title: Experiment3 shZFP819

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

country: United Kingdom

institute: Queen Mary University of London

description:
mESCs transduced with pLKO.1 (Addgene #10878) lentiviral vector expressing a shZfp819 hairpin (known as shZfp819 62) (see Fernandes et al., 2022 for shRNA sequences)
Sup_Table_TEcounts.xlsx

data_processing:
RNA-Seq and CUT&RUN fastq files were trimmed for quality using TrimGalore v0.4.1
For RNA-Seq samples, alignment of trimmed reads to mm10 version of the mouse genome was performed with Tophat 2.1.0 using the --max-multihits 100 option. The number of read counts per gene and repeat family was calculated using the multi option from Tecount. Differential expression analysis was performed with DESeq2. For further details see Fernandes et al., 2022.
For CUT&RUN samples, trimmed reads were aligned with STAR with the following parameters: --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06. Genomic coverage in form of bigwig files was calculated using the genomecov tool from bedtools using 10000000 / number_of_mapped_reads as a scaling factor.
For ChIP-Seq samples, reads were mapped to the mm10 version of the mouse genome using Bowtie2. ChIP-seq enriched peaks were called by MACS2 (v.2.1.2), and the common peaks were merged using bedtools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic coverage normalised to number of mapped reads. Excel spreadsheet with results of differential expression analysis. Bed files with ChIP-Seq peaks

source_name: mESC

growth_protocol: ES3 mESCs were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 100 U/ml penicillin/streptomycin, 10% fetal calf serum (FCS, Life Technologies), 2mM L-glutamine (Gibco, Thermo Fisher Scientific), 1mM Sodium pyruvate (Sigma), 1x MEM non-essential amino acids (Gibco, Thermo Fisher), 0.1mM  2-Mercaptoethanol (Life Technologies) and 1,000 units/ml Leukaemia inhibitory factor (LIF, Chemicon) and grown at 5% CO2 at 37 °C. mESC lines were split 1:4 every 2 days using accutase or trypsin.

extract_protocol:
RNA-seq - Total RNA was extracted using RNeasy Micro kit columns (Qiagen) and DNase treated according to the manufacturer’s instructions (Ambion AM1907). RNA was quality checked on a 4200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA Broad Range kit (Life Technologies, Paisley, UK)
CUT&RUN - We followed the EpiCypher® CUTANATM CUT&RUN Protocol (v1.6) (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol/). Briefly, CUT&RUN was performed using 100,000 sorted GFPBright cells (per antibody/sample combination). Cells were washed twice [20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1× protease inhibitors (cOmplete™, Mini, EDTA-free, Roche)], attached to Concanavalin A beads (BioMag®Plus, Generon) which were pre-activated in activation buffer (20mM HEPES pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Sample and bead slurry was resuspended in antibody buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× protease inhibitors, 0.01% w/v digitonin, 2mM EDTA) containing primary antibody. 1ug of anti-H3K9me3 (Abcam, ab8898) or anti-H3K27ac (Abcam, ab4729) was incubated overnight at 4°C with gentle shaking. IgG control Ab (Millipore, 12-370) alone was used in parallel. The samples were washed 3x in cold digitonin buffer (20 mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× Roche complete protease inhibitors, 0.01% digitonin). pA-MNase (2.5μl per tube, CUTANA™ pAG-MNase, Epicypher) was added incubated with the bead-cell slurry at room temperature for 10min. The beads were washed twice and resuspended in cold digitonin buffer. The pA-MNase was activated by addition of 2mM CaCl2 (final) and incubating at 4°C for 2h. The reaction was quenched using stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml glycogen, 50μg/ml RNase A), vortexing and incubating for 10 min at 37°C. A magnetic rack was used to separate cells and beads from the supernatant which was purified with a MinElute PCR Purification Kit (Qiagen).
ChIP - ES3 mESCs were transduced with ZFP819 and ZFP809-expressing lentiviral vectors (pRRLSIN.cPPT.PGK-ZFP.WPRE vectors with a triple HA tag). Cells were washed twice (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (10 min rotation in 1% formaldehyde), quenched with glycine (at 125 mM on ice), washed three times (PBS), and snap-frozen at 107 cells per tube. Cells were resuspended in sequential ChIP lysis buffers and then in 900ul of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors). Where a Covaris sonicator was used, 900ul was sonicated in one covaris glass tube with the settings: 20% duty cycle, intensity 5, 200 cycles/burst, 30 min. For sonication with a Bioruptor Pico, 300ul aliquots per 1.5ml tube were sonicated1. Immunoprecipitations were performed in duplicates as described2 using an HA Ab (Biolegend, 901501) and DNA extracted (Qiagen MinElute PCR purification kit, Cat. 28004) for PCR and sequencing. See Supplementary Information for primers.  1. Tie, C.H. et al. KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. EMBO Rep 19(2018).  2. Robbez-Masson, L. et al. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res (2018).
RNA-seq - 500 ng per sample was processed using KAPA’s stranded RNA HyperPrep RiboErase kit and sequenced on a NextSeq 500 instrument (Illumina Cambridge, Chesterford, UK) after pooling libraries in equimolar quantities, using a 2x 151 bp paired-end run, resulting in over 15 million reads per sample.
CUT&RUN - Illumina sequencing libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (New England BioLabs). Enrichment of DNA fragments was achieved by PCR (12 cycles). Libraries pooled in equimolar quantities were sequenced on Novaseq6000 for 150 paired-end reads.
ChIP-seq - Libraries were prepared following the ChIP-Seq library preparation protocol (Illumina, IP-102-1001). Ligation products were purified on 2% E Gels Size Select (Invitrogen; fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles). Sequencing was performed with Illumina HiSeq 2500 in 100-bp single-end reads.

treatment_protocol: mESCs were transduced with shRNA expressing lentiviral vectors. Puromycin selection was performed 2 days post transduction overnight (and control cells verified to die) and samples harvested 5 days post selection. Cells tranduced with GFP shRNA expressing lentiviral vectors were sorted on day 2 post transduction and harvested 5 days later.

tag: transduction

tag: time-point

value: Samples collected 5 days post puromycin selection

tag: full name


title: Experiment2 shEmpty

status: Public on Oct 31 2022

type: SRA

description:
mESCs transduced with empty pLKO.1 (Addgene #10878)  lentiviral vector (known as shControl) (see Fernandes et al., 2022 for shRNA sequences)
Sup_Table_TEcounts.xlsx

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

value: shEmpty


title: Experiment3 shEmpty


title: du145_DU145PS3B_D10_Enasidenib_1.5_24

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

country: USA

institute: Columbia University

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: prostate cancer

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

tag: treatment

value: Enasidenib

tag: cell line

tag: provider

value: ATCC

tag: vendor id

tag: age

tag: Sex

value: male


title: SAMPLE 26_hMSC_passage 5

type: RNA

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human mesenchymal stem cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and 480 ng cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software GX14.9.1 (Agilent) using default parameters.
Signal intensities of <1 were set to 1, and each chip was normalized to the 75th percentiles of all measurements from that chips. Baseline transformation of these data was not performed.

source_name: hMSC, passage 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human mesenchymal stem cells, hMSC, was cultured in MesenPRO RS medium (Gibco, 12746012) supplemented with 2 mM L-glutamine (Gibco, 25030-81) and 1 % Penicillin-Streptomycin (Gibco, 15140-122) at 37 ℃ in a humidified atmosphere of 5 % CO2.

extract_protocol: Total RNA was prepared by using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: hMSC

tag: tissue source

value: Human bone marrow

tag: cell type

value: Human mesenchymal stem cells (hMSC)

tag: passage

value: passage 5


title: SAMPLE 25_hMSC_passage 5


title: du145_DU145PS3B_D09_AZ12456623_1.5_24


title: SAMPLE 24_Yub622_passage 16

source_name: Yub622, passage 16

value: passage 16


title: SAMPLE 23_Yub622_passage 16


title: Experiment2 shZFP819


title: Experiment1 shEmpty


title: du145_DU145PS3B_D08_MGCD265_1_24


title: SAMPLE 17_Yub622_passage 13

source_name: Yub622, passage 13

value: passage 13


title: Experiment1 shZFP819


title: SAMPLE 18_Yub622_passage 13


title: SAMPLE 20_Yub622_passage 14

source_name: Yub622, passage 14

value: passage 14


title: du145_DU145PS3B_D07_Lonafarnib_0.3_24

value: Lonafarnib


title: SAMPLE 22_Yub622_passage 15

source_name: Yub622, passage 15

value: passage 15


title: SAMPLE 43_hMSC_passage 14

source_name: hMSC, passage 14


title: SAMPLE 19_Yub622_passage 14


title: SAMPLE 16_Yub622_passage 12

source_name: Yub622, passage 12

value: passage 12


title: SAMPLE 14_Yub622_passage 11

source_name: Yub622, passage 11

value: passage 11


title: SAMPLE 13_Yub622_passage 11


title: SAMPLE 21_Yub622_passage 15


title: XO (RRBS)

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to a bisulfite converted mm10 using Bismark
The percentage methylation at individual CpG sites was calculated at positions with at least 10 reads using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file percentage mC at individual CpGs that were covered by at least 10 reads.

molecule: genomic DNA

growth_protocol: Female Xmas mESC lines were established as described in the associated manuscript. Cells were grown by our new culture method for 7 passages.

extract_protocol:
DNA harvested using Zymo Quick DNA kit
Libraries were prepared using a NuGEN Ovation Methylseq library preparation kit

treatment_protocol: Cells were harvested and separated by FACS into XX and XO populations using the Xmas reporter alleles.

value: Female

value: Xmas mESC line

tag: karyotype

value: XO


title: du145_DU145PS3B_D06_DMSO__24

value: DMSO


title: XX (RRBS)

value: XX


title: SAMPLE 12_Yub622_passage 10

source_name: Yub622, passage 10

value: passage 10


title: Rep2 p20 New [DNA-2-p20-Off_S12]

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using bowtie2 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

growth_protocol: Male C57/Bl6 mESC lines were established as described in the associated manuscript.  Cells were expanded maintained in 2i media

extract_protocol:
Cells were split off the plate and DNA harvested using Zymo Quick DNA/RNA kit
Libraries were prepared according to standard Illumina Tru-seq protocols

treatment_protocol: Cells were harvested on the indicated passages.

