title: Mouse oocyte WT-14 months-GV-Rep1

description:
Aging-Mouse-FPKM.txt
WT-14 months-GV-Rep1


title: Mouse oocyte WT-4 weeks-MII-Rep3

status: Public on May 04 2022

type: SRA

city: Hangzhou

first: Yunwen

last: Wu

state: Zhejiang

address: Yu Hang Tang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-MII-Rep3

library_source: transcriptomic

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19), mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1 respectively. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

molecule: total RNA

organism: Mus musculus

source_name: Mouse WT young MII

extract_protocol:
Oocytes were collected from indicated species (1 oocyte per sample for human and 10 oocytes per sample for mouse). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

tag: tissue

value: oocyte


title: SC_NS-2

city: Pittsburgh

first: Chandan

middle: K

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

country: USA

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Quality control, clustering and differential gene expression analysis were performed using Seurat v.3.1.0
Genome_build: hg:38
Supplementary_files_format_and_content: barcode files
Supplementary_files_format_and_content: gene names file
Supplementary_files_format_and_content: count matrix file

organism: Homo sapiens

source_name: human unwounded skin tissue

growth_protocol: Human tissue samples

extract_protocol:
The tissue was chopped into small pieces and subjected to enzymatic dissociation using whole skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237) (Miltenyi Biotec Inc., San Diego, CA). The samples were incubated in a water bath at 37°C for approximately 3 hours. After incubation, the samples were diluted by adding 0.5 mL of cold cell culture medium in order to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentleMACS™ Octo dissociator and UW human skin dissociation program was performed. The cell suspension was subjected to a pre-Separation Filter, 70 µm, placed on a 15 mL tube in order to remove the debris. RBC were lysed using 10X RBC lysis buffer (cat. no. 420301, BioLegend, San Diego, CA).
The resulting cell suspension was utilized for single cell RNA sequencing using the 10x Genomics platform using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10x Genomics, Inc.) and sequenced on an Illumina NovaSeq 6000 (Illumina, Inc).

treatment_protocol: Single-cell suspensions were generated from theunwounded human skin biopsies.

tag: gender

value: M

tag: age (years)


title: Metabolic_syndrome (KC1-G36-H0915), total RNA

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

data_processing:
read trimming: skewer
mapping: STAR
quantification: Cuffquant
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Total RNA was isolated from   PBMC cell using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA) based method. The quantity and quality of the RNA were evaluated using Agilent Nono Kit and assessing the RNA integrity number (RIN >7). One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard MGI protocols

tag: cell type

value: PBMC

tag: Sex

value: Male

tag: disease state


title: 4-CCA2_EM

city: Guangzhou

first: Haoyu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
Bulk RNA-seq was performed by Novogene (Beijing, China) resulting in 20-30 million, 150 nucleotides long, paired-end reads.
Mapped reads were translated to counts using FeatureCounts (version 2.0.1) applying the built-in hg38 gernome annotation file.
CCA primary tissue bulk RNA-seq data from patient CCA1 was retrieved from a previously published manuscript [Broutier et al., Nat Med, 2017] (accession number GSE84073) and incorporated into our dataset. Raw counts were batch corrected using ComBat-seq (available via sva package version 3.36.0) using a negative binomial regression model.
Analysis of differential expression was performed using edgeR (version 3.32.1) and Limma (version 3.46.0) R packages. Genes were considered differentially expressed when the adjusted p-value was <0.05 (Benjamini Hochberg FDR corrected).
Subsequent GSEA on the log2FC values was done using fgsea (version 1.16.0) and gage (version 2.40.1) R packages. To increase specificity, fgsea results were filtered using gage results so that only pathways which are significant and in the same direction in both methods are retained.
Genome_build: Hg38
Supplementary_files_format_and_content: Dataframe counts and genes
Supplementary_files_format_and_content: Metadata information samples

source_name: Cholangiocarcinoma tumor organoids

growth_protocol: Broutier et al. Nat Med 2017. For BRCCAOs, branching organoids were created by switching culture conditions to non-canonical WNT stimulating conditions, consisting of William's E medium (WE, ThermoFisher Scientific) supplemented with 10 mM nicotinamide (Sigma), 17 mM sodium bicarbonate (Sigma), 0.2 mM 2-phospho-L-ascorbic acid trisodium salt (Sigma), 6.3 mM sodium pyruvate (Gibco), 14 mM glucose (Sigma), 20 mM HEPES (Fisher Scientific), ITS + premix (Life Technologies), 0.1 μM dexamethasone (Sigma), 2 mM Ultraglutamine (Fisher Scientific), 100 µg/mL penicillin/streptomycin (Fisher Scientific), 20 ng/mL EGF (Peprotech), 10% RSPO1 conditioned media (homemade) and 100 ng/mL DKK-1 (Abcam Ltd), after 3 passages.

extract_protocol:
RNA from CCA primary tissue and CCAOs cultured in EM and branching medium conditions was collected in lysis buffer (QIAzol lysing reagent, Qiagen) and the RNA was isolated using the miRNeasy mini kit (Qiagen) according to the manufacturer’s protocol
Sequencing data were uploaded to the Galaxy Web platform public server usegalaxy.org (Afgan E., Baker D., van den Beek M., Blankenberg D., Bouvier D., et al., 2016 The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44: W3–W10). Sequences were trimmed for adapters using Trim Galore! (version 0.4.3.1), and mapped using RNA STAR (version 2.6.8a) against the human reference genome GRCh38).

treatment_protocol: no treatment

value: human CCAOs

tag: medium

value: cultured in expansion medium


title: Metabolic_syndrome (KC1-G36-H1873), total RNA


title: YWT2

type: RNA

city: Duarte

first: WenYong

last: Chen

address: 1500 East Duarte Road

department: Cancer Biology

institute: City of Hope

hyb_protocol: Although RNA preparation and amplification were done separately for batches 1 and 2, all 8 samples were processed for Affymetrix GeneChip® Mouse Genome 430 2.0 Array analysis in the same batch by following Affymetrix Eukaryotic Target Hybridization protocol for 100 Format midi arrays (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 7G with Gen Chip Operating software (GCOS) software according to manufacturer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

data_processing: Partek Genomics Suite (Partek 6.6 beta, release 6.12.0530) was used to process and normalize expression from .CEL files

label: biotin

source_name: Hematopoietic Stem Cell (HSC) from Young WT mice

label_protocol: 500pg RNA per sample was amplified by Nugen Ovation Pico WTA system V2 (Part No.3302) and labeled by Nugen Encore Biotin Module  (Part No.4200), according to manufacturer's protocol

growth_protocol: Cells were harvested from BALB/c mice directly.

extract_protocol: RNA was extracted by using PicoPure RNA isolation kit (ABI/Arcturus)

tag: strain background

value: BALB/c

tag: genotype/variation

value: WT

tag: age group

value: young

value: Hematopoietic Stem Cells (HSCs)

tag: batch

value: Experimental Batch 2


title: Mouse oocyte WT-14 months-GV-Rep2

description:
Aging-Mouse-FPKM.txt
WT-14 months-GV-Rep2

source_name: Mouse WT old GV


title: YWT3


title: 2-CCA14_T

source_name: Cholangiocarcinoma tumor tissue

value: CCA tumor tissue


title: YWT4


title: Mouse oocyte WT-4 weeks-MII-Rep2

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-MII-Rep2


title: Mouse oocyte WT-4 weeks-MII-Rep1

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-MII-Rep1


title: KO2

source_name: Hematopoietic Stem Cell (HSC) from Old SIRT1 Knock-Out mice

value: SIRT1 Knock-Out

value: old

value: Experimental Batch 1


title: WT4

source_name: Hematopoietic Stem Cell (HSC) from Old WT mice


title: control (KC1-G36-H0613), total RNA

value: Female

value: control


title: 3-CCA1_EM


title: KO1


title: iBAT OB-3

first: Yanrui

last: Huang

address: 58 Zhongshan Er Lu

institute: Sun Yet-sen University

description: Gene expression of iBAT from 16-week-old male ob/ob mice

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: interscapular brown adipose tissues

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was determined by standard denaturing agarose gel electrophoresis.

treatment_protocol: Freshly iBATs were isolated from control mice and 16-week-old ob/ob mice.

value: interscapular brown adipose tissues

tag: age

value: 16 weeks

tag: background strain

tag: genotype

value: ob/ob


title: control (KC1-G36-H0907), total RNA

value: PBMC

value: Male


title: 5-CCA14_EM

value: human CCAOs

value: cultured in expansion medium


title: iBAT OB-2


title: YWT1

value: BALB/c

value: WT


title: Mouse oocyte WT-4 weeks-GV-Rep1

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-GV-Rep1

source_name: Mouse WT young GV

value: oocyte


title: 1-CCA27_T


title: control (KC1-G36-H1740), total RNA


title: Mouse oocyte WT-4 weeks-GV-Rep3

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-GV-Rep3


title: 4F-24h

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

data_processing:
Cell Ranger version 3.1.0 from 10x Genomics
The resulting files were processed in R using the package Seurat (version 3.1.3)
All cells with at least three detected genes and less than 30% of reads from mitochondrial genes and all genes that were detected in at least 200 cells were used in the further analyses
The remaining data were normalized using the “LogNormalize” method.
Genome_build: GRCh38
Supplementary_files_format_and_content: cloupe files

source_name: hiPS-CMs

growth_protocol: hiPS-CMs cultured for 60 days post differentiation

extract_protocol:
10X genomics single cell platform
Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3 (10X Cat # 1000092)

treatment_protocol: Adenovirus were added for 24, 48, or 72 hours

tag: time point

value: 60 days post differentiation

value: Cellular dymnamics medium


title: 5637 cells, siCDCA3-2

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
(1) Pre-processing of sequencing reads/Quality Control. 1) Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes. 2) Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
(2) Quantification of gene expression level. Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
(3) Differential expression analysis. The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(fold change)| > 1 using the DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

growth_protocol: 5637 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated from cells/tissues using the Trizol (invitrogen) according to the manufacturer's protocol. RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0. Briefly, rRNAs were removed from Total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified l library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) HiSeq3000.
Total RNA was extracted from cell/tissues using the Trizol (invitrogen) according to the manufacturer's protocol, and ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre, Madison, WI, USA).Fragmented RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA). The libraries were paired-end sequenced (PE150, Sequencing reads were 150 bp) at Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform.

treatment_protocol: Transfection of siRNA follows Lipofectamine 3000 Reagent’s (L3000015, Invitrogen) protocol.

tag: cell line

value: bladder cancer cells

tag: treatment

value: siRNA transfection (siCDCA3)


title: Mouse oocyte WT-4 weeks-GV-Rep2

description:
Aging-Mouse-FPKM.txt
WT-4 weeks-GV-Rep2

tag: tissue


title: control (KC1-G36-H1242), total RNA


title: WT3

value: old

value: Hematopoietic Stem Cells (HSCs)

value: Experimental Batch 1


title: Metabolic_syndrome (KC1-G36-H0113), total RNA


title: VS_NS9

data_processing:
Generated reads were pre-processed using the standard Space Ranger (https://support.10xgenomics.com/spatial-gene-expression/software) pipeline to align the raw sequencing reads onto hg38 genome and obtained the respective h5-format and spatial image files for UW human skin
Resulting pre-processed files were loaded in Seurat for further downstream data processing and analysis.
We loaded the .h5 and spatial image files using ‘Load10X_Spatial’ module in Seurat and created Seurat Object for data processing
Sample quality were assured by computing the mitochondrial content (MT-content <15% is retained) and filtering out the poor-quality spots using ‘subset’ module of Seurat. We used “SCTransform” method available in Seurat that implements the regularized negative binomial regression for normalizing the 10x spatial data
Spatial feature plot function in Seurat was used to visualize the spatial location and expression profile of candidate genes
Genome_build: hg:38
Supplementary_files_format_and_content: barcode files
Supplementary_files_format_and_content: gene names file
Supplementary_files_format_and_content: count matrix file

growth_protocol: Human tissue sample

extract_protocol:
20µm thick section was taken on visium spatial gene expression slide followed by permeabilization for 12 mins
cDNA libraries were synthesized using Visium spatial gene expression reagent kit as per manufacture’s recommendations (PN-100186, 100190; 10x Genomics) and sequenced using NovaSeq 6000 (Illumina, Inc)

