title: E18.5 Larynx Rep 2 [18-5L2]

source_name: E18.5 Larynx

value: E18.5 Larynx


title: E18.5 Esophagus Rep 2 [18-5E2]

status: Public on Jun 25 2022

type: SRA

city: Madison

first: Christina

last: Kendziorski

state: WI

address: 425, Henry Mall (2122 UWBC)

country: USA

institute: UW-Madison

library_source: transcriptomic

data_processing: Quality control on raw sequencing files was performed via FastQC v011.5(Andrews, 2010) using standard defaults. All samples appeared high quality based on available metrics and, in particular, passed our internal quality thresholds – 1) minimum per-base PHRED score of 5 and median per-base PHRED score of at least 20 and 2) modal per-sequence average PHRED score of at least 20 – and were used in downstream analysis. Sequenced reads were aligned to the GRCm39 reference genome, pre-indexed files accessed from the Bowtie2 repository, using Bowtie2 (v2.4.2), accessed by RSEM (v1.3.3) which was used quantify observed gene transcription levels, in units of expected counts from aligned reads(Langmead and Salzberg, 2012)(Li and Dewey, 2011). Expected counts were then normalized across samples by scaling observed expression using the method of Median-Ratio implemented in the EBSeq R package. Raw and normalized expression data were remapped to human ortholog gene symbols (HGNC format) using the mapping from the Molecular Signatures Database (Mouse_ENSEMBL_Gene_ID_Human_Orthologs_MSigDB.v7.3.chip),  53,647 Ensemble genes were mapped to 18,032 human orthologs in gene symbol notation (Daley and Vere-Jones, 2003)(Subramanian et al, 2005)(Mootha et al, 2003). All calculations were conducted in the R environment and with Bioconductor package management(R Core Team, 2013)(Gentleman et al, 2004).

molecule: total RNA

organism: Mus musculus

source_name: E18.5 Esophgaus

extract_protocol:
RNeasy Micro Kit 50 (Qiagen, Valencia, CA) was used for extraction of total RNA according to the manufacturer’s instructions. DNA digestion was performed using the DNase enzyme eliminator column- RNeasy MinElute spin columns. RNA concentration yield and integrity were evaluated using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), and samples that met the following three criteria were retained: a concentration of 1µg, an OD260−280 of 1.8–2.0 and an OD260:230 above two. Additionally, samples were evaluated for RNA integrity value (RIN) using the Agilent 2100 Bioanalyzer and RNA 6000 Pico kit (Agilent, Santa Clara, CA) according to the manufacturer’s instructions. Only samples with electropherograms exhibiting distinct 18S and 28S ribosomal RNA (rRNA) peaks and no evidence of degradation were retained.
Poly-A library preparation and RNA sequencing was performed by the DNA Sequencing facility at the University of Wisconsin-Madison Biotechnology Center per standard protocols. Briefly, first-strand cDNA using random hexamer-primed reverse transcription was generated, followed by second-strand cDNA synthesis using RNase MODULE and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of 350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. Sequencing of the prepared libraries was done on Illumina’s HiSeq 2000 and Illumina NovaSeq6000 2x150 S4 platforms with four RNA-Seq libraries per lane with a minimum depth of 2 × 100 bp paired-end reads by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.

tag: tissue

value: E18.5 Esophgaus

tag: treatment

tag: genotype

value: Wild type FVB/N

tag: age


title: 5IL22R KO Bladder UPEC 24hrs

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq Files were aligned to the mm10 genome using HISAT2
Counts table was produced using Rsubread
Normalisation was perfomed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Deseq2 normalized counts matrix
Supplementary_files_format_and_content: raw counts matrix

source_name: Bladder

growth_protocol: Mice were maintained in SPF conditions prior to the experement

extract_protocol:
RNA was extracted from bladders using Ambion RNA mini kit
Libraries were produced using Illumina TruSeq mRNA

treatment_protocol: Mice were cathaterised and injected with either UPEC or PBS. After 24 or 72 hours mice were culled and the bladders placed into RNAlater

value: UPEC

value: IL22R KO

tag: time point (hrs)

tag: strain


title: 4IL22R KO Bladder UPEC 24hrs


title: CD69+Ly108-, WT, Biol rep 2 [CL_WT_2]

city: San Antonio

first: Nu

last: Zhang

address: 7703 Floyd Curl Drive

institute: UTHSA

data_processing:
Data processing was performed by Novogene
Original image data file from Illumina is transformed to sequenced reads (Raw reads) by CASAVA base recognition
Raw reads of FASTQ format were firstly processed through fastp to obtain the clean reads
Paired-end clean reads were aligned to the reference genome (mm10) using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted using the Quick-RNA MiniPrep kit from Zymo Research
Libraray construction was performed by Novogene

value: spleen and lymph nodes

tag: cell line

tag: cell type

value: CD8 T cells

value: WT

value: LCMV Clone 13 infection


title: SciPlex Combo Library Well B06

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

data_processing:
First, data was demultiplexed by well. Cell barcode and UMI contained in Read1 were extracted, error corrected, and put into the header of each read.
Subsequently, reads were trimmed for polyA adaptors, mapped to the hg38 reference genome, and only transcripts mapping to the gencode annotated gene bodies were kept for further analysis
Reads were then deduplicated by UMI and assembled into a count matrix
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: sciPlex Combinations of Drugs

extract_protocol:
Resuspended cells were lsyed in a hypotonic buffer and fixed with a combination of DSP and 80% Methanol
Optimized sci-RNA-seq3 protocol was performed to make single cell sequencing libraries

treatment_protocol: Cells were treated with 2 drugs (or equivalent vehicle) at a concentration of 10uM at 24 hours post plating and then collected after 24 hours of treatment with compounds

value: Lung Adenocarcinoma

value: Combinations of drugs at 10uM


title: SciPlex Combo Library Well B03


title: CD69+Ly108-, KO, Biol rep 2 [CL_KO_2]

value: Tgfbr2 f/f distal Lck-cre


title: E15.5 Trachea Rep 1  [15-5T1]

source_name: E15.5 Trachea

value: E15.5 Trachea


title: CD69+Ly108-, WT, Biol rep 1 [CL_WT_1]


title: 3WT (C57BL/6N) Bladder PBS 24hrs

value: PBS


title: E15.5 Larynx Rep 1 [15-5L1]

source_name: E15.5 Larynx

value: E15.5 Larynx


title: SciPlex Combo Library Well B05


title: SciPlex Combo Library Well B04


title: E15.5 Trachea Rep 2 [15-5T2]


title: 1WT (C57BL/6N) Bladder PBS 24hrs


title: 266_ricEKO

city: Cologne

first: Sabine

last: Eming

state: NRW

address: Kerpener Str. 62

department: Department of Dermatology

country: Germany

institute: Uniklinik Koeln

description: processed data file: FPKM.txt

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads mapped to mouse genome (Ensembl version 87).
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks.
Genome_build: GRCm38 (Ensembl version 87)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Epidermis

extract_protocol:
Epidermis was separated and RNA was extracted using QIAGEN RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: Rictor -/-

