title: undifferentiated type (fibroblast) 2

description: fibroblast cells treated with saline for 48 h

value: fibroblast-like


title: differentiated type (myofibroblast) 1

status: Public on Sep 18 2019

type: SRA

city: Omaha

first: Tu

last: Yaping

state: NE

address: 2500 California Plaza

department: Pharmacology

country: USA

institute: Creighton University School of Medicine

description: fibroblast cells treated with 1 ng/mL TGF-β1 for 48 h

library_source: transcriptomic

data_processing:
trim adapter using cutadapt.
map trimmed reads on miRNA precursors using SHiMPS aligner
counts reads associated to mature miRNAs
Genome_build: miRBase 21
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: human primary lung fibroblast cells (HFL)

growth_protocol: Cells were cultured in DMEM/F12 medium with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated from samples using mirVana miRNA isolation kit (Invitrogen). NEXTflexTM Small RNA-Seq Kit v3 (Bioo Scientic #5132-05) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 1 ng/mL TGF-β1 or saline for 48 h.

tag: mophology

value: myofibroblast-like

tag: passage


title: undifferentiated type (fibroblast) 3


title: 05-30073

type: RNA

city: Vancouver

first: Christian

last: Steidl

state: British Columbia

address: 675 10th Avenue West

department: Lymphoid Cancer Research

country: Canada

institute: BC Cancer

hyb_protocol: Nucleic acids were diluted to a final concentration of 100ng/ul and array hybridization was performed at Sick Kids Hospital using the HumanHT-12 v4.0 Expression BeadChip.

scan_protocol: standard Illumina

data_processing: The limma and beadarray R packages were used to analyse probe-level expression data. A normal-exponential convolution model was applied for background correction and normalization of the data, followed by log2-transformation and quality assessment. Probes below the detection score (i.e. considered to be not expressed) in at least three arrays were removed (27,446 probes remained). One case of the sequencing cohort was identified as an outlier by both, multidimensional scaling and principal component analysis (PCA), and was therefore removed. Following exclusion of case PA012, 68 cases were available for integrative analyses. Annotation of probes with quality and gene symbol information was performed using the IlluminaHumanv4.db probe annotation database (Illumina). Probes annotated as having “bad” quality or had no gene match were removed. A total of 24,501 probes representing 17,027 genes remained, with 4,659 of those being represented by more than one probe (i.e. ambiguous transcript).

label: biotin

source_name: tumor

label_protocol: standard Illumina

extract_protocol: RNA was extracted using either the RNeasy mini kit or AllPrep FFPE kit and measured using a Nanodrop spectrophotometer

tag: patient diagnosis

value: primary mediastinal B-cell lymphoma

tag: tissue

value: tumor


title: undifferentiated type (fibroblast) 4


title: 01-13756


title: 06-10606


title: 05-28808


title: undifferentiated type (fibroblast) 1


title: 02-17975


title: 97-29186


title: 05-20696


title: 06-25118


title: 06-13965


title: AAV-TBG-Cre #1

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

data_processing:
Using a HiSeq SBS sequencing kit version 4, Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Trimmomatic ver 0.36 was used to remove sequence adapters and low-quality bases and quality control was checked by FastQC ver 0.11.5
Sequencing alignment was performed by STAR ver 2.5.0a.
The differential expression profiles of RNA-seq were analyzed by the edgeR-based R (ver 3.4.1) pipeline
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change, FDR between two conditions generated by edgeR

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA from the livers was isolated with the RNeasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols. The cDNA library was sequenced using an Illumina HiSeq2000 (Illumina, San Diego, CA) to produce paired-end 100 bp reads.

treatment_protocol: For liver-specific downregulation of Jmjd3, 8 week-old male Jmjd3 floxed mice were injected with AAV-TBG-Cre or -GFP (1.0 to 2.0 X 1011 active viral particles), and 12 weeks later the mice were fasted for 16 h.

tag: strain

value: Jmjd3 floxed mice

value: Liver

tag: treatment

value: AAV-TBG-Cre


title: AAV-TBG-Cre #2


title: AAV-GFP #1

value: AAV-GFP


title: AAV-TBG-Cre #3


title: 90-37635


title: AAV-GFP #3


title: 98-10389


title: 99-19873


title: 92-36297


title: Single Cell RNA-Seq for P17_94

city: Beijing

first: Xiannian

last: Zhang

address: Yiheyuan Road No.5

country: China

institute: Peking University

data_processing:
Align to gencode (release 25) using  SALMON (version 0.10).
Genome_build: hg38

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
The Smartseq2 protocol was immediately performed to rescue mRNAs from cell lysate
Libraries were constructed with a Tn5-based TruePrep DNA Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on the HiSeq 2500 platform (Illumina, USA).

tag: patient

value: Bone marrow

tag: cell type

value: myeloma


title: Single Cell RNA-Seq for P17_89


title: 06-30808


title: P35-45 3DIV ONCulture Control_4

city: Padova

first: Andrea

middle: Domenico

last: Rivera

address: Via Gabelli 67

department: Neuroscience

country: Italy

institute: University of Padova

description: Gene expression data of n=6 P35-45 optic nerves cultured for 3DIV in control conditions

hyb_protocol: 7µg of cRNA molecules were heat fragmented and applied to the Affymetrix Mouse Genechip 430 2.0. The hybridization solution was heated 2min. at 95°C and 5min. at 45°C. 200µl of this solution was filled in Affymetrix arrays and hybridized in GeneChip Hybridization Oven 640 for 16h at 45°C with 60 rpm rotation. Post hybridization washing was done using the GeneChip Fluidics Station 450 following the protocol FS450_0004 outlined in the Affymetrix instructions.

scan_protocol: The GeneChips were scanned in the Affymetrix GeneChip Scanner 7G  and the resultant image processed using the GCOS software package to prepare the CEL files and afterwards the expression console to generate CHP files.

data_processing: Data processing was performed using Agilent Genespring GX 12

label: Biotin

source_name: Mouse optic nerves cultured for 3DIV in control condition Sample 4

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: n=6 P35-45 C57BL/6 optic nerves were cultured for 3 day in vitro (DIV) with organotypic media containing saline or Lithium Chloride

extract_protocol: total RNA was extracted using Rneasy Mini Kit (Qiagen) according to manufacturer instructions

treatment_protocol: Optic nerves were collected in RNAlater (Qiagen) and stored at -80C until ready for RNA extraction

value: Optic nerve

tag: age

value: Saline


title: 98-17182


title: P35-45 3DIV ONCulture Lithium_2

description: Gene expression data of n=6 P35-45 optic nerves cultured for 3DIV with Lithium Chloride

source_name: Mouse optic nerves cultured for 3DIVwith Lithium Chloride Sample 2

value: Lithium


title: 03-25766


title: P35-45 3DIV ONCulture Lithium_4

source_name: Mouse optic nerves cultured for 3DIVwith Lithium Chloride Sample 4


title: 98-29355


title: 99-16291


title: P35-45 3DIV ONCulture Lithium_1

source_name: Mouse optic nerves cultured for 3DIVwith Lithium Chloride Sample 1


title: P35-45 3DIV ONCulture Lithium_3

source_name: Mouse optic nerves cultured for 3DIVwith Lithium Chloride Sample 3


title: AAV-GFP #2


title: 05-32897


title: Single Cell RNA-Seq for P17_84


title: Single Cell RNA-Seq for P17_82


title: Input IL1 5Z

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description:
Input sequencing of KB cells
ChIP-seq

library_source: genomic

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the human HG19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings.
Coverage vectors were extracted using deepTools bamCoverage function.
Genome_build: HG19
Supplementary_files_format_and_content: coverage Wiggle files were generated with Mscs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)

molecule: genomic DNA

source_name: KB cells

growth_protocol: cells were cultured in DMEM, 10% FCS, to subconfluency

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by purification of DNA
Sequencing libraries were prepared from 10 ng of DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: IL-1 alpha and the TAK1 inhibitor 5Z-oxozeaenol were added directly to the cell culture medium

value: 10ng/ml IL-1alpha for 1 h

value: 1uM 5Z-7-oxozeaenol for 1 h

tag: antibody

value: Input genomic DNA


title: Single Cell RNA-Seq for P17_81


title: P35-45 3DIV ONCulture Control_2

source_name: Mouse optic nerves cultured for 3DIV in control condition Sample 2


title: Input 5Z

description:
Input sequencing of KB cells
ChIP-seq


title: Single Cell RNA-Seq for P17_74


title: Single Cell RNA-Seq for P17_78


title: Single Cell RNA-Seq for P17_73


title: Input IL1

description:
Input sequencing of KB cells
ChIP-seq


title: Single Cell RNA-Seq for P17_70


title: Single Cell RNA-Seq for P17_66


title: Input

description:
Input sequencing of KB cells
ChIP-seq


title: 98-20177


title: 05-23168


title: 00-25381


title: Single Cell RNA-Seq for P17_65


title: P35-45 3DIV ONCulture Control_3

source_name: Mouse optic nerves cultured for 3DIV in control condition Sample 3


title: P35-45 3DIV ONCulture Control_1

source_name: Mouse optic nerves cultured for 3DIV in control condition Sample 1


title: Single Cell RNA-Seq for P17_62


title: Single Cell RNA-Seq for P17_64


title: CTCF IL1 5Z

description:
ChIP-seq analysis of CTCF in KB cells
ChIP-seq

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions


title: Single Cell RNA-Seq for P17_61


title: CTCF 5Z


title: Single Cell RNA-Seq for P17_59


title: Single Cell RNA-Seq for P17_54


title: 00-11328


title: Single Cell RNA-Seq for P17_53


title: 96-21505


title: Single Cell RNA-Seq for P17_57


title: CTCF IL1


title: CTCF


title: Single Cell RNA-Seq for P17_52


title: ATAC-seq KB IL1 5Z

description:
ATAC-seq analysis of KB cells
ATAC-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Reads were aligned to a pre-compiled index of the human hg19 genome using BWA with default settings.
Duplicate reads were removed with Samtools' rmdup function.
Virtual footprinting for motif analysis by adapting the HINT subroutine of the Regulatory Genomics Toolbox suite (http://www.regulatory-genomics.org/).
Peaks were called by using MACS2 (version 2.1.1.20160309) with the default setting the p-value threshold to -p 0.01 and using the -bampe option
Coverage plots were generated using ngs.plot (Shen, Shao et al., 2014),
hg19
Coverage bigwig files were generated with Deeptools bamCoverage function at 10 bp resolution.