value: Male

value: mESC line


title: du145_DU145PS3B_D05_Cediranib_0.22_24

value: Cediranib

value: ATCC

value: male


title: du145_DU145PS3B_D04_Telatinib_2_24

value: Telatinib


title: Rep2 p10 Old [DNA-2-p10-On_S4]


title: SAMPLE 10_Yub622_passage 9

source_name: Yub622, passage 9

value: Human bone marrow

value: Human mesenchymal stem cells (hMSC)

value: passage 9


title: SAMPLE 11_Yub622_passage 10


title: du145_DU145PS3B_D03_AZD5069_7_24


title: du145_DU145PS3B_D02_UNTREATED__24

value: UNTREATED


title: SAMPLE 8_Yub622_passage 8

source_name: Yub622, passage 8

value: passage 8


title: du145_DU145PS3B_D01_Cyclosporine_10_24

value: Cyclosporine


title: Rep2 p0 [DNA-2-p0_S2]


title: Rep1 p20 Old [DNA-1-p20-On_S5]


title: SAMPLE 7_Yub622_passage 8


title: SAMPLE 5_Yub622_passage 7

source_name: Yub622, passage 7

value: passage 7


title: SAMPLE 9_Yub622_passage 9


title: SAMPLE 4_Yub622_passage 6

source_name: Yub622, passage 6

value: passage 6


title: SAMPLE 3_Yub622_passage 6


title: SAMPLE 6_Yub622_passage 7


title: Aneurysm 2-9: macrophage, scRNAseq

city: Suita City

first: Akihiro

last: Okada

state: Osaka

address: 6-1 Kishibe-Shinmachi

department: Department of Molecular Pharmacology

institute: National Cerebral and Cardiovascular Center

library_source: transcriptomic single cell

data_processing:
Paired-end sequencing (2 × 75 base pair) was performed on a NextSeq500 (Illumina). Each read was then mapped to the Rattus norvegicus reference genome (Rnor6) using CLC genomics workbench (version 11, QIAGEN). Differential expression analyses, including principal component analysis and clustering analysis, were performed using the iDEP.951.
Assembly: Rnor6
Supplementary files format and content: Macrophages in aneurysm lesions.xlsx represents counts for all genes for all samples.

organism: Rattus norvegicus

source_name: Artery

extract_protocol:
DiI-containing nanoparticles were intravenously injected in rats to label macrophages infiltrating in lesions. After 3 days, DiI-labelled macrophages were then isolated from the lesions in a single-cell fashion by the laser-microdissection technique.
The library for single cell RNA-sequencing analysis was prepared by a SMART-Seq Single Cell Plus Kit.

treatment_protocol: Under general anesthesia by the inhalation of isoflurane (induction; 5.0 %, maintenance; 1.5~2.0 %), the left common carotid artery (CCA) was cut in the proximal portion and was anastomosed to the right CCA in an end-to-side fashion with a 10-0 nylon suture to create a bifurcation. Hyper-volemic state was also induced by salt overloading and ligation of the left renal artery. Immediately after the above surgical manipulations, animals were fed the chow containing 8 % sodium chloride and 0.12 % 3-aminopropionitrile, an inhibitor of lysyl oxidase that catalyzes the cross-linking of collagen and elastin.

tag: disease state

value: aneurysm model

tag: animal id

value: Macrophages

tag: tissue

value: Artery

value: Sprague Dawley

value: 7 weeks old


title: du145_DU145PS3B_C12_Volasertib_0.005_24

value: Volasertib


title: SAMPLE 2_Yub622_passage 5

source_name: Yub622, passage 5

value: passage 5


title: Rep1 p20 New [DNA-1-p20-Off_S11]

value: Male

value: mESC line


title: SAMPLE 1_Yub622_passage 5

value: Human bone marrow


title: du145_DU145PS3B_C10_Linsitinib_5.5_24

value: Linsitinib

value: ATCC

value: male


title: SAMPLE 15_Yub622_passage 12

value: Human mesenchymal stem cells (hMSC)

value: passage 12


title: du145_DU145PS3B_C11_Momelotinib_1_24

value: Momelotinib


title: Rep1 p10 Old [DNA-1-p10-On_S3]


title: Rep2 p10 New [DNA-2-p10-Off_S10]


title: hBMSC, siR-Ctrl-2

city: 桂林市

first: 陈琍

last: 陈

address: 临桂区临桂镇致远路

country: China

institute: 桂林医学院

description:
Gene expression data from human BMSC
hBMSC transfected by siR-Control, samples 2

hyb_protocol: Followed the GeneChip® Hybridization, Wash and Stain Kit, cRNA were hybridized for 18 hr at 45C on Affymetrix Whole-Transcript Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using  an Affymetrix GCS 3000 7G scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, and normalization was performed using Expression Console (Affymetrix, USA) with the RMA gene core algorithm.

label: biotin

source_name: hBMSC transfected by siR-Control

label_protocol: RNA was Biotinylated labeled according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay as provided by the manufacturer (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, then purified again by GenElute mammalian total RNA miniprep kit (Sigma-Aldrich). The quantification and quality analysis of RNA were analyzed by the 2100 Bioanalyzer (Agilent)

treatment_protocol: hBMSC cultured till confluent, then transfected by siRNA (non-targeting control or KIAA1199), after 72 hours, total RNAs were isolated separately

value: bone marrow stromal cell

tag: genotype

value: control


title: du145_DU145PS3B_C07_Copanlisib_0.16_24

source_name: prostate cancer

value: Copanlisib


title: Rep2 p20 New [RNA-2-p20-Off_S12]

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using TopHat v2.0.12 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo Quick DNA/RNA kit
Libraries were prepared according to standard Illumina RNA-seq protocols


title: Rep2 p20 Old [DNA-2-p20-On_S6]


title: hBMSC, siR-KIAA1199-2

description:
Gene expression data from human BMSC
hBMSC transfected by siR-KIAA1199, samples 2

source_name: hBMSC transfected by siR-KIAA1199

value: KIAA1199 knockdown


title: hBMSC, siR-KIAA1199-3

description:
Gene expression data from human BMSC
hBMSC transfected by siR-KIAA1199, samples 3


title: hBMSC, siR-Ctrl-1

description:
Gene expression data from human BMSC
hBMSC transfected by siR-Control, samples 1


title: hBMSC, siR-Ctrl-3

description:
Gene expression data from human BMSC
hBMSC transfected by siR-Control, samples 3


title: Rep1 p10 New [DNA-1-p10-Off_S9]


title: hBMSC, siR-KIAA1199-1

description:
Gene expression data from human BMSC
hBMSC transfected by siR-KIAA1199, samples 1


title: du145_DU145PS3B_C05_TAK700_10_24


title: du145_DU145PS3B_C04_Amonafide_0.335_24

value: Amonafide


title: Rep2 p10 New [RNA-2-p10-Off_S10]


title: du145_DU145PS3B_C09_Rucaparib_3.5_24

value: Rucaparib


title: du145_DU145PS3B_C08_Enzastaurin_0.24_24

value: Enzastaurin


title: Rep1 p0 [DNA-1-p0_S1]


title: Rep1 p20 Old [RNA-1-p20-On_S5]


title: du145_DU145PS3B_C06_DMSO__24

value: DMSO


title: Rep2 p10 Old [RNA-2-p10-On_S4]

value: Male


title: Rep2 p0 [RNA-2-p0_S2]

value: mESC line


title: du145_DU145PS3B_C03_AMG900_2.5_24


title: Rep1 p20 New [RNA-1-p20-Off_S11]


title: du145_DU145PS3B_C01_Aspirin_10_24

value: Aspirin


title: du145_DU145PS3B_B11_LY3023414_0.05_24


title: du145_DU145PS3B_B12_Calcitriol_0.005_24

value: Calcitriol


title: Rep2 p20 Old [RNA-2-p20-On_S6]


title: Rep1 p10 Old [RNA-1-p10-On_S3]


title: du145_DU145PS3B_C02_UNTREATED__24

value: UNTREATED

value: ATCC


title: Rep1 p10 New [RNA-1-p10-Off_S9]


title: N8_Mousebrain_n4_500ng_WT_E15-5_PFC_DF_pass2

city: Canberra

first: Pablo

last: Acera Mateos

state: ACT

address: 131 Garran Rd

department: The Shine-Dalgarno Centre for RNA Innovation

institute: ANU

description: Direct-RNA sequencing

data_processing:
The processed files were generating using the CHEUI pipeline (https://github.com/comprna/CHEUI-public)
Supplementary files format and content: data format is .xlsx containing significant RNA modifications called using CHEUI. Columns indicate Column 1: Chromosome; column 2: genomic start position (half-open) of the modified site; column 3: genomic end position of the modified site; column 4: transcript unique ID; column 5: score (not used); column 6: genomic strand; column 7: Transcript position (half-open) of the modified nucleotide; column 8: site motif; column 9: site coverage (number of reads); column 10: site stoichiometry; column 11: modified site probability; column 12: Transcript type; column 13: Gene name; column 14: Gene unique ID; column 15: transcript length (nts); column 16: transcript CDS length (nts); column 17: transcript 5’UTR length (nts); column 18: 3’UTR length (nts); column 19: CDS start in transcript coordinates; column 20: CDS end in transcript coordinates; column 21: site position relative to the transcript segments (see Methods). Ranges from 0 to 3. From 0-1 corresponds to start and end of 5’UTR; 1-2 corresponds to start and end of CDS, 2-3 corresponds to start and end of 3’UTR; column 22: abs_cds_start, absolute distance in nucleotides of the site from the annotated start of the CDS; column 23: abs_cds_end absolute distance in nucleotides of the site from the annotated end of the CDS; column 23: distance from the site to the closest junction upstream; column 24: distance from the site to the closest junction downstream; column 25: Sample name column 26: model (m6A or m5C).

molecule: polyA RNA

source_name: prefrontal cortex

growth_protocol: Embryonic mice were dissected on day (E) 12, E15 and E18.

extract_protocol:
All procedures were conducted in accordance with the Australian National University Animal Experimentation Ethics Committee (protocol number A2019/46). Pregnant females were cervically dislocated, and embryos extracted in cold sterile PBS. The frontal area of the cortex was then dissected with micro-knifes under a Zeiss STEMI 508 stereomicroscope and tissue samples were immediately placed in a 1.5 ml microcentrifuge tube (Eppendorf, DNA) containing 300 µl of denaturing lysis and binding buffer (100 mM Tris-HCl pH 7.4 at 25 °C, 1 % w/v lithium dodecyl sulfate (LDS), 0.8 M lithium chloride, 40 mM EDTA and 8 mM DTT; LBB). Samples were immediately agitated by vigorous pipetting until almost complete tissue dissolution, flash-frozen on dry ice and stored at – 80 °C until sequencing.
150 mg of frontal cortex (PFC) brain region tissue was lysed immediately upon extraction. The tissue/LBB mixture was thoroughly pipetted with 200 µl tip until the sample viscosity was reduced, and pipetting was seamless. 500 µl of oligo(dT)25 magnetic beads (New England BioLabs) suspension was used per replicate. The beads were washed with 1 ml of LBB twice, each time collecting the beads on a magnet and completely removing the supernatant. Upon washing, the oligo(dT)25 beads were resuspended in the tissue/LBB mixture and placed in a rotator set for 20 rpm at 25 °C for 5 minutes, followed by the same rotation at 4 °C for 30 minutes. The suspension was briefly spun down at 12,000 g, separated on a magnet, and the supernatant was discarded. The beads were then resuspended with 1 ml wash buffer (20 mM Tris-HCl pH 7.4, 0.2 % v/v Titron X-100, 0.4 M lithium chloride, 10 mM EDTA and 8 mM DTT; WB) and washed on a rotator set for 20 rpm at 4 °C for 5 minutes, 3 wash rounds in total. The beads were collected on a magnetic rack and the supernatant was discarded. The wash procedure was repeated three times. The elution was carried out stepwise. Washed bead pellet was first resuspended in 50 µl of the elution buffer (25 mM HEPES-KOH, 0.1 mM EDTA; HE). The first suspension was heated at 60 °C for 5 minutes to facilitate the elution, and the eluate was collected upon placing the bead-sample mixture on a magnetic rack, separating the beads, and recovering the clean supernatant. The resultant pellet was next resuspended in another 50 µl of HE buffer, and the process was repeated. The eluates were then combined and subjected to an additional solid-phase reversible immobilization (SPRI) bead purification step and stored frozen. The eluate from oligo(dT) bead extraction was further purified using AMPure XP SPRI beads (Beckman Coulter Life Sciences) according to the manufacturer’s recommendations. Briefly, the eluate samples were supplemented with 1.2× volumes of the SPRI bead suspension in its standard (supplied) binding buffer, and the resultant mixture was incubated at room temperature for 5 minutes with periodic mixing. The SPRI beads were brought down by a brief 2,000 g spin down and separated from the solution on a magnetic rack. The supernatant was removed, and the beads were resuspended in 1 ml of 80 % v/v ethanol, 20 % v/v deionized water mixture and further washed by tube flipping. The bead and solution separation procedure were repeated. The ethanol washing process was repeated one more time. Any remaining liquid was brought down by a brief spin and removed using a pipette, and the beads were allowed to air-dry while in the magnetic rack for 2 minutes. The purified RNA was then eluted in 20 µl of deionized water and the RNA content was assessed using absorbance readout via Nanodrop and fluorescence-based detection via Qubit RNA high sensitivity (HS) assay kit (Thermo Fisher Scientific).