value: epidermis


title: SciPlex Combo Library Well B02


title: E18.5 Esophagus Rep 1 [18-5E1]


title: E18.5 Larynx Rep 1 [18-5L1]

value: E18.5 Larynx


title: 265_ricEKO

description: processed data file: FPKM.txt


title: CD69+Ly108-, KO, Biol rep 1 [CL_KO_1]


title: E15.5 Esophagus Rep 1 [15-5E1]

source_name: E15.5 Esophgaus

value: E15.5 Esophgaus


title: 264_ctrl

description: processed data file: FPKM.txt

value: Control


title: SciPlex Combo Library Well B01


title: CD69-Ly108-, WT, Biol rep 2 [DN_WT_2]


title: E15.5 Esophagus Rep 2 [15-5E2]

value: Wild type FVB/N


title: E15,5 Larynx Rep 2 [15-5L2]


title: 2WT (C57BL/6N) Bladder PBS 24hrs


title: SciPlex Combo Library Well A12


title: 262_ctrl

description: processed data file: FPKM.txt


title: SciPlex Combo Library Well A11


title: Human ACP,scRNA-seq

city: Guangzhou

first: Yilamujiang

last: Ainiwan

state: Guangdong

address: No. 1838, Guangzhou North Road

department: Neurosurgery

country: China

institute: Southern Medical University , Nanfang Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads of mouse were aligned to the mouse genome (mm10) and raw reads of human were aligned to the human genome (hg38), cells were called and gene expression matrices were generated for each sample by the cellranger (v6.0.1) count function with default parameters.
Assembly: mm10 for the row reads of mouse , hg38 for the row reads of human
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: human ACP tumour

extract_protocol:
Mice were anesthetized 8 weeks after the operation. The hypothalamus of mice randomly selected from the cystic fluid group (1 case) and the sham operation group (1 case) were removed immediately under a light microscope for single-cell RNA sequencing. At the same time, a sample of fresh childhood ACP tumor tissue (with gliosis zone) immediately after collection during clinical surgery was also used for single-cell RNA sequencing.
The tissue was dissected out and flash frozen in liquid N2. Nuclei were isolated as followed by 10× Genomics demonstrate protocol (CG000375 • Rev A) .On the day of the experiment, frozen tissue was homogenized in NP40 Lysis Buffer with Protector RNAase Inhibitor (Sigma) and filtered through a 70μm strainer (falcon). Strained samples were centrifuged at 500 rcf × 5 min and pelleted nuclei were resuspended in wash buffer . Nuclei were strained again and recentrifuged at 500 rcf × 5 min. Washed nuclei were resuspended in wash buffer and stained nuclei underwent FACS sorting by 7-AAD (SML1633 sigma). Sorted nuclei were centrifuged at 500 rcf × 6 min and resuspended in wash buffer to obtain a concentration of 900 nuclei/μL. 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell G Chip (10× Genomics, 1000120), aiming for a recovery of 8000–9000 cells. The Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10× Genomics, 1000121) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3′ Reagent Kits User Guide Version 3.1. Libraries were sequenced using the NovaSeq 6000 platform (Illumina) to a depth of approximately 300 million reads per library with 2×150 read length.

value: human ACP tumour

value: surgecal removel


title: SciPlex Combo Library Well A08


title: SciPlex Combo Library Well A10


title: 261_ctrl

description: processed data file: FPKM.txt


title: E13.5 Esophagus Rep 2 [13-5E2]

source_name: E13.5 Esophagus

value: E13.5 Esophagus


title: SciPlex Combo Library Well A06

value: WT


title: E13.5 Trachea Rep 2 [13-5T2]

source_name: E13.5 Trachea

value: E13.5 Trachea


title: SciPlex Combo Library Well A07

value: Lung Adenocarcinoma


title: Intestine, SWM IP, Rep 1

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

description:
Raw_Read_Counts_Input_vs_IP.csv
DESeq2_Results_Input_vs_IP.csv

data_processing:
Quality trimming was performed using Cutadapt version 2.9.
Ribosomal RNA (rRNA) reads were removed using Tagdust2 version 2.2.
Remaining reads were aligned to the BDGP assembly release 6.28 (Ensembl release 100) reference genome using STAR version 2.7.3a.
Alignment output files were coordinate sorted and duplicated reades were removed using SAMtools version 1.10.
The Subread version 2.0.0 function featureCounts was used to count the number of aligned reads to the nearest overlapping feature.
Assembly: BDGP assembly release 6.28 (Ensembl release 100)
Supplementary files format and content: CSV file containing raw read counts
Supplementary files format and content: CSV file containing differential gene expression results obtained using DESeq2

organism: Drosophila melanogaster

source_name: Intestine

extract_protocol:
Gastrointestinal (GI) tracts of 100 adult female flies (per replicate) were dissected in ice-cold 1xPBS. Then cells were dissociated by treating intestines with 1mg/ml elastase at 27oC for 1 hour with agitation. Subsequently, ~30,000-50,000 GFP+ intestinal progenitor cells were sorted using a BD FACSAriaTM II flow cytometer equipped with a 100µm nozzle at the IUB Flow Cytometry Core Facility. For CLIP-seq analysis, dissected intestines were homogenized in lysis buffer and subjected to immunoprecipitation using SWM-coated magnetic beads. A portion of the total extract was used as control for this analysis. Total RNA was prepared using the TRIzol® LS reagent (Ambion). The rRNA-depleted libraries were prepared using the Ovation® SoLo RNA-seq system (Part No. 0502 including Parts 0407 and S02240) following manufacturer’s instructions. The quality and quantity of final libraries were assessed using Agilent 2200 TapeStation and KAPA Library Quantification Kit, respectively.
The rRNA-depleted RNA-seq/CLIP-seq libraries were prepared using the Ovation® SoLo RNA-seq system (Part No. 0502 including Parts 0407 and S02240) following manufacturer’s instructions.

value: Intestine

value: All intestinal cells


title: E13.5 Trachea Rep 1 [13-5T1]


title: E13.5 Esophagus Rep 1 [13-5E1]


title: SciPlex Combo Library Well A09

value: Combinations of drugs at 10uM


title: SciPlex Combo Library Well A05


title: Instestine, swm, Rep 3

description:
Raw_Read_Counts_RNAseq.csv
DESeq2_Results_RNAseq.csv

value: Intestinal progenitors

value: swm RNAi

value: Knocking down Swm


title: E11.5 Trachea Rep 1 [11-5T1]

source_name: E11.5 Trachea

value: E11.5 Trachea


title: E11.5 Trachea Rep 2 [11-5T2]


title: Instestine, swm, Rep 2


title: SciPlex Combo Library Well A04


title: E13.5 Larynx Rep 2 [13-5L2]

source_name: E13.5 Larynx

value: E13.5 Larynx


title: 4T1_shMCT-1_biological rep2

type: RNA

city: Zhunan

first: Hsin-Ling

last: Hsu

state: Miaoli

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

description: Gene-level analysis of 4T1 TNBC cells shMCT-4 vs. scramble (NC)

hyb_protocol: Samples were hybridized for 16 hours at 45° on GeneChip (Clariom D Assay, mouse) (Thermo Fisher Scientific). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.
MTA-1_0.r3.pgf
MTA-1_0.r3.Psrs.mps

label: biotin

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from fragmented cDNA.