extract_protocol: 130000 KB cells were harvested using trypsinization and washed with cold PBS. Cells were centrifuged in 50µl cold PBS (500xg, 5min, 4°C) and the supernatant was discarded. The cell pellet was resuspended in 50µl cold lysis buffer (10mM Tris HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and the supernatant was discarded after another centrifugation step (500xg, 10min, 4°C).

treatment_protocol: IL-1 alpha and 5Z-oxozeaenol inhibitor were added directly to the cell culture medium


title: 92-64389


title: Single Cell RNA-Seq for P17_41


title: Single Cell RNA-Seq for P17_43


title: ATAC-seq KB 5Z

description:
ATAC-seq analysis of CTCF in KB cells
ATAC-seq


title: ATAC-seq KB IL1

description:
ATAC-seq analysis of KB cells
ATAC-seq


title: Single Cell RNA-Seq for P17_37


title: Single Cell RNA-Seq for P17_39


title: Single Cell RNA-Seq for P17_34


title: Single Cell RNA-Seq for P17_32


title: Single Cell RNA-Seq for P17_31


title: 99-27271


title: Single Cell RNA-Seq for P17_29


title: ATAC-seq KB

description:
ATAC-seq analysis of KB cells
ATAC-seq

treatment_protocol: IL-1 alpha and 5Z-oxozeaenol inhibitors were added directly to the cell culture medium


title: 95-17581


title: Single Cell RNA-Seq for P17_27


title: THP1_ETOP_REP3

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

institute: University Medical Center, Johannes Gutenberg University of Mainz

data_processing:
The quality of raw sequencing reads was assessed using FastQC (v0.11.5, Babraham Bioinformatics, Cambridge, UK)
Sequencing reads were mapped to human reference genome using the STAR aligner (v2.5.3a, Dobin A et al., Bioinformatics, 2013, 29(1):15-21), with the option "--quantMode GeneCounts"
The quality of mapped expression data was assessed using NOISeq R package (v2.20.0, Tarazona S et al., Nucleic Acids Research, 2015, 43(21):e140)
Differential gene expression analysis using edgeR (v3.20.1, Robinson MD et al., Bioinformatics, 2010, 26(1):139-140). Genes with Log2(foldchange) > |1| and FDR < 0.05 were considered as significant.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include mapped gene counts for each sample
Supplementary_files_format_and_content: xlsx files include results from differential gene expression analysis performed using edgeR

source_name: AML

growth_protocol: All cell lines were cultured in respective enriched media and were maintained at 37OC and 5% CO2.

extract_protocol:
Cells from 3 wells were pooled together and total RNA was isolated using TriFast, peqGOLD total RNA kit and DNase I Digest kit (VWR PEQLAB GmbH, Germany) according to manufacturer's instructions.
The quality and integrity of the extracted RNA was examined using a 2100 Bioanalyzer (Agilent technologies). Library was constructed using Illumina HiSeq 2000 using TruSeq stranded mRNA HT sample prep kit at the Genomics Core Facility at the Institute of Molecular Biology (IMB, Mainz, Germany).

treatment_protocol: 1 X 10^6 cells per well were seeded in a 6 well plate containing 5 ml of the media. Cells were incubated overnight and then treated for 24 hours with either media or etoposide at cell line-specific IC50 concentrations.

tag: cell line

value: AML

value: Etoposide (IC50)


title: 10-19276


title: 92-50350


title: Single Cell RNA-Seq for P17_17


title: Single Cell RNA-Seq for P17_23


title: THP1_ETOP_REP2


title: Exo_Plus_small

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Base-calling and de-multiplexing in each Proton run was executed by Torrent Suite software by filtering subthreshold reads and trimming adapter sequences
UBAM or BAM files generated by Proton were used for the further analysis.
Total transcriptome reads were aligned to mm10 mouse genome reference with Proton instrument RNASeqAnalysis Plugin tool v5.2.0.5.  Absolute normalized reads table generated by above tools was used for the further data analyses
Human serum exosome or mouse liver small RNA sequencing data were aligned to mirBase21 reference (human or mouse respectively) using Proton SmallRNA v5.6.0.0 plugin tool
Genome_build: mmu10, miBase21 human (RNA) and mouse (RNA)
Supplementary_files_format_and_content: Tab-delimited text files were generated by Torrent Proton RNASeqAnalysis or SmallRNA plugin tools and include reads per mln values, absolute reads, FPKM values for isoforms

source_name: liver

extract_protocol:
Total liver RNA and exosome RNA were isolated with Norgen total RNA purification kit according to kit's protocols for each type of samples (Norgen Biotek Corp., Canada), small RNAs were enriched using Ion Total RNA-Seq Kit v2 (Life Technologies).
2 µg total RNA from the pool of 3 sampes per each condition was depleted for ribosomal RNA with RiboMinus Eukaryote System v2 (cat # A15026, Ambion, ThermoFisher Scientific), transcriptome RNA and small RNA  libraries were prepared with Ion Total RNA-Seq Kit v2 according to the kit manual

value: 500mg/kg acetaminophen + exosomes 5x108/mouse (from 1 ml of serum)


title: 06-12870

value: primary mediastinal B-cell lymphoma


title: THP1_ETOP_REP1


title: THP1_CTR_REP3

value: Untreated


title: DPP4-minus

description:
Transcriptome_mouse_APAP_toxicity_proton.rpm.bcmatrix.txt
Transcriptome_mouse_APAP_toxicity_proton.isoforms.txt

value: untreated control


title: GCSF

value: Liver

value: 500mg/kg acetaminophen+100µg/kg G-CSF


title: APAP

value: 500mg/kg acetaminophen


title: Exo_Plus


title: Nuc-603-30: Nucleosomal DNA (603 sequence) with 30bp linker

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Adapter DNAs were trimmed using Trim Galore (version 0.5.0) with the options: --paired –nextera.
The paired-end reads were concatenated into single-end reads using FLASh (version 1.2.11) with the options: -m 15 -M 101 (the reads that have the length within 101-180 base-pairs were analyzed).
The reads were mapped to the coordinate of 601 and 603 DNA sequences using bowtie (version 1.2.2) with the options: -v0 -m1 (retains exact hits and the ambiguous alignments of multi-reads were discarded).
Supplementary_files_format_and_content: The count matrix file (csv) contains the counts at 5'-end positions of sequenced DNA fragments with the strand infromation.

molecule: other

organism: synthetic construct

source_name: Synthetic DNA

extract_protocol:
The dinucleosome samples treated with Tn5 transposase complexed with adaptor DNAs were deproteinized, and approximately 100-300 base-pairs of DNA  fragments were purified by agaraose-TAE electrophoresis, followed by spin-column based DNA purification system.
The purified DNA fragments, in which the adopter DNA was ligated as a sequence tag by the transposase assay, were analyzed by massively parallel sequencing. The DNA fragments (10 ng) were ligated with the annealed Tn5MEDS-B oligonucleotides (Tn5MErev/Tn5ME-B, 2 mM) (Picelli et al. 2014) at blunt end side for 16°C at 30min using TaKaRa DNA ligation kit. The resulting DNA fragments were purified for excluding fragments shorter than 150 base-pair using AMPure XP beads (Beckman Coulter). The PCR amplification was performed using Ad1 (5’-AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG-3’) and Ad2 (5’-CAAGCAGAAGACGGCATACGAGAT[8mer_index]GTCTCGTGGGCTCGGAGATGT-3’) primers. PCR reaction was performed at the conditions, 72°C for 3 min and 95°C for 30 sec, followed by 7-8 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min, with a final extension at 72°C for 5 min using a LifeECO thermal cycler (Hangzhou Bioer Technology Co. Ltd., China). The amplified library was purified using a Qiagen MinElute Cleanup kit. The purified library was selected into 260–320 base-pairs fragments by E-Gel 2% SizeSelect electrophoresis (Invitrogen).

value: Synthetic DNA


title: THP1_CTR_REP2


title: 09-39172

value: tumor


title: 05-26031


title: Nuc-603-15: Nucleosomal DNA (603 sequence) with 15bp linker


title: THP1_CTR_REP1


title: Nuc-601-30: Nucleosomal DNA (601 sequence) with 30bp linker


title: Nuc-601-15: Nucleosomal DNA (601 sequence) with 15bp linker


title: 06-31586


title: 00-13084


title: 06-31916


title: 282TX

type: genomic

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description:
processed data file:
Plate_2_Full_Data_Table.txt

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned on iScan

data_processing:
no data processing was applied
Processed data files include: Genotype: AA,AB,BB,or NC (no call). The first 10 columns of  *Full_Data_Table.txt files contain info about probes, processed values start at 11th column.

source_name: blood

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA).

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

value: blood

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: 268TX

tag: tissue

tag: patient diagnosis


title: 231TX


title: OCIAML3_ETOP_REP3

tag: treatment


title: 213TX


title: 253TX


title: OCIAML3_ETOP_REP2

tag: cell type


title: 04-31184


title: 166TX


title: OCIAML3_CTR_REP2


title: 03-22426


title: 267TX


title: 10-26974


title: 03-29087


title: OCIAML3_CTR_REP1


title: 230TX


title: 99-29859


title: OCIAML3_ETOP_REP1


title: 06-13331


title: 252TX


title: 211TX


title: 280TX


title: 165TX


title: OCIAML2_ETOP_REP2


title: 193TX


title: 178TX


title: OCIAML3_CTR_REP3


title: 194TX


title: OCIAML2_ETOP_REP1


title: OCIAML2_ETOP_REP3


title: 91-31432


title: 179TX


title: 251TX


title: OCIAML2_CTR_REP3


title: 266TX


title: 229TX


title: 93-38062


title: 207TX


title: 191TX


title: 177TX


title: OCIAML2_CTR_REP2


title: OCIAML2_CTR_REP1


title: 164TX


title: NOMO1_ETOP_REP3


title: 279TX


title: 91-33532


title: 265TX


title: 91-33589


title: 03-27419


title: NOMO1_CTR_REP3


title: 250TX


title: 95-12514


title: 228TX


title: NOMO1_CTR_REP1


title: 206TX


title: NOMO1_ETOP_REP2


title: 94-22614


title: 92-30387


title: 190TX


title: NB4_ETOP_REP3


title: 91-31046


title: NB4_ETOP_REP2


title: 92-65678


title: 92-32297


title: 176TX


title: NB4_ETOP_REP1


title: 163TX


title: 92-34312


title: 277TX


title: NB4_CTR_REP3


title: 05-15712


title: 88-30447


title: 264TX


title: NB4_CTR_REP2


title: 93-34963


title: 247TX


title: NB4_CTR_REP1


title: 95-26081


title: 85-36643


title: 84-32502


title: MV411_ETOP_REP3


title: 227TX


title: 204TX


title: 281TX


title: 84-31698


title: MV411_ETOP_REP1


title: 90-33894


title: MV411_ETOP_REP2


title: 175TX


title: MV411_CTR_REP3


title: 189TX


title: 89-31121


title: 83-14779


title: 161TX


title: MV411_CTR_REP2


title: 82-62867


title: NOMO1_ETOP_REP1


title: 93-37171


title: 276TX


title: 88-33941


title: MV411_CTR_REP1


title: 03-29657


title: 245TX


title: 109T-O

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System.

