ cell like cells at day 4 of southern white rhinoceros induced by advanced RPMI 1640 with 10% KSR with BMP4, LIF, SCF, EGF, Y-27632, IWR1, bpV, and forskolin


title: SWR_PGCLCs(aRK10+BLSEYF2i)_rep1


title: kidney_es02_cells_myc_off_24hr

description: Date: 2013

value: doxycycline for 24 hours (MYC inactivated)


title: kidney_es01_cells_myc_off_72hr

description: Date: 2013

value: doxycycline for 72 hours (MYC inactivated)


title: V0774

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 230

value: Female


title: CVS_70625_Female_Spontaneous

tag: rnaseq dataset

value: ART Set2

tag: fetal sex


title: kidney_es01_cells_myc_off_24hr

description: Date: 2013


title: CVS_70629_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: NIFT

value: Male

tag: fetal race

tag: fetal ethnicity


title: V0772

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 229

tag: Sex


title: SWR_Preinduction(Ad)_rep1


title: CVS_70682_Male_NIFT

tag: gestational age_at_cvs_(days)


title: liver_hcc4-4_cells_myc_on

description: Date: 2013

value: LAP-tTA/TetO-MYC

value: MYC activated


title: SWR_ESCs(AF)_rep1

source_name: embryonic stem cells of southern white rhinoceros cultured with bFGF and Activin A

value: embryonic stem cells


title: V0770

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 228

tag: age

tag: bmi


title: SWR_ESCs(AF)_rep2


title: CVS_70594_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: IVF


title: SWR_PGCLCs(induced_by_exogenous_SOX17)_rep2

source_name: primordial germ cell like cells induced by exogenous SOX17 at day 4 of southern white rhinoceros

value: SOX17 Knockout and over-expressed


title: SWR_d6PGCLCs_rep1

value: WT


title: V0769

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 227

tag: fat mass

tag: muscle mass


title: SWR_PGCLCs(induced_by_exogenous_SOX17)_rep1


title: CVS_70579_Male_NIFT

tag: tissue

value: Caucasian


title: Sample infarcted cardiac tissue 20

city: La Jolla

first: Martin

last: Spang

address: 2880 Torrey Pines Scenic Dr

institute: University of California, San Diego

description: See protocols below

hyb_protocol: NanoString nCounter Prep Station performed automated fluidic sample processing to purify and immobilize hybridized sample to the cartridge surface.

scan_protocol: Digital barcode reads were analyzed by NanoString nCounter® Digital Analyzer

data_processing: Results were analyzed by manufacturer nSolverTM Analysis Software 4.0 and custom R scripts. Outliers were detected and excluded based on NanoString’s methods for outlier detection.

label: Capture ProbeSet

organism: Rattus

source_name: infarcted cardiac tissue

label_protocol: Samples were processed according to manufacturer instructions. In brief, RNA sample concentrations were measured on a Qubit 3.0 Fluorometer with a QubitTM RNA HS Assay kit. 70 µL of hybridization buffer was mixed with Immunology Panel Reporter CodeSet solution, and 8 µL of this master mix was mixed in a separate reaction vessel with 50-100 ng of RNA per tissue sample and RNA-free water up to 13 µL total. 2 µL of Capture ProbeSet was added to each vessel, mixed and placed on a thermocycler at 65ºC for 16-48 hours before being maintained at 4ºC for less than 24 hours

growth_protocol: Sprague Dawley rats, vivarium

extract_protocol: The LV free wall was isolated and flash frozen for subsequent RNA extraction using the RNEasy Mini Kit (Qiagen). RNA concentrations were measured using a NanoDrop spectrophotometer (Thermo Scientific)

treatment_protocol: 35 minute myocardial infarction, then infused with iECM

tag: strain

value: Sprague-Dawley

tag: time point

value: day 1

tag: agent

value: iECM


title: SWR_PGCLCs(GK15+BLSEYWi)_rep2

source_name: primordial germ cell like cells at day 4 of southern white rhinoceros induced by GMEM with 15% KSR supplemented with BMP4, LIF, SCF, EGF, Y-27632, and IWR1

tag: cell type

value: primordial germ cell like cells

tag: parental line


title: CVS_70551_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: genotype

tag: treatment

value: Spontaneous

value: NonHispanic


title: V0768

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 226

value: Female


title: SWR_PGCLCs(GK15+BLSEYWi)_rep1

tag: cell line


title: Sample infarcted cardiac tissue 18

description: See protocols below


title: CVS_70529_Male_IVF

description:
IVF Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: rnaseq dataset

value: ART Set2

tag: fetal sex

tag: fetal race


title: Sample infarcted cardiac tissue 19

description: See protocols below

value: control


title: SWR_Preinduction_rep2

source_name: pre-induced cells of southern white rhinoceros cultured with GMEM with 15% KSR

value: pre-induced cells


title: CVS_70623_Female_IVF

description:
IVF Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: CaucasianAsianBiracial

tag: fetal ethnicity

tag: gestational age_at_cvs_(days)


title: SWR_Preinduction_rep1


title: CVS_70514_Male_Spontaneous

value: Male


title: V0764

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 223

tag: Sex

tag: age

tag: bmi


title: V0761

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 222

tag: fat mass

tag: muscle mass


title: Sample infarcted cardiac tissue 16

description: See protocols below

tag: strain

tag: time point

value: day 3


title: SWR_ESCs_rep2

source_name: embryonic stem cells of southern white rhinoceros cultured with bFGF