growth_protocol: 4T1 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 100 U/ml Penicillin/Streptomycin. shMCT-1 clones were selected in the medium with 0.5 μg/ml puromycin for 2 weeks.

extract_protocol: Total mRNAs were isolated from 4T1 cancer cells by RNeasy Mini Kit (Qiagen) as per the manufacturer's protocol.

treatment_protocol: not applicable

value: breast cancer cell line


title: 4T1_scramble (NC)_biological rep2

description: Gene-level analysis of 4T1 TNBC cells shMCT-2 vs. scramble (NC)

source_name: scramble (NC)

value: NC


title: E13.5 Larynx Rep 1 [13-5L1]

value: Wild type FVB/N


title: 4T1_shMCT-1_biological rep1

description: Gene-level analysis of 4T1 TNBC cells shMCT-3 vs. scramble (NC)


title: 4T1_scramble (NC)_biological rep1

description: Gene-level analysis of 4T1 TNBC cells shMCT-1 vs. scramble (NC)


title: SciPlex Combo Library Well A03


title: Intestine, esgTS, Rep 3

value: Control


title: Intestine, Total Lysate, Rep 1


title: SciPlex Combo Library Well A02


title: E11.5 Larynx Rep 1 [11-5L1]

source_name: E11.5 Larynx

value: E11.5 Larynx


title: Mac UTI

data_processing:
Libraries were alligned to the mm10 genome using hisat2
Counts table produced using Rsubread
Normalisation of data with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts table
Supplementary_files_format_and_content: DESeq2 notmalised counts table

growth_protocol: Mice were housed in SPF conditions prior to the experement

extract_protocol:
Bladders were collected from the mice, the tissue digested with liberase and a single cell suspensions was produced. Macrophages were sorted based on live, CD45+ CD64+ cells into RLT+
RNA extraction was performed using quiagen micro RNA kit
Libraries were produced using Takara smarter stranded pico input

treatment_protocol: Mice were infected via a cathater with UPEC, PBS was used as the control

tag: group

value: UTI


title: SciPlex Combo Library Well A01

value: WT


title: Mac PBS

value: PBS


title: E11.5 Larynx Rep 2 [11-5L2]


title: E11.5 Esophgus Rep 1 [11-5E1]

source_name: E11.5 Esophagus

value: E11.5 Esophagus


title: Intestine, esgTS, Rep 2

value: Intestine


title: sdg26;aprf1_rep1

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
After removing adapter and filtering low-quality reads, the clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The differentially expressed genes were identified with log2(fold change) >=1 and p-value<0.01 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown at 23℃ under both long-day (16 h light and 8 h dark).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) from 10-day-old seedlings of fld, ld, sdg26aprf1-9, efl2/4, and Col-0 grown under long-day conditions at 23℃.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy).

treatment_protocol: The 10-day-old seedlings grown on MS plates were harvested and subjected to RNA extraction.

value: seedling


title: WT_CON2_IP

city: Tempe

first: Jason

middle: Marshall

last: Newbern

state: Arizona

address: ISTB1 320

department: School of Life Sciences

institute: Arizona State University

data_processing:
Fastq files were merged, qc filtered, and trimmed to 50bp using Trimmomatic.
Mapped to a modified GRCm38.p6 primary assembly file that includes information for "Cre recombinase" using RNA-STAR default settings
featureCounts used to quantify gene expression with a modified GRCm38.p6 annotation file limited to "gene_type = protein coding" and containing "Cre recombinase"
Differential gene expression was analyzed using DeSeq2, first, INPUT fractions were compared to IMMUNOPRECIPITATED fractions within a genotype (Table S1), then IMMUNOPRECIPITATED fractions were compared between genotypes (Table S2).
DeSeq2 derived mean normalized counts, log2fold-change, and unadjusted p-value were used to generate
Assembly: GRCm38.p6
Supplementary files format and content: xlsx files contain ENSEMBL Gene ID, sene symbol, gene name, average normalized counts for each sample under evaluation, log2foldchange, unadjusted p-value

source_name: Immunoprecipitated Cortical fraction

extract_protocol:
Whole P7.5 cortices were rapidly dissected, rinsed, and Dounce homogenized in 500 uL of ice-cold RNase-free buffer polysome buffer (50 mM Tris pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 200U/ml Promega RNasin, 1 mg/ml heparin, 100 ug/ml cycloheximide, and protease inhibitors). Lysate was cleared via centrifugation at 10,000g for 20min at 4ºC. 60 ul of supernatant (“Input”) was collected and lysed with 350 ul of buffer RLT from Qiagen RNeasy Kit supplemented with 10μl/ml bME. The remaining supernatant was gently mixed with 5ul of rabbit anti-HA antibody (#71–5500 Thermo Fisher Sci) and incubated with gentle rocking at 4°C for 2hrs before isolation with 50 ul of protein A/G magnetic beads previously equilibrated in polysome buffer and a magnetic stand. Immunoprecipitates were rinsed 3x with 800 ul of a high salt buffer (50 mM Tris pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 100 ug/ml cycloheximide) and then lysed in 350 ul of buffer RLT.  RNA isolation from Input and Immunoprecipitated fractions was performed following manufacturers instructions using Qiagen’s RNeasy extraction kit with DNAse digestion.
Following RNA quantitation using a Ribogreen RNA reagent and exclusion of samples with an RNA integrity number < 7 on an Agilent Bioanalyzer, 2 ng of RNA were used for single primer isothermal amplification (SPIA) amplification and generation of double-stranded cDNA with the Ovation RNAseq System V2 (Nugen Technologies). Library construction and sequencing was performed on the Illumina NextSeq 500 platform at the Arizona State University’s Genomics Core facility. Trimmed 50 bp single-end reads were quality checked and aligned to the mouse genome GRCm38.p6 primary assembly from Ensembl using RNA-STAR.

value: mixed

value: Cortex

value: postnatal day 7.5

value: Slc32A1:Cre +/-, Rpl22HA

tag: antibody

value: Rpl22HA immunoprecipitated RNA


title: Intestine, esgTS, Rep 1

value: Intestinal progenitors


title: E10.5 Trachea Rep 2 [10-5T2]

source_name: E10.5 Trachea

value: E10.5 Trachea


title: Intestine, SWM IP, Rep 2

value: All intestinal cells


title: sdg26;aprf1_rep2


title: ld_rep1


title: E10.5 Esophagus Rep 2 [10-5E2]

source_name: E10.5 Esophgaus

value: E10.5 Esophgaus

value: Wild type FVB/N


title: E10.5 Trachea Rep 1 [10-5T1]


title: ld_rep2


title: fld_rep1


title: 263_ricEKO

description: processed data file: FPKM.txt

value: Rictor -/-

value: epidermis


title: LF_CON3_IP

value: Erk1 -/-, Erk2 fl/wt, Slc32A1:Cre +/-, Rpl22HA


title: LF_MUT3_IP

value: Erk1 -/-, Erk2 fl/fl, Slc32A1:Cre +/-, Rpl22HA


title: fld_rep2


title: Instestine, swm, Rep 1

value: swm RNAi

value: Knocking down Swm


title: E10.5 Primitive Laryngopharynx Rep 1 [10-5L1]