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: Wilms organoid

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: Wilms organoid

tag: material

value: Frozen

tag: tumor identifier


title: 03-23736

source_name: tumor


title: 261TX


title: 02-25988


title: NOMO1_CTR_REP2

tag: cell line


title: 97T-O


title: 119M-O


title: 226TX

tag: (z)-4-oh-tam + 3-oh-tam


title: 95T-O


title: MONOMAC6_CTR_REP3


title: 203TX

tag: (z)-endoxifen + 3-oh-ndm-tam


title: 88T-O


title: 06-19999


title: 04-31838


title: 102T-O


title: 174TX

tag: tamoxifen


title: MONOMAC6_ETOP_REP2


title: 04-32225


title: MONOMAC6_CTR_REP1


title: MONOMAC6_ETOP_REP3


title: 05-16384


title: 101T-O


title: MOLM13_ETOP_REP3


title: 98T-O


title: 160TX

tag: ndm-tam


title: 80T-O


title: 03-25485


title: MOLM13_ETOP_REP2


title: 83T-O


title: 68T-O


title: 86T-O


title: 260TX

tag: (e)-endoxifen


title: MOLM13_ETOP_REP1


title: 05-17648


title: 57T-O


title: 94T-O


title: 04-32627


title: 243TX

tag: tam-n-oxide


title: MONOMAC6_ETOP_REP1


title: 52T-O


title: 187TX

tag: tam-n-gluc


title: 48T-O


title: 64T-O


title: 225TX

tag: (e)-a-oh-tam


title: 51T-O


title: MONOMAC6_CTR_REP2


title: MOLM13_CTR_REP2


title: 04-41579


title: 201TX

tag: (z)-a-oh-tam


title: 186TX

tag: z-endoxifen ratio


title: KASUMI1_ETOP_REP3


title: 274TX

tag: tissue


title: 172TX

tag: patient diagnosis


title: 158TX


title: 85T-O


title: KASUMI1_ETOP_REP1

tag: treatment


title: 05-23520


title: Poly 242 #3

city: Toulouse

first: Yvan

last: Martineau

address: 2 Avenue Hubert Curien, CS 53717,

department: UMR1037 Inserm CRCT

country: France

institute: Inserm

description:
polysomal RNA
MiaPaca-2 cells treated with pp242 for 12h followed by extraction of polysome-associated RNA

hyb_protocol: The resulting labelled samples were hybridized to the Human Genome U133 Plus 2.0 gene arrays from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data was extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label_protocol: 500 µg cytoplasmic or polysome-associated RNA was used as starting material for the 3’ IVT Express Kit (Affymetrix)

growth_protocol: MIAPACA-2 cells were grown in high glucose Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% defined fetal bovine serum (FBS), 2mM L-glutamine, 100 units/ml penicillin and 100 microgram/ml streptomycin. Cells were seeded in 150mm culture dishes and grown up to 70% confluence (about 20x10^6 cells).

extract_protocol: Cytosolic and polysome-associated RNA was collected from MIAPACA-2 cells (4 replicates). Briefly, total cytosolic mRNA (Cytosolic RNA) was extracted and sedimented on a 10%-50% sucrose gradient to separate mRNA according to the number of associated ribosomes. Polysome fractions with mRNA associated with >3 ribosomes were pooled (“polysome-associated” mRNA) and RNA was isolated using Trizol.

treatment_protocol: Cells were treated or not with PP242 at 2.5uM for 12 hours

tag: cell type

value: Pancreatic cancer cells


title: Total 242 #4

description:
Total RNA
MiaPaca-2 cells treated with pp242 for 12h followed by extraction of cytosolic RNA.


title: Total 242 #3

source_name: MiaPaca-2 cells treated with pp242 for 12h followed by extraction of cytosolic RNA.


title: KASUMI1_ETOP_REP2


title: 273TX


title: KASUMI1_CTR_REP3


title: Poly 242 #2

source_name: MiaPaca-2 cells treated with pp242 for 12h followed by extraction of polysome-associated RNA


title: KASUMI1_CTR_REP2


title: 242TX


title: KASUMI1_CTR_REP1


title: 259TX


title: MOLM13_CTR_REP1


title: HL60_ETOP_REP3


title: 107T-O

source_name: RCC organoid

value: RCC organoid

tag: material


title: 223TX


title: Total 242 #2


title: Poly 242 #4


title: 200TX


title: HL60_ETOP_REP2

value: AML


title: Total 242 #1


title: Poly 242  #1


title: 37T-O

tag: tumor identifier


title: Poly NT  #4

description:
polysomal RNA
MiaPaca-2 cells treated with vehicle (DMSO) for 12h followed by extraction of polysome-associated RNA

tag: cell line


title: HL60_ETOP_REP1

value: Etoposide (IC50)


title: 184TX

tag: (z)-4-oh-tam + 3-oh-tam


title: 60T-O

source_name: MRT organoid

value: MRT organoid


title: 171TX

tag: (z)-endoxifen + 3-oh-ndm-tam


title: HL60_CTR_REP3


title: 103T-O


title: PMC-O

description: PMC-O

value: PMC


title: HL60_CTR_REP2

value: Untreated


title: Poly NT  #3

source_name: MiaPaca-2 cells treated with vehicle (DMSO) for 12h followed by extraction of polysome-associated RNA


title: 119M-T

source_name: Wilms tumor

value: Wilms tumor


title: 102T-T


title: MOLM13_CTR_REP3


title: 155TX

tag: tamoxifen


title: 98T-T


title: 272TX

tag: ndm-tam


title: HL60_CTR_REP1


title: 258TX

tag: (e)-endoxifen


title: F36P_ETOP_REP3


title: 97T-T


title: 241TX

tag: tam-n-oxide


title: F36P_ETOP_REP2


title: Poly NT  #2


title: Total NT  #3

description:
Total RNA
MiaPaca-2 cells treated with vehicle (DMSO) for 12h followed by extraction of cytosolic RNA.


title: 220TX

tag: tam-n-gluc


title: F36P_ETOP_REP1


title: Total NT #1

source_name: MiaPaca-2 cells treated with vehicle (DMSO) for 12h followed by extraction of cytosolic RNA.


title: Total NT #2


title: 198TX

tag: (e)-a-oh-tam


title: Total NT  #4


title: Poly NT  #1


title: hnRNP M KD Salmonella-Typhimurium infected rep 2

city: Bryan

first: Robert

middle: O

last: Watson

state: TX

address: 8447 Riverside Pkwy

department: Microbial Pathogenesis and Immunology

institute: Texas A&M Health Science Center

data_processing:
Sample libraries have been sequenced using the Illumina HiSeq 4000.
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings.
Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench Transcriptome RNA-Seq Analysis program.
Genome_build: GRCm38 Ensembl
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: All cells were incubated at 37°C in 5% CO2 and were plated in 12-well tissue culture treated dishes at 7.5x10^5 and incubated for 12hrs before infecting cells with Salmonella-Typhimuirum. After Salmonella-Typhimuirum infection, RNA was collected with Trizol at 4hrs from infected cells and uninfected cells.

extract_protocol:
Cells were plated in a 12 well tissue culture treated dish at 7.5x10^5. RNA was harvested using Trizol reagent. Direct-zol RNA Miniprep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW 264.7 macrophages (ATCC) (originally isolated from male BALB/c mice) were cultured at 37°C with a humidified atmosphere of 5% CO2 in DMEM (Thermo Fisher) with 10% FBS (Sigma Aldrich) 0.5% HEPES (Thermo Fisher).

value: RAW 264.7 macrophages

value: macrophages

tag: genotype

value: hnRNP M shRNA Knockdown


title: hnRNP M KD Salmonella-Typhimurium infected rep 3


title: 85T-T


title: F36P_CTR_REP3


title: F36P_CTR_REP2


title: 88T-T


title: 78T-O


title: 183TX

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: hnRNP M KD Salmonella-Typhimurium infected rep 1

tag: tissue


title: 170TX

tag: patient diagnosis


title: 64T-T


title: SCR Control Salmonella-Typhimurium infected rep 3

value: scramble control shRNA Knockdown


title: 83T-T


title: 153TX


title: 293T miR-122

city: Nanjing

first: Yan

last: Zeng

address: No.1, Weigang

institute: Nanjing Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human.GRCh38 whole genome using hisat2-2.0.0.
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: human.GRCh38
Supplementary_files_format_and_content: abundance measurements

source_name: miR-122 transfected 293T cells

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS mRNA-seq v2 Library Prep Kit for Illumina (NR601-01) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: miR-122 overexpression

tag: time point

value: 48h of transfection


title: 293T miR-124

source_name: miR-124 transfected 293T cells

value: miR-124 overexpression


title: SCR Control Salmonella-Typhimurium infected rep 2


title: 257TX

value: blood

value: breast cancer


title: 293T miR-1

source_name: miR-1 transfected 293T cells

value: miR-1 overexpression


title: 271TX


title: hnRNP M KD Uninfected rep 3


title: 57T-T

tag: material

value: Frozen

tag: tumor identifier


title: 293T control

source_name: negative control transfected 293T cells

tag: cell line

value: negative control


title: 239TX

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam


title: 94T-T


title: hnRNP M KD Uninfected rep 2


title: 52T-T


title: 218TX

tag: tamoxifen

tag: ndm-tam


title: HKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 3

city: Adelaide

first: Sriganesh

last: Srihari

state: SA

address: North Terrace

department: Infection and Immunity

country: Australia

institute: South Australian Health and Medical Research Institute

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 machine using a v2 High Output 100 cycle Kit (1x 100 bp SR). The quality and number of reads for each sample were assessed with FastQC v0.11.3. Adaptors were trimmed from reads, and low quality bases with Phred scores < 28 were trimmed from ends of reads, using Trimgalore v0.4.0. Trimmed reads of less than 20 nucleotides were discarded.
Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using TopHat v2.1.0 (Kim et al., 2013),allowing for up to two mismatches. Reads not uniquely aligned to the genome were discarded. HTSeq-count v0.6.0 (Anders et al., 2015) was used in the union model to assign uniquely aligned reads to Ensembl Hg38.86-annotated genes.
Data were normalized across libraries by the trimmed mean of M-values (TMM) normalization method, implemented in the R v3.2.1., Bioconductor package, EdgeR v3.10.2 (Robinson et al., 2010). Only genes that had at least 5 reads per million in at least one cell-line were analysed for evidence of differential gene expression. Differentially expressed genes were identified using the glm model implemented in EdgeR (FDR < 0.05).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample

growth_protocol: All cell lines were maintained in DMEM (Dulbecco’s modified Eagle’s medium, Gibco) supplemented with 10% (v/v) foetal calf serum (Assay matrix), 2mM L-glutamine (Gibco) and incubated in a humidified atmosphere of 5% CO2 at 37ᵒC. Cells were routinely split every 2-3 days.