tag: cell type

value: embryonic stem cells


title: SWR_ESCs_rep1

tag: parental line


title: CVS_70507_Male_Spontaneous

tag: tissue

value: Placenta - chorionic villi

tag: genotype

value: Hispanic


title: Sample infarcted cardiac tissue 15

description: See protocols below

tag: agent


title: Sample infarcted cardiac tissue 14

description: See protocols below


title: CVS_70540_Female_IVF

value: WT

tag: treatment

value: IVF

tag: rnaseq dataset

value: Caucasian


title: Sample infarcted cardiac tissue 13

description: See protocols below

value: Sprague-Dawley


title: V0759

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 220


title: Sample infarcted cardiac tissue 12

description: See protocols below

value: day 1

value: iECM


title: V0767

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 225


title: V0765

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 224


title: CVS_70435_Female_IVF

tag: fetal sex

tag: fetal race

value: NonHispanic


title: Chronic cervicitis [cx-swab-2020-09]

city: Daegu

first: Yeseul

last: Choi

address: Chilgokjungang-daero 136 gil

country: South Korea

institute: KNU

data_processing:
Adapter sequence and the ends of the reads had Phred quality score less than 20 were trimmed
Reads shorter than 50 bp were removed by using cutadapt v.2.8.
Filtered reads were mapped to the reference genome using STAR v.2.7.1a, following ENCODE standard options with "quantMode TranscriptomeSAM" option for estimation of transcriptome expression level
Gene expression estimation was performed by RSEM v.1.3.1 with "strandedness" as direction of reads
Normalization performed with FPKM and TPM
Assembly: hg18
Supplementary files format and content: table with gene ID, ENSG ID, ENST ID, FPKM, TPM values, DEG information with logFC and p-values

source_name: cervical exfoliative cell

extract_protocol: RNA was extracted and library was generated with TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA) and sequenced for 151 bp paired-end

value: cervical exfoliative cell

tag: pathological diagnosis

value: Chronic cervicitis


title: V0756

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 219

tag: Sex


title: CVS_70281_Male_Spontaneous

value: Spontaneous

value: ART Set2

tag: fetal ethnicity

tag: gestational age_at_cvs_(days)


title: Sample infarcted cardiac tissue 11

description: See protocols below

value: control


title: V0760

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 221

value: Female

tag: age

tag: bmi

tag: fat mass


title: V0754

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 217

tag: muscle mass


title: Chronic cervicitis [cx-swab-2020-07]

tag: cell type


title: CVS_70273_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Sex Diff Set2

value: Male


title: SQCC, invasive [cx-swab-2020-06]

value: SQCC, invasive


title: V0755

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 218


title: CVS_70192_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: Sex Diff Set1


title: Sample infarcted cardiac tissue 10

description: See protocols below

tag: strain

tag: time point


title: SQCC, invasive [cx-swab-2020-05]


title: Sample infarcted cardiac tissue 8

description: See protocols below


title: CIS [cx-swab-2020-04]

value: CIS


title: CVS_70128_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: tissue

tag: genotype

value: WT

value: NIFT

value: Caucasian


title: CVS_70461_Male_NIFT

tag: treatment

value: Hispanic


title: V0750

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 214


title: Sample infarcted cardiac tissue 6

description: See protocols below

value: Sprague-Dawley

value: day 3

tag: agent

value: iECM


title: V0753

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 216


title: CIS [cx-swab-2020-03]

value: cervical exfoliative cell


title: V0752

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 215


title: Chronic cervicitis [cx-swab-2020-08]

value: Chronic cervicitis


title: CVS_70088_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: rnaseq dataset

value: ART Set2

tag: fetal sex

value: NonHispanic


title: V0747

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 213


title: V0745

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 212

value: Female


title: Sample infarcted cardiac tissue 9

description: See protocols below

value: day 1

value: control


title: HSIL(CIN2) [cx-swab-2020-02]

tag: pathological diagnosis


title: Sample infarcted cardiac tissue 4

description: See protocols below


title: Sample infarcted cardiac tissue 3

description: See protocols below


title: HSIL(CIN2) [cx-swab-2020-01]


title: V0793

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 244

tag: Sex


title: D50-U_rep3

city: Brno

first: Ece

last: Ergir

address: Studentska 6

department: Center for Translational Medicine (CTM)

country: Czech Republic

institute: St. Anne´s University Hospital Brno - International Clinical Research Centre (FNUSA-ICRC)

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
6-nt long UMIs were extracted and subseqeuntly used for deduplication of aligned reads by UMI-tools v. 1.1.1.
6-nt long barcode sequence related to Lexogen QuantSeq Library Prep Kit were trimmed using seqtk 1.3-r106, the adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using featureCounts tool v1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample gathered by featureCounts tool
Supplementary files format and content: Resulting table based on the analysis of differential gene expression performed by DESeq2 tool containing foldchanges and related statistics supplied with matrix with normalized counts for every gene and every sample