source_name: E10.5 Primitive Laryngopharynx

value: E10.5 Primitive Laryngopharynx


title: E10.5 Primitive Laryngopharynx Rep 2 [10-5L2]


title: LF_CON2_IP

value: mixed


title: SLK_K-Rta_stop+K-Rta_suppl_CHi-C

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Homo sapiens, KSHV

library_source: genomic

data_processing:
Basecalling and quality scoring were performed using Real-Time Analysis software (RTA2).
The HiC-Pro v2.11.1 pipeline was used to process the CHi-C data by performing read alignment, detection and filtering of valid interaction products, binning, and contact map normalization. Read alignment was performed with bowtie2 using a combined assembly of the human hg19 (GRCh37) and KSHV (NC_009333.1) reference genomes and by first mapping each read independently. The reads were filtered to remove duplicates and to keep only reads that mapped to the KSHV genome by using the Python module Pysam v0.14.1. Valid Hi-C interactions were detected based on several criteria, including the assignment of each read to a different restriction fragment and being located within a specified distance to a restriction site consistent with the size distribution of the sheared ligation products. Read pairs from invalid ligation products (e.g., self-circle ligation, dangling end, random breaks) and PCR duplicates were discarded. The valid reads were stored as matrices and binned with resolution of 500 bp (2 kb for density plots), the bins with more than 100 counts and at least 75% of cells with no-zero counts were used in the next steps. Iterative Correction and Eigenvector decomposition (ICE) normalization was used to treat the data with iteration of 100.
Genome_build: GRCh37 (hg19) + KSHV genome (GQ994935.1)
Supplementary_files_format_and_content: Processed data files are in hic format, which is an indexed binary format that is generated from Hi-C tag directories. This file format is designed to permit fast random access to contact matrix heatmaps in Juicebox.

molecule: genomic DNA

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: SLK cell line

growth_protocol: TREx-(F3H3)-K-Rta BCBL-1 (TREx-K-Rta BCBL-1, which have tetracycline/doxycycline (Dox)-inducible expression of N-terminal Flagx3- and HAx3-tagged K-Rta, were cultured in complete RPMI 1640 (supplemented with 10% FBS) containing blasticidin (50 ug/ml) and hygromycin B (100 mg/ml). BC-1 and BC-3 cells were obtained from the ATCC (Manassas, Va) and maintained in RPMI 1640 supplemented with 15% FBS, 2mM glutamine, and 1% penicillin-streptomycin. SLK cells were maintained in DMEM medium supplemented with 10% FBS, 2 mM glutamine, and 1% penicillin-streptomycin.

extract_protocol:
Chimeric DNA ligation products were prepared for KSHV Capture Hi-C (CHi-C) using kitted reagents from Arima Genomics (San Diego, CA) based on methods described for in situ Hi-C and CHi-C. Briefly, cells were crosslinked with 2% formaldehyde, lysed, and the genomic DNA digested with a cocktail of 4-cutter restriction endonucleases by incubation for 30 minutes at 37°C. The 5’-overhangs were then filled in and labeled with biotinylated dATP (biotin-14-dATP) by incorporation with Klenow fragment of DNA polymerase I (incubation for 45 minutes at 25°C). Ligation of the spatially proximal blunt-ended fragments was then performed with T4 DNA ligase (incubation for 15 minutes at 25°C). The formaldehyde crosslinks were reversed and the proximally-ligated, chimeric DNA products were purified with Agencourt AMPure XP paramagnetic beads (Beckman Coulter).
Hi-C and KSHV Capture Hi-C (CHi-C) libraries were prepared from the chimeric DNA ligation products using kitted reagents from Arima Genomics (San Diego, CA). The DNA was then sheared to an average length of 400 bp using a Covaris E220 Focused-ultrasonicator (Covaris, Inc.) and fragments size-selected with AMPure XP beads to achieve a size distribution of 200-600 bp. The biotin-marked ligation products were then enriched by affinity capture with streptavidin magnetic beads (DynaBeads MyOne Streptavidin C1; Invitrogen, Thermo Fisher Scientific). Subsequently, libraries were prepared from the bound ligation products with the Kapa HyperPrep Kit with Library Amplification Module (Roche) using an on-bead modification to the standard protocol for end repair, dA-tailing, and ligation of Illumina TruSeq sequencing adaptors. The KSHV CHi-C library was then prepared by target enrichment of the libraries for KSHV genomic content by solution hybridization with a custom-designed KSHV genomic capture probe library (xGen Lockdown Probes; Integrated DNA Technologies, Inc., Coralville, IA) as previously described (13). Briefly, libraries (500 ng) were hybridized with the KSHV genomic capture probe pool (3 pmol) in a mixture containing xGen 1X Hybridization Buffer, Cot-1 (5 µg), and xGen Universal Blocking Oligos for 4 hours at 65°C. The hybridized targets were then captured with streptavidin beads (DynaBeads MyOne Streptavidin C1; Thermo Fisher Scientific) by incubation for 45 minutes at 65°C. Unbound DNA was removed by a series of high-stringency (65°C) and low-stringency (room temperature) washes. The KSHV genome-enriched CHi-C library DNA was eluted and PCR enrichment (12 cycles) performed with high-fidelity KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems, Inc., Wilmington, MA).

treatment_protocol: TREx-(F3H3)-K-Rta BCBL-1 and iSLK.r219 cells were treated with doxyclyine for 24 hours in order to induce K-Rta expression, which consequently triggers KSHV reactivation.

tag: tissue or tumor of origin

value: human epithelial cells

value: SLK cells infected with KSHV harboring a K-Rta-Stop mutation

tag: viral infection

value: KSHV


title: Col-0_rep2

value: seedling

value: wild type


title: E11.5 Esophgus Rep 2 [11-5E2]

value: E11.5 Esophagus


title: HEKcells_CTLtreated_wRNH_IP_rep2

city: Tucson

first: Jacob

middle: C.

last: Schwartz

state: AZ

address: 1501 N Campbell Ave, LSN649

department: Pharmacology

institute: University of Arizona

data_processing:
library strategy: DRIP-seq
alignments made to hg38 refseq genes downloaded from UCSC genome browser
data was aligned using Tophat version 2.1.1
Reads were trimmed using TrimGalore (version 0.6.6) and aligned to GRCh38 using (version STAR 2.7.8a), essentially as previously described. Bam files were processed using the deepTools2.0 suite (version 3.5.1) to normalize to 1x depth (reads per genome coverage) with bamCoverage, merge replicates by bigwigCompare, and tags binned by computeMatrix, which was then used to compute scaling factors and generate heat maps and profiles. Merged bigwig files were converted to bedgraph then peaks called by Macs2 (version 2.1.1.20160309). HOMER (version v4.11.1) was used to calculate GC-content and annotate peaks.
Assembly: hg38
Supplementary files format and content: Reads were trimmed using TrimGalore (version 0.6.6) and aligned to GRCh38 using (version STAR 2.7.8a), essentially as previously described. Bam files were processed using the deepTools2.0 suite (version 3.5.1) to normalize to 1x depth (reads per genome coverage) with bamCoverage, merge replicates by bigwigCompare, and tags binned by computeMatrix, which was then used to compute scaling factors and generate heat maps and profiles. Merged bigwig files were converted to bedgraph then peaks called by Macs2 (version 2.1.1.20160309). HOMER (version v4.11.1) was used to calculate GC-content and annotate peaks.