treatment_protocol: Human tissue sample

value: skin


title: Metabolic_syndrome (KC1-G36-H2002), total RNA

value: Female


title: 4F-48h


title: LacZ


title: Mouse primary hepatocytes, IL6 negative, small RNA, 0h, rep3

status: Public on May 03 2022

city: Brisbane

first: Samuel

last: Lukowski

state: Queensland

address: 306 Carmody Road, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

description:
36bp
mmPH-r3_IL6neg0h_smallRNA

data_processing:
FASTQ files containing paired-end reads (mRNA only) were mapped to the human (Homo sapiens; UCSC hg19) and mouse (Mus musculus; UCSC mm10) reference genomes using TopHat2 (v2.06) with default parameters. Reads were then mapped to known exons annotated by GENCODE v12 (human). For mouse annotations, we used the UCSC Table Browser to derive a table of known mouse genes. Read counts for each gene were obtained using the HTSeq python script.
Single-end reads (small RNA-seq) were filtered prior to mapping using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to (i) remove adapter-only reads, (ii) retain reads with a quality score ≥ 10 for 50% of bases/read, (iii) discard N-only reads and (iv) retain reads between 16 and 27 nt. The remaining reads were mapped to the reference genomes and annotated as for paired-end reads.
Assembly: hg19; mm10
Supplementary files format and content: comma-delimited text files include raw read count values for each Sample

source_name: Primary hepatocytes

growth_protocol: Hepatocytes were seeded at 0.75 × 10^5 cells/cm2 on collagen plates and incubated at 37 °C and 5% CO2 with culture medium

extract_protocol:
At the appropriate time point, cells were washed in PBS, scraped and centrifuged before RNA was extracted using the standard Qiagen miRNeasy (Qiagen) protocol as per the manufacturer's instructions, which retains the total RNA, including the small RNA fraction. cDNA from mRNA was synthesized using SuperScript II (Invitrogen), and from miRNA using the Exiqon Universal cDNA Synthesis kit II, according to the manufacturer's protocols.
For mRNA-seq of 6 conditions (IL-6 (+/−) at 0, 6, 24 h), two biological replicates for HepG2 cells (12 samples) and three biological replicates each for human and mouse primary hepatocytes (18 samples each) were prepared using the standard Illumina TruSeq RNA v2 protocol. Libraries were randomized and sequenced as 49 bp paired-end reactions using 6 samples per lane. For small RNA-seq, four biological replicates for HepG2 cells (24 samples) and three biological replicates each for human and mouse primary hepatocytes (18 samples) were prepared using the standard Illumina TruSeq small RNA protocol. The libraries were randomized and sequenced as 36 bp single-end reactions using 15 samples per lane. All library preparations were checked for quality using an Agilent Bioanalyzer (Agilent) and sample concentration was measured with a Qubit spectrophotometer (Invitrogen). All sequencing was performed on an Illumina HiSeq 2000.

treatment_protocol: Human and mouse hepatocytes were cultured for 48 h post-plating (24 h for HepG2). Cells were then washed twice in PBS then serum-starved for 24 h. Recombinant human or mouse interleukin-6 (Gibco), depending on the cell origin, was added to the media at a concentration of 50 ng/mL. Cells were collected at 0 h (untreated), 6 h and 24 h following exposure to human or mouse IL-6.

value: Primary hepatocytes

value: Hepatocytes

value: WT 129Sv/C57Bl6J

value: No treatment

tag: time


title: Mouse primary hepatocytes, IL6 positive, small RNA, 0h, rep3

description:
36bp
mmPH-r3_IL6pos0h_smallRNA

value: IL6 stimulated


title: Mouse primary hepatocytes, IL6 positive, small RNA, 24h, rep3

description:
36bp
mmPH-r3_IL6pos24h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, small RNA, 24h, rep2

description:
36bp
mmPH-r2_IL6pos24h_smallRNA


title: Mouse primary hepatocytes, IL6 negative, small RNA, 24h, rep3

description:
36bp
mmPH-r3_IL6neg24h_smallRNA


title: Mouse primary hepatocytes, IL6 negative, small RNA, 6h, rep3

description:
36bp
mmPH-r3_IL6neg6h_smallRNA


title: Metabolic_syndrome (KC1-G36-H1870), total RNA

value: PBMC

value: Male


title: iBAT Ctrl-3

description: Gene expression of iBAT from 16-week-old male control mice

value: interscapular brown adipose tissues

value: 16 weeks

tag: gender

value: control


title: Mouse primary hepatocytes, IL6 positive, small RNA, 0h, rep2

description:
36bp
mmPH-r2_IL6pos0h_smallRNA

tag: cell type


title: Mouse primary hepatocytes, IL6 negative, small RNA, 6h, rep2

description:
36bp
mmPH-r2_IL6neg6h_smallRNA


title: iBAT Ctrl-2


title: Mouse primary hepatocytes, IL6 positive, small RNA, 6h, rep1

description:
36bp
mmPH-r1_IL6pos6h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, small RNA, 24h, rep1

description:
36bp
mmPH-r1_IL6pos24h_smallRNA


title: 5637 cells, siNC

value: bladder cancer cells

value: WT

value: siRNA transfection (siNC)


title: 4F-72h

value: 60 days post differentiation

value: Cellular dymnamics medium


title: iBAT OB-1

value: ob/ob


title: Mouse primary hepatocytes, IL6 negative, small RNA, 24h, rep1

description:
36bp
mmPH-r1_IL6neg24h_smallRNA


title: Metabolic_syndrome (KC1-G36-H0833), total RNA

tag: Sex


title: Mouse primary hepatocytes, IL6 positive, small RNA, 6h, rep3

description:
36bp
mmPH-r3_IL6pos6h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, 6h, rep3

description:
49bp
mmPH-r3_IL6pos6h

molecule: polyA RNA


title: Mouse primary hepatocytes, IL6 positive, 24h, rep3

description:
49bp
mmPH-r3_IL6pos24h


title: Mouse primary hepatocytes, IL6 negative, 24h, rep3

description:
49bp
mmPH-r3_IL6neg24h


title: Mouse primary hepatocytes, IL6 positive, 24h, rep2

description:
49bp
mmPH-r2_IL6pos24h


title: VS_NS5

data_processing:
Generated reads were pre-processed using the standard Space Ranger (https://support.10xgenomics.com/spatial-gene-expression/software) pipeline to align the raw sequencing reads onto hg38 genome and obtained the respective h5-format and spatial image files for UW human skin
Resulting pre-processed files were loaded in Seurat for further downstream data processing and analysis.
We loaded the .h5 and spatial image files using ‘Load10X_Spatial’ module in Seurat and created Seurat Object for data processing
Sample quality were assured by computing the mitochondrial content (MT-content <15% is retained) and filtering out the poor-quality spots using ‘subset’ module of Seurat. We used “SCTransform” method available in Seurat that implements the regularized negative binomial regression for normalizing the 10x spatial data
Spatial feature plot function in Seurat was used to visualize the spatial location and expression profile of candidate genes
Genome_build: hg:38
Supplementary_files_format_and_content: barcode, gene names, count matrix and filtered feature barcode matrix h5 files

value: male

tag: age (years)

value: unwounded skin tissue


title: 5637 cells, siCDCA3-1

value: siRNA transfection (siCDCA3)


title: iBAT Ctrl-1


title: Mouse primary hepatocytes, IL6 positive, small RNA, 6h, rep2

description:
36bp
mmPH-r2_IL6pos6h_smallRNA

value: Primary hepatocytes

value: Hepatocytes

value: WT 129Sv/C57Bl6J


title: Mouse primary hepatocytes, IL6 positive, 6h, rep1

description:
49bp
mmPH-r1_IL6pos6h

value: IL6 stimulated


title: Mouse primary hepatocytes, IL6 negative, 0h, rep2

description:
49bp
mmPH-r2_IL6neg0h

value: No treatment


title: Mouse primary hepatocytes, IL6 positive, 0h, rep1

description:
49bp
mmPH-r1_IL6pos0h


title: Mouse primary hepatocytes, IL6 negative, 6h, rep1

description:
49bp
mmPH-r1_IL6neg6h


title: Mouse primary hepatocytes, IL6 negative, small RNA, 24h, rep2

description:
36bp
mmPH-r2_IL6neg24h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, 24h, rep1

description:
49bp
mmPH-r1_IL6pos24h


title: Mouse primary hepatocytes, IL6 negative, small RNA, 0h, rep2

description:
36bp
mmPH-r2_IL6neg0h_smallRNA


title: Mouse primary hepatocytes, IL6 negative, 0h, rep3

description:
49bp
mmPH-r3_IL6neg0h


title: Mouse primary hepatocytes, IL6 negative, small RNA, 6h, rep1

description:
36bp
mmPH-r1_IL6neg6h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, small RNA, 0h, rep1

description:
36bp
mmPH-r1_IL6pos0h_smallRNA


title: Mouse primary hepatocytes, IL6 negative, small RNA, 0h, rep1

description:
36bp
mmPH-r1_IL6neg0h_smallRNA


title: Mouse primary hepatocytes, IL6 positive, 0h, rep3

description:
49bp
mmPH-r3_IL6pos0h


title: Mouse primary hepatocytes, IL6 positive, 6h, rep2

description:
49bp
mmPH-r2_IL6pos6h


title: Mouse primary hepatocytes, IL6 negative, 6h, rep3

description:
49bp
mmPH-r3_IL6neg6h


title: Mouse primary hepatocytes, IL6 positive, 0h, rep2

description:
49bp
mmPH-r2_IL6pos0h


title: Mouse primary hepatocytes, IL6 negative, 6h, rep2

description:
49bp
mmPH-r2_IL6neg6h


title: Mouse primary hepatocytes, IL6 negative, 24h, rep2

description:
49bp
mmPH-r2_IL6neg24h


title: Mouse primary hepatocytes, IL6 negative, 24h, rep1

description:
49bp
mmPH-r1_IL6neg24h


title: Mouse primary hepatocytes, IL6 negative, 0h, rep1

description:
49bp
mmPH-r1_IL6neg0h


title: genomic DNA from OB-D-2

type: genomic

city: Ulm

first: Julian

middle: Philipp

last: Giesche

address: Albert-Einstein-Allee 23

department: Institute of Pathology

country: Germany

institute: University Hospital Ulm

description: OB

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio (v2011.1; methylation module 1.9.0; Illumina)

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA of formalin-fixed, paraffin-embedded tissue was extracted and purified using the truXTRAC FFPE DNA microTUBE Kit (Covaris) according to manufacturer’s instructions. Genomic DNA of cryo-preserved fresh tissue and cell lines was extracted and purified using the QIAamp DNA Mini Kit (Qiagen) according to manufacturer’s instructions.

value: female

tag: sample type

value: cultivated cells

tag: disease state

value: normal, passage 2-3

tag: source

value: Charité, Berlin

tag: h3f3a status

tag: location

tag: tumour size

tag: tissue acquisition


title: genomic DNA from OB-2

description: OB

value: WT

tag: age


title: genomic DNA from MSC-D-3

description: MSC


title: genomic DNA from MSC-D-1

description: MSC


title: genomic DNA from MSC-2

description: MSC


title: genomic DNA from BT-2R

description: BT

value: recurrence

value: University of Ulm

value: right mandibula


title: genomic DNA from OB-D-3

description: OB


title: genomic DNA from MSC-3

description: MSC


title: genomic DNA from CB-3P

description: CB

value: primary tumour

value: medial distal femur


title: genomic DNA from CB-1P

description: CB

value: male


title: genomic DNA from OB-D-1

description: OB


title: genomic DNA from MSC-1

description: MSC


title: genomic DNA from ABC-3P

description: ABC


title: genomic DNA from CB-2P

description: CB

value: left acetabular region


title: genomic DNA from NOF-3P

description: NOF

value: left distal tibia


title: genomic DNA from U-GCT-1

description: GCTB

value: cell line of GCTB1P

value: proximal tibia


title: genomic DNA from BT-1P

description: BT

value: right distal femur and proximal tibia


title: genomic DNA from U-GCT-3R

description: GCTB

value: cell line of GCTB3R1

value: left distal femur


title: genomic DNA from U-GCT-2

description: GCTB

value: female

value: cell line of GCTB2P


title: genomic DNA from NOF-1P

description: NOF


title: genomic DNA from OB-1

description: OB

value: cultivated cells

value: normal, passage 2-3

value: Charité, Berlin


title: genomic DNA from ABC-2P

description: ABC

value: University of Ulm

value: WT

value: vertebral C2


title: genomic DNA from U-GCT-7

description: GCTB

value: cell line of GCTB7P

value: primary tumour


title: genomic DNA from U-GCT-3M

description: GCTB

value: cell line of GCTB3M

value: pulmonary metastasis

value: left lobe of the lung


title: genomic DNA from ABC-1P

description: ABC

value: male

value: left 5. digit


title: Met/ΔN90-catenin_3wks_Cre- 8125

city: piscataway

first: Junrong

last: Yan

state: NJ

address: 164 frelinghuysen road

department: Chemical Biology

institute: Rutgers University

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with the reference genome (UCSC mouse genome build mm9) using HISAT2 default settings.
The BAM files obtained after alignment were processed using featurecounts to obtain the counts per gene in all samples (Anders et al., 2015).
Assembly: UCSC mouse genome build mm9
Supplementary files format and content: The processed data files are in txt format.  The first column contains the gene ID and the other columns contain the read counts of the gene

source_name: liver tissue from male mice

growth_protocol: Glulf/f (mixed 129/Ola and C57BL/6) and Albumin-Cre (The Jackson Laboratory, Strain 003574, C57Bl/6) were used