source_name: 2D monolayer cardiac differentiation - hiPSC derived

growth_protocol: hiPSC culture an maintenance was described previously by Pagliari et al (1). Cardiac differentiation was achieved by using the human iPSC cell line DF 19–9-7 T (iPS, karyotype: 46, XY) was purchased from WiCell (Madison, WI, USA), and was  performed following the Wnt signalling modulation protocol by Lian et.al. (2,3), with slight modifications as previously described by Pagliari et al (1). Briefly, prior to cardiovascular differentiation, hiPSCs were dissociated into single cells (TrypLE Select, Thermo Fisher Scientific) and re-seeded onto 12-well Matrigel-coated plates with 2.0 × 10^5 cells/cm2, with complete Essential 8 medium including Y27632 Rock Inhibitor (RI) (1:4000 dilution from 10 μM stock, 2.5 μM final, Selleck chemicals, Houston, TX, USA). The next day, the medium was replaced with complete Essential 8 medium without RI, and the medium exchange was performed daily until the cells reached 100% confluency. On day 0, to start mesoderm differentiation, the medium was changed with RPMI 1640 with L-Glutamine (Biosera) media supplemented with P/S, B-27™ supplement minus insulin (1×, Thermo Fisher Scientific) and CHIR99021 (8 µM, Sigma-Aldrich). On day 2, the medium was exchanged with RPMI 1640+B-27 minus insulin (RPMI+B27-Ins), supplemented with IWP-2 (5 µM, Selleck chemicals). On day 4, the medium was replaced with RPMI+B27-Ins, and medium exchange was performed every 2 days until the cells started beating (usually on day 7, but may depend on the iPSC line). Once beating clusters started to emerge, the medium was replaced with RPMI 1640+B-27™ supplement (RPMI+B27+Ins) (1×, Thermo Fisher Scientific), and medium exchange was performed every 2-3 days until day 15 of differentiation. From day 15 on, the cells were used either for generation of 3D hOCMTs, or were continued to be cultured as 2D monolayers as controls, with medium exchange every 3-4 days until the end of experiments, on day 30 or day 50 endpoints.    REFERENCES:  1. Pagliari, S. et al. YAP–TEAD1 control of cytoskeleton dynamics and intracellular tension guides human pluripotent stem cell mesoderm specification. Cell Death Differ. 2020 284 28, 1193–1207 (2020).  2. Lian, X. et al. Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling. Proc. Natl. Acad. Sci. U. S. A. 109, E1848–E1857 (2012).  3. Lian, X. et al. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nat. Protoc. 8, 162–175 (2013).

extract_protocol:
For RNA isolation, 3D microtissue and 2D controls were dissociated by using MACS MultiTissue Dissociation Kit 3 on day 30 and day 50. After cell dissociation, RNA was extracted with High Pure RNA Isolation Kit (Roche) according to manufacturer’s instructions, and quantified with Nanodrop 2000 Spectrophotometer (Thermo Fisher Scientific). Quality control for RNA integrity number (RIN) was also determined with Agilent 2100 Bioanalyzer.
500 nanograms of total RNA per sample was used as an input for library preparation using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Briefly, RNA was transcribed into cDNA using oligodT primer (FS1) at half volume compared to the manufacturer's instructions to minimize the off-target products. Following the first strand synthesis, RNA removal and second strand synthesis were performed using the UMI Second Strand Synthesis Mix (USS) containing Unique Molecular Identifiers (UMIs) that allow detection and removal of PCR duplicates. Finally, sequencing libraries were created by PCR with i5 Unique Dual Indexing Add-on Kit for Illumina (Lexogen). The quality and quantity of libraries was determined using Fragment Analyzer by DNF-474 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and QuantiFluor dsDNA System (Promega). Final library pool was sequenced on Illumina NextSeq 500 with 75 bp single-ends

tag: time-point

value: Day 50

tag: strain origin

value: iPSC DF 19-9-7 (karyotype:46, XY, WiCell)


title: V0742

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 210

tag: age


title: CVS_70089_Male_IVF

description:
IVF Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

source_name: Placenta - chorionic villi

value: Placenta - chorionic villi

value: IVF

value: Male

tag: fetal race

value: CaucasianAsianBiracial

tag: fetal ethnicity

tag: gestational age_at_cvs_(days)


title: Sample infarcted cardiac tissue 7

description: See protocols below


title: V0744

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 211

tag: bmi

tag: fat mass

tag: muscle mass


title: D50-U_rep2


title: V0740

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 209


title: Liver, H12h, 3 (miRNA-seq)

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
The clean miRNA reads were obtained from raw reads after discarding sequences, adaptor-ligated contaminants, and reads shorter than 18 nt.
Clean reads were compared against small RNAs in Rfam database to identify and remove rRNA, scRNA, sonRNA, snRNA, and tRNA.
Known miRNAs were identified by aligning against the miRbase database (v.22), and unannotated reads were considered as novel miRNAs according to their genome positions and hairpin structures using Mireap_v0.2.
Assembly: miRbase database (v.22)
Supplementary files format and content: tab-delimited text file includes TPM values for miRNAs for each Sample

organism: Carassius auratus

source_name: liver

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: stress

value: hypoxia, 12 hr

value: wild-type


title: SUM225_NRAS_OE_rep1

first: Jonathan

middle: Thomas

last: Lei

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

description:
EC_SUM225_RNAseq_Log2plus1_RSEM_UQ.txt
NRW

data_processing:
Paired-end 150 bp reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2.
Log2 RSEM counts of protein-coding genes were upper quantile normalized and used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Processed tab-delimited files are provided for each cell line containing upper quantile log2+1 RSEM counts

growth_protocol: SUM102PT cells carrying DOX-inducible shRNA against NRAS were cultured in F12 medium supplemented with 1 g/L bovine serum albumin, 10 mM HEPES, 5mM ethanolamine, 5μg/mL transferrin, 10 nM triiodo thyronine, 50 nM sodium selenite, 5  μg/ml human insulin, 1  μg/ml hydrocortisone, and 10 ng/ml epidermal growth factor. SUM225 cells were cultured in DMEM/F12 medium (Thermo Fisher Scientific) supplemented with 5% fetal bovine serum, 10 mM HEPES, non-essential amino acids, 5 µg/mL human insulin, and 1 µg/mL hydrocortisone.

extract_protocol:
RNA was isolated with Qiagen RNeasy kit
Illumina TruSeq Stranded mRNA prep kit was used for library preparation

treatment_protocol: SUM102PT cells carrying DOX-inducible shRNA against NRAS were treated with or without 2 μg/ml doxycycline for 3 months. SUM225 cells were grown in their growth medium for 5 weeks.