source_name: CTL treated (SCR) DRIP replicate 2 - Neg control IP with S9.6 antibody after RNaseH1 treatment

extract_protocol:
Between 7 and 9 x 106 cells were harvested at 72 hours post-siRNA treatment, and cell pellets frozen in liquid nitrogen. Pellets were later resuspended in 1.6 mL of TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) that was added to include 0.6% sodium dodecyl sulfate (SDS) and 60 µg/mL Proteinase K. After Proteinase K digested lysates overnight at 37 ºC, DNA was extracted using the MaXtract High Density tubes (Qiagen, 129065). DNA was spooled by glass Pasteur pipette, transferred, then ethanol precipitated. DNA was digested overnight in TE buffer with 1x NEBuffer™ 2 (New England Biolabs Inc., #B6002), BSA (95 µg/mL), spermidine (1 mM), and 30 U each of restriction enzymes BsrGl, EcoRI, HindIII, SspI, and XbaI. Efficient restriction digest was confirmed by agarose (0.8% w/v) gel electrophoresis. Samples were sonicated for 30 cycles (30 sec on / 30 sec off). Negative control samples were digested by 20U RNaseH (Fisher Scientific, 50-811-717) per 10 µg DNA. After restriction enzyme and RNaseH digests, DNA was extracted by Phase Lock Gel™ (VWR, 10847-800) per manufacturer instructions. 50 µg of DNA was incubated overnight at 4 ºC with 20 µg S9.6 antibody and in 500 µL DRIP buffer (1x TE buffer, 10 mM Na phosphate pH 7, 140 mM NaCl, 0.05% Triton X-100). 5 µg of DNA was kept for input samples. Antibody precipitated with 100 µL Protein A/G beads (Millipore, IP05-1.5ML) was washed twice in 700 µL DRIP buffer. Hybrids were eluted by incubating beads with 300 µL DRIP Elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 0.5% SDS, 0.5 µg/µL Proteinase K) for 45 minutes at 55 ºC, then extracted by Phase Lock Gel™.
Sample libraries were prepared and sequenced to by Novogene Corporation Inc. using a NovaSeq 6000 with 150 base paired-end reads (8 G raw data per sample).

treatment_protocol: HEK293T/17 cells (ATCC, CRL-11268) grown and passaged in DMEM (5% FBS) were transfected by siRNA using RNAiMax™ (Invitrogen, 13778150) in Optimem (Invitrogen, 31985070). Between 7 and 9 x 106 cells were harvested at 72 hours post-siRNA treatment, and cell pellets frozen in liquid nitrogen.

tag: cell line source

tag: cell origin

value: Embryonic Kidney

tag: time point

value: 72 hours post-siRNA transfection

value: siRNA "SCR", 5' GAUGCAGACAUUCAGGAUGUU 3'


title: LF_CON1_IP

tag: tissue

value: Cortex

value: postnatal day 7.5

value: Rpl22HA immunoprecipitated RNA


title: BCBL-1_reactivated_CHi-C_Rep3

description: Homo sapiens, KSHV

source_name: TREx-(F3H3)-K-Rta BCBL-1 cell line

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cell line with doxycycline-inducible expression of Flagx3-tagged K-Rta

tag: virus status

value: reactivated


title: WT_CON1_IP

tag: genotype

value: Slc32A1:Cre +/-, Rpl22HA


title: Col-0_rep1


title: E10.5 Esophagus Rep 1 [10-5E1]

value: E10.5 Esophgaus

tag: treatment

value: Wild type FVB/N

tag: age


title: LF_MUT1_IP

tag: strain

value: mixed

value: Erk1 -/-, Erk2 fl/fl, Slc32A1:Cre +/-, Rpl22HA


title: elf2/4_rep1

value: seedling


title: HEKcells_CTLtreated_wRNH_IP_rep1

source_name: CTL treated (SCR) DRIP replicate 1 - Neg control IP with S9.6 antibody after RNaseH1 treatment


title: LF_MUT2_IP


title: WT_CON1_PUT

source_name: Whole Cortical Input fraction


title: HEKcells_CTLtreated_IP_rep2

source_name: CTL treated (SCR) DRIP replicate 2 - IP with S9.6 antibody


title: BCBL-1_latent_CHi-C_Rep3

description: Homo sapiens, KSHV

value: KSHV

value: latent


title: WT_CON2_PUT


title: elf2/4_rep2


title: LF_CON3_PUT

value: Erk1 -/-, Erk2 fl/wt, Slc32A1:Cre +/-, Rpl22HA


title: BCBL-1_reactivated_CHi-C_Rep2

description: Homo sapiens, KSHV


title: LF_CON2_PUT


title: SLK_K-Rta_stop_CHi-C

description: Homo sapiens, KSHV

value: human epithelial cells

value: SLK cells infected with KSHV harboring a K-Rta-Stop mutation


title: HEKcells_CTLtreated_IP_rep1

source_name: CTL treated (SCR) DRIP replicate 1 - IP with S9.6 antibody

value: Embryonic Kidney

value: 72 hours post-siRNA transfection

value: siRNA "SCR", 5' GAUGCAGACAUUCAGGAUGUU 3'


title: HEKcells_siFtreated_wRNH_IP_rep2

source_name: FUS knockdown (siFUS) DRIP replicate 2 - Neg control IP with S9.6 antibody after RNaseH1 treatment

value: siRNA "siFUS", 5' CGGACAUGGCCUCAAACGAdTdT 3'


title: BCBL-1_reactivated_CHi-C_Rep1

description: Homo sapiens, KSHV

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cell line with doxycycline-inducible expression of Flagx3-tagged K-Rta


title: LF_CON1_PUT

value: Cortex

value: postnatal day 7.5


title: BCBL-1_latent_CHi-C_Rep1

description: Homo sapiens, KSHV


title: HEKcells_siFtreated_wRNH_IP_rep1

source_name: FUS knockdown (siFUS) DRIP replicate 1 - Neg control IP with S9.6 antibody after RNaseH1 treatment


title: irisin-treated 3D-cultured human periodontal ligament cells, biological rep2

city: Oslo

first: Yang

last: Yang

address: Geitmyrsveien 71

department: Faculty of dentistry

country: Norway

institute: University of Oslo

description: Gene expression data from human periodontal ligament cells cultured in 3D for 14 days with irisin treatment

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix)