extract_protocol:
RNA was isolated from the cell lines at 0, 15, 30, 60, 90 and 120 mins post-stimulation using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA was extracted from 3 biological replicates at each timepoint. An ethanol precipitation was used to further purify the RNA. Briefly, 0.1x final volume of 3 M sodium acetate, 20 µg glycogen (Life Technologies) and 2.5X 100% ethanol was used to resuspend RNA. RNA was precipitated at -80ᵒC for a minimum of 2 hours. The precipitant was spun at 13,000 x g for 30 min at 4 ᵒC. The supernatant was removed and the pellet was washed with twice with 75% ethanol, before resuspending in a final volume of 50 µL of RNase-free water. All RNA samples were treated with DNase (Ambion) to remove any contaminating DNA from the purified RNA. Briefly, 2 Units/µL of rDNase I enzyme was added to RNA in 10x DNase I Buffer and incubated at 37ᵒC for 30 min. The reaction was inactivated by addition of DNase Inactivation Reagent and purified DNA-free RNA was extracted from the resultant supernatant. RNA concentration was determined by spectrophotometry on the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and by Qubit assay (Thermo Fisher Scientific). RNA integrity was assessed using a Bioanalyzer 2100 (Agilent).
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the NEXTflex Rapid Directional mRNA-Seq library Kit from BIOO Scientific (Austin, Texas) as per the manufacturer’s instructions (v14.10), by staff at the SAHMRI David R. Gunn Genomics facility. Briefly, 200ng of total RNA was polyA selected and the mRNA chemically fragmented prior to reverse transcription and second strand cDNA synthesis using dUTP. The resultant cDNA was poly adenylated before the ligation of Illumina-compatible barcoded sequencing adapters. The cDNA libraries were treated with UDG to degrade the second strand and PCR amplified for 15 cycles prior to assessment using a TapeStation 2200 (Agilent) for quality and Qubit fluorescence assay for quantification. In total, 36 cDNA libraries (2 cell lines X 6 time-points X 3 replicates per timepoint) were generated for sequencing.

treatment_protocol: For the stimulation studies, cells were seeded onto 6 well plates until confluent. Cells were then starved for 18 hours and subsequently stimulated with transforming growth factor alpha (TGF-α) (0.01 µg/mL, Abcam).

value: Colon

value: HKE3 colorectal cancer cells

tag: treatment


title: 51T-T


title: F36P_CTR_REP1

source_name: AML

tag: cell type

value: AML


title: hnRNP M KD Uninfected rep 1


title: HKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 2


title: 197TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam


title: Hepatocellular carcinoma YSH048

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

description: Methylation data from early HCC.

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina scan protocol.

data_processing: Illumina BeadStudio software.

label: Cy5 and Cy3

source_name: Hepatocellular carcinoma

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted from fresh frozen tissue with the DNeasy Blood & Tissue Kit (Qiagen).

tag: tissue

value: Liver

tag: disease stage

value: eHCC


title: 182TX

tag: patient diagnosis

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Hepatocellular carcinoma YSH047

description: Methylation data from early HCC.


title: HKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 1


title: SCR Control Uninfected rep 2

value: RAW 264.7 macrophages

tag: genotype


title: High grade dysplastic nodules YSH044

description: Methylation data from dysplastic nodules.

source_name: High grade dysplastic nodules


title: 80T-T

value: Wilms tumor

tag: material

tag: tumor identifier


title: HKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 3

tag: cell line

value: 90 mins post stimulation with TGF-alpha


title: SCR Control Uninfected rep 3

value: macrophages

value: scramble control shRNA Knockdown


title: 107T-T

source_name: RCC tumor

value: RCC tumor


title: HKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 2


title: 86T-T


title: 152TX

source_name: blood

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen


title: HKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 1

tag: treatment


title: SCR Control Salmonella-Typhimurium infected rep 1


title: 270TX

tag: ndm-tam

tag: (e)-endoxifen


title: HKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 3

value: 60 mins post stimulation with TGF-alpha


title: Hepatocellular carcinoma YSH039

description: Methylation data from early HCC.


title: 103T-T

source_name: MRT tumor

value: MRT tumor


title: High grade dysplastic nodules YSH045


title: Lymph Node Metastatic Site [P9_M1]

city: London

first: Matthew

last: Davies

address: Fulham Road

country: United Kingdom

institute: Institute of Cancer Research

description: Biotinylated oligo hybridised overnight

hyb_protocol: DNA was processed with Molecular Inversion Probe technology. Samples underwent exonuclease addition and PCR amplified, fragmented, labeled and hybridized to array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the OncoScan® FFPE Assay Kit

data_processing:
Samples of 0.2-0.5 ug of DNA were analyzed by the Affymetrix service laboratory on the OncoScan® FFPE Assay Kit that is optimised for the analysis of FFPE samples. Nexus software was used to center the data to probes located in diploid regions according to the user manual and raw log-ratio (LogR) and B-allele frequency data from 217,612 probes were extracted. LogR data was winorised to remove outliers and joint segmentation of all samples within a patient was carried using the copynumber R package. In order to convert segmented logR data into integer copy number data, we first generated frequency plots of the segmented log ratio data by binning the whole genome into 50,000 bp windows. A frequency distribution of this data was plotted with a smooth bandwidth of 0.01.
LogR and B-Allele frequency data from OncoScan® FFPE Assay Kit

source_name: GEA Patient 9

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from samples using the QIAamp DNA FFPE Tissue Kit. DNA quality and quantity was assessed using Qubit and agarose gel electrophoresis

tag: region

value: Lymph Node Metastatic Site

value: gastric adenocarcinoma


title: 238TX

value: blood

value: breast cancer

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam


title: HKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 2

tag: tissue

value: Colon


title: Invasive Front [P9_R3]

description: Biotinylated oligo hybridised overnight

value: Invasive Front


title: Liver cirrhosis YSH040

description: Methylation data from liver cirrhosis.

source_name: Liver cirrhosis

tag: disease stage

value: LC


title: 37T-T

value: Frozen


title: 48T-T


title: High grade dysplastic nodules YSH042

value: Liver


title: 216TX

tag: patient diagnosis

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: High grade dysplastic nodules YSH046


title: 169TX


title: Lateral Margin [P9_R2]

description: Biotinylated oligo hybridised overnight

value: Lateral Margin


title: 256TX


title: HKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 1

value: HKE3 colorectal cancer cells


title: 196TX


title: HKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 3

value: 30 mins post stimulation with TGF-alpha


title: Main Mass [P9_R1]

description: Biotinylated oligo hybridised overnight

value: Main Mass


title: High grade dysplastic nodules YSH036


title: 181TX


title: Omental Metastatic Site [P8_M2]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 8

value: Omental Metastatic Site


title: 168TX


title: HKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 1


title: Lymph Node Metastatic Site [P8_M1]

description: Biotinylated oligo hybridised overnight


title: HKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 2


title: 151TX


title: HKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 3

value: 15 mins post stimulation with TGF-alpha


title: Hepatocellular carcinoma YSH037

description: Methylation data from progressed HCC.

value: HCC


title: Invasive Front [P8_R3]

description: Biotinylated oligo hybridised overnight


title: 78T-T

value: MRT tumor

tag: material

tag: tumor identifier


title: 269TX

tag: (z)-4-oh-tam + 3-oh-tam


title: Hepatocellular carcinoma YSH031

description: Methylation data from early HCC.

value: eHCC


title: High grade dysplastic nodules YSH034


title: HKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 2

tag: cell line


title: 60T-T


title: Lateral Margin [P8_R2]

description: Biotinylated oligo hybridised overnight

value: gastric adenocarcinoma


title: SCR Control Uninfected rep 1

value: RAW 264.7 macrophages

value: macrophages

tag: genotype

value: scramble control shRNA Knockdown


title: Main Mass [P8_R1]

description: Biotinylated oligo hybridised overnight


title: HKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 1

value: Colon

tag: treatment


title: Unstimulated HKE3 cells (time 0 mins) - Replicate 3

value: unstimulated


title: 236TX

value: blood

value: breast cancer

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: Lymph Node Metastatic Site [P7_M1]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 7

tag: region

value: Lymph Node Metastatic Site


title: Hepatocellular carcinoma YSH030

description: Methylation data from progressed HCC.

value: Liver


title: 214TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc


title: Invasive Front [P7_R3]

description: Biotinylated oligo hybridised overnight

value: Invasive Front

tag: tissue


title: Unstimulated HKE3 cells (time 0 mins) - Replicate 2

value: HKE3 colorectal cancer cells


title: Lateral Margin [P7_R2]

description: Biotinylated oligo hybridised overnight

value: Lateral Margin


title: Liver cirrhosis YSH029

description: Methylation data from liver cirrhosis.

tag: disease stage

value: LC


title: 195TX

tag: patient diagnosis

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: Hepatocellular carcinoma YSH028

description: Methylation data from early HCC.


title: 180TX

tag: z-endoxifen ratio


title: HCT116 cells 120 mins post stimulation with TGF-alpha - Replicate 3

value: HCT116 colorectal cancer cells


title: HCT116 cells 120 mins post stimulation with TGF-alpha - Replicate 2


title: Main Mass [P7_R1]

description: Biotinylated oligo hybridised overnight

value: Main Mass


title: 255TX

tag: (z)-4-oh-tam + 3-oh-tam


title: Lymph Node Metastatic Site [P6_M1]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 6


title: Unstimulated HKE3 cells (time 0 mins) - Replicate 1

tag: cell line


title: 167TX


title: Hepatocellular carcinoma YSH026

description: Methylation data from progressed HCC.