tag: cell line

tag: cell type

value: luminal-like DCIS, NRAS overexpressing

tag: treatment

value: growth medium, 5weeks


title: Liver, H12h, 2 (miRNA-seq)

tag: genotype


title: ABC multiplex K562 rep3 (originally rep1)

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

description: ABC CLIP-seq IP library, multiplex with 10 conjugated antibodies

data_processing:
Data is processed in a similar way to standard eCLIP pipeline, except for a few adjustments to ABC’s multiplex design and library structure. UMI are extracted using umitools 1.0.0 and adaptors are removed using cutadapt 2.8, then fastqs are demultiplexed based on the 5nt barcode sequence using fastx toolkit. Since ABC is sequenced on the reverse strand, we reverse complement sequences. Alignment to the repetitive regions removes multi-mapped reads, then aligned to the genomic sequences using STAR 2.7.6. The pipeline is available at https://github.com/algaebrown/oligoCLIP.git
Given the genome alignment, we subsequently follow the steps to do peak call using CLIPper, then rank the peaks comparing to “backgrounds”, either SMInput (eCLIP), RNA-seq (ABC), or to other multiplex libraries (internal normalization). CLIPper uses nearby regions (+/- 500 b.p.) to estimate the background, followed by a Poisson distribution to assess the significance of a peak, whereas “normalization” takes into account of another background library. In the eCLIP protocol, the SMInput library is prepared the same way as the IP library, which estimates the background crosslinking rate of other RBPs with similar size ranges as well as the RNA expression level and all other bias in library preparation. Since ABC does not have a SMInput, we realize that a total RNA-seq library can capture part of the bias. Furthermore, internal normalization to other multiplexed library can estimate not only the expression level, but also other biases introduced within the protocol. Ideally, as the number of RBP approaches infinity, the summation of “other RBPs in the multiplexed library” should approach the SMI-input. To estimate the significance of the peak based on backgrounds, we used a chi-square test (or Fisher Exact test, if the number of reads < 5) to compare the number of reads in the IP library and the background library within and outside of the peak region. The pipeline is available at https://github.com/algaebrown/oligoCLIP.git
Assembly: GRCh38
Supplementary files format and content: bed (unnormalized CLIPper peak)
Supplementary files format and content: bed (normalized to RNA-seq)
Supplementary files format and content: bed (normalized to other multiplex library, repeat element removed)

growth_protocol: K562 and HEK293 cells were cultured in DMEM media supplemented with 10% FBS following the standard tissue culture technique. Cell pellets were generated by washing 10 cm plates (~15 million cells) once with cold 1X phosphate-buffered saline (PBS) and overlaid or resuspended with minimal (3 mL per 10 cm plate) cold 1X PBS and UV crosslinked (254 nm, 400 mJ/cm2) on ice. After crosslinking, cells were scraped and spun down, the supernatant removed, and washed with cold 1X PBS. Cell pellets (10 million each) were flash-frozen on dry ice and stored at -80°C.

extract_protocol: Frozen HEK293 or K562 cell pellets were lysed in 1 mL lysis buffer (50mM Tris pH 7.4, 100mM NaCl, 1% Igepal, 0.1% SDS, 0.5% Sodium Deoxycholate) supplemented with 5 µl protease inhibitor cocktail and 10 µl RNase inhibitor and sonicated for 5 min with 30 second on/off cycles. The lysate was then treated with 10 µl diluted (1:25) RNase I and 5 µl TurboDNase and incubated at 37°C for 5 min. Cellular debris was removed by centrifugation at 12,000 x g for 3 min.

tag: clip antibody

value: Bethyl A300-864A (RBFOX2)

value: Bethyl A300-202A (PUM2)

value: Bethyl A300-474A (DDX3)

value: Bethyl A303-889A (FAM120A)

value: Bethyl A301-524A (ZC3H11A)

value: Bethyl A303-588A (LIN28B)

value: Bethyl A303-950A (SF3B4)

value: Bethyl A301-755A (EIF3G)

value: Bethyl A303-921A (PRPF8)

value: MBL RN008P (IGF2BP2)


title: SUM225_NRAS_OE_rep2

description:
EC_SUM225_RNAseq_Log2plus1_RSEM_UQ.txt
S2NW5W


title: V0738

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 208

source_name: Peripheral blood

tag: Sex

value: Female


title: SUM225_control_rep1

description:
EC_SUM225_RNAseq_Log2plus1_RSEM_UQ.txt
NRC

value: luminal-like DCIS, empty vector control


title: Liver, H12h, 1 (miRNA-seq)

value: liver


title: D30-U_rep3

tag: time-point

value: Day 30

value: iPSC DF 19-9-7 (karyotype:46, XY, WiCell)


title: V0736

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 207


title: SUM102PT_plusDOX_rep2

description:
EC_SUM102_RNAseq_Log2plus1_RSEM_UQ.txt
SB2DOXV12W

value: basal-like DCIS, DOX-inducible NRAS shRNA

value: growth medium, +DOX, 13weeks


title: D30-U_rep2

tag: strain origin


title: D30-U_rep1


title: V0734

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 206

value: Male

tag: age


title: SUM102PT_minusDOX_rep2

description:
EC_SUM102_RNAseq_Log2plus1_RSEM_UQ.txt
SB2V12W

value: growth medium, -DOX, 13weeks


title: Sample infarcted cardiac tissue 2

description: See protocols below

tag: strain

value: Sprague-Dawley

tag: time point

value: day 3

tag: agent

value: iECM


title: Liver, N, 2 (miRNA-seq)