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues using a TRIzol™ (Invitrogen #15596026) and PureLink RNA Mini Kit (Invitrogen, #12183018A) combined method.
Approximately 500 ng Total RNA was used for RNA-seq library preparation by following kapa rRNA depletion Total RNA-se sample preparation kit

treatment_protocol: Seven-week-old GS wild-type and knockout male mice were injected with vehicle or c-Met/ΔN90-β-catenin/SB10 plasmids, and livers were harvested 0, 2 or 3 weeks after the injection for RNA-sequencing analysis

tag: strain

value: mixed 129/Ola and C57BL/6

value: 9-weeks old

value: Male


title: Met/ΔN90-catenin_3wks_Cre+ 8085


title: genomic DNA from NOF-2P

description: NOF

value: female


title: genomic DNA from GCTB-13P

description: GCTB

value: cryo-preserved fresh tissue

value: right proximal humerus


title: genomic DNA from U-GCT-6

description: GCTB

value: cell line

value: recurrence

value: left distal femur


title: genomic DNA from U-GCT-4

description: GCTB

value: cell line of GCTB4P

value: University of Ulm

value: left distal humerus


title: Met/ΔN90-catenin_3wks_Cre- 8092


title: Met/ΔN90-catenin_2wks_Cre+ 8130


title: Met/ΔN90-catenin_3wks_Cre- 8095


title: genomic DNA from GCTB-14R

description: GCTB

value: left metacarpal D1


title: Met/ΔN90-catenin_2wks_Cre+ 7424


title: Met/ΔN90-catenin_2wks_Cre+ 6857


title: Met/ΔN90-catenin_2wks_Cre- 6863


title: Met/ΔN90-catenin_3wks_Cre+ 8123


title: genomic DNA from GCTB-11P

description: GCTB

value: primary tumour

value: left proximal tibia


title: Met/ΔN90-catenin_2wks_Cre- 6855


title: Untreated_Cre+ 7687


title: Met/ΔN90-catenin_2wks_Cre- 8121


title: Met/ΔN90-catenin_3wks_Cre+ 8084


title: genomic DNA from OB-3

description: OB

value: cultivated cells

value: normal, passage 2-3

value: Charité, Berlin

value: WT


title: Untreated_Cre+ 7685

value: mixed 129/Ola and C57BL/6

value: 9-weeks old

value: Male


title: Untreated_Cre- 7684


title: Untreated_Cre- 7682


title: Untreated_Cre- 7628


title: Met/ΔN90-catenin_2wks_Cre+ 6862


title: HEK293, YAP knockout SA infected, rep2

city: Saint-Priest-en-Jarez

first: Robin

last: Caire

address: 10 rue de la Marandière

department: Biology

country: France

institute: Université Jean Monnnet Saint-Etienne

hyb_protocol: 70µl of hybridization buffer was added to the reporter codeset to create Mastermix which was aliquoted (8µl) in 12 tubes. 5µl of samples at 10ng/µl were added to each tube. 2µl of capture Probeset was added to each tube. Tubes were placed for 16 hours at 65°C in thermocycler.

scan_protocol: Instrument: nCounter SPRINT, used with standard procedure

data_processing: Normalization was performed using housekeeping genes that were identify with geNorm analysis using nanostring advance software

label: Nanostring CodeSet

source_name: HEK293 cells

label_protocol: 50 ng of total RNA per sample was labeled with Nanostring CodeSet, which are target specific reporter (color coded) and capture probes.

growth_protocol: HEK293 cells were cultivated in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) with 10% fetal bovine serum (FBS), 1% non-essential amino acid solution. HEK293 YAP-/- were generated using specific CRISPR cas-9 and homology direct repair plasmid targeting YAP sequence (Santa Cruz Biotechnology), CRISPR clones generation was done following manufacturer instructions, and validated by western blot and DNA sequencing. 12 well plates were coated with fibronectin (1:100, Sigma) for 2 hours at 37°C before seeding. HEK293 WT (n=6) or YAP-/- (n=6) were plated at 100,000 cells/cm2 to obtain medium cell density the next day.

extract_protocol: RNA was extracted using Allprep RNA/protein kit (Qiagen Inc.). Quality and quantity of RNA were assessed by Experion RNA analysis (BioRad) and QuantIT RiboGreen RNA assay (Thermo Fisher Scientifc), respectively.

treatment_protocol: 24 hours after seeding, 3 wells for WT cells and 3 wells for YAP-/- cells were infected with S. aureus at a multiplicity of infection of 10. After 2 hours of bacterial contact, lysostaphin was added in all wells to kill extracellular S. aureus without affecting internalized bacteria and kept in the culture medium for 5 h (Thus, cells were infected with S. aureus for 7 h in total).  3 wells for WT cells and 3 wells for YAP-/- cells were used as controls.

tag: cell line

tag: genotype

value: YAP knockout

tag: infection

value: Staphylococcus aureus


title: genomic DNA from GCTB-12P

description: GCTB

value: female

value: cryo-preserved fresh tissue

value: right hip bone


title: HEK293, YAP knockout SA infected, rep3


title: Met/ΔN90-catenin_2wks_Cre- 8124


title: Met/ΔN90-catenin_3wks_Cre+ 8091


title: HEK293, YAP knockout control, rep2

value: Control


title: HEK293, Wild type SA infected, rep3

value: wild type


title: HEK293, YAP knockout SA infected, rep1


title: HEK293, YAP knockout control, rep1


title: genomic DNA from GCTB-9P

description: GCTB

value: University of Ulm

value: left distal femur


title: genomic DNA from GCTB-8P

description: GCTB

value: male

value: primary tumour

value: right proximal tibia


title: HEK293, YAP knockout control, rep3


title: genomic DNA from GCTB-4P

description: GCTB

value: left distal humerus


title: Met/ΔN90-catenin_3wks_Cre- 8122


title: HEK293, Wild type control, rep2


title: HEK293, Wild type SA infected, rep1


title: HEK293, Wild type control, rep1


title: imr90_4_cardiomyocytes_13_07_21

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Second reads were aligned using the human reference transcriptome from the UCSC website (hg38) with BWA version 0.7.4.4 and parameter “-l 24”
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

source_name: hiPSC-derived cardiomyocyte

growth_protocol: Two hiPSC lines were used: BiONi010-C (Bioneer A/S, Denmark), which stems from the skin of a teenage male (Rasmussen et al., 2014) and IMR90-1 (WiCell, USA), which stems from lung tissue from a female fetus (Yu et al., 2007). Cells were cultured using mTeSR1 medium (Stemcell Technologies, USA) in 6 cm dishes coated with Matrigel (BD Biosciences, USA) at 37°C and 5% CO2. Cells were passaged once a week by washing with D-PBS (Sigma-Aldrich, USA) and treatment with 0.02% EDTA for 3 minutes using a split ratio of 1:10-1:40.

extract_protocol:
RNA was isolated using Kit from Qiagen and stored at -80 ℃.
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.

treatment_protocol: PFOS were mixed with the medium from D1 through D6 with either DMSO (vehicle), 6.25 µM, 12.5 µM, or 25 µM PFOS, maintaining a solvent concentration of 0.1% in all treatments.

tag: treatment

tag: tissue

value: cardiomyocytes

tag: Stage

value: late (Day 7)


title: imr90_4_cardiomyocytes_01_06_21


title: imr90_4_cardiomyocytes_20_07_21


title: genomic DNA from GCTB-7P

description: GCTB

tag: gender


title: Untreated_Cre+ 7629

value: mixed 129/Ola and C57BL/6

value: 9-weeks old

tag: Sex


title: imr90_4_early_cardiomyocytes_25_05_21


title: imr90_5_cardiomyocytes_13_07_21


title: genomic DNA from GCTB-2P

description: GCTB

tag: sample type

value: left proximal tibia


title: imr90_4_cardiomyocytes_10__05__21


title: imr90_5_cardiomyocytes_20_07_21


title: imr90_5_cardiomyocytes_10_05_21


title: imr90_6_cardiomyocytes_20_07_21


title: genomic DNA from GCTB-3R

description: GCTB

tag: disease state

value: recurrence


title: HEK293, Wild type SA infected, rep2

value: Staphylococcus aureus


title: imr90_6_cardiomyocytes_13_07_21


title: genomic DNA from GCTB-4R

description: GCTB

value: cryo-preserved fresh tissue

tag: source

value: left metacarpal D4


title: imr90_6_cardiomyocytes_01_06_21


title: imr90_5_early_cardiomyocytes_25_05_21


title: imr90_4_early_cardiomyocytes_16_07_21

value: early (Day 3)


title: imr90_6_cardiomyocytes_10_05_21


title: imr90_Ctrl_cardiomyocytes_20_07_21

value: Ctrl (DMSO)


title: imr90_Ctrl_cardiomyocytes_13_07_21


title: genomic DNA from GCTB-5P

description: GCTB

value: University of Ulm

tag: h3f3a status

value: left proximal fibula


title: HEK293, Wild type control, rep3

value: wild type

value: Control


title: imr90_4_early_cardiomyocytes_21_05_21


title: genomic DNA from GCTB-3P

description: GCTB

value: female

value: primary tumour

tag: location

value: left distal femur


title: imr90_Ctrl_cardiomyocytes_01__06__21

value: cardiomyocytes

value: late (Day 7)


title: imr90_5_early_cardiomyocytes_10_05_21


title: imr90_5_early_cardiomyocytes_28_05_21


title: imr90_4_early_cardiomyocytes_09_07_21


title: genomic DNA from GCTB-3M

description: GCTB

value: pulmonary metastasis

value: left lobe of the lung

tag: tumour size


title: imr90_6_early_cardiomyocytes_28_05_21


title: imr90_4_early_cardiomyocytes_28_05_21


title: imr90_6_early_cardiomyocytes_25_05_21


title: imr90_Ctrl_cardiomyocytes_25_05_21


title: imr90_5_early_cardiomyocytes_09_07_21


title: imr90_6_early_cardiomyocytes_10_05_21


title: imr90_5_cardiomyocytes_01_06_21


title: imr90_Ctrl_cardiomyocytes_10_05_21


title: imr90_Ctrl_early_cardiomyocytes_10_05_21


title: genomic DNA from GCTB-10P

description: GCTB

value: male

value: left proximal humerus

tag: tissue acquisition


title: imr90_5_early_cardiomyocytes_16_07_21


title: imr90_4_early_cardiomyocytes_10_05_21


title: imr90_Ctrl_early_cardiomyocytes_09_07_21


title: bioni_4_cardiomyocytes_10_05_21

value: bioni


title: bioni_4_cardiomyocytes_17_11_20


title: genomic DNA from GCTB-1P

description: GCTB

value: proximal tibia

tag: age


title: imr90_Ctrl_early_cardiomyocytes_16_07_21

value: early (Day 3)


title: bioni_4_cardiomyocytes_10_11_20


title: bioni_5_cardiomyocytes_24_11_20


title: imr90_Ctrl_early_cardiomyocytes_28_05_21

value: Ctrl (DMSO)