value: prefrontal cortex

value: WT


title: Vata [S220]

city: New Delhi

first: Mitali

last: Mukerji

state: Delhi

address: Near Mathura Road, Sukhdev Vihar

department: CSIR TRISUTRA UNIT

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was extracted using GenomeStudio Software and background correction was performed in R using nec function available in limma package. Further preprocessing and filtering based on the detection p-value was performed to retain 16857 high confident probes. Next the filtered  data  was normalised and corrected for unknown and known batch effects using surrogate variable analysis (SVA package) and supervised normalization method (SNM package) available in R.

source_name: Peripheral Blood Mononuclear Cell (PBMC)

label_protocol: Biotinylated cRNA were prepared with the IlluminaTotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

tag: prakriti

value: V

tag: gender

value: Female

tag: batch


title: Vata-Pitta [S224]

value: VP


title: Vata-Pitta [S221]


title: Pitta [S223]

value: P


title: du145_DU145PS3B_B10_AZ13064550_10_24

tag: treatment

value: male


title: Kapha [S225]

value: K


title: Vata [S219]


title: Vata [S217]


title: Pitta-Kapha [S215]

value: PK


title: Vata-Kapha [S212]

value: VK


title: Vata [S216]


title: Rep1 p0 [RNA-1-p0_S1]

tag: strain


title: N7_Mousebrain_n4_500ng_WT_E15-5_PFC_DF_pass1

description: Direct-RNA sequencing


title: Pitta-Kapha [S222]


title: Pitta-Kapha [S210]


title: du145_DU145PS3B_B07_Pimasertib_0.31_24

value: Pimasertib

tag: cell line

tag: provider


title: Vata [S214]

tag: age


title: Vata [S218]


title: Vata-Pitta [S211]


title: du145_DU145PS3B_B08_Dovitinib_0.31_24

value: Dovitinib

tag: vendor id

tag: Sex


title: AR18_Mousebrain_n4_1546ng_WT_E12_LB_pass3

description: Direct-RNA sequencing


title: Vata [S209]


title: du145_DU145PS3B_B09_AZ12419304_0.5_24


title: du145_DU145PS3B_B05_EpothiloneD_0.04_24

value: EpothiloneD


title: AR16_Mousebrain_n4_1546ng_WT_E12_LB_pass1

description: Direct-RNA sequencing


title: du145_DU145PS3B_B04_ABT888_10_24


title: Kapha [S206]


title: N16_Mousebrain_n2_500ng_WT_E12_DF_pass1

description: Direct-RNA sequencing


title: du145_DU145PS3B_B03_AEE788_0.17_24


title: du145_DU145PS3B_B06_Saridegib_1_24

value: Saridegib


title: Vata-Pitta [S207]


title: du145_DU145PS3B_B02_DMSO__24

value: DMSO


title: AR17_MouseBrain_n4_1546ng_WT_E12_LB_pass2

description: Direct-RNA sequencing


title: Vata-Pitta [S213]


title: du145_DU145PS3B_B01_Hydroxychloroquine_0.5_24

value: Hydroxychloroquine


title: Vata-Pitta [S204]


title: AR14_Mousebrain_n4_2573ng_WT_E18_DF_pass1

description: Direct-RNA sequencing


title: AR15_Mousebrain_n4_2573ng_WT_E18_DF_pass2

description: Direct-RNA sequencing


title: Vata [S208]


title: Vata [S202]

value: Male


title: Pitta [S203]


title: AR13_Mousebrain_n4_2573ng_WT_E18_DF_pass2

description: Direct-RNA sequencing

value: prefrontal cortex


title: Pitta-Kapha [S205]


title: AR12_Mousebrain_n4_2573ng_WT_E18_DF_pass1

description: Direct-RNA sequencing

value: WT


title: du145_DU145PS3B_A11_Pracinostat_0.03_24

value: Pracinostat

value: ATCC


title: Pitta-Kapha [S199]

value: Female


title: N17_Mousebrain_n2_500ng_WT_E18_DF_pass1

description: Direct-RNA sequencing


title: du145_DU145PS3B_A10_AMG337_9.5_24


title: Vata-Pitta [S198]

value: VP


title: Vata-Pitta [S196]


title: Vata [S194]

value: V


title: du145_DU145PS3B_A12_Duvelisib_5_24

value: Duvelisib

value: male


title: AR2_Mousebrain_n2_812ng_WT_E18_DF_pass1

description: Direct-RNA sequencing


title: AR9_Mousebrain_n4_4720ng_WT_E18_BF_pass2

description: Direct-RNA sequencing


title: du145_DU145PS3B_A09_GDC0068_0.5_24


title: Kapha [S200]

value: K


title: Kapha [S201]


title: Pitta-Kapha [S195]

value: PK


title: Vata [S193]


title: du145_DU145PS3B_A08_PF04691502_0.24_24


title: du145_DU145PS3B_A07_Tivozanib_0.175_24

value: Tivozanib


title: AR1_Mousebrain_n2_386ng_WT_E18_DF_pass1

description: Direct-RNA sequencing


title: Vata [S190]


title: Vata [S197]


title: Pitta-Kapha [S188]


title: du145_DU145PS3B_A06_Apremilast_0.5_24

value: Apremilast


title: Pitta [S191]

value: P


title: Vata [S189]


title: Vata [S192]


title: Vata [S186]


title: AR8_Mousebrain_n4_4720ng_WT_E18_BF_pass1

description: Direct-RNA sequencing


title: du145_DU145PS3B_A05_Zibotentan_1.5_24

value: Zibotentan


title: Vata [S184]


title: du145_DU145PS3B_A03_Icotinib_1_24

value: Icotinib


title: du145_DU145PS3B_A04_Onalespib_0.065_24

value: Onalespib


title: du145_DU145PS3B_A01_Mycophenolate_1.5_24

value: Mycophenolate


title: Kapha [S183]


title: Vata-Pitta [S185]


title: Vata [S181]


title: Kapha [S187]


title: Vata [S182]


title: du145_DU145PS3A_H12_Vatalanib_0.115_24

value: Vatalanib


title: Pitta [S178]


title: du145_DU145PS3A_H11_UNTREATED__24

value: UNTREATED


title: Kapha [S175]

value: Male


title: Liver-Females-Control1-Rep6

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

description: wash bath 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 58 out of 72 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 36501 spots out of 62976 were selected.  The mean signal of the 24 first samples, 24 next and 24 last ones were substracted to individuals signals to correct the batch effect of the 3 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33847 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were housed at 20-22°C under 12h/12h light/dark conditions.

extract_protocol: RNAs were extracted from liver samples in males and females mice using the method Chomczynski P and Sacchi N (1987) with Tri-reagent (Sigma Aldrich).

treatment_protocol: Mice were fed one of the 6 diets for 15 weeks.

value: Liver

value: Females

tag: diet


title: Vata-Pitta [S177]

value: VP

value: Female


title: Pitta-Kapha [S176]


title: Vata [S179]

value: V


title: Liver-Females-Control2-Rep6

description: wash bath 3


title: Vata [S180]


title: Liver-Females-Choline deficient High Fat Diet-Rep6

description: wash bath 3

value: Cholin deficient High Fat Diet


title: du145_DU145PS3B_A02_DMSO__24

value: DMSO

value: ATCC

value: male


title: Pitta-Kapha [S173]

value: PK


title: Kapha [S172]

value: K


title: du145_DU145PS3A_H10_CC223_1_24


title: du145_DU145PS3A_H09_Mocetinostat_0.165_24

value: Mocetinostat


title: Vata [S170]


title: Kapha [S171]


title: Liver-Males-Western Diet-Rep6

description: wash bath 3

value: Males

value: Western Diet


title: Liver-Males-High Fat Diet-Rep6

description: wash bath 3

value: High Fat Diet


title: Vata-Pitta [S168]


title: Vata [S169]


title: Vata [S167]


title: du145_DU145PS3A_H08_Triciribine_0.135_24

value: Triciribine


title: Pitta-Kapha [S174]


title: Vata [S166]


title: Pitta [S165]

value: P


title: du145_DU145PS3A_H07_LY2603618_0.5_24


title: Pitta [S163]


title: Liver-Males-Control2-Rep6

description: wash bath 3

value: Liver


title: Liver-Males-Control1-Rep6

description: wash bath 3


title: Pitta-Kapha [S164]


title: Kapha [S161]


title: du145_DU145PS3A_H06_Nintedanib_0.135_24

value: Nintedanib


title: Vata-Kapha [S162]

value: VK


title: du145_DU145PS3A_H05_CP724714_1.5_24


title: Vata [S159]

value: Female


title: Liver-Females-Control2-Rep5

description: wash bath 3

value: Females


title: du145_DU145PS3A_H04_Givinostat_0.025_24

value: Givinostat


title: Pitta [S158]


title: du145_DU145PS3A_H03_ABT751_1_24


title: Vata [S157]

value: V


title: Liver-Males-Choline deficient High Fat Diet-Rep6

description: wash bath 3

value: Cholin deficient High Fat Diet


title: Liver-Females-Control1-Rep5

description: wash bath 3


title: du145_DU145PS3A_H02_Savolitinib_10_24

value: Savolitinib

value: ATCC

value: male


title: Vata [S160]


title: Pitta-Kapha [S156]

value: PK


title: Kapha [S155]

value: K


title: du145_DU145PS3A_H01_Phenelzine_1_24

value: Phenelzine


title: Liver-Males-Western Diet-Rep5

description: wash bath 3

value: Males

value: Western Diet


title: du145_DU145PS3A_G11_UNTREATED__24

value: UNTREATED


title: Liver-Males-Western Diet Glucose Fructose-Rep6

description: wash bath 3

value: Liver

value: Western Diet Glucose Fructose


title: Kapha [S152]