value: control

value: wild-type


title: SUM225_control_rep2

description:
EC_SUM225_RNAseq_Log2plus1_RSEM_UQ.txt
S2C5W

value: growth medium, 5weeks


title: Sample infarcted cardiac tissue1

description: See protocols below

value: day 1


title: V0732

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 205

tag: bmi


title: D50-U_rep1

value: Day 50


title: V0730

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 203

tag: fat mass


title: V0731

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 204

tag: muscle mass


title: Liver, N, 1 (miRNA-seq)

tag: tissue


title: SUM102PT_minusDOX_rep1

description:
EC_SUM102_RNAseq_Log2plus1_RSEM_UQ.txt
EC13W


title: V0729

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 202

value: Female


title: sample65_adjacent_non_HCC_tissue

city: Nanning

first: Meiying

last: Long

state: Guangxi

address: Guangxi nanning of China

institute: Guangxi Medical University

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L65_sample_N

data_processing:
The raw sequencing reads were preprocessed by fastp v0.23.0
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align the transcriptome sequencing Reads to the reference genome
HTSeq was used for Reads Count calculation
Transcripts Per Million of library size (TPM) 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.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: tissue: liver

extract_protocol:
(1) NanoDrop™ One/OneC for RNA purity (OD260/280, OD260/230 ratios); (2) Life Invitrogen Qubit® 3.0 fluorescence quantification instrument with Qubit™ RNA HS Assay Kit for precise quantification; (3) Agilent 4200 (3) Agilent 4200 TapeStation System for accurate detection of RNA integrity (RIN value).
(1) Capture mRNA with polyA structure using magnetic beads with Oligo (DT); (2) Synthesize cDNA using fragmented mRNA as template; (3) Purify cDNA with end repair, A-tailing and sequencing connectors; (4) Screen cDNA of 200bp with AMPure XP beads, perform PCR amplification and sequencing library. (4) Screen the 200bp cDNA with AMPure XP beads, amplify the PCR and purify the PCR

value: paracancerous normal tissues


title: sample64_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L64_sample_N


title: sample63_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L63_sample_N


title: V0725

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 199


title: V0727

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 201


title: V0726

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 200


title: Liver, N, 3 (miRNA-seq)

value: liver

tag: stress


title: sample62_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L62_sample_N


title: V0720

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 197


title: HCV_SARS-CoV-2.2

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Sequence alignment: RNA-seq analysis was performed on data from SARS infected cells (n=3) and HCV+SARS co-infected cells (n=3) obtained in this study, and HCV infected cells (n=6) and uninfected cells adopted from Perez et al (1). Raw reads were aligned to the NCBI RefSeq genes from GRCh37/hg19 human genome assembly using RNA-seq by expectation maximization pipeline (RSEM)
Differential expression analysis: Differential gene expression analysis was conducted using the DESeq2 (3) package (release 1.30.1) in R (version 4.0.5). Specifically, HCV, SARS, co-infected data were compared separately against non-infected, using p-value (adjusted by Benjamini–Hochberg method) of 10e-5 and the absolute fold change of 0.5 as cutoffs. To avoid biases resulted from different number of replicates, we iteratively sampled three out of six samples for the HCV and non-infected categories, and use the average value over iterations.
Pathway enrichment analysis: Pathway analysis of differentially expressed genes (both up and down regulated genes) was performed with ‘KEGGprofile’ R package (release 1.32.0) (4) using the find_enriched_pathway function with the following parameters: returned_adjpvalue = 0.05, download_latest=T.
Assembly: human GRCh37/hg19

growth_protocol: Huh 7.5 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco), supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptavidin and 1% non-essential amino acids (NEAA).

extract_protocol:
Total RNA from HCV/ SARS-CoV-2 monoinfected, coinfected and non-infected Huh7.5 cells (generated as described above) was purified using the RNeasy Mini Kit (Qiagene).
1 μg of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB). RNA-seq libraries were produced using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). For each tested group three biological replicates were performed.

treatment_protocol: For all experiments with 100% HCV-infected Huh7.5, cells were infected with HJ3-5 at a multiplicity of infection (MOI) of 0.1, and passaged for at least 2 weeks until approximately 100% of the cells were HCV-positive, as determined by immunofluorescence. for HCV-SARS-CoV-2 coinfection experiments, 100% HCV-infected or non-infected Huh7.5 cells were seeded in 12- or 24-well plates, or on 8-well chamber slides (Thermo) and grown overnight. The next day, SARS-CoV-2 stock was used to infect the cells at a MOI of 0.01 for 1, 5, 24 or 48 h. Then, cells were lysed for RNA purification, or fixed for immunostaining for detection of infection.

value: Hepatocyte

value: HCV-SARS-CoV-2 coinfected

value: WT

value: Carcinoma

value: Unknown

tag: source gender

value: male


title: HCV_SARS-CoV-2.3

tag: cell type


title: sample61_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L61_sample_N


title: HCV_SARS-CoV-2.1

tag: treatment


title: SUM102PT_plusDOX_rep1

description:
EC_SUM102_RNAseq_Log2plus1_RSEM_UQ.txt
EC13WD

tag: cell line

value: basal-like DCIS, DOX-inducible NRAS shRNA

value: growth medium, +DOX, 13weeks


title: sample60_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L60_sample_N


title: sample59_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L59_sample_N


title: SARS-CoV-2.3

tag: genotype


title: SARS-CoV-2.2


title: V0718

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 195

tag: Sex


title: sample57_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L57_sample_N


title: V0719

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 196


title: sample58_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L58_sample_N


title: SARS-CoV-2.1


title: sample56_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L56_sample_N


title: sample55_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L55_sample_N


title: V0717

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 194


title: V0715

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 192


title: V0724

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 198

value: Male


title: sample54_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L54_sample_N


title: V0713

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 191


title: V0711

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 190


title: sample53_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L53_sample_N