title: bioni_6_cardiomyocytes_10_05_21


title: imr90_6_early_cardiomyocytes_21_05_21


title: imr90_6_early_cardiomyocytes_09_07_21


title: bioni_5_cardiomyocytes_10_11_20


title: imr90_5_early_cardiomyocytes_21_05_21


title: bioni_5_cardiomyocytes_17_11_20


title: bioni_4_cardiomyocytes_24_11_20


title: bioni_6_cardiomyocytes_10_11_20


title: bioni_5_cardiomyocytes_10_05_21


title: imr90_6_early_cardiomyocytes_16_07_21


title: bioni_6_cardiomyocytes_17_11_20


title: imr90_Ctrl_early_cardiomyocytes_21_05_21


title: bioni_Ctrl_cardiomyocytes_24_11_20


title: bioni_Ctrl_cardiomyocytes_17_11_20


title: bioni_4_cardiomyocytes_01_12_20


title: bioni_4_early_cardiomyocytes_10_05_21


title: bioni_Ctrl_cardiomyocytes_01_12_20


title: bioni_Ctrl_cardiomyocytes_10_11_20


title: bioni_5_cardiomyocytes_01_12_20


title: bioni_6_cardiomyocytes_01_12_20


title: bioni_Ctrl_cardiomyocytes_10_05_21


title: bioni_4_early_cardiomyocytes_20_11_20


title: bioni_6_cardiomyocytes_24_11_20


title: bioni_4_early_cardiomyocytes_13_11_20


title: bioni_4_early_cardiomyocyte_06_11_20


title: bioni_5_early_cardiomyocytes_10_05_21


title: bioni_5_early_cardiomyocytes_27_11_20


title: bioni_5_early_cardiomyocytes_20_11_20


title: bioni_5_early_cardiomyocytes_13_11_20


title: bioni_4_early_cardiomyocytes_27_11_20


title: bioni_6_early_cardiomyocytes_13_11_20


title: bioni_5_early_cardiomyocyte_06_11_20


title: bioni_6_early_cardiomyocytes_20_11_20


title: bioni_Ctrl_early_cardiomyocytes_10_05_21


title: bioni_6_early_cardiomyocytes_27_11_20


title: bioni_6_early_cardiomyocytes_10_05_21


title: bioni_Ctrl_early_cardiomyocytes_20_11_20


title: bioni_Ctrl_early_cardiomyocytes_06_11_20


title: bioni_Ctrl_early_cardiomyocytes_27_11_20


title: LuCaP_243_s3_ET7555_PDX_Tumor

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 243 PDX Tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from flash frozen LuCaP xenograft tissue with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: cell type

value: prostate cancer

tag: molecular phenotype


title: LuCaP_243_s4_ET7751_PDX_Tumor


title: bioni_6_early_cardiomyocyte_06_11_20

tag: cell line


title: LuCaP_173.1_s17_ET4905_PDX_Tumor

source_name: LuCaP 173.1 PDX Tumor


title: LuCaP_173.1_s25_ET7161_PDX_Tumor


title: bioni_Ctrl_early_cardiomyocytes_13_11_20


title: LuCaP_235.2_s0_ET5576_PDX_Tumor

source_name: LuCaP 235.2 PDX Tumor


title: LuCaP_189.3CR_s2_ET7532_PDX_Tumor

source_name: LuCaP 189.3CR PDX Tumor


title: LuCaP_176CR_s5_ET5973_PDX_Tumor

source_name: LuCaP 176CR PDX Tumor


title: LuCaP_235.2_s2_ET5967_PDX_Tumor


title: LuCaP_235.3_s2_ET6075_PDX_Tumor

source_name: LuCaP 235.3 PDX Tumor


title: LuCaP_235.3CR_s1_ET7179_PDX_Tumor

source_name: LuCaP 235.3CR PDX Tumor


title: LuCaP_176CR_s1_ET5147_PDX_Tumor


title: LuCaP_235.3_s3_ET6287_PDX_Tumor


title: AML707B-D0

city: Toronto

first: Andy

last: Zeng

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
Paired-end sequence data was aligned against GRCh38 and transcript annotations from GENCODE v37 using STAR 2.7.9a. Default parameters were used except for the following: “–chimSegmentMin 12 –chimJunctionOverhangMin 8 –alignSJDBoverhangMin 10 –alignSJstitchMismatchNmax 5 -1 5 5.”
Raw counts were obtained using HTSeq v0.7.2 with strand specified.
For TPM normalization, raw counts for each gene were divided by the median length in kilobases of all GRCh38 annotated transcripts corresponding to a given gene. Sample-based normalization was subsequently performed such that the sum of all estimated transcript abundances for each sample equals 1,000,000. For VST normalized expression, variance-stabilizing transformation was performed on the raw counts using the vst function in DESeq2 v1.32.0.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files depict raw counts for each sample. Supplementary files contain processed data for all samples, including raw counts (ideal for differential expression), TPM-normalized expression (ideal for deconvolution), and VST-normalized expression (ideal for clustering, visualization, and precise quantification of specific genes) for each sample.

source_name: Human acute myeloid leukemia cells

extract_protocol:
RNA was extracted from bulk bone marrow mononuclear cells using an RNeasy Micro Kit (Qiagen).
Libraries were constructed using the Kapa mRNA Hyper Prep (Roche).

tag: patientid

value: Human acute myeloid leukemia cells


title: AML916-D0


title: AML921A-D0


title: LuCaP_235.3CR_s6_ET7819_PDX_Tumor


title: ChIP-pSer2_shNonT_DLD1

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

library_source: genomic

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality sequences (-q 25)
The remaining reads were aligned to the human genome hg19 assembly using Bowtie2 v2.3.5.1 (Amemiya et al., 2019)
PCR duplicates and low mapping quality reads (MAPQ < 30) were removed using Picard tools v2.23.3 (https://broadinstitute.github.io/picard/) (REMOVE_DUPLICATES = True) and SAMtools v1.9 (Li et al., 2009)
Aligned read counts were then normalized to reads per million mapped reads (RPM) using deeptools v3.5.0 (Ramírez et al., 2016)
Blacklist regions for hg19 genome annotation from ENCODE project were removed (Amemiya et al., 2019).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and protein was isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: The cell was  treated with relevant lentivirus

value: colorectal adenocarcinoma cell lines

tag: chip antibody

value: Phospho-Rpb1 CTD (Ser2)

tag: treatment

value: untreated


title: LuCaP_136CR2_s2_ET7670_PDX_Tumor

source_name: LuCaP 136CR2 PDX Tumor


title: ChIP-pSer2_shRPAP2_DLD1


title: ChIP-Input_shRPAP2_DLD1

value: input


title: AML556-D0


title: LuCaP_235.3CR_S4_ET7643_PDX_Tumor


title: ChIP-Input_shNonT_DLD1


title: ChIP-TFIIF_dTAG_RPAP2-rtTA-DLD1_rep2

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality sequences (-q 25) and then aligned to the human genome hg19 assembly using Bowtie2 v2.3.5.1 (Amemiya et al., 2019).
PCR duplicates and low mapping quality reads (MAPQ < 30) were removed using Picard tools v2.23.3 (https://broadinstitute.github.io/picard/) (REMOVE_DUPLICATES = True) and SAMtools v1.9 (Li et al., 2009).
Aligned read counts were then normalized to Reads Per Million mapped reads (RPM) using deeptools v3.5.0 (Ramirez et al., 2016)
Blacklist regions for hg19 genome annotation from ENCODE project were removed (Amemiya et al., 2019).
Reads aligned to human genome were normalized based on 1e6/ mm10_count calculated by SAMtools v1.9 (Li et al., 2009).
Normalized bigwig files were generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: RPAP2-dTAG DLD1

treatment_protocol: The cell was  treated with relevant lentivirus and dTAG13

value: treated with dTAG13 for 3 hours


title: LuCaP_189.3CR_s3_ET7777_PDX_Tumor


title: ChIP-TFIIF_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep2

value: treated with dTAG13 for 3 hours,overexpress Y127A-RPAP2


title: LuCaP_136CR2_ET7674_PDX_Tumor


title: ChIP-TFIIF_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep1


title: ChIP-TFIIF_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep2

value: treated with dTAG13 for 3 hours,overexpress WT-RPAP2


title: ChIP-TFIIF_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep1


title: ChIP-TFIIF_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep1

value: treated with dTAG13 for 3 hours,overexpress DEL-RPAP2


title: ChIP-TFIIF_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep2


title: ChIP-PolII-NTD_dTAG_RPAP2-rtTA-DLD1_rep2

value: Rpb1 NTD


title: ChIP-PolII-NTD_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep1


title: ChIP-PolII-NTD_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep2


title: ChIP-PolII-NTD_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep2


title: ChIP-PolII-NTD_dTAG_RPAP2-rtTA-DLD1_rep1


title: ChIP-PolII-NTD_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep2


title: ChIP-Input_dTAG_RPAP2-rtTA-DLD1_rep2

value: Input


title: ChIP-Input_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep2


title: ChIP-Flag_dTAG-3h_RPAP2-rtTA-DLD1

value: Flag


title: ChIP-Input_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep2


title: ChIP-PolII-NTD_shNonT-DLD1


title: ChIP-Input_dTAG_Dox-Y127A-RPAP2-rtTA-DLD1_rep1


title: ChIP-Input_shNonT-DLD1


title: ChIP-Input_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep1


title: TT-seq_DMSO-6h.DRB-3h.release-40min_RPAP2-fkbp-DLD1

data_processing:
Library strategy: TT-seq
Raw reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality sequences (-q 25)
The remaining reads were mapped to hg19 or mm10 genome with STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate”
Duplicates and low-quality reads were removed, and only properly paired reads were kept.
The counts of reads mapping to spike-in mm10 reads were used to generate the normalization factor.
Strand-specific normalized bigwigs and metaplots of DRB/TT-seq signal were generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 6h, DRB for 3hours

value: colorectal adenocarcinoma cell line


title: ChIP-Flag_DMSO-3h_RPAP2-rtTA-DLD1


title: TT-seq_dTAG-6h.DRB-3h.release-30min_RPAP2-fkbp-DLD1

value: treated with dTAG13 for 6 hours, DRB for 3hours


title: ChIP-Input_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep1


title: ChIP-PolII-NTD_dTAG_Dox-WT-RPAP2-rtTA-DLD1_rep1


title: TT-seq_DMSO-6h.DRB-3h.release-30min_RPAP2-fkbp-DLD1


title: ChIP-Input_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep2


title: TT-seq_dTAG-6h.DRB-3h.release-40min_RPAP2-fkbp-DLD1


title: ChIP-PolII-NTD_dTAG_Dox-DEL-RPAP2-rtTA-DLD1_rep1


title: ChIP-Input_dTAG_RPAP2-rtTA-DLD1_rep1


title: Lin− CD34+ c-Kit+

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Cellranger Pipeline 3.0.1 for Lin− c-Kit+ cells and Cellranger Pipeline 5.0.1 for Lin− CD34+ c-Kit+ cells with spike-in hashtagged cells
Genome_build: GRCh38
Supplementary_files_format_and_content: tar.gz files containing matrix table with gene counts, features counts (for Lin− CD34+ c-Kit+ cells), corresponding barcodes, and 10X .h5 file

source_name: Human Peripheral Blood

extract_protocol:
Lin− (CD3− CD14− CD15− CD19−) c-Kit+ cells from peripheral blood were analyzed using the 10X Genomics single-cell RNA sequencing platform (version 2 kit). Lin− CD34+ c-Kit+ and Lin− CD34+ c-Kit+ FcεRI+ PE_hashtag_oligonucleotide+ peripheral blood cells were FACS isolated, pooled, and analyzed using the 10X Genomics single-cell RNA sequencing platform (version 3.1 kit).
The Lin− c-Kit+ scRNAseq library was prepared according to the instructions in the Chromium Single Cell 3' Reagent Kits v2 User Guide. The Lin− CD34+ c-Kit+ scRNA-seq library and the corresponding hashtag oligonucleotide library were prepared according to the user guide of the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein.

tag: tissue

value: Human Peripheral Blood

tag: cell population

value: Lin− CD34+ c-Kit+

tag: spike-in cells

value: Lin− c-Kit+ CD34+ FcεRI+ PE_hashtag_oligonucleotide+

tag: 10x genomics kit version


title: ChIP-Input_shRPAP2-DLD1


title: Lin− c-Kit+

value: Lin− c-Kit+


title: hEST_N_18_493_hEST_N_18.Warfarin.6

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Base-calling was performed with Illumina NovaSeq 6000 Sequencing System.
Alignment was performed with Bowtie2 (2.3.5)
Quantification of amplicon-mapping reads was performed with BEDtools (2.29.2)
QC and filtering was performed with BioQC (1.20.0), ribiosExpression (1.1.9), and ribiosNGS (1.1.30), as well as custom software.
Factor analysis was performed with R (4.0.1) and the psych package (2.1.6)
Differential gene expression was performed with edgeR (3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements are tab-delimited files, containing genes and number of reads mapped to the pre-defined amplicons; raw counts are in the GCT (version 1.2) file, a tab-delimited format of aggregated gene counts.

source_name: Human induced pluripotent-stem-cell derived embryoid body

growth_protocol: The cells were passaged twice a week with a defined cell number of 2.4 × 104 cells/cm2 (three-day culture) or 1.2 × 104 cells/cm2 (four-day culture) to achieve a maximum confluence of 80%. The medium was removed and the cells were detached with StemPro Accutase™ Cell Dissociation Reagent (Thermo Fisher Scientific) for five minutes at 37°C/ 5% CO2. Cell detachment was stopped by adding StemFlex™ Medium (Thermo Fisher Scientific) to the detached cells, followed by centrifugation for five minutes at 240 × g. Afterwards, the cell pellet was gently suspended in culture medium and the cells were seeded into Geltrex™ coated culture flasks with complete StemFlex™ (containing 10% StemFlex™ Supplement and 1% RevitaCell™). StemFlex™ w/o RevitaCell™ replaced the medium completely the day after cell propagation. The cells were cultured throughout in a humidified incubator (Binder, Germany) at 37°C and 5% CO2.