title: Pitta [S154]

value: P


title: Vata [S151]

value: Female


title: Vata [S150]

value: Male


title: Liver-Females-Western Diet Glucose Fructose-Rep6

description: wash bath 3

value: Females


title: Liver-Females-High Fat Diet-Rep6

description: wash bath 3

value: High Fat Diet


title: Liver-Females-Western Diet-Rep6

description: wash bath 3


title: Liver-Males-High Fat Diet-Rep5

description: wash bath 3


title: Kapha [S153]


title: Vata [S147]

value: V


title: Liver-Females-Control1-Rep4

description: wash bath 3


title: Vata [S149]


title: Vata [S146]


title: Vata-Pitta [S145]

value: VP


title: Pitta [S144]


title: du145_DU145PS3A_G09_AZ12609721_1_24

value: ATCC


title: Kapha [S143]


title: Liver-Females-Choline deficient High Fat Diet-Rep5

description: wash bath 3

value: Cholin deficient High Fat Diet


title: du145_DU145PS3A_G12_Cyproterone_0.165_24

value: Cyproterone

value: male


title: Liver-Males-Control2-Rep5

description: wash bath 3


title: Kapha [S142]

value: K


title: Liver-Females-Western Diet Glucose Fructose-Rep5

description: wash bath 3


title: Vata [S141]


title: Liver-Males-Control1-Rep5

description: wash bath 3

value: Males


title: Vata [S148]


title: du145_DU145PS3A_G10_INK128_0.015_24


title: du145_DU145PS3A_G07_Rocilinostat_0.16_24

value: Rocilinostat


title: Vata [S140]


title: du145_DU145PS3A_G06_RAF265_0.04_24


title: Pitta-Kapha [S138]

value: PK


title: du145_DU145PS3A_G05_Eniluracil_4_24

value: Eniluracil


title: Vata [S139]


title: Pitta [S137]


title: du145_DU145PS3A_G04_Brigatinib_0.035_24

value: Brigatinib


title: du145_DU145PS3A_G03_Ispinesib_0.001_24

value: Ispinesib


title: du145_DU145PS3A_G02_Banoxantrone_5_24

value: Banoxantrone


title: du145_DU145PS3A_G08_AZ12823138_10_24


title: Kapha [S135]

value: Female


title: Liver-Males-Western Diet-Rep4

description: wash bath 3

value: Liver

value: Western Diet


title: Liver-Males-Western Diet-Rep3

description: wash bath 2


title: Liver-Females-High Fat Diet-Rep5

description: wash bath 3

value: Females

value: High Fat Diet


title: Vata-Pitta [S136]

value: VP


title: Vata-Kapha [S130]

value: VK


title: Liver-Males-Choline deficient High Fat Diet-Rep5

description: wash bath 3

value: Cholin deficient High Fat Diet


title: Kapha [S133]


title: Vata [S129]

value: V

value: Male


title: Liver-Females-Control2-Rep4

description: wash bath 2


title: du145_DU145PS3A_G01_Berberine_7_24

value: Berberine

value: ATCC

value: male


title: du145_DU145PS3A_F12_Cilengitide_10_24

value: Cilengitide


title: Pitta-Kapha [S128]

value: PK


title: Liver-Males-Control1-Rep4

description: wash bath 2

value: Males


title: Kapha [S126]

value: K


title: Kapha [S134]

value: Female


title: Vata-Pitta [S125]


title: du145_DU145PS3A_F11_DMSO_0_24

value: DMSO


title: Liver-Females-Western Diet Glucose Fructose-Rep4

description: wash bath 2

value: Liver

value: Western Diet Glucose Fructose


title: Vata [S123]


title: Liver-Females-High Fat Diet-Rep4

description: wash bath 2

value: Females

value: High Fat Diet


title: Vata [S124]


title: Vata-Pitta [S122]

value: VP


title: Liver-Males-Choline deficient High Fat Diet-Rep4

description: wash bath 2

value: Cholin deficient High Fat Diet


title: Kapha [S127]


title: Vata [S131]

value: V


title: du145_DU145PS3A_F10_MLN2480_6.5_24


title: Liver-Females-Western Diet Glucose Fructose-Rep3

description: wash bath 2


title: Vata [S121]

value: Male


title: du145_DU145PS3A_F09_Tacedinaline_1_24

value: Tacedinaline


title: Kapha [S120]


title: Vata-Kapha [S132]

value: VK


title: du145_DU145PS3A_F08_Quizartinib_1.5_24

value: Quizartinib

value: ATCC

value: male


title: du145_DU145PS3A_F07_Ganetespib_0.005_24

value: Ganetespib


title: Kapha [S118]

value: K


title: du145_DU145PS3A_F06_UNTREATED__24

value: UNTREATED


title: du145_DU145PS3A_F05_AT9283_1_24


title: Kapha [S114]

value: Female


title: Kapha [S117]


title: Pitta [S113]

value: P


title: Pitta [S112]


title: Vata-Pitta [S119]


title: Pitta [S115]


title: Liver-Males-Western Diet-Rep2

description: wash bath 2

value: Liver

value: Males

value: Western Diet


title: Liver-Males-Control2-Rep4

description: wash bath 2


title: Liver-Females-Western Diet-Rep5

description: wash bath 2

value: Females


title: du145_DU145PS3A_F04_Dacomitinib_0.001_24

value: Dacomitinib


title: Liver-Males-Western Diet Glucose Fructose-Rep5

description: wash bath 2

value: Western Diet Glucose Fructose


title: Vata [S111]

value: V

value: Male


title: Liver-Females-Control2-Rep3

description: wash bath 2


title: du145_DU145PS3A_F02_ARN509_10_24


title: Vata [S108]


title: Pitta [S107]


title: Vata [S109]


title: Liver-Males-High Fat Diet-Rep4

description: wash bath 2

value: High Fat Diet


title: Liver-Females-Western Diet Glucose Fructose-Rep2

description: wash bath 2


title: Liver-Females-Choline deficient High Fat Diet-Rep4

description: wash bath 2

value: Cholin deficient High Fat Diet


title: Vata [S103]


title: Vata [S104]


title: Liver-Males-Control1-Rep3

description: wash bath 2


title: du145_DU145PS3A_F03_Acalabrutinib_1.5_24

value: Acalabrutinib

value: ATCC


title: Vata [S110]


title: du145_DU145PS3A_F01_Aminopterin_1_24

value: Aminopterin

value: male


title: Kapha [S106]

value: K


title: du145_DU145PS3A_E11_DMSO_0_24

value: DMSO


title: Vata [S102]

value: Female


title: Liver-Females-High Fat Diet-Rep3

description: wash bath 2

value: Liver


title: Pitta [S100]

value: P


title: Pitta [S99]


title: du145_DU145PS3A_E12_Sotrastaurin_3_24

value: Sotrastaurin


title: Vata-Pitta [S105]

value: VP


title: Kapha [S98]


title: Kapha [S97]


title: Pitta [S101]


title: Liver-Males-High Fat Diet-Rep3

description: wash bath 2

value: Males


title: Kapha [S96]


title: Liver-Females-Control1-Rep3

description: wash bath 2

value: Females


title: du145_DU145PS3A_E10_RO4929097_0.5_24


title: du145_DU145PS3A_E08_Galunisertib_2.5_24

value: Galunisertib


title: du145_DU145PS3A_E07_Crenolanib_0.145_24

value: Crenolanib


title: du145_DU145PS3A_E09_CPI613_0.005_24


title: Liver-Males-Western Diet Glucose Fructose-Rep4

description: wash bath 2

value: Western Diet Glucose Fructose


title: du145_DU145PS3A_E06_UNTREATED__24

value: UNTREATED


title: du145_DU145PS3A_E05_Varlitinib_0.005_24

value: Varlitinib


title: du145_DU145PS3A_E04_Combretastatin_0.2_24

value: Combretastatin

value: ATCC


title: Vata [S92]

value: V

value: Male


title: Vata [S90]


title: Liver-Females-Choline deficient High Fat Diet-Rep3

description: wash bath 2

value: Cholin deficient High Fat Diet


title: Liver-Females-Western Diet-Rep4

description: wash bath 2

value: Western Diet


title: Liver-Males-Western Diet Glucose Fructose-Rep3

description: wash bath 2

value: Liver


title: Vata [S89]

value: Female


title: Vata [S94]


title: Vata [S88]


title: du145_DU145PS3A_E03_TAK733_0.08_24

value: male


title: du145_DU145PS3A_E02_Valproic acid_2_24

value: Valproic acid


title: Vata-Pitta [S87]

value: VP


title: Kapha [S93]

value: K


title: Liver-Males-Cholin deficient High Fat Diet-Rep3

description: wash bath 1

value: Males


title: Liver-Males-Control2-Rep3

description: wash bath 2


title: Pitta [S85]

value: P


title: du145_DU145PS3A_E01_Tacrolimus_10_24

value: Tacrolimus


title: Pitta [S83]


title: Pitta [S82]


title: du145_DU145PS3A_D12_SAR245409_0.5_24


title: Vata [S91]


title: Liver-Males-Western Diet-Rep1

description: wash bath 1


title: Liver-Females-Choline deficient High Fat Diet-Rep2

description: wash bath 1

value: Females


title: Vata-Kapha [S81]

value: VK


title: Vata-Pitta [S86]


title: du145_DU145PS3A_D11_MK0752_10_24


title: Liver-Males-Western Diet Glucose Fructose-Rep2

description: wash bath 1

value: Western Diet Glucose Fructose


title: Pitta [S95]


title: Vata [S80]


title: du145_DU145PS3A_D10_Enasidenib_1.5_24

value: Enasidenib

value: ATCC


title: Vata [S79]

value: V

value: Male


title: Vata [S78]


title: Liver-Females-Western Diet-Rep3

description: wash bath 1

value: Western Diet


title: du145_DU145PS3A_D09_AZ12456623_1.5_24


title: Vata [S116]


title: Kapha [S74]


title: Kapha [S73]


title: Vata-Pitta [S76]


title: du145_DU145PS3A_D07_Lonafarnib_0.3_24

value: Lonafarnib


title: Liver-Females-High Fat Diet-Rep2

description: wash bath 1

value: Liver

value: High Fat Diet


title: du145_DU145PS3A_D06_DMSO_0_24

value: DMSO

value: male


title: Kapha [S67]

value: K


title: Kapha [S68]


title: du145_DU145PS3A_D08_MGCD265_1_24


title: Liver-Males-Control2-Rep2

description: wash bath 1

value: Males


title: Liver-Females-Cholin deficient High Fat Diet-Rep1

description: wash bath 1

value: Cholin deficient High Fat Diet


title: du145_DU145PS3A_D05_Cediranib_0.22_24

value: Cediranib


title: Vata-Pitta [S75]

value: VP


title: Vata-Kapha [S64]

value: VK


title: Vata-Pitta [S69]


title: Pitta [S84]

value: P


title: Kapha [S66]


title: Pitta [S70]


title: Vata-Pitta [S63]


title: Kapha [S62]


title: Vata-Kapha [S71]