value: HCC


title: High grade dysplastic nodules YSH038


title: HCT116 cells 120 mins post stimulation with TGF-alpha - Replicate 1


title: HCT116 cells 90 mins post stimulation with TGF-alpha - Replicate 3

value: 90 mins post stimulation with TGF-alpha


title: 128TX

description:
processed data file:
Plate_1_Full_Data_Table.txt


title: 150TX


title: HCT116 cells 90 mins post stimulation with TGF-alpha - Replicate 2


title: Lateral Margin [P6_R2]

description: Biotinylated oligo hybridised overnight

value: gastric adenocarcinoma


title: Main Mass [P6_R1]

description: Biotinylated oligo hybridised overnight


title: Invasive Front [P6_R3]

description: Biotinylated oligo hybridised overnight


title: Hepatocellular carcinoma YSH022

description: Methylation data from progressed HCC.


title: Hepatocellular carcinoma YSH020

description: Methylation data from early HCC.

value: eHCC


title: HCT116 cells 90 mins post stimulation with TGF-alpha - Replicate 1


title: 149TX


title: Omental Metastatic Site [P5_M2]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 5

value: Omental Metastatic Site


title: Hepatocellular carcinoma YSH019

description: Methylation data from progressed HCC.


title: 93TX


title: HCT116 cells 60 mins post stimulation with TGF-alpha - Replicate 3

value: Colon

value: 60 mins post stimulation with TGF-alpha


title: High grade dysplastic nodules YSH014


title: 108TX

value: blood


title: Lymph Node Metastatic Site [P5_M1]

description: Biotinylated oligo hybridised overnight


title: 72TX

value: breast cancer


title: Lateral Margin [P5_R2]

description: Biotinylated oligo hybridised overnight


title: Liver cirrhosis YSH013

description: Methylation data from liver cirrhosis.


title: 53TX


title: High grade dysplastic nodules YSH012


title: Main Mass [P5_R1]

description: Biotinylated oligo hybridised overnight


title: 40TX


title: ONC201, U87 glioblastoma cells

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from U87 glioblastoma cells treated with ONC201.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0).

source_name: U87 glioblastoma cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Human glioma cells (U87) were cultured in DMEM (Corning, New York, USA) supplemented with 10% FBS at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hiden, Germany) according to the manufacturer's protocol.

treatment_protocol: After one day of cell seeding, U87 cells were treared with 10 µM of ONC201 for 72 hours in DMEM supplemented with 1.5% FBS.

value: U87 glioblastoma cells


title: Invasive Front [P4_R3]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 4


title: DMSO, U87 glioblastoma cells

description: Gene expression data from U87 glioblastoma cells treated with DMSO.

value: DMSO


title: HCT116 cells 60 mins post stimulation with TGF-alpha - Replicate 2


title: HCT116 cells 60 mins post stimulation with TGF-alpha - Replicate 1


title: HCT116 cells 30 mins post stimulation with TGF-alpha - Replicate 2

value: 30 mins post stimulation with TGF-alpha


title: HCT116 cells 30 mins post stimulation with TGF-alpha - Replicate 1


title: 21TX


title: HCT116 cells 30 mins post stimulation with TGF-alpha - Replicate 3


title: Lymph Node Metastatic Site [P4_M1]

description: Biotinylated oligo hybridised overnight

value: Lymph Node Metastatic Site


title: Lateral Margin [P4_R2]

description: Biotinylated oligo hybridised overnight

value: Lateral Margin


title: Hepatocellular carcinoma YSH024

description: Methylation data from early HCC.

value: Liver


title: High grade dysplastic nodules YSH006


title: Hepatocellular carcinoma YSH021

description: Methylation data from early HCC.


title: 144TX


title: HCT116 cells 15 mins post stimulation with TGF-alpha - Replicate 3

value: HCT116 colorectal cancer cells

value: 15 mins post stimulation with TGF-alpha


title: Undifferentiated NCH690

description: Gene expression data from undifferentiated NCH644 cells.

source_name: NCH644 cells

growth_protocol: Human stem cell like glioma cells (NCH644 and NCH690) were cultured in GBM-MG medium (CLS, Heidelberg, Germany) and their differentiated cells were cultured in DMEM (Corning, New York, USA) supplemented with 10% FBS at 37°C in 5% CO2.

treatment_protocol: Differentiation of NCH644 and NCH690 was performed by incubating the cells in DMEM containing 10% FBS and 10 µM retinoic acid or in DMEM containg 10% FBS, respectively.

value: Undifferentiated NCH690

tag: state

value: undifferentiated


title: 127TX


title: Main Mass [P4_R1]

description: Biotinylated oligo hybridised overnight

value: Main Mass

value: gastric adenocarcinoma


title: Differentiated NCH690

description: Gene expression data from differentiated NCH690 cells.

source_name: NCH690 cells

value: Differentiated NCH690

value: differentiated


title: Undifferentiated NCH644

value: Undifferentiated NCH644


title: Differentiated NCH644

value: Differentiated NCH644


title: 107TX

value: blood

value: breast cancer


title: Liver cirrhosis YSH005

description: Methylation data from liver cirrhosis.

value: LC


title: Lymph Node Metastatic Site [P3_M1]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 3


title: High grade dysplastic nodules YSH002


title: 92TX


title: 71TX


title: Invasive Front/Metastatic [P3_R3M]

description: Biotinylated oligo hybridised overnight

value: Invasive Front/Metastatic


title: SYN library DNA plasmid pool

city: St. Louis

first: Dana

middle: M

last: King

state: Missouri

address: 4523 CLAYTON AVE, CB 8510

department: Department of Genetics

institute: Washington University

description: Demultiplexing barcode sequence of 'TCAGTCT' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library

data_processing:
All raw reads (SRA accession number SRR7515851) were process regardless of quality scores. Briefly, reads with the expected in-line multiplexing barcode sequence for each replicate followed by the restriction site used for library construction were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were then written to file along with the barcode's raw read count, all other counts were discarded.
Supplementary_files_format_and_content: Processed count text files include read counts in first column, barcode sequence in second column, and the putative regulatory element/sequence identifier in the last column.

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: RW4 mouse ESCs (ATCC SCRC-1018) were cultured on on 2% gelatin coated plates in standard media (DMEM, 10% fetal bovine serum, 10% newborn calf serum, nucleoside supplement, 1000 U/ml leukemia inhibitory factor (LIF), and 0.1 uM B-mercaptoethanol)

extract_protocol:
Total RNA was extracted from approximately 9 million cells using the PureLink RNA mini kit (Life Technologies) according to the manufactor's instructions, removing any residual DNA from the RNA pool using TURBO DNA-free kit (Life Technologies).
First strand cDNA was prepared from total RNA using SuperScript RT III (Life Technologies) with oligo dT primers. Target library reporter sequences were amplified from cDNA and DNA pools using primers CF150, 'TACACCGTGGTGGAGCAGTA', and CF151b, 'AGCGTACTCGAGTTGTTAACTTGTTTATTGCAGCTT', followed by digestion with XbaI and XhoI (NEB). Digested amplicons were then ligated to custom Illumina adapters,each including an in-line barcode sequence to identify each sample. Ligated products were then further amplified using primers CF52, 'AATGATACGGCGACCACCGAG', and CF53, 'CAAGCAGAAGACGGCATACGA'.

treatment_protocol: Approximately 1 million RW.4 cells were seeded in 6-well plates and transfected with 3 ug of MPRA library plasmid (SYN or gWT/gMUT ) and 0.3 ug of CF128, a GFP control plasmid.

tag: strain background


title: Lateral Margin [P3_R2]

description: Biotinylated oligo hybridised overnight


title: Liver cirrhosis YSH001

description: Methylation data from liver cirrhosis.


title: HCT116 cells 15 mins post stimulation with TGF-alpha - Replicate 1

value: Colon

tag: treatment


title: gWT/gMUT library DNA plasmid pool

description: Demultiplexing barcode sequence of 'TTCCAAG' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library


title: HCT116 cells 15 mins post stimulation with TGF-alpha - Replicate 2


title: Liver cirrhosis YSH011

description: Methylation data from liver cirrhosis.


title: Unstimulated HCT116 cells (time 0 mins) - Replicate 2

value: unstimulated


title: 39TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen


title: Main Mass [P3_R1]

description: Biotinylated oligo hybridised overnight

tag: region


title: 52TX

tag: ndm-tam

tag: (e)-endoxifen


title: Unstimulated HCT116 cells (time 0 mins) - Replicate 3


title: Lymph Node Metastatic Site [P2_M1]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 2

value: Lymph Node Metastatic Site


title: Unstimulated HCT116 cells (time 0 mins) - Replicate 1

value: HCT116 colorectal cancer cells


title: 20TX

tag: tam-n-oxide

tag: tam-n-gluc


title: Main Mass 2 [P2_R1b]

description: Biotinylated oligo hybridised overnight

value: Main Mass 2

tag: tissue


title: vehicle control, U87 glioblastoma cells

description: Gene expression data from U87 glioblastoma cells treated with vehicle control.

growth_protocol: U87 MG (ATCC® HTB-14™) glioblastoma cells were cultured under normal complete medium (Ctr) or complete medium with 30nM Panobinostat (PbR) for 3 weeks. Cells were passaged when confluent.

extract_protocol: RNAs of the U87 cells in each culture medium were collected and extracted at the same time with RNeasy Mini Kit (Qiagen Cat No./ID: 74104).

treatment_protocol: U87 cells were cultured in complete medium with or without 30nM Panobinostat for 3 weeks.

value: U87 glioblastoma cells

value: vehicle control


title: 143TX

tag: patient diagnosis


title: ChIP_JASPer_gst_RNAi_2

city: Planegg-Martinsried

first: Christian

last: Albig

address: Großhaderner Strasse 9

department: Biomedical Center

institute: Ludwig-Maximilians-University Munich

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1).
To generate bigWig files, reads were extended to 150 bp and per base normalized genome coverage vectors were calculated as described in (Villa et al., 2016).
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files with coverage

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2‑DRSC (DGRC stock # 181) cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1 mg/mL streptomycin (Sigma‑Aldrich) at 26°C.