extract_protocol:
Differentiated EBs were lysed after 7 days of differentiation in 350 μl MagNA Pure LC RNA Buffer (Roche Diagnostics) and purified by using the automated MagNA Pure 96 system (Roche Diagnostics).
The total RNA was quantified using the Qubit RNA Assay Kit (Thermo Fisher) on the Fluorometer Glomax (Promega). Total RNA with a maximum of 10 ng from each biological replicate was reverse transcribed to cDNA using Superscript IV Vilo (Thermo Fisher). Libraries were generated with the AmpliSeq Library Plus Kit (Illumina) according to the reference guide. Pipetting steps for target amplification, primer digestion, and adapter ligation were done with the mosquito automatic pipettor (SPT Labtech) in miniaturization. For the purifications before and after final library amplification, solid phase reversible immobilization magnetic bead purification (Clean NGS, LABGENE Scientific SA) was performed on the multidrop automated pipetting station (Thermo Fisher). We measured both amplicon sizes and cDNA concentrations using an Agilent High Sensitivity DNA Kit (Agilent Technologies) according to the manufacturer’s recommendation. Prior to sequencing, cDNA contents of the samples were normalized and pooled to 2 nM final concentration on Biomek FXP workstation.
RNA-Seq (Amplicon-based molecular phenotyping)

treatment_protocol: To start, human induced pluripotent stem cells (hiPSC) are seeded at a density of 120000 cells per well in 96-well microwell plates. They form homogenous embryoid bodies (EBs) which are spontaneously differentiated over 7 days. Compounds are added as six-point concentration range on day 0, day 3 and day 5. Single wells containing about 70 differentiated EBs are lysed to generate one sample for the viability assay and gene expression profiling.