title: Pitta [S61]


title: Liver-Males-Control1-Rep2

description: wash bath 1


title: Kapha [S65]


title: du145_DU145PS3A_D04_Telatinib_2_24

value: Telatinib


title: Liver-Males-Western Diet Glucose Fructose-Rep1

description: wash bath 1

value: Western Diet Glucose Fructose


title: Kapha [S59]


title: Liver-Females-Western Diet-Rep2

description: wash bath 1

value: Females


title: Vata-Pitta [S60]

value: Male


title: Liver-Females-Control1-Rep1

description: wash bath 1


title: Liver-Males-High Fat Diet-Rep2

description: wash bath 1


title: du145_DU145PS3A_D03_AZD5069_7_24

value: ATCC


title: Kapha [S58]


title: du145_DU145PS3A_D02_UNTREATED__24

value: UNTREATED


title: Liver-Males-Choline deficient High Fat Diet-Rep2

description: wash bath 1

value: Liver


title: du145_DU145PS3A_D01_Cyclosporine_10_24

value: Cyclosporine


title: Pitta [S56]


title: Liver-Females-Control2-Rep2

description: wash bath 1


title: du145_DU145PS3A_C12_Volasertib_0.005_24

value: Volasertib


title: Vata-Pitta [S55]

value: Female


title: Pitta-Kapha [S54]

value: PK


title: Liver-Females-Control2-Rep1

description: wash bath 1


title: Pitta [S53]


title: du145_DU145PS3A_C10_Linsitinib_5.5_24

value: Linsitinib

value: male


title: Liver-Males-High Fat Diet-Rep1

description: wash bath 1

value: Males

value: High Fat Diet


title: Kapha [S51]

value: K


title: Kapha [S50]


title: du145_DU145PS3A_C09_Rucaparib_3.5_24

value: Rucaparib


title: Vata-Pitta [S47]

value: VP


title: du145_DU145PS3A_C08_Enzastaurin_0.24_24

value: Enzastaurin


title: Pitta [S46]

value: P


title: Vata [S57]

value: V


title: Liver-Females-Western Diet Glucose Fructose-Rep1

description: wash bath 1

value: Females

value: Western Diet Glucose Fructose


title: Kapha [S45]

value: Male


title: Vata [S44]


title: Liver-Males-Control2-Rep1

description: wash bath 1

value: Liver


title: du145_DU145PS3A_C11_Momelotinib_1_24

value: Momelotinib

value: ATCC


title: Pitta [S52]


title: Kapha [S42]


title: du145_DU145PS3A_C06_DMSO_0_24

value: DMSO


title: Liver-Females-Western Diet-Rep1

description: wash bath 1

value: Western Diet


title: Liver-Males-Control1-Rep1

description: wash bath 1


title: Vata [S48]


title: Kapha [S49]


title: Kapha [S40]


title: Pitta [S41]


title: Liver-Females-High Fat Diet-Rep1

description: wash bath 1


title: du145_DU145PS3A_C05_TAK700_10_24

value: male


title: Vata-Pitta [S37]


title: Liver-Males-Choline deficient High Fat Diet-Rep1

description: wash bath 1

value: Males

value: Cholin deficient High Fat Diet


title: du145_DU145PS3A_C07_Copanlisib_0.16_24

value: Copanlisib


title: Pitta [S43]


title: du145_DU145PS3A_C04_Amonafide_0.335_24

value: Amonafide


title: Kapha [S38]

value: K


title: PPARaLKO_Males_Fasted_rep6

description: Serial Wash Batch22

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE V2 microarray (8X60K, Design 074809)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34786 spots out of 62976 were selected.  The mean signal of the 16 first samples, 8 next, 16 other and 8 last ones were substracted to individuals signals to correct the batch effect of the 4 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32131 rows each corresponding to a unique ProbeName (provided as data Matrix).

treatment_protocol: Mice were fasted for 24 hours.

value: liver

value: PPARaLKO

tag: nutrition

value: Fasted

value: 14 weeks


title: du145_DU145PS3A_C03_AMG900_2.5_24


title: PPARaLWT_Females_Fed_rep6

description: Serial Wash Batch22

value: PPARaLWT

value: Females

value: Fed


title: PPARaLWT_Females_Fasted_rep5

description: Serial Wash Batch22


title: Vata [S36]

value: V

value: Male


title: Pitta [S35]

value: P


title: Pitta-Kapha [S77]

value: PK

value: Female


title: PPARaLKO_Males_Fed_rep2

description: Serial Wash Batch22

value: Males


title: Pitta [S32]


title: Kapha [S31]


title: du145_DU145PS3A_B12_Calcitriol_0.005_24

value: Calcitriol

value: ATCC

value: male


title: Kapha [S39]

value: K


title: du145_DU145PS3A_C02_UNTREATED__24

value: UNTREATED


title: du145_DU145PS3A_B10_AZ13064550_10_24


title: Pitta-Kapha [S30]


title: PPARaLWT_Males_Fed_rep5

description: Serial Wash Batch22

value: liver


title: du145_DU145PS3A_C01_Aspirin_10_24

value: Aspirin


title: du145_DU145PS3A_B09_AZ12419304_0.5_24


title: PPARaLWT_Males_Fasted_rep6

description: Serial Wash Batch22

value: Fasted

value: 14 weeks


title: du145_DU145PS3A_B08_Dovitinib_0.31_24

value: Dovitinib


title: du145_DU145PS3A_B11_LY3023414_0.05_24


title: Pitta [S25]


title: PPARaLWT_Males_Fasted_rep3

description: Serial Wash Batch21

value: PPARaLWT


title: du145_DU145PS3A_B07_Pimasertib_0.31_24

value: Pimasertib


title: PPARaLKO_Females_Fasted_rep3

description: Serial Wash Batch22

value: PPARaLKO

value: Females


title: Vata [S34]

value: V

value: Male


title: Pitta-Kapha [S29]

value: PK


title: du145_DU145PS3A_B06_Saridegib_1_24

value: Saridegib


title: Kapha [S28]


title: Vata-Pitta [S22]

value: VP


title: PPARaLKO_Females_Fed_rep1

description: Serial Wash Batch22

value: Fed


title: Vata-Pitta [S27]


title: Vata-Pitta [S23]


title: PPARaLWT_Males_Fed_rep2

description: Serial Wash Batch21

value: Males


title: Vata-Kapha [S72]

value: VK


title: Kapha [S26]

value: K


title: Pitta-Kapha [S17]


title: Liver-Females-Control1-Rep2

description: wash bath 1

value: Liver


title: du145_DU145PS3A_B05_EpothiloneD_0.04_24

value: EpothiloneD

value: ATCC

value: male


title: du145_DU145PS3A_B04_ABT888_10_24


title: du145_DU145PS3A_B03_AEE788_0.17_24


title: Kapha [S20]


title: Vata-Kapha [S24]


title: Kapha [S18]


title: Pitta [S21]

value: P


title: PPARaLKO_Males_Fasted_rep4

description: Serial Wash Batch21

value: liver

value: Fasted

value: 14 weeks


title: du145_DU145PS3A_B02_DMSO_0_24

value: DMSO


title: PPARaLKO_Females_Fasted_rep2

description: Serial Wash Batch21

value: PPARaLKO

value: Females


title: du145_DU145PS3A_B01_Hydroxychloroquine_0.5_24

value: Hydroxychloroquine


title: Pitta-Kapha [S33]

value: PK

value: Male


title: PPARaLKO_Males_Fed_rep6

description: Serial Wash Batch21

value: Males

value: Fed


title: du145_DU145PS3A_A12_Duvelisib_5_24

value: Duvelisib


title: Kapha [S9]

value: K


title: Pitta [S15]


title: Pitta-Kapha [S13]


title: Kapha [S14]


title: PPARaLWT_Females_Fasted_rep3

description: Serial Wash Batch21

value: PPARaLWT


title: Pitta-Kapha [S7]


title: Vata-Pitta [S11]

value: VP


title: PPARaLWT_Females_Fed_rep4

description: Serial Wash Batch21


title: Kapha [S19]


title: PPARaLKO_Females_Fed_rep4

description: Serial Wash Batch21


title: Kapha [S3]


title: Vata-Kapha [S8]

value: VK


title: Vata [S4]

value: V


title: du145_DU145PS3A_A11_Pracinostat_0.03_24

value: Pracinostat

value: ATCC

value: male


title: Pitta [S10]

value: P


title: du145_DU145PS3A_A10_AMG337_9.5_24


title: Pitta-Kapha [S12]


title: PPARaLWT_Females_Fed_rep3

description: Serial Wash Batch21

value: liver

value: 14 weeks


title: du145_DU145PS3A_A09_GDC0068_0.5_24


title: Pitta-Kapha [S16]


title: PPARaLKO_Males_Fasted_rep1

description: Serial Wash Batch21

value: PPARaLKO

value: Fasted


title: PPARaLWT_Males_Fasted_rep5

description: Serial Wash Batch21


title: du145_DU145PS3A_A08_PF04691502_0.24_24


title: du145_DU145PS3A_A06_Apremilast_0.5_24

value: Apremilast


title: du145_DU145PS3A_A05_Zibotentan_1.5_24

value: Zibotentan


title: du145_DU145PS3A_A07_Tivozanib_0.175_24

value: Tivozanib


title: CMZ173 [NPB-4]

city: New York

first: Juan

middle: M

last: Arriaga

address: 1425 Madison Ave

department: Oncological Sciences, Urology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Libraries were sequenced using Illumina HiSeq2500/4000 or NovaSeq6000 at Columbia Genome Center, or Genewiz. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp or 150bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
Reads were pseudo-aligned to mouse reference genome version GRCm38 mm10, using kallisto v0.44.0 (Bray et al., 2016) with sequence-based bias correction.
Genome_build: Mouse: UCSC/mm10
Supplementary_files_format_and_content: Tab-delimited text files include kallisto estimated counts for each gene in each sample
Supplementary_files_format_and_content: Gemms_counts.xlsx: Includes 19 NPK samples from GSE143815

source_name: Mouse prostate primary tumor

extract_protocol:
RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.
Libraries were prepared by the Columbia Genome Center or Genewiz. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using TruSeq RNA library prep kit v2 or TruSeq Stranded mRNA library prep kit.