extract_protocol:
ChIP‑seq was performed as previously described (Albig et al., 2019). In brief, S2 cells (~1x10e8 cells) after RNAi were harvested and chilled on ice. Cells were cross‑linked with 1% formaldehyde for 55 min on ice and the reaction was stopped by adding glycine. Isolated nuclei were resuspended in RIPA (10 mM Tris/HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton‑X 100, 0.1%(v/v) SDS, 0.1% (v/v) DOC) at 1x10e8 cells/mL in 1 mL for shearing with Covaris AFA S220 using 12x12 tubes at 100 W peak incident power, 20% duty factor and 200 cycles per burst for 25 min at 5°C to generate 150‑200 bp fragments. 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 200 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and icubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

treatment_protocol: RNAi against target genes in S2 was performed as previously described (Albig et al., 2019). In brief, double-stranded RNA fragments (dsRNA) were generated with MEGAscript kit (Thermo Fisher) from PCR products. Cells were incubated with 4.2 µg dsRNA at 6.3 µg/mL serum free medium per 1x10e6 cells (12x10e6 cells in 75 cm^2 flask for ChIP‑seq) for 1 hour. Two volumes of growth medium were added and cells were incubated for 5 days at 26°C. Then, 1x of initial volume (6‑well plate) or 0.75x of initial volume (75 cm2 flask) of growth medium was added and cells were incubated for further 2 days at 26°C.

tag: gender

value: male

value: gst RNAi

tag: antibody

value: JASPer (GP13)


title: panobinostat, U87 glioblastoma cells

description: Gene expression data from U87 glioblastoma cells treated with panobinostat.

value: panobinostat


title: Hepatocellular carcinoma YSH008

description: Methylation data from early HCC.

source_name: Hepatocellular carcinoma

value: Liver

tag: disease stage

value: eHCC


title: Hepatocellular carcinoma YSH004

description: Methylation data from progressed HCC.

value: HCC


title: Invasive Front [P2_R3]

description: Biotinylated oligo hybridised overnight

value: Invasive Front

value: gastric adenocarcinoma


title: 126TX

source_name: blood

value: blood

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Old rep5

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description:
data.counts.csv
O_5

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
The raw reads were quality-trimmed and filtered for low complexity with the tool preprocess from the SGA assembler v0.10.13 (-q 30 -m 50 --dust) .
The passed reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 85) with TopHat2 v2.1.0.
All reads mapping uniquely to an Ensembl gene were counted using FeatureCounts v1.5.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

source_name: sciatic nerve

extract_protocol:
Sciatic nerves were homogenized in peqGOLD TriFast™ (VWR Peqlab, Darmstadt, Germany), total RNA was isolated from the aqueous phase with the PureLink RNA Mini Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA) accoding to manufactures instructions.
Preparation of libraries was done using Illumina’s TruSeq stranded mRNA kit following the manufacturer’s instruction.

treatment_protocol: Six intact (non-injured) sciatic nerves each from young (3 months) and old C57BL6 mice (20 months) were dissected and used for Anaylsis.

tag: strain

tag: Sex

value: female

tag: age

value: 20 months

value: sciatic nerve


title: 105TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen


title: ChIPseq.s2.jasper_4

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1).
To generate bigWig files, reads were extended to 150 bp and per base normalized genome coverage vectors were calculated as described in (Villa et al., 2016) and raw per base genome coverage vectors were generated by summing up all reads and normalizing to million mapped reads (rpm).
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files with coverage

growth_protocol: S2‑DRSC (DGRC stock # 181), Kc167 (DGRC stock # 1) cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1 mg/mL streptomycin (Sigma‑Aldrich) at 26°C.

extract_protocol:
ChIP-seq was performed on MNase digested chromatin as described previously (Straub et al., 2008 and Kasinathan et al., 2013) with some modifications. Cells were fixed in 1% formaldehyde for 1 min at 26°C, followed by quenching with 125 mM glycine and washing with PBS. Nuclei were released by resuspending in TM2+ with NP-40. MNase digestion was performed in TM2+IC using 4U MNase (Sigma Aldrich, resuspended in EX50 (Bonte & Becker, 1999)) in the presence of CaCl2 for 13 min at 37 °C. Reaction was stopped with EGTA and Triton-X-100, SDS, NaDOC and NaCl was added to final concentration as in RIPA Buffer. MNase digested chromatin was incubated for 1 h at 4°C while slight agitation and chromatin was solubilized by passing ten times through 27 G needle and centrifuged for 30 min at 15,000 g at 4°C. 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 200 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and icubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

tag: cell line

value: JASPer (GP14)


title: Main Mass [P2_R1a]

description: Biotinylated oligo hybridised overnight

tag: region

value: Main Mass


title: ChIPseq.s2.jasper_2


title: Old rep4

description:
data.counts.csv
O_4


title: Old rep2

description:
data.counts.csv
O_2


title: ChIPseq.s2.jasper_3


title: Old rep3

description:
data.counts.csv
O_3


title: 91TX

tag: ndm-tam

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc


title: Old rep6

description:
data.counts.csv
O_6

tag: tissue


title: Main Mass 2 [P1_R1b]

description: Biotinylated oligo hybridised overnight

source_name: GEA Patient 1

value: Main Mass 2


title: Lateral Margin [P2_R2]

description: Biotinylated oligo hybridised overnight

value: Lateral Margin


title: ChIPseq.s2.jasper_1

tag: gender

value: male

tag: antibody


title: 70TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (e)-a-oh-tam


title: Metastatic Site (perf. into colon) [P1_M2]

description: Biotinylated oligo hybridised overnight

value: Metastatic Site (perf. into colon)


title: 51TX

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Old rep1

description:
data.counts.csv
O_1

tag: strain

tag: Sex

tag: age


title: Young rep6

description:
data.counts.csv
Y_6

value: 3 months


title: Invasive Front [P1_R3]

description: Biotinylated oligo hybridised overnight


title: ChIPseq.kc.jasper_3

source_name: Kc cells

tag: cell line

value: Kc


title: Young rep5

description:
data.counts.csv
Y_5


title: ChIPseq.kc.jasper_2

value: JASPer (GP13)


title: ChIP_JASPer_gst_RNAi_3

tag: treatment

value: gst RNAi


title: Lateral Margin [P1_R2]

description: Biotinylated oligo hybridised overnight

tag: region


title: ChIPseq.kc.jasper_1


title: Young rep4

description:
data.counts.csv
Y_4


title: 18TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam

tag: (e)-endoxifen


title: Main Mass [P1_R1a]

description: Biotinylated oligo hybridised overnight

tag: tissue


title: 141TX

tag: tam-n-oxide

tag: tam-n-gluc


title: 124TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam


title: Young rep1

description:
data.counts.csv
Y_1


title: Young rep3

description:
data.counts.csv
Y_3


title: Young rep2

description:
data.counts.csv
Y_2


title: mtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T120_Rep3

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 machine using a v2 High Output 100 cycle Kit (1x 100 bp SR). The quality and number of reads for each sample were assessed with FastQC v0.11.3. Adaptors were trimmed from reads, and low quality bases with Phred scores < 28 were trimmed from ends of reads, using Trimgalore v0.4.0. Trimmed reads of less than 20 nucleotides were discarded.
Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using TopHat v2.1.0 (Kim et al., 2013),allowing for up to two mismatches. Reads not uniquely aligned to the genome were discarded. HTSeq-count v0.6.0 (Anders et al., 2015) was used in the union model to assign uniquely aligned reads to Ensembl Hg38.86-annotated genes.
Data were normalized across libraries by the trimmed mean of M-values (TMM) normalization method, implemented in the R v3.2.1., Bioconductor package, EdgeR v3.10.2 (Robinson et al., 2010). Only genes that had at least 5 reads per million in at least one cell-line were analysed for evidence of differential gene expression. Differentially expressed genes were identified using the glm model implemented in EdgeR (FDR < 0.05).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file includes read counts for each sample

value: Colon

value: mtHKE3 colorectal cancer cells

tag: genotype

value: mutant-KRAS

value: TGF-alpha

tag: time

value: 120 mins


title: RNAseq.s2.jasper5.batch1

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using STAR (Dobin et al., 2013) version 2.6.0 (parameters --quantMode TranscriptomeSAM GeneCounts, --outFilterMultimapNmax 1).
Gene quantification was performed using RSEM (Li and Dewey, 2011) version 1.3.0 (parameters –bam, --paired-end, --forward-prob 0).
Genome_build: BDGP6
Supplementary_files_format_and_content: tsv with reads per gene

extract_protocol:
2 million S2 cells or Kc cells after RNAi treatment were resuspended in Trizol and RNA was purified using the RNeasy Mini Kit (QIAGEN).
1 µg of purified total RNA’s was used for rRNA depletion using Ribo-Zero Gold rRNA Removal Kit (Illumnia, MRZG 12324) or NEBNext rRNA Depletion Kit (NEB, E6310). Library preparation was done according to the manufacturer’s instructions with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760).

treatment_protocol: For RNAi against target genes in S2 and Kc cells for RNA-seq, cells were washed with serum‑free medium and 10 µg dsRNA per 10^6 cells at a concentration of 10 µg/mL in serum‑free medium (10^6 cells in 6‑well plate) was added, incubated for 10 min at room temperature (RT) with slight agitation and further 50 min at 26°C. Two volumes of complete growth medium were added and cells were incubated for 3 days at 26°C. At day 3, cells were split, and reseeded and retreated as at day 1. Cells were incubated for further 4 days at 26°C.

tag: gender

value: jasper RNAi


title: mtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T120_Rep2


title: 66TX

value: blood

value: breast cancer

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: RNAseq.s2.jasper8.batch2

tag: cell line

tag: treatment


title: 88TX

tag: (z)-endoxifen + 3-oh-ndm-tam


title: mtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T120_Rep1


title: 50TX

tag: tamoxifen


title: RNAseq.kc.jasper4.batch2

value: female


title: RNAseq.kc.jasper3.batch2


title: RNAseq.kc.jasper2.batch1


title: mtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T90_Rep1

value: 90 mins


title: mtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T90_Rep2


title: 36TX

tag: ndm-tam


title: RNAseq.s2.jasper9.batch2


title: cancer, hepatic duct bifurcation site, ECCA-1

city: Seoul

first: HONG JOO

last: KIM

address: 29, Saemunan-Ro, Jongno-Gu

institute: Kangbuk Samsung Hospital

description: miRNA

hyb_protocol: Hybridizations were performed with GeneChip® Hybridization, Wash, and Stain Kit (P/N 900720, Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Affymetrix 7G scanner and miRNA QCtool were used to scan each microarray chip and to determine the signal intensity.

data_processing: RMA-DABG, Cluster 3.0, TreeView software, and TargetScan 5.1 were used to normalize and analyze miRNA expression levels.