tag: run

tag: plate

value: Warfarin

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity

value: Positive


title: hEST_N_18_505_hEST_N_18.Warfarin.5

tag: cell type

value: Human induced pluripotent-stem-cell derived embryoid body


title: hEST_N_18_529_hEST_N_18.Warfarin.3


title: hEST_N_18_517_hEST_N_18.Warfarin.4


title: hEST_N_18_553_hEST_N_18.Warfarin.1


title: hEST_N_18_510_hEST_N_18.Misoprostol.5

value: Misoprostol


title: hEST_N_18_534_hEST_N_18.Misoprostol.3


title: hEST_N_18_541_hEST_N_18.Warfarin.2


title: hEST_N_18_558_hEST_N_18.Misoprostol.1


title: hEST_N_18_498_hEST_N_18.Misoprostol.6


title: hEST_N_18_546_hEST_N_18.Misoprostol.2


title: hEST_N_18_509_hEST_N_18.Lazabemide.5

value: Lazabemide

value: Negative


title: hEST_N_18_521_hEST_N_18.Lazabemide.4


title: hEST_N_18_545_hEST_N_18.Lazabemide.2


title: hEST_N_18_533_hEST_N_18.Lazabemide.3


title: hEST_N_18_497_hEST_N_18.Lazabemide.6


title: hEST_N_18_515_hEST_N_18.Ibuprofen.5

value: Ibuprofen


title: hEST_N_18_557_hEST_N_18.Lazabemide.1


title: hEST_N_18_527_hEST_N_18.Ibuprofen.4


title: hEST_N_18_539_hEST_N_18.Ibuprofen.3


title: ChIP-TFIIF_dTAG_RPAP2-rtTA-DLD1_rep1

value: colorectal adenocarcinoma cell lines

value: treated with dTAG13 for 3 hours


title: hEST_N_18_551_hEST_N_18.Ibuprofen.2


title: hEST_N_18_563_hEST_N_18.Ibuprofen.1


title: hEST_N_18_492_hEST_N_18.DMSO

value: DMSO


title: hEST_N_18_491_hEST_N_18.DMSO


title: hEST_N_18_489_hEST_N_18.DMSO


title: hEST_N_18_522_hEST_N_18.Misoprostol.4


title: hEST_N_18_488_hEST_N_18.DMSO


title: hEST_N_18_487_hEST_N_18.DMSO


title: hEST_N_18_485_hEST_N_18.DMSO


title: hEST_N_18_526_hEST_N_18.Cetirizine.4

value: Cetirizine


title: hEST_N_18_486_hEST_N_18.DMSO


title: hEST_N_18_482_hEST_N_18.DMSO


title: hEST_N_18_502_hEST_N_18.Cetirizine.6


title: hEST_N_18_531_hEST_N_18.Ascorbic.acid.3

value: Ascorbic acid


title: hEST_N_18_538_hEST_N_18.Cetirizine.3


title: hEST_N_18_481_hEST_N_18.DMSO


title: hEST_N_18_503_hEST_N_18.Ibuprofen.6


title: hEST_N_18_495_hEST_N_18.Ascorbic.acid.6


title: hEST_N_18_506_hEST_N_18.Acitretin.5

value: Acitretin


title: hEST_N_18_555_hEST_N_18.Ascorbic.acid.1


title: hEST_N_18_562_hEST_N_18.Cetirizine.1


title: hEST_N_18_519_hEST_N_18.Ascorbic.acid.4


title: hEST_N_18_543_hEST_N_18.Ascorbic.acid.2


title: hEST_N_18_507_hEST_N_18.Ascorbic.acid.5


title: hEST_N_18_494_hEST_N_18.Acitretin.6


title: hEST_N_18_542_hEST_N_18.Acitretin.2


title: hEST_N_18_530_hEST_N_18.Acitretin.3


title: hEST_N_18_554_hEST_N_18.Acitretin.1


title: hEST_N_18_496_hEST_N_18.5.Fu.6


title: ChIP-PolII-NTD_shRPAP2-DLD1

value: Rpb1 NTD


title: hEST_N_18_550_hEST_N_18.Cetirizine.2


title: hEST_N_18_508_hEST_N_18.5.Fu.5


title: hEST_N_18_484_hEST_N_18.DMSO


title: hEST_N_18_514_hEST_N_18.Cetirizine.5


title: hEST_N_17_409_hEST_N_17.Warfarin.5


title: hEST_N_18_544_hEST_N_18.5.Fu.2


title: hEST_N_18_520_hEST_N_18.5.Fu.4


title: hEST_N_17_397_hEST_N_17.Warfarin.6


title: hEST_N_17_445_hEST_N_17.Warfarin.2


title: hEST_N_18_556_hEST_N_18.5.Fu.1


title: hEST_N_17_450_hEST_N_17.Misoprostol.2


title: hEST_N_18_518_hEST_N_18.Acitretin.4


title: hEST_N_17_426_hEST_N_17.Misoprostol.4


title: hEST_N_17_462_hEST_N_17.Misoprostol.1


title: hEST_N_17_433_hEST_N_17.Warfarin.3


title: hEST_N_17_402_hEST_N_17.Misoprostol.6


title: hEST_N_17_457_hEST_N_17.Warfarin.1


title: hEST_N_17_413_hEST_N_17.Lazabemide.5


title: hEST_N_17_401_hEST_N_17.Lazabemide.6


title: hEST_N_17_437_hEST_N_17.Lazabemide.3


title: hEST_N_18_532_hEST_N_18.5.Fu.3


title: hEST_N_17_461_hEST_N_17.Lazabemide.1


title: hEST_N_17_407_hEST_N_17.Ibuprofen.6


title: hEST_N_17_419_hEST_N_17.Ibuprofen.5


title: hEST_N_17_425_hEST_N_17.Lazabemide.4


title: hEST_N_17_443_hEST_N_17.Ibuprofen.3


title: hEST_N_17_431_hEST_N_17.Ibuprofen.4


title: hEST_N_17_396_hEST_N_17.DMSO


title: hEST_N_17_467_hEST_N_17.Ibuprofen.1


title: hEST_N_17_391_hEST_N_17.DMSO


title: hEST_N_17_390_hEST_N_17.DMSO


title: hEST_N_17_388_hEST_N_17.DMSO


title: hEST_N_17_385_hEST_N_17.DMSO


title: hEST_N_17_430_hEST_N_17.Cetirizine.4


title: hEST_N_18_483_hEST_N_18.DMSO


title: hEST_N_17_387_hEST_N_17.DMSO


title: hEST_N_17_395_hEST_N_17.DMSO


title: hEST_N_17_393_hEST_N_17.DMSO


title: hEST_N_17_442_hEST_N_17.Cetirizine.3


title: hEST_N_17_399_hEST_N_17.Ascorbic.acid.6


title: hEST_N_17_455_hEST_N_17.Ibuprofen.2


title: hEST_N_17_449_hEST_N_17.Lazabemide.2


title: hEST_N_17_394_hEST_N_17.DMSO


title: hEST_N_17_392_hEST_N_17.DMSO


title: hEST_N_17_414_hEST_N_17.Misoprostol.5


title: hEST_N_17_406_hEST_N_17.Cetirizine.6


title: hEST_N_17_454_hEST_N_17.Cetirizine.2


title: hEST_N_17_466_hEST_N_17.Cetirizine.1


title: hEST_N_17_411_hEST_N_17.Ascorbic.acid.5


title: hEST_N_17_423_hEST_N_17.Ascorbic.acid.4


title: hEST_N_17_435_hEST_N_17.Ascorbic.acid.3


title: hEST_N_17_389_hEST_N_17.DMSO


title: hEST_N_17_447_hEST_N_17.Ascorbic.acid.2


title: hEST_N_17_418_hEST_N_17.Cetirizine.5


title: hEST_N_17_410_hEST_N_17.Acitretin.5


title: hEST_N_17_386_hEST_N_17.DMSO


title: hEST_N_17_459_hEST_N_17.Ascorbic.acid.1


title: hEST_N_17_398_hEST_N_17.Acitretin.6


title: hEST_N_17_458_hEST_N_17.Acitretin.1


title: hEST_N_17_434_hEST_N_17.Acitretin.3


title: hEST_N_17_400_hEST_N_17.5.Fu.6


title: hEST_N_17_412_hEST_N_17.5.Fu.5


title: hEST_N_17_446_hEST_N_17.Acitretin.2


title: hEST_N_17_436_hEST_N_17.5.Fu.3


title: hEST_N_17_460_hEST_N_17.5.Fu.1


title: hEST_N_14_178_hEST_N_14.Dexamethasone.1

value: Dexamethasone

value: FALSE


title: hEST_N_14_179_hEST_N_14.Progesterone.1

value: Progesterone


title: hEST_N_14_174_hEST_N_14.Amoxycillin.1

value: Amoxycillin

value: TRUE


title: hEST_N_14_177_hEST_N_14.Penicillin.G.1

value: Human induced pluripotent-stem-cell derived embryoid body

value: Penicillin G


title: hEST_N_14_175_hEST_N_14.SB431542.1


title: hEST_N_14_176_hEST_N_14.Metformin.1

value: Metformin


title: hEST_N_14_171_hEST_N_14.Phenytoin.1

value: Phenytoin


title: hEST_N_14_170_hEST_N_14.Cisplatin.1

value: Cisplatin


title: hEST_N_18_490_hEST_N_18.DMSO


title: hEST_N_17_422_hEST_N_17.Acitretin.4

value: Positive


title: hEST_N_14_173_hEST_N_14.Hydroxyurea.1

value: Hydroxyurea


title: hEST_N_14_172_hEST_N_14.Folic.acid.1

value: Folic acid


title: hEST_N_17_424_hEST_N_17.5.Fu.4


title: hEST_N_14_165_hEST_N_14.Penicillin.G.2


title: hEST_N_14_169_hEST_N_14.5.Azacitidine.1


title: hEST_N_14_167_hEST_N_14.Progesterone.2


title: hEST_N_14_164_hEST_N_14.Metformin.2


title: hEST_N_17_448_hEST_N_17.5.Fu.2


title: hEST_N_14_166_hEST_N_14.Dexamethasone.2


title: hEST_N_14_161_hEST_N_14.Hydroxyurea.2


title: hEST_N_14_159_hEST_N_14.Phenytoin.2


title: hEST_N_14_160_hEST_N_14.Folic.acid.2


title: hEST_N_14_162_hEST_N_14.Amoxycillin.2


title: hEST_N_14_163_hEST_N_14.SB431542.2


title: hEST_N_14_158_hEST_N_14.Cisplatin.2


title: hEST_N_14_157_hEST_N_14.5.Azacitidine.2


title: hEST_N_14_152_hEST_N_14.Metformin.3


title: hEST_N_14_153_hEST_N_14.Penicillin.G.3


title: hEST_N_14_154_hEST_N_14.Dexamethasone.3


title: hEST_N_14_155_hEST_N_14.Progesterone.3


title: hEST_N_14_150_hEST_N_14.Amoxycillin.3


title: hEST_N_14_142_hEST_N_14.Dexamethasone.4


title: hEST_N_14_141_hEST_N_14.Penicillin.G.4


title: hEST_N_14_149_hEST_N_14.Hydroxyurea.3


title: hEST_N_14_151_hEST_N_14.SB431542.3


title: hEST_N_14_146_hEST_N_14.Cisplatin.3


title: hEST_N_14_147_hEST_N_14.Phenytoin.3


title: hEST_N_14_143_hEST_N_14.Progesterone.4


title: hEST_N_14_145_hEST_N_14.5.Azacitidine.3


title: hEST_N_14_140_hEST_N_14.Metformin.4


title: hEST_N_14_137_hEST_N_14.Hydroxyurea.4


title: hEST_N_14_139_hEST_N_14.SB431542.4


title: hEST_N_14_136_hEST_N_14.Folic.acid.4


title: hEST_N_14_138_hEST_N_14.Amoxycillin.4


title: hEST_N_14_135_hEST_N_14.Phenytoin.4


title: hEST_N_14_133_hEST_N_14.5.Azacitidine.4


title: hEST_N_14_130_hEST_N_14.Dexamethasone.5


title: hEST_N_14_131_hEST_N_14.Progesterone.5


title: hEST_N_14_126_hEST_N_14.Amoxycillin.5


title: hEST_N_14_148_hEST_N_14.Folic.acid.3


title: hEST_N_14_127_hEST_N_14.SB431542.5


title: hEST_N_14_125_hEST_N_14.Hydroxyurea.5


title: hEST_N_14_123_hEST_N_14.Phenytoin.5


title: hEST_N_17_421_hEST_N_17.Warfarin.4

value: Warfarin


title: hEST_N_14_134_hEST_N_14.Cisplatin.4


title: hEST_N_14_121_hEST_N_14.5.Azacitidine.5


title: hEST_N_14_122_hEST_N_14.Cisplatin.5


title: hEST_N_14_129_hEST_N_14.Penicillin.G.5


title: hEST_N_14_128_hEST_N_14.Metformin.5


title: Human primary hepatocytes, IL6 positive, small RNA, 24h, rep3

description:
36bp
hPH-r3_IL6pos24h_smallRNA

tag: cell line

value: Primary hepatocytes

value: Hepatocytes

tag: genotype

value: WT

value: IL6 stimulated

tag: time


title: hEST_N_14_118_hEST_N_14.Dexamethasone.6

value: Dexamethasone

value: FALSE


title: Human primary hepatocytes, IL6 positive, small RNA, 6h, rep3

description:
36bp
hPH-r3_IL6pos6h_smallRNA

tag: treatment


title: hEST_N_14_116_hEST_N_14.Metformin.6


title: Human primary hepatocytes, IL6 positive, small RNA, 0h, rep3

description:
36bp
hPH-r3_IL6pos0h_smallRNA


title: Human primary hepatocytes, IL6 negative, small RNA, 6h, rep3

description:
36bp
hPH-r3_IL6neg6h_smallRNA

value: No treatment


title: hEST_N_14_114_hEST_N_14.Amoxycillin.6

value: Amoxycillin

value: TRUE


title: hEST_N_14_124_hEST_N_14.Folic.acid.5

value: Human induced pluripotent-stem-cell derived embryoid body


title: hEST_N_14_117_hEST_N_14.Penicillin.G.6

value: Penicillin G


title: hEST_N_14_113_hEST_N_14.Hydroxyurea.6


title: hEST_N_14_112_hEST_N_14.Folic.acid.6


title: hEST_N_14_115_hEST_N_14.SB431542.6


title: Human primary hepatocytes, IL6 positive, small RNA, 6h, rep2

description:
36bp
hPH-r2_IL6pos6h_smallRNA


title: hEST_N_14_119_hEST_N_14.Progesterone.6

value: Progesterone


title: Human primary hepatocytes, IL6 negative, small RNA, 0h, rep3

description:
36bp
hPH-r3_IL6neg0h_smallRNA


title: hEST_N_14_111_hEST_N_14.Phenytoin.6

value: Phenytoin


title: Human primary hepatocytes, IL6 positive, small RNA, 24h, rep2

description:
36bp
hPH-r2_IL6pos24h_smallRNA


title: hEST_N_14_109_hEST_N_14.5.Azacitidine.6


title: Human primary hepatocytes, IL6 positive, small RNA, 0h, rep2

description:
36bp
hPH-r2_IL6pos0h_smallRNA


title: hEST_N_14_108_hEST_N_14.DMSO

value: DMSO


title: No_dox_M1_1 [JB_3]

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from Lentiviral transduced C2C12 cell line upon differentiation without induction of MyoD

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

source_name: C2C12 cell line transduced with MyoD Lentivirus: differentiated - dox treatment

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

extract_protocol:
cell isolation protocol: Cells were directly lysed in Trizol
Trizol-based extraction of total RNA was performed according to the manufacturer's instructions.

value: Lentiviral-transduced with integrating transgene encoding Myod1

tag: tissue/cell type

value: Muscle; myoblast


title: Control_2 [JB_2]

description: Gene expression data from control (naïve/nontransduced) C2C12 cell line upon differentiation

source_name: Nontransduced (naïve) C2C12 cell line: differentiated + dox treatment

value: No viral transduction


title: Dox_M1_1 [JB_5]

description: Gene expression data from Lentiviral transduced C2C12 cell line upon differentiation with doxycycline-induced expression of MyoD

source_name: C2C12 cell line transduced with MyoD Lentivirus: differentiated + dox treatment


title: No_dox_M1_2 [JB_4]


title: Dox_M1_2 [JB_6]


title: Control_1 [JB_1]


title: hEST_N_14_106_hEST_N_14.DMSO


title: hEST_N_14_105_hEST_N_14.DMSO


title: Human primary hepatocytes, IL6 negative, small RNA, 6h, rep2

description:
36bp
hPH-r2_IL6neg6h_smallRNA

source_name: Primary hepatocytes

value: Primary hepatocytes


title: hEST_N_14_107_hEST_N_14.DMSO


title: hEST_N_17_438_hEST_N_17.Misoprostol.3

value: Misoprostol

value: Positive


title: Human primary hepatocytes, IL6 positive, small RNA, 6h, rep1

description:
36bp
hPH-r1_IL6pos6h_smallRNA

value: Hepatocytes

value: WT

value: IL6 stimulated


title: Human primary hepatocytes, IL6 negative, small RNA, 0h, rep2

description:
36bp
hPH-r2_IL6neg0h_smallRNA

value: No treatment


title: Human primary hepatocytes, IL6 positive, small RNA, 0h, rep1

description:
36bp
hPH-r1_IL6pos0h_smallRNA


title: Human primary hepatocytes, IL6 positive, small RNA, 24h, rep1

description:
36bp
hPH-r1_IL6pos24h_smallRNA


title: Human primary hepatocytes, IL6 negative, small RNA, 24h, rep2

description:
36bp
hPH-r2_IL6neg24h_smallRNA


title: hEST_N_14_104_hEST_N_14.DMSO


title: Human primary hepatocytes, IL6 negative, small RNA, 6h, rep1

description:
36bp
hPH-r1_IL6neg6h_smallRNA


title: Human primary hepatocytes, IL6 negative, small RNA, 24h, rep1

description:
36bp
hPH-r1_IL6neg24h_smallRNA


title: Human primary hepatocytes, IL6 negative, small RNA, 0h, rep1

description:
36bp
hPH-r1_IL6neg0h_smallRNA


title: Human primary hepatocytes, IL6 negative, small RNA, 24h, rep3

description:
36bp
hPH-r3_IL6neg24h_smallRNA


title: hEST_N_14_101_hEST_N_14.DMSO


title: hEST_N_14_103_hEST_N_14.DMSO


title: hEST_N_14_99_hEST_N_14.DMSO


title: hEST_N_14_110_hEST_N_14.Cisplatin.6

value: Cisplatin

value: FALSE


title: hEST_N_14_102_hEST_N_14.DMSO

value: Human induced pluripotent-stem-cell derived embryoid body

value: TRUE


title: hEST_N_14_100_hEST_N_14.DMSO


title: HepG2 cells, IL6 positive, small RNA, 6h, rep4

description:
36bp
HepG2-r4_IL6pos6h_smallRNA


title: hEST_N_14_97_hEST_N_14.DMSO


title: hEST_N_14_98_hEST_N_14.DMSO


title: HepG2 cells, IL6 positive, small RNA, 24h, rep4

description:
36bp
HepG2-r4_IL6pos24h_smallRNA


title: HepG2 cells, IL6 positive, small RNA, 0h, rep4

description:
36bp
HepG2-r4_IL6pos0h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 6h, rep4

description:
36bp
HepG2-r4_IL6neg6h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 24h, rep4

description:
36bp
HepG2-r4_IL6neg24h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 0h, rep4

description:
36bp
HepG2-r4_IL6neg0h_smallRNA


title: hEST_N_13_80_hEST_N_13.Metformin.1

value: Metformin


title: HepG2 cells, IL6 positive, small RNA, 24h, rep3

description:
36bp
HepG2-r3_IL6pos24h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 24h, rep3

description:
36bp
HepG2-r3_IL6neg24h_smallRNA


title: hEST_N_13_78_hEST_N_13.Amoxycillin.1

value: Amoxycillin


title: HepG2 cells, IL6 negative, small RNA, 6h, rep3

description:
36bp
HepG2-r3_IL6neg6h_smallRNA


title: hEST_N_13_76_hEST_N_13.Folic.acid.1

value: Folic acid


title: HepG2 cells, IL6 positive, small RNA, 6h, rep3

description:
36bp
HepG2-r3_IL6pos6h_smallRNA


title: hEST_N_13_77_hEST_N_13.Hydroxyurea.1

value: Hydroxyurea


title: hEST_N_13_73_hEST_N_13.5.Azacitidine.1


title: HepG2 cells, IL6 negative, small RNA, 0h, rep3

description:
36bp
HepG2-r3_IL6neg0h_smallRNA


title: hEST_N_13_82_hEST_N_13.Dexamethasone.1

value: Dexamethasone


title: hEST_N_13_75_hEST_N_13.Phenytoin.1

value: Phenytoin


title: HepG2 cells, IL6 positive, small RNA, 24h, rep2

description:
36bp
HepG2-r2_IL6pos24h_smallRNA


title: HepG2 cells, IL6 positive, small RNA, 6h, rep2

description:
36bp
HepG2-r2_IL6pos6h_smallRNA


title: hEST_N_13_74_hEST_N_13.Cisplatin.1


title: HepG2 cells, IL6 positive, small RNA, 0h, rep2

description:
36bp
HepG2-r2_IL6pos0h_smallRNA


title: hEST_N_13_71_hEST_N_13.Progesterone.2

value: Progesterone


title: hEST_N_13_69_hEST_N_13.Penicillin.G.2

value: Penicillin G


title: hEST_N_13_79_hEST_N_13.SB431542.1


title: hEST_N_13_81_hEST_N_13.Penicillin.G.1


title: hEST_N_13_83_hEST_N_13.Progesterone.1


title: HepG2 cells, IL6 negative, small RNA, 6h, rep2

description:
36bp
HepG2-r2_IL6neg6h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 24h, rep2

description:
36bp
HepG2-r2_IL6neg24h_smallRNA


title: HepG2 cells, IL6 positive, small RNA, 0h, rep3

description:
36bp
HepG2-r3_IL6pos0h_smallRNA


title: hEST_N_13_68_hEST_N_13.Metformin.2


title: HepG2 cells, IL6 positive, small RNA, 6h, rep1

description:
36bp
HepG2-r1_IL6pos6h_smallRNA


title: hEST_N_13_66_hEST_N_13.Amoxycillin.2


title: HepG2 cells, IL6 negative, small RNA, 0h, rep2

description:
36bp
HepG2-r2_IL6neg0h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 6h, rep1