title: sample51_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L51_sample_N


title: V0710

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 189


title: ABC multiplex HEK293T rep1 (originally rep2)

description: ABC CLIP-seq IP library, multiplex with 10 conjugated antibodies

tag: clip antibody

value: Bethyl A300-864A (RBFOX2)

value: Bethyl A300-202A (PUM2)

value: Bethyl A300-474A (DDX3)

value: Bethyl A303-889A (FAM120A)

value: Bethyl A301-524A (ZC3H11A)

value: Bethyl A303-588A (LIN28B)

value: Bethyl A303-950A (SF3B4)

value: Bethyl A301-755A (EIF3G)

value: Bethyl A303-921A (PRPF8)

value: MBL RN008P (IGF2BP2)


title: sample52_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L52_sample_N

value: paracancerous normal tissues


title: ABC multiplex HEK293T rep1 (originally rep1)


title: ABC singleplex SLBP K562 rep2

description: ABC CLIP-seq IP library, singleplex

value: Bethyl A303-968A (SLBP)


title: ABC singleplex RBFOX2 HEK293T rep2

description: ABC CLIP-seq IP library, singleplex


title: sample50_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L50_sample_N


title: ABC singleplex SLBP K562 rep1

description: ABC CLIP-seq IP library, singleplex


title: V0716

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 193

value: Female


title: V0704

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 185


title: V0705

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 186


title: ABC multiplex K562 rep2 (originally rep6)


title: sample48_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L48_sample_N


title: RD-EWS_FLI1-OE-ETV6

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Raw reads from RNA-seq were mapped to reference genome hg38 using RNA STAR with default parameters. Read count tables were created using FeatureCounts with a custom GTF file containing protein coding genes only. Differentially expressed genes were analyzed using DESeq2 with two independent replicates using default parameters.
Raw reads from ChIP-seq were aligned to the reference genome hg38 using Bowtie2 with sensitive end-to-end setting. After removal of PCR duplication reads by SAMtools, peaks were identified using MACS2, with narrow peak option for TFs and broad peak option for H3K27Ac. Genome-wide read coverage was calculated by deepTools with a bin size of 50 bp.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: peaks .bed file
Supplementary_files_format_and_content: DESeq2 .tabular file with (basemean, log2FoldChange, lfcSE, stat, pvalue, padj)

source_name: human Rhabdomyosarcoma cancer cell

growth_protocol: Ewing sarcoma cell line A673 (ATCC, CRL-1598), Rhabdomyosarcoma cell line RD (ATCC, CCL-136) and Osteosarcoma cell line U2OS were cultured in DMEM supplemented with 10% FBS (Corning, 35-010-CV). Ewing sarcoma cell line TC71 (DSMZ, ACC-516) was cultured in Iscove’s MDM supplemented with 15% FBS. Ewing sarcoma cell line RH1 (DSMZ, ACC-493) and leukemia cell line HEL (ATCC, TIB-180) were cultured in RPMI 1640 supplemented with 10% FBS. Penicillin_Streptomycin was added to all media. All cell lines were cultured at 37 °C with 5% CO2 and periodically tested for mycoplasma infections.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For ChIP_seq experiments, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
was constructed using the Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions.

treatment_protocol: Samples were collected 5 days post guide RNA infection or 48h after doxycycline treatment (1μg_ml)

value: RD

tag: chip antibody

value: ETV6, Bethyl, A303-674A


title: sample49_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L49_sample_N


title: ABC singleplex RBFOX2 HEK293T rep1

description: ABC CLIP-seq IP library, singleplex


title: ABC multiplex K562 rep1 (originally rep4)


title: V0702

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 184

tag: age


title: RD-EV-ETV6


title: V0707

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 187


title: sample47_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L47_sample_N


title: sample46_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L46_sample_N


title: V0701

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 183


title: sample45_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L45_sample_N


title: V0700

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 182


title: V0708

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 188


title: sample44_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L44_sample_N


title: sample43_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L43_sample_N


title: A673-SAM-Dox-EWS_FLI1

source_name: human Ewing sarcoma cancer cell

value: Treat with 1ug_ml doxycycline for 48h

value: FLI1, Abcam, ab15289


title: A673-SAM-Control-EWS_FLI1


title: V0699

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 181


title: V0698

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 180


title: A673-SAM-Dox-ETV6


title: sample42_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L42_sample_N


title: V0696

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 179


title: V0695

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 178


title: V0692

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 177


title: A673-sgETV6_1-EWS_FLI1


title: RD-Input


title: A673-sgNEG-EWS_FLI1


title: sample40_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L40_sample_N


title: A673-sgEWS_FLI1-ETV6


title: sample39_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L39_sample_N


title: sample38_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L38_sample_N


title: V0691

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 176


title: A673-sgETV6_2-EWS_FLI1


title: V0689

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 174


title: A673-sgETV6_1-ETV6


title: V0690

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 175


title: A673-SAM-Control-ETV6


title: sample37_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L37_sample_N


title: V0688

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 173


title: A673-sgNEG-ETV6


title: A673-Input


title: sample36_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L36_sample_N


title: sample34_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L34_sample_N


title: sample41_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L41_sample_N


title: V0687

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 172


title: V0686

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 171


title: V0685

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 170


title: sample33_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L33_sample_N


title: A673-SAM-Dox_rep1


title: sample32_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L32_sample_N


title: V0683

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 169


title: A673-SAM-Control_rep2


title: sample31_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L31_sample_N


title: sample35_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L35_sample_N


title: A673-SAM-Control_rep1


title: V0682

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 168


title: U2OS_sgETV6_2_rep2

source_name: human osteosarcoma cancer cell

value: Infect with guide RNA for 5 days


title: sample30_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L30_sample_N


title: V0679

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 166


title: U2OS-sgETV6_1_rep2


title: sample27_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L27_sample_N


title: sample28_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L28_sample_N


title: V0677

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 164


title: A673-SAM-Dox_rep2


title: V0680

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 167


title: U2OS-sgNEG-rep2


title: AML346, WT1 KO, 3

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

description:
Read_Counts.txt column:
ATCGCTGCTCAG

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to a combined Human Genome (hg38) and Mouse Genome (mm10) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Assembly: hg38
Supplementary files format and content: cell (columns) and gene (rows) -wise raw counts expression table

source_name: AML PDX line

growth_protocol: The PDX cell mixture of WT KO, DNMT3A KO and CTRL in a 1:1:1 ratio were injected into NSG mice.