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

source_name: periodontal ligament cells

label_protocol: 150 ng of total RNA was subjected to the GeneChip WT PLUS Reagent Kit (WT PLUS Kit), following the manufacturer’s protocol for whole-genome gene expression analysis (Affymetrix)

growth_protocol: Approximately 6.5×10^6 human periodontal ligament cells were cultured in CelVivo 10 mL bioreactors (CelVivo, Blommenslyst, Denmark), and the 3D hPDL cell spheroids were acquired in the rotational 3D cell culture system (CelVivo) in a humidified atmosphere with 5% CO2 at 37 °C at the rotation speed of 2 rpm.

extract_protocol: Total RNA was extracted from 3D-culutred human periodontal ligament cells using TRIzol (Ambion, Life Technologies, Carlsbad CA, USA) method

treatment_protocol: Once the 3D human periodontal ligament cell spheroids formed, 10 ng/mL recombinant irisin (Adipogen, Liestal, Switzerland) or equal volume of sterile milliQ water (control for recombinant irisin) were administered to the culture medium, the human periodontal ligament cells were cultured in 3D for 14 days.

value: Periodontal ligament tissues

tag: treatement

value: 10 ng/ml irisin


title: UPEC Thy 1

data_processing:
Fastq were aligned to mm10 using hisat2
Counts table was produced using Rsubread
Normalisation was carried out using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq 2 nomalised counts

source_name: bladder

growth_protocol: Mice were maintaind in SPF

extract_protocol:
Bladders were taken and RNA extracted using ambion RNA mini kit
Takara smarta high input

treatment_protocol: Mice were pretreate with either isotype control or anti thy 1.1 and subsequently given a UTI through infection with UPEC.

value: bladder

value: anti thy1.1

value: RAG KO

tag: disease state

value: UTI


title: LF_MUT3_PUT

value: mixed

value: Erk1 -/-, Erk2 fl/fl, Slc32A1:Cre +/-, Rpl22HA


title: irisin-treated 3D-cultured human periodontal ligament cells, biological rep3


title: BCBL-1_latent_CHi-C_Rep2

description: Homo sapiens, KSHV

tag: cell type

value: KSHV

value: latent


title: HEKcells_CTLtreated_Input_rep1

source_name: CTL treated (SCR) input sample

value: Embryonic Kidney

value: 72 hours post-siRNA transfection


title: irisin-treated 3D-cultured human periodontal ligament cells, biological rep1


title: HEKcells_siFtreated_IP_rep1

source_name: FUS knockdown (siFUS) DRIP replicate 1 - IP with S9.6 antibody

value: siRNA "siFUS", 5' CGGACAUGGCCUCAAACGAdTdT 3'


title: HEKcells_siFtreated_IP_rep2

source_name: FUS knockdown (siFUS) DRIP replicate 2 - IP with S9.6 antibody


title: LF_MUT2_PUT


title: BC1_latent_CHi-C

description: Homo sapiens, KSHV

source_name: BC1 cell line

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells

value: KSHV+EBV


title: 3D-cultured human periodontal ligament cells, biological rep3

description: Gene expression data from human periodontal ligament cells cultured in 3D for 14 days

value: miliQ water


title: BC3_latent_CHi-C

description: Homo sapiens, KSHV

source_name: BC3 cell line


title: LF_MUT1_PUT

value: Cortex

value: postnatal day 7.5


title: HEKcells_siFtreated_Input_rep1

source_name: FUS knockdown (siFUS) input sample


title: 3D-cultured human periodontal ligament cells, biological rep1

value: Periodontal ligament tissues


title: 49.Acitretin

status: Public on Jun 24 2022

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the statistical software R, version 4.0.5. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

source_name: SBAD2 iPS cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: Cells were differentiated in RPMI 1640 GlutaMAX™ medium (Thermo Fisher Scientific, Germany) plus B-27™ Supplement, minus insulin (Thermo Fisher Scientific, Germany) spiked with 10 µM Wnt activator small molecule CHIR99021 (R&D Systems, Minneapolis, USA).

extract_protocol: The cells were homogenised with TRIzol lysis reagent (Thermo Fisher Scientific, Germany), and the total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.

treatment_protocol: Cells were incubated (5 % CO2, 37 °C) with the test compounds at different concentrations and a DMSO concentration of 0.1 % or 0.5 %.

tag: gender

value: male

value: SBAD2 iPS cells

value: Acitretin


title: 55.Isotretinoin

value: Isotretinoin


title: 3D-cultured human periodontal ligament cells, biological rep2


title: 57.Isotretinoin


title: 45.Favipiravir

value: Favipiravir


title: 47.Favipiravir


title: 51.Acitretin


title: 42.Carbamazepin

value: Carbamazepin


title: 53.Acitretin


title: 43.Favipiravir


title: 41.Carbamazepin


title: 33.9-cis retinoic acid

value: 9-cis retinoic acid


title: 39.Carbamazepin


title: 52.Acitretin


title: 40.Carbamazepin


title: 50.Acitretin


title: 54.Acitretin


title: 30.Vismodegib

value: Vismodegib


title: 32.9-cis retinoic acid


title: 44.Favipiravir


title: 31.9-cis retinoic acid


title: 48.Favipiravir


title: 29.Vismodegib


title: 38.Carbamazepin


title: 35.9-cis retinoic acid


title: 36.9-cis retinoic acid


title: 56.Isotretinoin


title: 46.Favipiravir


title: 37.Carbamazepin


title: 27.5,5-Diphenylhydantoin


title: 28.Vismodegib


title: 21.Teriflunomide

value: Teriflunomide


title: 25.5,5-Diphenylhydantoin


title: 26.5,5-Diphenylhydantoin


title: 22.Leflunomide

value: Leflunomide


title: 10.Retinol

value: Retinol


title: 15.DPH

value: DPH


title: 18.DPH


title: 24.Leflunomide


title: 6.0,5Dmso


title: 17.DPH


title: 5.0,5Dmso


title: 20.Teriflunomide


title: 16.DPH


title: 11.Retinol


title: 13.DPH


title: 8.Retinol


title: 23.Leflunomide


title: 3.0,1Dmso


title: 78.Thalidomide

value: Thalidomide


title: 19.Teriflunomide


title: 12.Retinol


title: 1.0,1Dmso


title: 4.0,5Dmso


title: 9.Retinol


title: 75.Thalidomide


title: 7.Retinol


title: 2.0,1Dmso


title: 76.Thalidomide


title: 14.DPH


title: 77.Thalidomide


title: 3DBT4743

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

description: RMA expression value derived from Affymetrix GeneChip command console software v4.0.

hyb_protocol: Labeled samples were then hybridized with Affymetrix Clariom D human (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Samples were washed and stained with the Affymetrix GeneChip2 hybridization wash and stain kit, and then scanned with the Affymetrix GeneChip Scanner 3000 7G to generate fluorescent images, as described in the manufacturer’s protocol.

data_processing: For lncRNAs array analysis, CEL-files of the raw data were produced with Affymetrix GeneChip command console software v4.0.

source_name: 3D cultures on matrigel

label_protocol: RNA was labeled with the flash tag biotin HSR kit (Genisphere, Hatfield, PA, USA) according to the manufacturer’s instructions for poly(A)-tailing.

growth_protocol: Establishment of 3D organotypic cultures of the BT-474 cell line grown on geltrex and 2D cultures of the BT-474 cell line.