description:
36bp
HepG2-r1_IL6neg6h_smallRNA


title: hEST_N_13_70_hEST_N_13.Dexamethasone.2


title: HepG2 cells, IL6 negative, small RNA, 24h, rep1

description:
36bp
HepG2-r1_IL6neg24h_smallRNA


title: hEST_N_13_65_hEST_N_13.Hydroxyurea.2


title: HepG2 cells, IL6 positive, small RNA, 24h, rep1

description:
36bp
HepG2-r1_IL6pos24h_smallRNA


title: HepG2 cells, IL6 positive, small RNA, 0h, rep1

description:
36bp
HepG2-r1_IL6pos0h_smallRNA


title: HepG2 cells, IL6 negative, small RNA, 0h, rep1

description:
36bp
HepG2-r1_IL6neg0h_smallRNA


title: Human primary hepatocytes, IL6 positive, 6h, rep3

description:
49bp
hPH-r3_IL6pos6h

value: Primary hepatocytes


title: hEST_N_13_64_hEST_N_13.Folic.acid.2


title: hEST_N_13_63_hEST_N_13.Phenytoin.2


title: hEST_N_13_62_hEST_N_13.Cisplatin.2


title: Human primary hepatocytes, IL6 positive, 0h, rep3

description:
49bp
hPH-r3_IL6pos0h

value: Hepatocytes


title: Human primary hepatocytes, IL6 positive, 24h, rep3

description:
49bp
hPH-r3_IL6pos24h

value: WT


title: hEST_N_13_67_hEST_N_13.SB431542.2


title: hEST_N_13_57_hEST_N_13.Penicillin.G.3


title: hEST_N_13_59_hEST_N_13.Progesterone.3


title: Human primary hepatocytes, IL6 negative, 24h, rep3

description:
49bp
hPH-r3_IL6neg24h


title: Human primary hepatocytes, IL6 positive, 24h, rep2

description:
49bp
hPH-r2_IL6pos24h

value: IL6 stimulated


title: hEST_N_13_54_hEST_N_13.Amoxycillin.3


title: hEST_N_13_61_hEST_N_13.5.Azacitidine.2


title: hEST_N_13_55_hEST_N_13.SB431542.3


title: hEST_N_13_58_hEST_N_13.Dexamethasone.3


title: hEST_N_13_56_hEST_N_13.Metformin.3


title: Human primary hepatocytes, IL6 positive, 6h, rep2

description:
49bp
hPH-r2_IL6pos6h


title: Human primary hepatocytes, IL6 negative, 6h, rep3

description:
49bp
hPH-r3_IL6neg6h

value: No treatment


title: hEST_N_13_53_hEST_N_13.Hydroxyurea.3


title: hEST_N_13_50_hEST_N_13.Cisplatin.3

value: Cisplatin


title: hEST_N_13_51_hEST_N_13.Phenytoin.3

value: FALSE


title: Human primary hepatocytes, IL6 negative, 0h, rep3

description:
49bp
hPH-r3_IL6neg0h


title: Human primary hepatocytes, IL6 negative, 6h, rep2

description:
49bp
hPH-r2_IL6neg6h


title: Human primary hepatocytes, IL6 negative, 24h, rep2

description:
49bp
hPH-r2_IL6neg24h


title: Human primary hepatocytes, IL6 positive, 0h, rep2

description:
49bp
hPH-r2_IL6pos0h


title: Human primary hepatocytes, IL6 negative, 0h, rep2

description:
49bp
hPH-r2_IL6neg0h


title: hEST_N_13_52_hEST_N_13.Folic.acid.3

value: Human induced pluripotent-stem-cell derived embryoid body


title: hEST_N_13_47_hEST_N_13.Progesterone.4

value: TRUE


title: hEST_N_13_49_hEST_N_13.5.Azacitidine.3


title: Human primary hepatocytes, IL6 positive, 24h, rep1

description:
49bp
hPH-r1_IL6pos24h


title: hEST_N_13_45_hEST_N_13.Penicillin.G.4


title: Human primary hepatocytes, IL6 positive, 0h, rep1

description:
49bp
hPH-r1_IL6pos0h


title: hEST_N_13_46_hEST_N_13.Dexamethasone.4


title: Human primary hepatocytes, IL6 positive, 6h, rep1

description:
49bp
hPH-r1_IL6pos6h


title: hEST_N_13_42_hEST_N_13.Amoxycillin.4


title: hEST_N_13_43_hEST_N_13.SB431542.4


title: Human primary hepatocytes, IL6 negative, 6h, rep1

description:
49bp
hPH-r1_IL6neg6h


title: Human primary hepatocytes, IL6 negative, 24h, rep1

description:
49bp
hPH-r1_IL6neg24h


title: HepG2 cells, IL6 positive, 0h, rep2

description:
49bp
HepG2-r2_IL6pos0h


title: hEST_N_13_41_hEST_N_13.Hydroxyurea.4


title: HepG2 cells, IL6 positive, 24h, rep2

description:
49bp
HepG2-r2_IL6pos24h


title: hEST_N_13_39_hEST_N_13.Phenytoin.4


title: hEST_N_13_40_hEST_N_13.Folic.acid.4


title: HepG2 cells, IL6 positive, 6h, rep1

description:
49bp
HepG2-r1_IL6pos6h


title: HepG2 cells, IL6 negative, 6h, rep2

description:
49bp
HepG2-r2_IL6neg6h


title: hEST_N_13_37_hEST_N_13.5.Azacitidine.4


title: HepG2 cells, IL6 negative, 0h, rep2

description:
49bp
HepG2-r2_IL6neg0h


title: hEST_N_13_35_hEST_N_13.Progesterone.5


title: hEST_N_13_34_hEST_N_13.Dexamethasone.5


title: hEST_N_13_33_hEST_N_13.Penicillin.G.5


title: hEST_N_13_32_hEST_N_13.Metformin.5

value: Metformin


title: HepG2 cells, IL6 positive, 0h, rep1

description:
49bp
HepG2-r1_IL6pos0h


title: HepG2 cells, IL6 negative, 6h, rep1

description:
49bp
HepG2-r1_IL6neg6h


title: hEST_N_13_44_hEST_N_13.Metformin.4


title: Human primary hepatocytes, IL6 negative, 0h, rep1

description:
49bp
hPH-r1_IL6neg0h


title: HepG2 cells, IL6 positive, 24h, rep1

description:
49bp
HepG2-r1_IL6pos24h


title: hEST_N_13_29_hEST_N_13.Hydroxyurea.5


title: HepG2 cells, IL6 negative, 24h, rep1

description:
49bp
HepG2-r1_IL6neg24h


title: hEST_N_13_30_hEST_N_13.Amoxycillin.5

value: Amoxycillin


title: HepG2 cells, IL6 positive, 6h, rep2

description:
49bp
HepG2-r2_IL6pos6h


title: hEST_N_13_38_hEST_N_13.Cisplatin.4


title: HepG2 cells, IL6 negative, 0h, rep1

description:
49bp
HepG2-r1_IL6neg0h


title: hEST_N_13_28_hEST_N_13.Folic.acid.5

value: Folic acid


title: hEST_N_13_27_hEST_N_13.Phenytoin.5


title: hEST_N_13_25_hEST_N_13.5.Azacitidine.5


title: A20913

data_processing:
Raw Data (BAM Files): Paired-end sequence data were analyzed with BWA/v0.6 alignment software with option (-s) to disable Smith-Waterman alignment. Reads were mapped onto GRCh37-lite reference genome and exon-exon junction reference whose coordinates were defined based on transcript annotations in Ensembl/v59. Reads with mapping quality < 10 were discarded and duplicate reads were tagged using the Picard's MarkDuplicates program. JAGuaR 2.1 was used to incorporate reads spanning multiple exons into the alignment by introducing large alignment gaps.
Processed Data (Normalized Expression): All transcripts of a given gene were collapsed into a single gene model such that exonic bases were the union of exonic bases that belonged to all known transcripts of the gene. FPKM transcript abundance levels were obtained by quantifying the fraction of each read that overlapped with an exonic region for that gene. Sample-based normalization was subsequently performed such that the sum of all estimated transcript abundances for each sample equals 1,000,000 culminating in TPM normalized expression levels.
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files depict FPKM-normalized expression for each sample. Supplementary files contain FPKM and TPM-normalized expression levels for all samples. Metadata for all samples is included as a separate tab-delimited text file.

source_name: patient-derived xenograft cells

growth_protocol: Primary AML cells were xenotransplanted into immunosuppressed NOD.SCID and NSG mice.

extract_protocol:
RNA was extracted from human CD45+ cells out of patient-derived xenografts using an RNeasy Micro Kit (Qiagen).
Libraries were constructed using SMART-Seq (Clonetec)

treatment_protocol: Xenotransplanted mice were treated with either Fedratinib (60mg/kg) or Vehicle control (0.5% methylcellulose) by oral gavage twice daily for 14 days.

tag: patientid

tag: fedratinibresponse

value: Non-Responder

value: Fedratinib

value: patient-derived xenograft cells


title: A20912

value: Vehicle


title: A19778

value: Responder


title: A19779


title: hEST_N_13_31_hEST_N_13.SB431542.5

tag: run


title: hEST_N_13_23_hEST_N_13.Progesterone.6

tag: plate

value: Progesterone


title: hEST_N_13_21_hEST_N_13.Penicillin.G.6

value: Penicillin G

tag: usedforfactoranalysis


title: A18789

value: Partial-Responder


title: A18790


title: hEST_N_13_22_hEST_N_13.Dexamethasone.6

value: Dexamethasone

tag: usedformodelbuilding


title: HepG2 cells, IL6 negative, 24h, rep2

description:
49bp
HepG2-r2_IL6neg24h

value: Hepatocytes

value: WT

value: No treatment


title: A18738


title: A18739


title: hEST_N_13_20_hEST_N_13.Metformin.6

value: Human induced pluripotent-stem-cell derived embryoid body

value: FALSE

tag: contrast


title: hEST_N_13_19_hEST_N_13.SB431542.6

value: TRUE

tag: concentration


title: hEST_N_13_26_hEST_N_13.Cisplatin.5

value: Cisplatin

tag: conclabel


title: hEST_N_13_15_hEST_N_13.Phenytoin.6

value: Phenytoin

tag: concstr


title: A18733

value: Non-Responder


title: hEST_N_13_17_hEST_N_13.Hydroxyurea.6

value: Hydroxyurea

tag: teratogenicity


title: A18732

tag: cell type

value: patient-derived xenograft cells


title: A18729

value: Fedratinib


title: hEST_N_13_14_hEST_N_13.Cisplatin.6


title: A18731


title: hEST_N_13_13_hEST_N_13.5.Azacitidine.6


title: A18730

value: Vehicle


title: hEST_N_13_18_hEST_N_13.Amoxycillin.6

value: Amoxycillin


title: A18727

value: Responder


title: A18101


title: A18728

value: Partial-Responder


title: hEST_N_13_16_hEST_N_13.Folic.acid.6

value: Folic acid


title: A18726


title: A17909


title: hEST_N_13_12_hEST_N_13.DMSO

value: DMSO


title: hEST_N_13_11_hEST_N_13.DMSO


title: A17908


title: A14971


title: hEST_N_13_7_hEST_N_13.DMSO


title: hEST_N_13_5_hEST_N_13.DMSO


title: hEST_N_13_8_hEST_N_13.DMSO


title: A18102


title: hEST_N_13_6_hEST_N_13.DMSO


title: A12246


title: hEST_N_13_4_hEST_N_13.DMSO


title: hEST_N_13_10_hEST_N_13.DMSO


title: hEST_N_13_2_hEST_N_13.DMSO


title: A31467

extract_protocol:
RNA was extracted from bulk peripheral blood mononuclear cells using an RNeasy Micro Kit (Qiagen).
Libraries were constructed using SMART-Seq (Clonetec)

value: Human acute myeloid leukemia cells


title: A33903


title: A14970


title: hEST_N_12_84_hEST_N_12.Ibuprofen.1

value: Ibuprofen


title: A12187


title: A12186


title: A31428


title: hEST_N_13_1_hEST_N_13.DMSO

value: Human induced pluripotent-stem-cell derived embryoid body


title: hEST_N_12_81_hEST_N_12.Retinoic.acid.1

value: Retinoic acid

value: FALSE


title: hEST_N_13_3_hEST_N_13.DMSO

value: TRUE


title: A12245


title: hEST_N_12_83_hEST_N_12.Methotrexate.1

value: Methotrexate


title: hEST_N_12_80_hEST_N_12.R.Thalidomide.1

value: R-Thalidomide


title: hEST_N_12_82_hEST_N_12.Valproic.acid.1

value: Valproic acid


title: A31459


title: hEST_N_12_79_hEST_N_12.S.Thalidomide.1

value: S-Thalidomide


title: A31432


title: hEST_N_12_78_hEST_N_12.Thalidomide.1

value: Thalidomide


title: hEST_N_12_71_hEST_N_12.Methotrexate.2


title: A31360


title: hEST_N_12_72_hEST_N_12.Ibuprofen.2


title: A31406


title: A31390


title: hEST_N_12_69_hEST_N_12.Retinoic.acid.2


title: A31387

value: Non-Responder


title: A31372


title: A31288


title: A31338


title: hEST_N_12_67_hEST_N_12.S.Thalidomide.2


title: hEST_N_12_68_hEST_N_12.R.Thalidomide.2


title: A30212


title: A37133_Selinexor_3

growth_protocol: Primary AML cells were xenotransplanted into immunosuppressed NSG mice.