label_protocol: 1 μg sample of total RNA was labeled with GeneChip® One-Cycle Target Labeling and Control Reagents (P/N 900493, Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Human hepatic duct bifurcation site cancer cell line SNU-1196 (KCLB No. 01196, population doubling time 48h), and human common bile duct cancer cell line SNU-245 (KCLB No. 00245, population doubling time 54h) were maintained in RPMI1640 medium supplemented with L-glutamine (300mg/L), 25mM HEPES, 25mM NaHCO3 (90%) and 10 % heat inactivated fetal bovine serum (FBS). Normal human biliary epithelial cell (NHBEC) lines were established by primary culture of normal extrahepatic bile duct epithelium obtained from surgically resected specimens and cultured in DMEM/F12 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with fetal bovine serum (CellGro, Manassas, VA, USA), penicillin/streptomycin, vitamin solution, MEM solution, CD lipid concentrate, L-glutamine, soybean trypsin inhibitor, insulin/transferrin/selenium-A, bovine pituitary extract, epidermal growth factor, 3,3′5-triiodo-L-thyronine, dexamethasone, and forskolin.

extract_protocol: Total RNA extraction was performed using RecoverAll™ Total Nucleic Acid Isolation Kit (AM1975, Life technologies, Carlsbad, CA, USA).

tag: cell population doubling time


title: cancer, bile duct, ECCA-2

description: miRNA

source_name: human common bile duct cancer cell

treatment_protocol: Human hepatic duct bifurcation site cancer cell line SNU-1196 (KCLB No. 01196, population doubling time 48h), and human common bile duct cancer cell line SNU-245 (KCLB No. 00245, population doubling time 54h) were maintained in RPMI1640 medium supplemented with L-glutamine (300mg/L), 25mM HEPES, 25mM NaHCO3 (90%) and 10 % heat inactivated fetal bovine serum (FBS). Normal human biliary epithelial cell (NHBEC) lines were established by primary culture of normal extrahepatic bile duct epithelium obtained from surgically resected specimens and cultured in DMEM/F12 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with fetal bovine serum (CellGro, Manassas, VA, USA), penicillin/streptomycin, vitamin solution, MEM solution, CD lipid concentrate, L-glutamine, soybean trypsin inhibitor, insulin/transferrin/selenium-A, bovine pituitary extract, epidermal growth factor, 3,3′5-triiodo-L-thyronine, dexamethasone, and forskolin.


title: 38TX

tag: tissue

tag: (e)-endoxifen


title: RNAseq.s2.jasper4.batch1


title: mtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T90_Rep3


title: normal, biliary epithelial cell, NHBEC

description: miRNA

source_name: human biliary epithelial cell

tag: cell type

value: primary culture of normal extrahepatic bile duct epithelium obtained from surgically resected specimens


title: mtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T60_Rep2

value: 60 mins


title: 15TX

tag: patient diagnosis

tag: tam-n-oxide

tag: tam-n-gluc


title: 104TX

tag: (z)-4-oh-tam + 3-oh-tam


title: ChIPseq.s2.msl3_jil2_3

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1) and to D. virilis FlyBase release r1.07_FB2018_05 reference genome using Bowtie with standard settings.
To generate bigWig files, reads were extended to 150 bp and per base genome coverage vectors normalized to the sum of D. virilis genome coverage vectors multiplied by 20 to adjust for difference in cell number were calculated as described in (Villa et al., 2016).
Genome_build: BDGP6
Supplementary_files_format_and_content: *bw: bigWig files with coverage.

extract_protocol:
For ChIP-seq on MNase-digested chromatin in combination with mild sonication, S2 cells (~3 * 10^8 cells) after RNAi treatment were cross‑linked with 1% formaldehyde for 8 min at room temperature and the reaction was stopped by adding glycine. 5% 79f7Dv3 cells, processed as described for S2 cells without RNAi treatment, relative to S2 cells were added. Isolated nuclei were resuspended in RIPA (10 mM Tris/HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton‑X 100, 0.1%(v/v) SDS, 0.1% (v/v) DOC) supplemented with PI and 2 mM CaCl2 at 7 * 10^7 cells/mL and digested in 1 mL aliquots by adding 0.6 U MNase (Sigma Aldrich), resuspended in EX50 at 0.6 U/µL (Bonte and Becker, 1999), and incubating at 37°C for 35 min with slight agitation. The reaction was stopped by adding 10 mM EGTA and placing on ice. Digested chromatin was sheared with Covaris AFA S220 using 12x12 tubes at 50 W peak incident power, 20% duty factor and 200 cycles per burst for 8 min at 5°C. Subsequent steps were performed as described in (Albig et al., 2019). In brief, 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 300 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and incubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

treatment_protocol: RNAi against target genes in S2 was performed as previously described (Albig et al., 2019). In brief, double-stranded RNA fragments (dsRNA) were generated with MEGAscript kit (Thermo Fisher) from PCR products. Cells were incubated with 4.2 µg dsRNA at 6.3 µg/mL serum free medium per 1x10^6 cells (12x10^6 cells in 75 cm^2 flask for ChIP‑seq) for 1 hour. Two volumes of growth medium were added and cells were incubated for 5 days at 26°C. Then, 0.75x of initial volume (75 cm2 flask) of growth medium was added and cells were incubated for further 2 days at 26°C.

tag: gender

value: Male

value: jil-1_2 RNAi

tag: chip antibody

value: MSL3 (GP)


title: mtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T60_Rep1

tag: genotype

tag: time


title: ChIPseq.s2.msl3_jil2_2

tag: cell line


title: 140TX

description:
processed data file:
Plate_1_Full_Data_Table.txt

data_processing:
no data processing was applied
Processed data files include: Genotype: AA,AB,BB,or NC (no call). The first 10 columns of  *Full_Data_Table.txt files contain info about probes, processed values start at 11th column.

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: aortic_TAA_rep19

city: Luxembourg

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: Labeled miRNAs were hybridized to Agilent G3 Human miRNA Microarray (G4872A) overnight at 55°C. After hybridization, microarrays were washed, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent high-resolution Scanner (G2565C) using one color scan setting for 8x60k array slides (Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters. Data was normlised using RMA (Robust Microarray Analysis).

source_name: aortic median from TAA patient 19

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA using miRNA Complete Labeling and Hyb kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using miRVana kit (Life technologies), according to provider recommendations. Concentration of RNA samples were checked using a Nanodrop spectrophotometer.

treatment_protocol: Aortic media were recovered from aortic biopsies and directly frozen at -80°C for long term storage. Aortic media were thawed and approximatively 45 mg of aortic media were crushed in Lysis Binding Buffer (Ambion) and frozen at -80°C for storage before RNA extraction.

value: aortic media

tag: disease state

value: Thoracic Aortic Aneurysm patient


title: 103TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: aortic_control_rep18

source_name: aortic media from healthy control 18

tag: tissue

value: male

value: healthy control


title: 123TX

tag: patient diagnosis

tag: (e)-endoxifen


title: mtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T30_Rep2

value: Colon

value: mtHKE3 colorectal cancer cells

value: mutant-KRAS

tag: treatment

value: 30 mins


title: aortic_control_rep19

source_name: aortic media from healthy control 19


title: mtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T60_Rep3

value: TGF-alpha


title: mtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T30_Rep1


title: 87TX

value: blood

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: tam-n-oxide

tag: tam-n-gluc


title: ChIPseq.s2.msl3_gst_2

tag: gender

value: gst RNAi

tag: chip antibody


title: aortic_TAA_rep17

source_name: aortic median from TAA patient 17


title: RNAseq.kc.jasper1.batch1

tag: cell line

value: Kc

value: female

value: jasper RNAi


title: ChIPseq.s2.jasper_jil2_3

value: Male

value: jil-1_2 RNAi

value: JASPer (GP13)


title: 64TX

tag: (e)-a-oh-tam


title: ChIPseq.s2.jasper_jil2_2


title: aortic_control_rep17

source_name: aortic media from healthy control 17

value: aortic media


title: 49TX

tag: (z)-a-oh-tam


title: mtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T15_Rep2

tag: genotype

tag: time

value: 15 mins


title: aortic_TAA_rep16

source_name: aortic median from TAA patient 16

value: male

tag: disease state

value: Thoracic Aortic Aneurysm patient


title: ChIPseq.s2.msl3_gst_3

value: MSL3 (GP)


title: mtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T15_Rep1

value: Colon

value: mtHKE3 colorectal cancer cells

value: mutant-KRAS


title: ChIPseq.s2.jasper_jil1_1

value: jil-1_1 RNAi


title: 14TX

value: blood

value: breast cancer

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: z-endoxifen ratio


title: aortic_TAA_rep18

source_name: aortic median from TAA patient 18

tag: tissue


title: ChIPseq.s2.jasper_gst_3

value: gst RNAi


title: aortic_control_rep15

source_name: aortic media from healthy control 15

value: healthy control


title: aortic_control_rep16

source_name: aortic media from healthy control 16


title: 138TX

tag: patient diagnosis

tag: ndm-tam

tag: (e)-endoxifen


title: ChIPseq.s2.jasper_gst_2

source_name: S2 cells

tag: treatment


title: mtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T30_Rep3

value: TGF-alpha

value: 30 mins


title: aortic_TAA_rep15

source_name: aortic median from TAA patient 15


title: Unstimulated mtHKE3 cells (time 0 mins) - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T0_Rep2

source_name: Unstimulated mtHKE3 cells (time 0 mins)

value: Unstimulated

value: 0 mins


title: Unstimulated mtHKE3 cells (time 0 mins) - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T0_Rep1


title: 102TX

source_name: blood

tag: (z)-4-oh-tam + 3-oh-tam

tag: tam-n-oxide

tag: tam-n-gluc


title: ChIPseq.s2.input_jil2_3

tag: cell line

tag: gender

value: Male

value: jil-1_2 RNAi

tag: chip antibody


title: wtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T120_Rep3

value: wtHKE3 colorectal cancer cells

tag: genotype

value: wildtype-KRAS

value: 120 mins


title: ChIPseq.s2.jasper_gfp_1

value: gfp RNAi

value: JASPer (GP13)


title: aortic_control_rep14

source_name: aortic media from healthy control 14

value: aortic media

value: male


title: 34TX

value: blood

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: 86TX

value: breast cancer

tag: (z)-endoxifen + 3-oh-ndm-tam


title: aortic_control_rep13

source_name: aortic media from healthy control 13

tag: disease state


title: aortic_TAA_rep14

source_name: aortic median from TAA patient 14

value: Thoracic Aortic Aneurysm patient


title: ChIPseq.s2.input_jil2_2


title: 120TX

tag: tamoxifen

tag: z-endoxifen ratio


title: wtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T120_Rep2

tag: tissue

value: Colon

tag: time


title: 62TX

tag: patient diagnosis

tag: ndm-tam

tag: (e)-endoxifen


title: ChIPseq.s2.input_jil1_1

tag: treatment

value: jil-1_1 RNAi


title: mtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T15_Rep3

value: mtHKE3 colorectal cancer cells

value: mutant-KRAS

value: TGF-alpha

value: 15 mins


title: wtHKE3 cells 120 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T120_Rep1