extract_protocol: RNA was isolated from 2D and 3D cultures using the RNeasy plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

tag: cell line

value: Luminal B breast cancer cell line


title: pig-Morula-H2AZ-1

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

data_processing:
All reads were mapped to the mouse reference genome mm10 or pig reference genome susScr11 using Bowtie2 (version 2.4.1).
The Samtools (version ) was used to remove low quality reads (MAPQ < 30) and Picard (version 1.9) was used to remove PCR duplicates.
The MACS2 (version 2.2.7.1) software calls the ChIP-seq peak with the parameters “--nolambda –nomodel --broad”
RPKM-normalized bigwig files were generated by bamCoverage subcommand in deepTools (version 3.5.0) and the tracks were visualized with Integrative Genomics Viewer (IGV, version 2.6.2).
Genome_build: mm10 (GRCm38) or susScr11 (Sscrofa11.1)
Supplementary_files_format_and_content: bigWig files

organism: Sus scrofa

source_name: embryo

extract_protocol:
ULI-NChIP-seq was performed as previously described with some modifications. Embryos and cells were then added into 20 μL Nuclear Isolation buffer and 30 μL 10 U/ mL MNase Master mix to digest chromatin for 7 min at 25℃, and added 5.5 μL 100 mM EDTA and 5.5 μL 1% Triton X-100 plus 1% deoxycholate solution to finish digestion. Next, samples were incubated with antibody-bead complexes in 130 μL Complete Immunoprecipitation buffer overnight at 4°C. After two washes with 200 μL Low Salt Wash buffer and 200 μL High Salt Wash buffer, chromatin was dissolved in 100 μL ChIP Elution buffer for 2 h at 65℃.
DNA was then extracted by 100 μL phenol-chloroform-isoamyl alcohol (25:24:1), and used for library generation by using KAPA HyperPrep Kit (KK8504, Roche) following the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on Illumina HiSeq X-Ten.

treatment_protocol: Small interference RNAs (siRNAs) against mouse H2A.Z were designed and synthesized for three pairs by GenePharma, Shanghai, China. All three pairs of siRNAs for each gene were diluted and mixed in nuclease-free water with a working concentration of 20 μM. Mouse zygotes at the pronuclear stage 3 (20-22 h post hCG injection) were injected with approximately 10 pl of siRNAs using a PiezoXpert micromanipulator (Eppendorf), and cultured in G1-plus medium at 37℃ under 5% CO2 in air. The injected embryos were observed at 44 h, 55 h, 68 h, 78 h and 94 h post hCG injection to summary the developmental phenotypes.

tag: developmental stage

value: Morula

value: Large White

value: IVF

tag: chip antibody


title: 3DBT4741


title: pig-Morula-H2AZ-2


title: 2DBT4742

source_name: 2D cultures


title: Isolated pancreatic islets A0BΔpanc rep3 [LAB_276_19]

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
Sequencing reads were mapped to the Ensembl mouse genome (release GRCm38.102) using subread (version 2.0.2) (PMID:23558742) and the read counts  aligning to known genes were generated by featureCounts (PMID: 24227677).
The read counts were normalized with the iDEGES/edgeR method implemented in TCC (version 1.34.0) (PMID:12770646), and pairwise comparisons of gene expression between islets from WT, A0B2 control and A0BΔpanc were conducted with the edgeR (version 3.36.0) (PMID:19910308). The false discovery rate (FDR) adjustments (DOI:http://www.jstor.org/stable/2346101) were applied to correct for multiple testing, and differentially expressed genes (DEGs) were identified with an FDR cutoff of 0.05.
Assembly: GRCm38.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Isolated pancreatic islets

extract_protocol:
Total RNA from the islets was isolated using the TRIZOL reagent (Thermo Fisher Scientific). RNA quality was examined by RNA 6000 Pico kit (Agilent, Santa Clara, CA). An amount of 50 ng total RNA was used for RNA-seq library preparation with NEB NEBNext rRNA Depletion Kit and ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA); 2x36 base paired-end sequencing was performed with NextSeq500 (Illumina, San Diego, CA) by Tsukuba i-Laboratory LLP (Tsukuba, Ibaraki, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Isolated pancreatic islets

value: post natal 10 weeks


title: Isolated pancreatic islets A0B2 rep3 [LAB_276_16]

value: MafA-/-;MafB flox/flox (A0B2)


title: Isolated pancreatic islets A0BΔpanc rep1 [LAB_276_17]


title: 3DBT4742


title: 65.Control

value: male

value: SBAD2 iPS cells

value: Control


title: 74.Thalidomide


title: 62.Control


title: 59.Sucralose

value: Sucralose


title: 64.Control


title: 73.Thalidomide


title: 34.Lithium

value: Lithium


title: 60.Sucralose


title: 61.Control


title: Isolated pancreatic islets A0B2 rep2 [LAB_276_15]


title: 55.Sucralose


title: 58.Sucralose


title: 33.Lithium


title: 2DBT4743


title: 31.Lithium


title: 2DBT4741


title: 57.Sucralose


title: Isolated pancreatic islets A0BΔpanc rep2 [LAB_276_18]


title: 30.MethylMerc

value: MethylMerc


title: 56.Sucralose


title: AAV_NULL_optic_nerve_sham_rep6

city: Miami

first: Kyung (Kevin)

last: Park

state: FL

address: 1095 NW 14th Terrace, Miami Project to Cure Paralysis, LPLC room 4-20

department: Neurological Surgery

institute: University of Miami

data_processing:
FASTQ data were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.
Reads were aligned to the mm10 human genome using STAR aligner v 2.5.3a with default parameters and RSEM v1.2.31 to obtain expected gene counts against the mouse Ensembl (version 96). The differential expression analysis was determined between AAV_CNTF_optic_nerve_crush_VS_AAV_NULL_optic_nerve_crush, AAV_CNTF_optic_nerve_crush_VS_AAV_NULL_optic_nerve_sham, and  AAV_NULL_optic_nerve_crush_VS_AAV_NULL_optic_nerve_sham animals using DESeq2 (5) and R v3.2.3. A gene was considered detected if the FPKM was > 1 in three replicates of at least one sample and significantly changed if the adjusted p-values < 0.05 and a fold change >1.5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM and counts values for each sample and replicate and the log2 Fold change and adjusted p-values for each comparison.

source_name: Optic nerve

extract_protocol:
Libraries were prepared with the Nugen Universal RNASeq with AnyDeplete Mouse kit using 20ng RNA input and sequenced on Illumina Novaseq 6000.
Total RNA was extracted from the optic nerve using RNeasy Micro Kit (Qiagen 74004) and treated with DNAse I to remove contaminating genomic DNA.
Total RNA-seq (ribo-depleted) libraries were produced using Truseq Stranded Total RNA library prep kit (Illumina, #20020596) with 500 ng of DNase-treated Input RNA.

treatment_protocol: Animal received either intravitreal AAV-CNTF and AAV-Null injection followed by optic nerve crush or sham injury.