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26R+/+

value: intact

tag: mouse id

tag: use

value: Interactome + VIPER analysis


title: CMZ176 [NPB-3]

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26RLSL-EYFP/+


title: Pitta-Kapha [S6]

value: PK

value: Male


title: Pitta-Kapha [S5]


title: PPARaLKO_Females_Fed_rep2

description: Serial Wash Batch21

value: Females

value: Fed


title: Vata [S2]

value: V


title: PPARaLKO_Males_Fed_rep1

description: Serial Wash Batch21

value: liver

value: Males


title: du145_DU145PS3A_A04_Onalespib_0.065_24

value: Onalespib

value: ATCC

value: male


title: TRP_2

city: Guang Zhou

first: Qun

last: Miao

address: Huangpu avenue

institute: Jinan University

data_processing:
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colorectum

extract_protocol: Total RNA was extracted using TRIzol Reagent (Servicebio, Wuhan, China) at a ratio of 106 cells per mL of reagent according to the manufacturer’s instructions.

value: colorectum

value: Pericyte

tag: cell type

value: Tumor pericyte

value: overexpression of TRPM8


title: TRP_3

tag: tissue


title: vec_1

value: vector


title: PPARaLKO_Females_Fed_rep5

description: Serial Wash Batch12

tag: genotype

value: PPARaLKO

value: 14 weeks


title: PPARaLKO_Females_Fasted_rep5

description: Serial Wash Batch21

value: Fasted


title: vec_2


title: vec_3


title: TRP_1


title: PPARaLKO_Males_Fed_rep5

description: Serial Wash Batch12


title: PPARaLWT_Females_Fasted_rep6

description: Serial Wash Batch21

value: PPARaLWT


title: Vata-Pitta [S1]

tag: prakriti

value: VP

value: Male


title: CMZ175 [NPB-2]

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26RLSL-EYFP/+

value: intact

value: Interactome + VIPER analysis


title: du145_DU145PS3A_A03_Icotinib_1_24

value: Icotinib

value: ATCC


title: CMZ174 [NPB-1]

value: Nkx3.1CreERT2/+; Ptenflox/flox; B-RafV6E/+; R26R+/+


title: CMZ170 [NPS-5]

value: Nkx3.1CreERT2/+; Ptenflox/flox; SMAD4flox/flox; R26R+/+


title: du145_DU145PS3A_A02_DMSO_0_24

value: DMSO

value: male


title: CMZ169 [NPS-2]

value: Nkx3.1CreERT2/+; Ptenflox/flox; SMAD4flox/flox; R26R-CAGLSL-EYFP/+


title: du145_DU145PS3A_A01_Mycophenolate_1.5_24

value: Mycophenolate


title: CMZ168 [NPS-1]


title: CMZ172 [NPS-4]


title: du145_DU145PS2B_H12_Dactinomycin_0.00265_24

value: Dactinomycin


title: CMZ134 [NPMycWT-6]

value: castrated

value: Interactome


title: CMZ171 [NPS-3]


title: CMZ131 [NPMycWT-3]


title: du145_DU145PS2B_H11_UNTREATED__24

value: UNTREATED


title: CMZ132 [NPMycWT-5]


title: CMZ129 [NPMycWT-2]


title: CMZ139 [NPMycTA-6]


title: CMZ133 [NPMycWT-4]


title: du145_DU145PS2B_H10_Rigosertib_0.075_24

value: Rigosertib


title: CMZ138 [NPMycTA-5]

value: Mouse prostate primary tumor


title: CMZ130 [NPMycWT-1]


title: du145_DU145PS2B_H09_MK1775_0.115_24


title: CMZ140 [NPMycTA-4]


title: PPARaLWT_Males_Fed_rep6

description: Serial Wash Batch21

value: liver

value: PPARaLWT

tag: gender

value: Males

value: Fed

value: 14 weeks


title: du145_DU145PS2B_H08_Amuvatinib_0.02_24

value: Amuvatinib

value: ATCC


title: CMZ136 [NPMycTA-2]

value: intact


title: du145_DU145PS2B_H07_BI2536_0.0029_24

value: male


title: CMZ177 [NPMycTA-1]


title: PPARaLWT_Males_Fed_rep3

description: Serial Wash Batch12


title: du145_DU145PS2B_H06_AZD5363_0.5_24


title: CMZ149 [NPM-4]

value: Nkx3.1CreERT2/+; Ptenflox/flox; ARR2/Pbsn-MYCTg/; R26R+/+

value: Interactome + VIPER analysis


title: PPARaLKO_Females_Fasted_rep4

description: Serial Wash Batch12

value: PPARaLKO

value: Females

value: Fasted


title: CMZ178 [NPMycTA-3]

value: Interactome


title: CMZ179 [NPM-3]

value: Nkx3.1CreERT2/+; Ptenflox/flox; ARR2/Pbsn-MYCTg/; R26R-CAGLSL-EYFP/+


title: du145_DU145PS2B_H05_Elesclomol_0.07_24

value: Elesclomol


title: CMZ150 [NPM-1]

value: Mouse prostate primary tumor


title: CMZ166 [NPp53 H/L-11]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R+/+

value: castrated


title: PPARaLWT_Females_Fasted_rep2

description: Serial Wash Batch12

value: liver

value: PPARaLWT


title: CMZ165 [NPp53 H/L-9]


title: du145_DU145PS2B_H04_AUY922_0.005_24


title: CMZ164 [NPp53 H/L-10]


title: du145_DU145PS2B_H03_Floxuridine_0.5_24

value: Floxuridine


title: CMZ167 [NPp53 H/L-8]


title: CMZ161 [NPp53 H/L-2]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R-CAGLSL-EYFP/+


title: CMZ163 [NPp53 H/L-7]


title: du145_DU145PS2B_H02_Prednisone_1_24

value: Prednisone

value: ATCC


title: PPARaLWT_Females_Fed_rep2

description: Serial Wash Batch12

value: Fed

value: 14 weeks


title: CMZ162 [NPp53 H/L-1]

value: intact

value: Interactome + VIPER analysis


title: du145_DU145PS2B_H01_Oxaliplatin_2.5_24

value: Oxaliplatin

value: male


title: CMZ157 [NPp53 H/+-7]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/+; R26R-CAGLSL-EYFP/+

value: Interactome


title: PPARaLKO_Males_Fasted_rep2

description: Serial Wash Batch12

value: PPARaLKO

value: Males

value: Fasted


title: du145_DU145PS2B_G12_Bosutinib_0.375_24

value: Bosutinib


title: PPARaLWT_Females_Fasted_rep1

description: Serial Wash Batch11

value: liver

value: PPARaLWT

value: Females


title: PPARaLKO_Males_Fasted_rep5

description: Serial Wash Batch11


title: CMZ153 [NPM-5]

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; ARR2/Pbsn-MYCTg/; R26R+/+

value: castrated


title: CMZ158 [NPp53 H/+-5]


title: CMZ156 [NPp53 H/+-3]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/+; R26R+/+


title: PPARaLWT_Males_Fasted_rep4

description: Serial Wash Batch11

value: 14 weeks


title: CMZ159 [NPp53 H/+-4]


title: du145_DU145PS2B_G10_Flavopiridol_0.06_24

value: Flavopiridol

value: ATCC


title: CMZ115 [NPp53-15]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox; R26R-CAGLSL-EYFP/+

value: Interactome + VIPER analysis


title: du145_DU145PS2B_G11_UNTREATED__24

value: UNTREATED

value: male


title: CMZ154 [NPp53 H/+-2]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/+; R26R-CAGLSL-EYFP/+

value: intact

value: Interactome


title: PPARaLWT_Females_Fed_rep5

description: Serial Wash Batch11

value: liver

value: Fed


title: du145_DU145PS2B_G09_Obatoclax Mesylate_0.1_24

value: Obatoclax Mesylate


title: CMZ114 [NPp53-13]

value: Mouse prostate primary tumor


title: PPARaLKO_Females_Fasted_rep1

description: Serial Wash Batch11

value: PPARaLKO

value: Females

value: Fasted


title: CMZ010 [NPp53-12]

value: castrated


title: du145_DU145PS2B_G08_HMN214_0.5_24


title: CMZ009 [NPp53-11]


title: CMZ155 [NPp53 H/+-1]


title: CMZ008 [NPp53-10]


title: du145_DU145PS2B_G07_GSK461364_0.005_24


title: CMZ113 [NPp53-6]


title: CMZ145 [NPBRCA2-5]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Brca2flox/flox; R26R+/+


title: du145_DU145PS2B_G06_Navitoclax_0.5_24

value: Navitoclax

value: ATCC


title: CMZ112 [NPp53-5]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53flox/flox; R26R-CAGLSL-EYFP/+

value: Interactome + VIPER analysis


title: CMZ143 [NPBRCA2-3]

value: Nkx3.1CreERT2/+; Ptenflox/flox; Brca2flox/flox; R26R-CAGLSL-EYFP/+


title: du145_DU145PS2B_G05_Gossypol_2_24

value: Gossypol

value: male


title: CMZ144 [NPBRCA2-4]

value: intact


title: du145_DU145PS2B_G04_Sonidegib_8_24

value: Sonidegib


title: CMZ142 [NPBRCA2-2]


title: CMZ141 [NPBRCA2-1]


title: CMZ128 [NPE6]


title: CMZ127 [NPE5]


title: PPARaLWT_Males_Fasted_rep1

description: Serial Wash Batch12

value: liver

value: PPARaLWT

value: Males

value: 14 weeks


title: CMZ126 [NPE4]

value: Mouse prostate primary tumor


title: du145_DU145PS2B_G03_Bicalutamide_10_24

value: Bicalutamide


title: CMZ123 [NPE3]


title: du145_DU145PS2B_G02_Albendazole_1_24

value: Albendazole


title: CMZ124 [NPE2]


title: du145_DU145PS2B_G01_Arsenic_0.5_24

value: Arsenic


title: PPARaLKO_Males_Fed_rep3

description: Serial Wash Batch11

value: PPARaLKO

value: Fed


title: PPARaLWT_Males_Fed_rep1

description: Serial Wash Batch11


title: CMZ002 [NP-14]

value: castrated


title: du145_DU145PS2B_F12_Amsacrine_0.11_24

value: Amsacrine

value: ATCC


title: PPARaLKO_Males_Fed_rep4

description: Serial Wash Batch11


title: PPARaLKO_Males_Fasted_rep3

description: Serial Wash Batch11

value: Fasted


title: PPARaLKO_Females_Fasted_rep6

description: Serial Wash Batch11

value: Females


title: CMZ001 [NP-11]

value: Interactome + VIPER analysis


title: CMZ004 [NP-12]


title: PPARaLKO_Females_Fed_rep6

description: Serial Wash Batch11


title: PPARaLWT_Males_Fasted_rep2

description: Serial Wash Batch11


title: Liver - Male_PPARaLKO_Vehicle - Rep6

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 38 out of 47 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 39696 spots out of 62976 were selected.  The mean signal of the 31 first samples and 16 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 37027 rows each corresponding to a unique ProbeName (provided as data Matrix).

growth_protocol: Mice were housed at 20-22°C under 12h/12h light/dark conditions and fed a chow diet.

treatment_protocol: Mice either received the PPARα agonist pemafibrate (0,1 mg/kg/day) or vehicle (Carboxymethyl cellulose 0,5%) by gavage for 14 days.

value: Male

value: LKO

value: Vehicle

tag: washbatch


title: CMZ125 [NPE1]

tag: treatment

value: intact


title: CMZ122 [NP-8]


title: du145_DU145PS2B_F10_Entinostat_0.12_24

value: Entinostat

value: male


title: CMZ120 [NP-7]

value: Mouse prostate primary tumor


title: CMZ119 [NP-6]


title: du145_DU145PS2B_F09_Epigallocatechin_0.5_24

value: Epigallocatechin


title: CMZ121 [NP-5]


title: du145_DU145PS2B_F11_DMSO__24

value: DMSO


title: CMZ116 [NP-3]

value: Interactome


title: CMZ118 [NP-2]


title: CMZ117 [NP-1]


title: du145_DU145PS2B_F07_Brivanib_10_24

value: Brivanib


title: hdac2 rep3

city: Houston

first: Hui-Lin

last: Pan

state: Tx

address: 1515 Holcomb Blvd

institute: MD Anderson Cancer Center

data_processing:
Reads were mapped to mouse genome (mm10) using Hisat2.
The mapped files were converted and sorted into bam files using samtools.
Then reads abundant of each gene were calculated using FeatureCounts.
Differential expressed gene were analysis using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FeatureCounts values for each Sample.