treatment_protocol: Xenotransplanted mice were treated with either Selinexor (20mg/kg) or Vehicle control by oral gavage three times per week for four weeks.

tag: patient

value: Selinexor (KPT-330)

value: patient-derived xenograft cells


title: hEST_N_12_70_hEST_N_12.Valproic.acid.2


title: hEST_N_12_66_hEST_N_12.Thalidomide.2


title: A30231

value: Partial-Responder


title: A37130_Veh_3

value: Vehicle


title: A31388

value: Responder


title: A37129_Veh_2


title: A37131_Selinexor_1


title: A37128_Veh_1


title: hEST_N_12_58_hEST_N_12.Valproic.acid.3


title: hEST_N_12_54_hEST_N_12.Thalidomide.3


title: hEST_N_12_55_hEST_N_12.S.Thalidomide.3


title: LSC0077_Bl_CD34pCD38p

data_processing:
Raw Data (BAM Files): Paired-end sequence data were analyzed with BWA/v0.6 alignment software with option (-s) to disable Smith-Waterman alignment. Reads were mapped onto GRCh37-lite reference genome and exon-exon junction reference whose coordinates were defined based on transcript annotations in Ensembl/v59. Reads with mapping quality < 10 were discarded and duplicate reads were tagged using the Picard's MarkDuplicates program. JAGuaR 2.1 was used to incorporate reads spanning multiple exons into the alignment by introducing large alignment gaps.
Processed Data (Raw Counts): Paired-end sequence data was aligned against GRCh38 and transcript sequences downloaded from Ensembl build 90 using STAR 2.5.2a. Default parameters were used except for the following: “–chimSegmentMin 12 –chimJunctionOverhangMin 12 –alignSJDBoverhangMin 10 –alignMatesGapMax 100000 –alignIntronMax 100000 –chimSegmentReadGapMax parameter 3 –alignSJstitchMismatchNmax 5 -1 5 5.” Raw counts were obtained using HTSeq v0.9.1.
Supplementary Files (Normalized Expression): For TPM normalization, raw counts for each gene were divided by the median length in kilobases of all GRCh38 annotated transcripts corresponding to a given gene. Sample-based normalization was subsequently performed such that the sum of all estimated transcript abundances for each sample equals 1,000,000. For VST normalized expression, variance-stabilizing transformation was performed on the raw counts using the vst function in DESeq2 v1.32.0.
Assembly: Raw BAM Files: GRCh37; Processed Data: GRCh38
Supplementary files format and content: Tab-delimited text files depict raw counts for each sample. Supplementary files contain processed data for all samples, including raw counts (ideal for differential expression), TPM-normalized expression (ideal for deconvolution), and VST-normalized expression (ideal for clustering, visualization, and precise quantification of specific genes) for each sample. Metadata for all samples is included as a separate tab-delimited text file.

treatment_protocol: T-cell depleted mononuclear cells from primary acute myeloid leukemia patients were thawed and flow-sorted according to expression of CD34 and CD38.

tag: fraction

tag: lsc activity

value: LSC+

value: Human acute myeloid leukemia cells


title: hEST_N_12_56_hEST_N_12.R.Thalidomide.3

value: Human induced pluripotent-stem-cell derived embryoid body


title: hEST_N_12_60_hEST_N_12.Ibuprofen.3

value: Ibuprofen


title: A37132_Selinexor_2

tag: treatment


title: hEST_N_12_59_hEST_N_12.Methotrexate.3

value: FALSE


title: LSC0077_Bl_CD34pCD38m


title: hEST_N_12_57_hEST_N_12.Retinoic.acid.3

value: Retinoic acid

value: TRUE


title: hEST_N_12_46_hEST_N_12.Valproic.acid.4


title: LSC0076_Bl_CD34mCD38p

value: LSC-


title: hEST_N_12_47_hEST_N_12.Methotrexate.4

value: Methotrexate


title: hEST_N_12_45_hEST_N_12.Retinoic.acid.4


title: LSC0074_Bl_CD34mCD38p


title: hEST_N_12_44_hEST_N_12.R.Thalidomide.4

value: R-Thalidomide


title: LSC0071_Bl_CD34mCD38p


title: LSC0074_Bl_CD34pCD38p


title: LSC0072_Bl_CD34pCD38p


title: LSC0073_Bl_CD34mCD38p


title: hEST_N_12_48_hEST_N_12.Ibuprofen.4


title: hEST_N_12_35_hEST_N_12.Methotrexate.5


title: hEST_N_12_34_hEST_N_12.Valproic.acid.5

value: Valproic acid


title: hEST_N_12_36_hEST_N_12.Ibuprofen.5


title: LSC0071_Bl_CD34mCD38m


title: hEST_N_12_31_hEST_N_12.S.Thalidomide.5

value: S-Thalidomide


title: LSC0069_Bl_CD34pCD38m


title: LSC0068_Bl_CD34mCD38p


title: LSC0069_Bl_CD34pCD38p


title: LSC0076_Bl_CD34mCD38m


title: hEST_N_12_43_hEST_N_12.S.Thalidomide.4


title: LSC0069_Bl_CD34mCD38p


title: hEST_N_12_33_hEST_N_12.Retinoic.acid.5


title: hEST_N_12_24_hEST_N_12.Ibuprofen.6


title: hEST_N_12_30_hEST_N_12.Thalidomide.5

value: Thalidomide


title: LSC0066_Bl_CD34mCD38p


title: LSC0065_Bl_CD34pCD38m


title: hEST_N_12_22_hEST_N_12.Valproic.acid.6


title: hEST_N_12_23_hEST_N_12.Methotrexate.6


title: LSC0064_Bl_CD34pCD38p


title: LSC0064_Bl_CD34mCD38p


title: hEST_N_12_42_hEST_N_12.Thalidomide.4


title: LSC0067_Bl_CD34pCD38p


title: hEST_N_12_21_hEST_N_12.Retinoic.acid.6


title: hEST_N_12_32_hEST_N_12.R.Thalidomide.5


title: hEST_N_12_18_hEST_N_12.Thalidomide.6


title: LSC0063_Bl_CD34mCD38p


title: LSC0061_Bl_CD34pCD38p


title: LSC0062_Bl_CD34mCD38p


title: hEST_N_12_20_hEST_N_12.R.Thalidomide.6


title: hEST_N_12_19_hEST_N_12.S.Thalidomide.6


title: hEST_N_12_12_hEST_N_12.DMSO

value: DMSO


title: LSC0061_Bl_CD34mCD38p


title: LSC0060_Bl_CD34mCD38p


title: hEST_N_12_10_hEST_N_12.DMSO


title: hEST_N_12_8_hEST_N_12.DMSO


title: hEST_N_12_9_hEST_N_12.DMSO


title: LSC0060_Bl_CD34pCD38p


title: LSC0059_Bl_CD34mCD38p


title: LSC0059_Bl_CD34mCD38m


title: hEST_N_12_6_hEST_N_12.DMSO


title: LSC0060_Bl_CD34pCD38m


title: hEST_N_12_7_hEST_N_12.DMSO


title: LSC0058_Bl_CD34mCD38m


title: LSC0058_Bl_CD34pCD38m


title: hEST_N_12_2_hEST_N_12.DMSO


title: hEST_N_12_4_hEST_N_12.DMSO


title: hEST_N_12_3_hEST_N_12.DMSO


title: hEST_N_12_1_hEST_N_12.DMSO


title: LSC0061_Bl_CD34mCD38m


title: LSC0055_Bl_CD34mCD38p


title: hEST_N_12_11_hEST_N_12.DMSO


title: hEST_N_11_83_hEST_N_11.Methotrexate.1


title: LSC0056_Bl_CD34pCD38m

value: Non-leukemic graft


title: hEST_N_11_84_hEST_N_11.Ibuprofen.1


title: hEST_N_12_5_hEST_N_12.DMSO


title: hEST_N_11_79_hEST_N_11.S.Thalidomide.1


title: LSC0054_Bl_CD34mCD38p


title: LSC0052_Bl_CD34pCD38p


title: hEST_N_11_82_hEST_N_11.Valproic.acid.1


title: LSC0051_Bl_CD34pCD38p


title: hEST_N_11_78_hEST_N_11.Thalidomide.1


title: hEST_N_11_72_hEST_N_11.Ibuprofen.2


title: LSC0053_Bl_CD34pCD38m


title: hEST_N_11_80_hEST_N_11.R.Thalidomide.1


title: LSC0057_Bl_CD34pCD38m


title: LSC0053_Bl_CD34mCD38p


title: LSC0049_Bl_CD34pCD38p


title: LSC0053_Bl_CD34pCD38p


title: LSC0058_Bl_CD34mCD38p


title: LSC0050_Bl_CD34mCD38p


title: hEST_N_11_71_hEST_N_11.Methotrexate.2


title: hEST_N_13_9_hEST_N_13.DMSO


title: LSC0049_Bl_CD34mCD38p


title: hEST_N_11_69_hEST_N_11.Retinoic.acid.2


title: LSC0048_Bl_CD34mCD38p


title: LSC0046_Bl_CD34mCD38p


title: LSC0045_Bl_CD34mCD38p


title: hEST_N_11_68_hEST_N_11.R.Thalidomide.2


title: hEST_N_11_67_hEST_N_11.S.Thalidomide.2


title: hEST_N_11_66_hEST_N_11.Thalidomide.2


title: hEST_N_11_60_hEST_N_11.Ibuprofen.3


title: hEST_N_11_70_hEST_N_11.Valproic.acid.2


title: hEST_N_11_56_hEST_N_11.R.Thalidomide.3


title: LSC0041_Bl_CD34pCD38p


title: LSC0043_Bl_CD34mCD38m


title: LSC0042_Bl_CD34pCD38p


title: LSC0043_Bl_CD34pCD38p


title: LSC0040_Bl_CD34mCD38p


title: hEST_N_11_81_hEST_N_11.Retinoic.acid.1


title: hEST_N_11_59_hEST_N_11.Methotrexate.3


title: hEST_N_11_48_hEST_N_11.Ibuprofen.4


title: LSC0041_Bl_CD34mCD38m


title: LSC0041_Bl_CD34pCD38m


title: LSC0039_Bl_CD34mCD38p


title: LSC0038_Bl_CD34mCD38p


title: hEST_N_11_44_hEST_N_11.R.Thalidomide.4


title: LSC0039_Bl_CD34pCD38m


title: hEST_N_11_47_hEST_N_11.Methotrexate.4


title: hEST_N_11_54_hEST_N_11.Thalidomide.3


title: hEST_N_11_46_hEST_N_11.Valproic.acid.4


title: LSC0037_Bl_CD34mCD38p


title: LSC0036_Bl_CD34mCD38p


title: LSC0038_Bl_CD34mCD38m


title: LSC0038_Bl_CD34pCD38p


title: hEST_N_11_35_hEST_N_11.Methotrexate.5


title: hEST_N_11_58_hEST_N_11.Valproic.acid.3


title: hEST_N_11_42_hEST_N_11.Thalidomide.4


title: hEST_N_11_43_hEST_N_11.S.Thalidomide.4


title: hEST_N_11_34_hEST_N_11.Valproic.acid.5


title: LSC0024_Bl_CD34mCD38m


title: hEST_N_11_31_hEST_N_11.S.Thalidomide.5


title: hEST_N_11_33_hEST_N_11.Retinoic.acid.5


title: hEST_N_11_36_hEST_N_11.Ibuprofen.5


title: LSC0027_Bl_CD34mCD38m


title: hEST_N_11_32_hEST_N_11.R.Thalidomide.5


title: hEST_N_11_45_hEST_N_11.Retinoic.acid.4


title: LSC0023_Bl_CD34mCD38p


title: LSC0027_Bl_CD34pCD38m


title: hEST_N_11_30_hEST_N_11.Thalidomide.5


title: hEST_N_11_24_hEST_N_11.Ibuprofen.6


title: LSC0025_Bl_CD34pCD38p


title: LSC0032_Bl_CD34pCD38m


title: LSC0022_Bl_CD34pCD38p


title: hEST_N_11_22_hEST_N_11.Valproic.acid.6


title: hEST_N_11_21_hEST_N_11.Retinoic.acid.6


title: hEST_N_11_19_hEST_N_11.S.Thalidomide.6


title: LSC0031_Bl_CD34mCD38p


title: LSC0019_Bl_CD34mCD38m


title: LSC0021_Bl_CD34mCD38p


title: hEST_N_11_20_hEST_N_11.R.Thalidomide.6


title: LSC0023_Bl_CD34pCD38p


title: hEST_N_11_23_hEST_N_11.Methotrexate.6


title: LSC0018_Bl_CD34pCD38p