title: 48TX

tag: (z)-4-oh-tam + 3-oh-tam

tag: tam-n-oxide

tag: tam-n-gluc


title: wtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T90_Rep3

tag: cell line

value: 90 mins


title: Unstimulated mtHKE3 cells (time 0 mins) - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
mtHKE3_T0_Rep3

tag: genotype

value: Unstimulated

value: 0 mins


title: ChIPseq.s2.input_gst_2

tag: gender

value: Male

value: gst RNAi

tag: chip antibody


title: ChIPseq.s2.input_gfp_1

value: gfp RNAi


title: wtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T90_Rep1

value: wtHKE3 colorectal cancer cells

value: wildtype-KRAS


title: 13TX

value: blood

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: aortic_TAA_rep12

source_name: aortic median from TAA patient 12

value: aortic media

value: male

tag: disease state


title: 119TX

tag: tissue

value: breast cancer

tag: tamoxifen

tag: z-endoxifen ratio


title: aortic_control_rep12

source_name: aortic media from healthy control 12

value: healthy control


title: aortic_control_rep11

source_name: aortic media from healthy control 11

value: female


title: 137TX

tag: patient diagnosis

tag: ndm-tam


title: ChIPseq.s2.input_gst_3

tag: treatment


title: ChIPseq.s2.h4k16ac_jil2_2

value: jil-1_2 RNAi

value: H4K16ac (Millipore, 07-329)


title: ChIPseq.s2.h4k16ac_jil1_1

value: jil-1_1 RNAi


title: 101TX

tag: (z)-4-oh-tam + 3-oh-tam

tag: (e)-endoxifen


title: aortic_TAA_rep10

source_name: aortic median from TAA patient 10

value: Thoracic Aortic Aneurysm patient


title: 85TX

tag: tam-n-oxide

tag: tam-n-gluc


title: 33TX


title: aortic_TAA_rep11

source_name: aortic median from TAA patient 11


title: wtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T60_Rep2

value: Colon

tag: cell line

tag: genotype

value: TGF-alpha

tag: time

value: 60 mins


title: wtHKE3 cells 90 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T90_Rep2

value: 90 mins


title: ChIPseq.s2.h4k16ac_gst_3

tag: gender

value: Male

value: gst RNAi

tag: chip antibody


title: ChIPseq.s2.h4k16ac_gst_2


title: 60TX

description:
processed data file:
Plate_1_Full_Data_Table.txt

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: aortic_TAA_rep9

source_name: aortic median from TAA patient 9

tag: tissue

tag: disease state


title: aortic_control_rep9

source_name: aortic media from healthy control 9


title: ChIPseq.s2.h4k16ac_jil2_3


title: wtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T30_Rep2

value: wtHKE3 colorectal cancer cells

value: wildtype-KRAS

value: 30 mins


title: ChIPseq.s2.h4k16ac_gfp_1

value: gfp RNAi


title: wtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T60_Rep3


title: aortic_control_rep8

source_name: aortic media from healthy control 8

value: aortic media

value: male


title: 47TX

value: blood

tag: patient diagnosis

value: breast cancer

tag: tamoxifen

tag: z-endoxifen ratio


title: aortic_control_rep10

source_name: aortic media from healthy control 10

value: healthy control


title: 31TX

tag: (z)-4-oh-tam + 3-oh-tam

tag: ndm-tam


title: wtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T30_Rep1

tag: treatment


title: 12TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc


title: ChIPseq.s2.h3k9me2_jil2_2

tag: cell line

value: jil-1_2 RNAi

value: H3K9me2 (Abcam, ab1220)


title: wtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T15_Rep3

value: Colon

tag: genotype

tag: time

value: 15 mins


title: ChIPseq.s2.h3k9me2_jil2_3

tag: gender

tag: chip antibody


title: wtHKE3 cells 30 mins post stimulation with TGF-alpha - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T30_Rep3

value: TGF-alpha


title: aortic_TAA_rep13

source_name: aortic median from TAA patient 13

value: Thoracic Aortic Aneurysm patient


title: wtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T15_Rep2


title: ChIPseq.s2.h3k9me2_jil1_1

source_name: S2 cells

value: Male

value: jil-1_1 RNAi


title: 113TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: aortic_control_rep7

source_name: aortic media from healthy control 7

tag: tissue

value: female

tag: disease state


title: wtHKE3 cells 15 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T15_Rep1

value: wtHKE3 colorectal cancer cells

value: wildtype-KRAS


title: aortic_TAA_rep8

source_name: aortic median from TAA patient 8


title: ChIPseq.s2.h3k9me2_gst_2

value: gst RNAi


title: 100TX

source_name: blood

tag: patient diagnosis

tag: tamoxifen

tag: z-endoxifen ratio


title: aortic_TAA_rep7

source_name: aortic median from TAA patient 7

value: aortic media


title: aortic_TAA_rep6

source_name: aortic median from TAA patient 6

value: male


title: ChIPseq.s2.h3k9me2_gst_3

tag: treatment


title: aortic_control_rep6

source_name: aortic media from healthy control 6


title: ChIPseq.s2.h3k9me2_gfp_1

value: gfp RNAi


title: Unstimulated wtHKE3 cells (time 0 mins) - Replicate 3

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T0_Rep3

source_name: Unstimulated wtHKE3 cells (time 0 mins)

value: Unstimulated

value: 0 mins


title: 84TX

value: blood

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: ndm-tam

tag: (e)-endoxifen


title: Unstimulated wtHKE3 cells (time 0 mins) - Replicate 2

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T0_Rep2

value: Colon

tag: cell line


title: 59TX

tag: tam-n-oxide

tag: tam-n-gluc


title: 135TX


title: Unstimulated wtHKE3 cells (time 0 mins) - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T0_Rep1

tag: genotype

tag: time


title: ChIPseq.s2.msl3_2

tag: gender

tag: antibody

value: MSL3 (GP)


title: ChIPseq.s2.msl3_7


title: aortic_TAA_rep5

source_name: aortic median from TAA patient 5


title: aortic_control_rep5

source_name: aortic media from healthy control 5

value: healthy control


title: ChIPseq.s2.msl3_6


title: Q114_CONTROL

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total cellular RNA was extracted from endometrial samples using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s recommendations. After extraction, RNA concentration and quality were analyzed using a NanoDrop DP-1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and a Bioanalyzer® (Agilent, Santa Clara, CA). All samples had a 260/280 ratio > 2.0 and RNA integrity number (RIN) > 8 (8.95±0.4, mean ± SEM). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions.
The extracted RNA (1ng), was used for library preparation and RNA Sequencing. Paired-end reads with 150 nucleotides in length were produced. The RNAseq libraries were prepared with Illumina's TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, CA). Read 1 aligns to the antisense strand and Read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.  The lane produced a total of 700 million reads. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: Mares received a urea-treatment or control infusion (n = 7 mares/group) in a crossover design. The intervening estrous cycle was skipped and served as a washout cycle. Mares received 2500 IU of human chorionic gonadotropin (hCG) (Chorulon; Intervet, Millsboro, DE) intravenously when they had a follicle of at least 35 mm in diameter and pronounced uterine edema. Animals were scanned daily by ultrasound for ovulation detection (Day 0 = ovulation) and infusions were initiated at Day 7 of diestrus (D7). On the day of infusion, both jugular veins were catheterized using. Treatment consisted of a loading dose of 0.03 g/kg of urea (Sigma-Aldrich Company, St. Louis, MO) diluted in 100 mL of saline solution (Hospira, Inc, Lake Forest, IL) (15 g of urea for a 500 kg horse) to achieve a rapid increase in urea concentrations, and control mares received 100 mL of saline solution. Subsequently, mares received a bolus injection of urea (0.03 g/kg/hr) diluted in 15 mL of saline solution every 30 minutes over 6 hours (90 g of urea during 6 hours for a 500 kg horse). The control group received the same amount of saline solution as the urea group, 100 mL of saline solution as a loading dose and 15 mL of saline solution every 30 minutes over 6 hours. A uterine biopsy was collected from the base of the uterine horn.

value: Endometrium

value: control


title: Q114_UREA

value: urea


title: 30TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: 45TX

tag: tissue

tag: patient diagnosis


title: aortic_control_rep4

source_name: aortic media from healthy control 4

tag: disease state


title: Q112_UREA

tag: treatment


title: 11TX

tag: (z)-4-oh-tam + 3-oh-tam

tag: tamoxifen

tag: z-endoxifen ratio


title: Q112_CONTROL


title: ChIPseq.s2.jil_5_hope

tag: cell line

value: JIL-1 (Hope)


title: ChIPseq.s2.jil_5_R69S


title: 134TX

tag: ndm-tam

tag: (e)-endoxifen

tag: tam-n-oxide


title: wtHKE3 cells 60 mins post stimulation with TGF-alpha - Replicate 1

description:
RNAseq_Counts_wtHKE3_mtHKE3.txt
wtHKE3_T60_Rep1

value: wtHKE3 colorectal cancer cells

tag: genotype

value: TGF-alpha

tag: time

value: 60 mins


title: Q111_UREA


title: 112TX

tag: tam-n-gluc


title: ChIPseq.s2.jil_5_R69AP

tag: gender

tag: antibody

value: JIL-1 (R69AP)


title: 97TX

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: aortic_control_rep2

source_name: aortic media from healthy control 2

tag: tissue

value: aortic media

value: female

tag: disease state


title: Q111_CONTROL

tag: treatment


title: aortic_TAA_rep4

source_name: aortic median from TAA patient 4

value: Thoracic Aortic Aneurysm patient


title: aortic_TAA_rep2

source_name: aortic median from TAA patient 2

value: male


title: aortic_TAA_rep3

source_name: aortic median from TAA patient 3


title: aortic_TAA_rep1

source_name: aortic median from TAA patient 1


title: 82TX

value: blood

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: tamoxifen


title: aortic_control_rep3

source_name: aortic media from healthy control 3


title: ChIPseq.s2.jil_4

source_name: S2 cells

tag: cell line

value: JIL-1 (R70AP)


title: ChIPseq.s2.jil_3


title: ChIPseq.s2.input_7

value: none (Input)


title: Q108_CONTROL


title: 44TX

value: breast cancer

tag: ndm-tam

tag: (e)-endoxifen

tag: z-endoxifen ratio