extract_protocol:
[harvest protocol] The mixture of the cells were harvested from bone marrow of the mice that had reached advanced leukemia stage and sorted for single KOs.
prime-seq
Library was constructed using the prime-seq protocol

value: patient derived xenograft cells

tag: disease  state

value: acute myeloid leukemia

value: sgWT1 KO


title: AML661, WT1 KO, 3

description:
Read_Counts.txt column:
AAGAGCTGGTCT


title: V0676

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 163


title: sample25_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L25_sample_N


title: sample24_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L24_sample_N


title: AML346, WT1 KO, 2

description:
Read_Counts.txt column:
GTGCGATAGTCC


title: sample23_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L23_sample_N


title: V0674

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 161


title: U2OS_sgETV6_2_rep1


title: AML356, WT1 KO, 3

description:
Read_Counts.txt column:
AATGCATCAGCA


title: SUIT2_sgETV6_2_rep1

source_name: human pancreatic cancer cell


title: sample29_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L29_sample_N


title: AML388, WT1 KO, 2

description:
Read_Counts.txt column:
AGAACGACACAA


title: V0672

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 160


title: V0671

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 159


title: V0678

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 165


title: SUIT2-sgETV6_1_rep2


title: U2OS-sgETV6_1_rep1


title: sample22_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L22_sample_N


title: SUIT2-sgETV6_1_rep1


title: AML661, WT1 KO, 2

description:
Read_Counts.txt column:
CTTCTCGCTACA


title: sample26_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L26_sample_N


title: V0669

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 158


title: sample21_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L21_sample_N


title: U2OS-sgNEG-rep1


title: V0668

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 157


title: V0675

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 162


title: sample20_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L20_sample_N


title: SUIT2_sgETV6_2_rep2


title: SUIT2-sgNEG-rep2


title: AML356, WT1 KO, 2

description:
Read_Counts.txt column:
TCACGACGACAG


title: sample19_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L19_sample_N


title: SUIT2-sgNEG-rep1


title: V0665

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 156


title: AML661, WT1 KO, 1

description:
Read_Counts.txt column:
CACCGTGGATCA


title: sample18_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L18_sample_N


title: AML346, WT1 KO, 1

description:
Read_Counts.txt column:
GGATATTCCACA


title: V0664

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 155


title: sample17_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L17_sample_N


title: RD-EF-sgETV6_2_rep1


title: AML356, WT1 KO, 1

description:
Read_Counts.txt column:
TCTTGCGTTCAA


title: V0663

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 154


title: RD-EF-sgETV6_2_rep2


title: V0662

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 153


title: RD-EF-sgETV6_1_rep2


title: AML388, WT1 KO, 1

description:
Read_Counts.txt column:
ACGTATTGTCCA


title: sample15_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L15_sample_N


title: RD-EF-sgETV6_1_rep1


title: sample16_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L16_sample_N


title: sample14_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L14_sample_N


title: AML356, DNMT3A KO, 3

description:
Read_Counts.txt column:
GCCTCAAGATAA

value: sgDNMT3A KO


title: AML388, DNMT3A KO, 2

description:
Read_Counts.txt column:
CCAGTGTCCTTG


title: RD-EF-sgNEG-rep2


title: V0661

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 152


title: AML356, DNMT3A KO, 2

description:
Read_Counts.txt column:
ATTCGAATTCCG


title: RD-EF-sgNEG-rep1


title: AML346, DNMT3A KO, 3

description:
Read_Counts.txt column:
GTCACCAAGCCA


title: sample13_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L13_sample_N


title: V0658

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 149


title: sample12_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L12_sample_N


title: RD_sgETV6_2_rep2


title: V0659

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 150


title: RD_sgETV6_2_rep1


title: V0660

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 151


title: AML346, DNMT3A KO, 2

description:
Read_Counts.txt column:
CGCGGTCAAGAA


title: V0654

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 148


title: RD-sgETV6_1_rep2


title: V0653

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 147


title: sample10_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L10_sample_N


title: AML388, DNMT3A KO, 1

description:
Read_Counts.txt column:
TTAGCACACCTT


title: AML661, DNMT3A KO, 3

description:
Read_Counts.txt column:
TTGAATGTGCGA


title: V0652

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 146


title: sample9_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L09_sample_N


title: V0651

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 145


title: RD-sgNEG-rep2


title: sample7_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L07_sample_N


title: sample8_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L08_sample_N


title: AML356, DNMT3A KO, 1

description:
Read_Counts.txt column:
TCAGGTCGTGGA


title: RD-sgNEG-rep1


title: V0650

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 144


title: AML661, DNMT3A KO, 1

description:
Read_Counts.txt column:
CCACGTAAGAGG


title: V0649

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 143


title: sample11_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L11_sample_N