source_name: Dorsal root ganglion

extract_protocol:
Dorsal root ganglia were removed, flash frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Libraries were constructed and sequenced on the Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Dorsal root ganglion

value: post natal 8-week


title: hdac2 rep2


title: hdac2 rep1


title: du145_DU145PS2B_F08_Tivantinib_0.5_24

value: Tivantinib

tag: cell line

value: ATCC


title: WT rep3


title: Liver - Female_PPARaLWT_Pemafibrate - Rep6

value: liver

value: Female

value: LWT

value: Pemafibrate


title: du145_DU145PS2B_F05_-__24

tag: provider


title: PPARaLKO_Females_Fed_rep3

description: Serial Wash Batch11

value: PPARaLKO

value: Females

value: Fed

tag: age

value: 14 weeks


title: WT rep1


title: WT rep2


title: du145_DU145PS2B_F04_Omacetaxine_0.015_24

value: Omacetaxine

tag: vendor id

value: male


title: Liver - Male_PPARaLWT_Pemafibrate - Rep5

value: Male


title: PPARaLWT_Females_Fed_rep1

description: Serial Wash Batch11

value: PPARaLWT


title: PPARaLWT_Males_Fed_rep4

description: Serial Wash Batch11

value: Males


title: PPARaLWT_Females_Fasted_rep4

description: Serial Wash Batch11

value: Fasted


title: Liver - Male_PPARaLWT_Vehicle - Rep6

value: Vehicle


title: du145_DU145PS2B_F02_Thalidomide_8.5_24

value: Thalidomide

tag: Sex


title: CMZ160 [NPp53 H/+-6]

value: Mouse prostate primary tumor

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/+; R26R-CAGLSL-EYFP/+

value: castrated

value: Interactome


title: du145_DU145PS2B_F03_Finasteride_5.5_24

value: Finasteride

value: ATCC


title: Liver - Female_PPARaLKO_Pemafibrate - Rep4

value: liver

value: Female

value: LKO

value: Pemafibrate


title: Liver - Male_PPARaLKO_Pemafibrate - Rep6


title: Liver - Female_PPARaLKO_Vehicle - Rep6


title: Liver - Female_PPARaLKO_Vehicle - Rep5


title: du145_DU145PS2B_F06_UNTREATED__24

value: UNTREATED

value: male


title: du145_DU145PS2B_F01_Carmustine_1.5_24

value: Carmustine


title: Liver - Male_PPARaLKO_Pemafibrate - Rep5

value: Male


title: du145_DU145PS2B_E12_Idarubicin_0.02_24

value: Idarubicin


title: du145_DU145PS2B_E11_DMSO__24

value: DMSO


title: SQR_3_S_STRIGA_REP3

city: Davis

first: Dorota

last: Kawa

state: CA

address: 451 Health Science Dr

institute: University of California DAvis

description: 3'mRNA-Seq library

data_processing:
Technical replicates of the libraries were pooled before reads were processed
Barcodes were trimmed from raw reads with fastx-trimmer with parameters: -v -f 12 -Q33
Adaptor trimming and quality filtering was performed with reaper from Kraken Suite  with options: -geom no-bc -tabu $tabu -3pa $seqAdapt -noqc -dust-suffix 6/ACTG -dust-suffix-late 6/ACTG -nnn-check 1/1 -qqq-check 35/10 -clean-length 30 -polya 5.
Trimmed reads were mapped to the reference genome of Sorghum bicolor BTx623 (McCormick et al., 2018) using STAR (Dobin et al., 2013) with options: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignIntronMin 20 --alignIntronMax 10000 --outFilterMismatchNmax 5 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
Assembly: Sorghum bicolor v3.1.1 (https://phytozome.jgi.doe.gov/pz/portal.html)
Supplementary files format and content: Table with raw gene counts for every gene and every sample

organism: Sorghum bicolor

source_name: whole root tissue

growth_protocol: Four day old seedlings of approximately the same radicle length were transferred to a soil plug (natural or sterile soil), that is, a 50 mL falcon tube filled with sterile soil (soil collected from the Clue Field in the Netherlands; 52° 03’ 37.91’’ N and 5° 45’ 7.074’’ E, which was further dried, sieved through 4 mm mesh and sterilized by gamma irradiation) mixed with 5% sterile water (w/v). Seedlings were watered with autoclaved water every second day. On day ten, seedlings together with the soil plug were transferred to 40 cm long cones (Greenhouse Megastore, catalog number CN-SS-DP) filled with 700 mL of 0.5-1.0 mm filter sand (filcom.nl/). The bottom layer of the cones was filled with 350 mL of filter sand (0.5-1.0 mm, filcom.nl/)  and the upper layer was filled with 350 mL preconditioned sand without (control) or with Striga seeds (3000 germinable Striga seeds per cone). Plants were organized in a randomized manner in a greenhouse compartment with a temperature of 28°C during the day (11 hours) and 25°C at night (13 hours), with 70% relative humidity and light intensity of 450mmol/m2/s. At days zero, seven and 14, plants were watered with 50 mL of modified half-strength Hoagland solution with 0.05 mM KH2PO4. On days one, four, ten, 13 and 17, plants were watered with 50 mL deionized sterile water. Two and three weeks after transfer to the cones (corresponding to 28 and 35 day old plants) root material was harvested two hours after the light turned on. Each sorghum plant was gently taken from the cone and the whole root system was cleaned from the sand and soil by washing in water, dried with paper towel and snap frozen in liquid nitrogen (taking approximately 3 minutes per plant).

extract_protocol:
Root tissue was manually ground and RNA was extracted with RNaesy Plus Mini kit (Qiagen) with application of QIAshredder columns (Qiagen) and on-column Dnase I (Qiagen) treatment. Total RNA obtained was precipitated with 3M NaOAc pH 5.2 (Thermo Scientific) in 100% ethanol and washed with 70% (v/v) ethanol
RNA‑seq libraries were synthesized with QuantSeq 3’ mRNA‑Seq Library Prep Kit (Lexogen) according to manufacturer protocol.

treatment_protocol: Striga infection = 3000 germinable Striga seeds

value: whole root tissue

tag: plant age

value: 35 day old, 3 weeks post infection

value: Shanqui Red

tag: soil

value: sterile

value: Striga


title: SQR_3_S_STRIGA_REP4

description: 3'mRNA-Seq library


title: Liver - Male_PPARaLKO_Vehicle - Rep5

value: Vehicle


title: Liver - Female_PPARaLWT_Vehicle - Rep6

value: LWT


title: Liver - Male_PPARaLWT_Pemafibrate - Rep4

value: liver


title: Liver - Male_PPARaLWT_Vehicle - Rep5


title: du145_DU145PS2B_E10_YM155_0.015_24

value: ATCC


title: SQR_3_S_CTR_REP1

description: re-analysis of GSE167101

value: control


title: SQR_3_S_CTR_REP4

description: 3'mRNA-Seq library


title: SQR_3_N_STRIGA_REP4

description: 3'mRNA-Seq library

value: natural


title: SQR_3_N_STRIGA_REP3

description: 3'mRNA-Seq library


title: SQR_3_S_CTR_REP3

description: re-analysis of GSE167101


title: SQR_3_S_STRIGA_REP1

description: 3'mRNA-Seq library


title: SQR_3_S_CTR_REP2

description: re-analysis of GSE167101


title: SQR_3_S_STRIGA_REP2

description: 3'mRNA-Seq library


title: du145_DU145PS2B_E09_Neratinib_0.225_24

value: Neratinib


title: du145_DU145PS2B_E08_Linifanib_1_24

value: Linifanib

value: male


title: SQR_3_N_STRIGA_REP2

description: 3'mRNA-Seq library


title: SQR_3_N_CTR_REP4

description: 3'mRNA-Seq library


title: SQR_3_N_CTR_REP3

description: 3'mRNA-Seq library


title: SQR_2_S_STRIGA_REP4

description: 3'mRNA-Seq library

value: 28 day old, 2 weeks post infection


title: SQR_3_N_STRIGA_REP1

description: 3'mRNA-Seq library


title: SQR_3_N_CTR_REP1

description: 3'mRNA-Seq library


title: SQR_3_N_CTR_REP2

description: 3'mRNA-Seq library


title: Liver - Female_PPARaLKO_Pemafibrate - Rep5

value: Female

value: LKO

value: Pemafibrate


title: SQR_2_S_STRIGA_REP3

description: 3'mRNA-Seq library

value: whole root tissue


title: du145_DU145PS2B_E07_PD0325901_0.015_24


title: Liver - Female_PPARaLWT_Vehicle - Rep4


title: du145_DU145PS2B_E06_UNTREATED__24

value: UNTREATED


title: SQR_2_S_STRIGA_REP1

description: 3'mRNA-Seq library

value: Shanqui Red

value: sterile


title: SQR_2_S_CTR_REP4

description: re-analysis of GSE167101


title: SQR_2_S_CTR_REP3

description: re-analysis of GSE167101


title: du145_DU145PS2B_E05_AZD2014_0.35_24


title: SQR_2_S_CTR_REP2

description: re-analysis of GSE167101


title: SQR_2_S_STRIGA_REP2

description: 3'mRNA-Seq library

value: Striga


title: du145_DU145PS2B_E04_Rosiglitazone_2_24

value: Rosiglitazone


title: Liver - Male_PPARaLWT_Pemafibrate - Rep3

value: liver

value: Male

value: LWT


title: SQR_2_S_CTR_REP1

description: re-analysis of GSE167101

value: control


title: Liver - Male_PPARaLKO_Pemafibrate - Rep4


title: SQR_2_N_STRIGA_REP4

description: 3'mRNA-Seq library

value: natural


title: SQR_2_N_STRIGA_REP3

description: 3'mRNA-Seq library


title: Liver - Female_PPARaLKO_Vehicle - Rep4

value: Vehicle


title: CMZ003 [NP-13]

value: Mouse prostate primary tumor

value: castrated

tag: mouse id

value: Interactome + VIPER analysis


title: Liver - Male_PPARaLWT_Vehicle - Rep4


title: SQR_2_N_STRIGA_REP2

description: 3'mRNA-Seq library

value: 28 day old, 2 weeks post infection


title: SQR_2_N_STRIGA_REP1

description: 3'mRNA-Seq library


title: du145_DU145PS2B_E02_Fludarabine_3_24

value: Fludarabine

value: ATCC

value: male


title: du145_DU145PS2B_E01_Pipobroman_10_24

value: Pipobroman


title: du145_DU145PS2B_E03_Altretamine_10_24

value: Altretamine


title: du145_DU145PS2B_D12_Daunorubicin_0.03_24

value: Daunorubicin


title: SQR_2_N_CTR_REP3

description: 3'mRNA-Seq library

value: whole root tissue

value: Shanqui Red


title: SQR_2_N_CTR_REP1

description: 3'mRNA-Seq library


title: tumor sample 10

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

description:
Test
SAMPLE 10

data_processing:
miRNAs with Ct>35 were considered as not expressed and excluded from further analysis.
Matrix normalized worksheet reports normalized signals. The normalization was performed according to the manufacturers instructions and array data were normalized using the average of RNU-U6  as endogenous control and after the review of the Literature and the assessment of its stability in our study cohort.
miRNA data were analyzed with SDS Relative Quantification Software version 2.4. (Applied Biosystems); miRNAs with Ct values ≥35 were considered as not expressed and were excluded from further analysis. Normalization was carried out by subtracting the U6 mean Ct from individual Ct values

label: FAM

source_name: tumor sample

label_protocol: Total RNA was isolated from fresh tumor tissue. tTotal RNA was retrotranscribed through the TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems) and MegaPlex RT primers (Applied Biosystems) pools A and B. cDNAs were preamplified using TaqMan PreAmp Master Mix and PreAmp primers (pools A and B; Applied Biosystems). The miRNA arrays were loaded with the preampli-fied samples and run on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

extract_protocol: Total RNA was isolated using miRVana PARIS kit (Invitrogen Cat No. AM1556) according to the manufacturer’s protocol.