title: RD-sgETV6_1_rep1


title: RH1_sgETV6_2_rep2


title: sample6_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L06_sample_N


title: AML346, DNMT3A KO, 1

description:
Read_Counts.txt column:
CAGCGGAACTTA


title: sample5_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L05_sample_N


title: sample4_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L04_sample_N


title: RH1-sgETV6_1_rep2


title: AML661, Control, 3

description:
Read_Counts.txt column:
GACAAGAGCTTA

value: CTRL


title: sample3_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L03_sample_N


title: V0645

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 141


title: AML661, DNMT3A KO, 2

description:
Read_Counts.txt column:
CTTCCTTGTCGG


title: AML346, Control, 3

description:
Read_Counts.txt column:
ATCTCGATACGA


title: sample2_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L02_sample_N


title: V0644

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 140


title: RH1-sgETV6_1_rep1


title: RH1-sgNEG-rep2


title: AML356, Control, 3

description:
Read_Counts.txt column:
CCACTCTAGGCT


title: RH1-sgNEG-rep1


title: AML356, Control, 2

description:
Read_Counts.txt column:
ACCAGCCACCTA


title: sample1_adjacent_non_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L01_sample_N


title: V0641

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 138


title: V0642

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 139


title: AML661, Control, 2

description:
Read_Counts.txt column:
AGCATAGCCACA


title: TC71_sgETV6_2_rep2


title: sample65_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L65_sample_T

value: hepatocellular carcinoma


title: RH1_sgETV6_2_rep1


title: V0640

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 137


title: V0647

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 142


title: V0610

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 136


title: sample64_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L64_sample_T


title: TC71_sgETV6_2_rep1


title: sample63_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L63_sample_T


title: AML388, Control, 3

description:
Read_Counts.txt column:
GAGTGTCATGTT


title: V0598

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 135


title: TC71-sgETV6_1_rep2


title: AML346, Control, 2

description:
Read_Counts.txt column:
CTCTTCTACTAG


title: sample62_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L62_sample_T


title: TC71-sgETV6_1_rep1


title: AML388, Control, 2

description:
Read_Counts.txt column:
TCGGTTCGCTCA


title: V0571

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 134


title: V0545

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 133

value: Male


title: TC71-sgNEG-rep2


title: sample61_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L61_sample_T


title: sample60_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L60_sample_T


title: AML661, Control, 1

description:
Read_Counts.txt column:
GATTCATTCGGA


title: V0544

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 132


title: TC71-sgNEG-rep1


title: AML346, Control, 1

description:
Read_Counts.txt column:
GTAGGCGCATGA


title: sample59_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L59_sample_T


title: A673_sgEWS_FLI1_rep2


title: sample58_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L58_sample_T


title: A673_sgETV6_2_rep2


title: sample57_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L57_sample_T


title: V0539

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 131


title: sample56_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L56_sample_T


title: V0538

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 130


title: A673_sgETV6_2_rep1


title: V0513

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 128


title: A673-sgETV6_1_rep2


title: V0506

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 127


title: lung_normal_rep1

description: Date: 2009

source_name: normal lung tissue

tag: strain

value: FVB/N


title: lung_normal_rep2

description: Date: 2009


title: AML356, Control, 1

description:
Read_Counts.txt column:
TAGCGGTCTGCA


title: A673-sgETV6_1_rep1


title: V0364

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 126


title: sample54_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L54_sample_T


title: sample53_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L53_sample_T


title: lung_tumor_myckras_rep4

description: Date: 2009

source_name: lung adenocarcinoma

value: on doxycycline (MYC and KRAS activated)


title: AML388, Control, 1

description:
Read_Counts.txt column:
TGTTATGGCCAA


title: V0314

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 125


title: A673-sgNEG-rep2


title: A673_sgEWS_FLI1_rep1


title: A673-sgNEG-rep1


title: V0299

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 124


title: V0514

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 129


title: lung_tumor_myckras_rep3

description: Date: 2009


title: sample50_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L50_sample_T


title: V0281

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 123


title: sample55_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L55_sample_T


title: sample51_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L51_sample_T


title: Breast cancer epithelial cells, 72h Treated

city: PORTLAND

first: Hongmei

last: Zhang

state: OR

address: 2730 SW Moody Ave

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
Raw base call files were demultiplexed with 'cellranger mkfastq' into fastq files (cellranger 2.0).
We applied 'cellranger count' to performs genome alignment, filtering, barcode counting, and UMI counting for fastq files with default parameters. The feature-barcode matrices were generated by sample.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI count for each gene in cell populations.

source_name: Breast cancer epithelial cells

growth_protocol: HCC1143 cells were maintained in RPMI1640 growth medium (Life Technologies Inc.) supplemented with 10% fetal bovine serum (Hyclone) incubating at 37°C with 5%.

extract_protocol:
Cell were incubated with Gel Bead-In-Emulsions(GEM) using Chromium Controller of 10x Genomics for 6.5 min. Barcoded and full length cDNA from poly A mRNA by reverse transcription were produced after incubation. The GEMs were broken and full length cDNA were pooled together.
Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass, QC(200-9000bp) with Agilent Bioanalyzer chip for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size (peaks 400-600bp) with Agilent D1000 ScreenTape prior to library construction.  P5, P7, a sample index and R2 were added during library construction via End repair, A-tailing, Adaptor ligation and PCR. The final libraries contain the P5 and P7 primers were used in Illumina bridge amplification.

treatment_protocol: Cells were seeded into 6-well plate allowed to attach for 24 hours prior to treatment with DMSO or Paclitaxel (P-9600, LC Labs) 1nM for 24 or 72 hours then collected for single cell sequence.

value: Treated with Paclitaxel

tag: time point


title: V0243

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 122

data_processing: Results were analyzed using TaqMan Genotyper software.

extract_protocol: Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen Sciences, Inc, Germantown, MD, USA)

tag: bmi