tag: disease

value: Gastrointestinal stromal tumor

tag: driver gene

value: PDGFRA

tag: mutation

value: PDGFRA non D842V


title: tumor sample 8

description:
Test
SAMPLE 8


title: tumor sample 7

description:
Test
SAMPLE 7


title: Liver - Female_PPARaLWT_Pemafibrate - Rep2

tag: tissue

value: liver

value: Female

tag: genotype

value: LWT

value: Pemafibrate


title: du145_DU145PS2B_D11_Disulfiram_0.015_24

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

value: Disulfiram


title: tumor sample 6

description:
Test
SAMPLE 6


title: Liver - Female_PPARaLKO_Pemafibrate - Rep6

tag: gender

value: LKO


title: tumor sample 5

description:
Test
SAMPLE 5

value: PDGFRA D842V


title: Liver - Male_PPARaLKO_Vehicle - Rep4

value: Male

value: Vehicle

tag: washbatch


title: Liver - Female_PPARaLWT_Vehicle - Rep5

tag: treatment


title: Liver - Female_PPARaLKO_Pemafibrate - Rep3

tag: strain


title: du145_DU145PS2B_D10_KX2391_0.03_24

tag: cell line

value: ATCC

value: male


title: Liver - Male_PPARaLKO_Pemafibrate - Rep1


title: tumor sample 4

description:
Test
SAMPLE 4


title: SQR_2_N_CTR_REP4

description: 3'mRNA-Seq library

value: 28 day old, 2 weeks post infection

value: natural

value: control


title: du145_DU145PS2B_D09_Dinaciclib_0.005_24

value: Dinaciclib

tag: provider


title: Liver - Female_PPARaLWT_Vehicle - Rep3


title: Liver - Male_PPARaLWT_Vehicle - Rep1


title: Liver - Female_PPARaLWT_Pemafibrate - Rep3


title: tumor sample 3

description:
Test
SAMPLE 3

value: Gastrointestinal stromal tumor

value: PDGFRA


title: Liver - Male_PPARaLWT_Pemafibrate - Rep1

value: liver


title: Liver - Female_PPARaLKO_Vehicle - Rep3

value: Female


title: tumor sample 2

description:
Test
SAMPLE 2


title: Liver - Male_PPARaLKO_Vehicle - Rep3


title: tumor sample 9

description:
Test
SAMPLE 9

value: PDGFRA non D842V


title: du145_DU145PS2B_D08_BGJ398_8_24

tag: age


title: du145_DU145PS2B_D05_Selumetinib_10_24

value: Selumetinib

tag: vendor id


title: Liver - Female_PPARaLKO_Pemafibrate - Rep2

value: Pemafibrate


title: 99R_OR_89_G6

city: Loughborough

first: Gabriel

last: Castrillo

address: Nr Loughborough

department: School of Biosciences

institute: University of Nottingham

data_processing:
For the analysis of the RNASeq data, reads were first subjected to quality control and filtering via fastp v0.20.1 (59). The resulting high-quality reads were pseudo-aligned to the Arabidopsis thaliana genome deposited in the Ensembl Plants version 52, using salmon v1.6.0 (60). Gene level summarization from the salmon quantification was performed with the tximport function from the tximport v.1.22.0 R package (50).
Assembly: Ensembl Plants version 52
Supplementary files format and content: Gene level summarization from the salmon quantification

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
RNA was extracted from plant roots following Logemann et al.
RNA libraries were prepared following Finkel et al. with modification

value: Root


title: 9R

value: Col 0


title: 99R_OR_89_G7

value: arf7 arf19


title: 98R


title: 97R


title: du145_DU145PS2B_D04_Bosentan_1_24

value: Bosentan

tag: Sex


title: 95R


title: 94R


title: tumor sample 1

description:
Test
SAMPLE 1

value: PDGFRA D842V


title: 93R


title: 91R


title: 92R


title: du145_DU145PS2B_D07_PKC412_0.23_24

value: ATCC

value: male


title: du145_DU145PS2B_D06_DMSO__24

value: DMSO


title: 96R


title: Liver - Female_PPARaLWT_Pemafibrate - Rep5

value: LWT


title: Liver - Male_PPARaLKO_Pemafibrate - Rep2

value: Male

value: LKO


title: 90R


title: Liver - Male_PPARaLWT_Vehicle - Rep2

value: Vehicle


title: Liver - Female_PPARaLWT_Vehicle - Rep2

value: liver


title: Liver - Male_PPARaLKO_Vehicle - Rep2


title: 8R


title: du145_DU145PS2B_D02_UNTREATED__24

value: UNTREATED


title: Liver - Female_PPARaLWT_Pemafibrate - Rep4

value: Female


title: Liver - Female_PPARaLKO_Vehicle - Rep2


title: Liver - Female_PPARaLKO_Pemafibrate - Rep1


title: du145_DU145PS2B_D03_Leucovorin_2_24

value: Leucovorin


title: du145_DU145PS2B_C12_Tofacitinib_0.305_24

value: Tofacitinib


title: 86R

value: Root


title: 88R


title: du145_DU145PS2B_D01_Thiotepa_3.5_24

value: Thiotepa


title: 85R


title: Liver - Female_PPARaLKO_Vehicle - Rep1


title: du145_DU145PS2B_C10_GDC0941_0.5_24


title: 84R


title: 83R


title: du145_DU145PS2B_C09_Alisertib_0.17_24

value: Alisertib


title: 81R


title: 82R


title: Liver - Female_PPARaLWT_Vehicle - Rep1


title: du145_DU145PS2B_C11_Azathioprine_0.25_24

value: Azathioprine


title: 79R


title: 7R

value: Col 0


title: Liver - Female_PPARaLWT_Pemafibrate - Rep1

value: Pemafibrate


title: 78R


title: du145_DU145PS2B_C07_Bafetinib_8.5_24

value: Bafetinib

value: ATCC

value: male


title: 77R


title: 76R


title: Liver - Male_PPARaLKO_Vehicle - Rep1

value: Male


title: 75R


title: du145_DU145PS2B_C06_DMSO__24

value: DMSO


title: du145_DU145PS2B_C05_Azacitidine_0.02_24

value: Azacitidine


title: 80R


title: Liver - Male_PPARaLKO_Pemafibrate - Rep3

value: liver

value: LKO


title: 72R


title: 74R


title: cervical cancer-Genistein-rep2

city: YangZhou

first: Shuna

last: Cui

state: JiangSu

address: Jiang Yang Middle Road 136,

department: Medical College of Yangzhou University

institute: YangZhou university

description:
Geni_2
Replicate 2 of Hela cells treated by genistein for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt

data_processing:
RNA quality was evaluated and sequenced using Illumina Hiseq X ten platform in GeneChem, raw data from the sequencer were first underwent quality control using FastQC.
Reads are treated using trim_galore, where Illumina adapter sequence and low quality (phred score <20) at the 3’ end were trimmed, and the paired reads were removed if any of the two reads doesn’t meet the minimum length (20bp).
Duplicates in all data samples are removed using Picard. For each sample, we count the reads hitted on each transcript using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM_matrix.txt: Matrix table with FPKM values for every gene and every sample.
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: human cervical cancer

growth_protocol: HeLa Cells were cultured in the DMEM medium with 10% FBS, penicillin (100 units/ml) and streptomycin (100 µg/ml) in the incubator with 37°C and 5% CO2.

extract_protocol:
Cells were washed with PBS, and Trizol reagent was added. Total RNA of different treatment was isolated by RNeasy Plus Mini Kit according to the manufacturer's instruction (Qiagen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HeLa Cells were treated with genistein (50 μM) or Tanshinone I (50 μM) and the same amount of solvent control (DMSO) for 5 h, respectively.

value: HeLa

value: 50 uM genistein


title: cervical cancer-Genistein-rep3

description:
Geni_3
Replicate 3 of Hela cells treated by genistein for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt


title: du145_DU145PS2B_C08_JNJ26854165_0.155_24

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: cervical cancer-Genistein-rep1

description:
Geni_1
Replicate 1 of Hela cells treated by genistein for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt


title: 73R


title: Liver - Male_PPARaLWT_Pemafibrate - Rep6

value: LWT


title: 71R

value: Root


title: cervical cancer-Tanshinone I-rep3

description:
TanI_3
Replicate 3 of Hela cells treated by Tanshinone I for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt

value: 50 uM Tanshinone I


title: 70R


title: du145_DU145PS2B_C03_Gefitinib_0.5_24

value: Gefitinib


title: 6R


title: Liver - Male_PPARaLWT_Vehicle - Rep3

value: Vehicle


title: du145_DU145PS2B_C02_UNTREATED__24

value: UNTREATED


title: cervical cancer-Tanshinone I-rep2

description:
TanI_2
Replicate 2 of Hela cells treated by Tanshinone I for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt


title: 69R


title: 68R


title: 67R


title: du145_DU145PS2B_C04_Clarithromycin_1_24

value: Clarithromycin


title: du145_DU145PS2B_C01_Hydroxyurea_10_24

value: Hydroxyurea


title: cervical cancer-Control-rep3

description:
Ctrl_3
Replicate 3 of Hela cells treated by DMSO for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt

value: solvent control (DMSO)


title: du145_DU145PS2B_B12_Busulfan_0.295_24

value: Busulfan

value: ATCC

value: male


title: cervical cancer-Control-rep2

description:
Ctrl_2
Replicate 2 of Hela cells treated by DMSO for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt


title: 63R

value: arf7 arf19

value: NB


title: du145_DU145PS2B_B11_Teniposide_0.045_24

value: Teniposide


title: du145_DU145PS2B_B10_SNX2112_0.02_24


title: cervical cancer-Control-rep1

description:
Ctrl_1
Replicate 1 of Hela cells treated by DMSO for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt

value: HeLa


title: 60R