tag: injury type

value: sham injury

tag: intravitreal injections

value: Adeno-associated virus serotype-2 (AAV2)  (AAV2-Null without a transgene)

value: Adult


title: Isolated pancreatic islets A0B2 rep1 [LAB_276_14]


title: Isolated pancreatic islets WT rep3 [LAB_276_13]

value: wild type


title: Isolated pancreatic islets WT rep2 [LAB_276_12]


title: AAV_NULL_optic_nerve_sham_rep5


title: AAV_NULL_optic_nerve_sham_rep4


title: 36.Lithium


title: AAV_NULL_optic_nerve_sham_rep3


title: Isolated pancreatic islets WT rep1 [LAB_276_11]


title: AAV_NULL_optic_nerve_sham_rep2


title: 35.Lithium


title: AAV_NULL_optic_nerve_crush_rep6

value: optic nerve crush injury


title: 32.Lithium


title: AAV_NULL_optic_nerve_crush_rep3


title: AAV_NULL_optic_nerve_crush_rep5


title: 26.MethylMerc


title: AAV_NULL_optic_nerve_crush_rep4


title: AAV_CNTF_optic_nerve_crush_rep5

value: Adeno-associated virus serotype-2 (AAV2) expressing a secretable form of CNTF (AAV-CNTF )


title: AAV_CNTF_optic_nerve_crush_rep6


title: 28.MethylMerc


title: AAV_NULL_optic_nerve_crush_rep2


title: AAV_CNTF_optic_nerve_crush_rep3


title: 29.MethylMerc


title: 23.Entinostat

value: Entinostat


title: 22.Entinostat


title: 20.Entinostat


title: 24.Entinostat


title: 19.Entinostat


title: 21.Entinostat


title: 25.MethylMerc


title: 27.MethylMerc


title: 3.TSA

value: TSA


title: 2.TSA


title: mm DRG culture rep4

city: Madison

first: Zachary

middle: T

last: Campbell

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

data_processing:
FastQ file generation was followed by quality check via FastQC 0.11.5
Adaptor sequences were trimmed and read mapping was performed using TopHat 2.1.1
Reads were mapped to their respective reference genomes and transcriptomes.
Gene abundance quantification was performed using Cufflinks 2.2.1 with option --no-length-correction
FPKM values were converted first to TPM values and then to uqTPM values.
Genome_build: mm10 and h19
Supplementary_files_format_and_content: xlsx workbook with uqTPM values for all samples
Supplementary_files_format_and_content: xlsx workbook with uqTPM values, fold changes, and p-values for all samples and their respective comparisons

source_name: DRG

extract_protocol:
Mouse DRGs were excised. Tissue samples were homogenized. Cultures were generated. hiPSC samples were lysed. RNA was harvested using Trizol reagent. Lexogen QuantSeq 3'mRNA-seq library kit and RiboCop rRNA depletion kit were used with 50ng-1ug total RNA.
RNA libraries were prepared for sequencing using maufacturer's protocols

value: Swiss Webster

value: DRG

tag: culture method

value: DRG culture


title: mm DRG culture rep3


title: mm DRG culture rep2


title: mouse_brain_rep2

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

institute: Max Delbrück Center for Molecular Medicine

data_processing:
We processed raw paired-end sequencing data using Spacemake v.0.4.2 with default parameters
We selected the top 100,000 barcodes from every sample
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression (DGE) Matrix

source_name: E12 mouse brain

growth_protocol: Wild-type E12 mouse brain was processed and analyzed

extract_protocol:
RNA extraction was performed according to the published Slide-seq protocol (Rodriguez et al., 2019)
scRNAseq libraries were generated according to Illumina sequencing protocol. Libraries were prepared following the published Slide-Seq protocol (Rodriguez et al., 2019)

value: brain


title: mouse_brain_rep3


title: mouse_brain_rep1


title: mm DRG tissue rep2

value: DRG tissue


title: 1.TSA

value: male

value: SBAD2 iPS cells


title: 55.Ranitidine

value: Ranitidine


title: 54.Dextrometh

value: Dextrometh


title: AAV_CNTF_optic_nerve_crush_rep4


title: mm DRG culture rep1


title: 52.Dextrometh


title: 51.Dextrometh


title: 60.Ranitidine


title: 59.Ranitidine


title: 57.Ranitidine


title: 53.Dextrometh


title: 58.Ranitidine


title: 50.Dextrometh


title: 56.Ranitidine


title: AAV_CNTF_optic_nerve_crush_rep2


title: mm DRG tissue rep3


title: mm DRG tissue rep5


title: brain cortex, EAE replicate2

city: Muenster

first: Hyun-Woo

last: Jeong

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: brain cortex single cells

data_processing:
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98  nt RNA sequence.
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v0.5.3) used for cell barcode and UMI counting
STAR (v2.5.3a_modified) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.1) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

molecule: polyA RNA

source_name: brain cortex

extract_protocol:
Mice were perfused transcardially with ice-cold PBS under anesthesia. Brain cortex tissues were dissected and digested using the enzyme-cocktail solution of 30U/ml papain (LK003153; Worthington) and 0.125mg/ml Liberase TM (5401119001; Sigma-Aldrich) in DMEM (Sigma-Aldrich) for 60 min at 37 °C. Homogenized tissues were added by 1.7-fold volume of 22% bovine serum albumin in PBS and then centrifuged at 1,000 rcf for 10 min for myelin removal. After washing with ice-cold DMEM, dead cells and debris were removed using ClioCell nanoparticles (amsbio) according to the manufacturer’s instructions. Single cells were counted using Luna-II automated cell counter (Logos Biosystems) and captured using the 10X Chromium system (10X Genomics). We pooled tissues from three (for Aged and EAE samples) or six (for Juvenile and Adult samples) mice to reduce individual variations.
Libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics)
3' single cell RNA-Seq using cell barcodes and unique molecular identifiers (UMIs).

treatment_protocol: Active EAE induction : 150 ul of 0.75mg/ml myelin oligodendrocyte glycoprotein 33 to 55 peptides (MOG35–55) mixed with Complete Freund's Adjuvant (FS8810; Sigma-Aldrich) was injected into the tail base spine of 7 to 11 wk-old female mice. On day 2, 100 ul of 2ug/ml pertussis toxin (P7208; Sigma-Aldrich) was injected intravenously.

value: EAE, disease peak

value: brain cortex


title: brain cortex, Juvenile replicate1

description: brain cortex single cells

value: Juvenile


title: brain cortex, Juvenile replicate4

description: brain cortex single cells


title: 48.L-Thyronine

value: L-Thyronine


title: brain cortex, Juvenile replicate3

description: brain cortex single cells


title: 44.L-Thyronine


title: 49.Dextrometh


title: mm DRG tissue rep1


title: 46.L-Thyronine


title: mm DRG tissue rep4


title: brain cortex, Juvenile replicate2

description: brain cortex single cells


title: brain cortex, EAE replicate1

description: brain cortex single cells

value: Adult


title: brain cortex, Adult replicate2

description: brain cortex single cells


title: brain cortex, Aged replicate2

description: brain cortex single cells

value: Aged

value: 18 mo


title: brain cortex, Adult replicate3

description: brain cortex single cells


title: brain cortex, Aged replicate1

description: brain cortex single cells


title: Iswi male, rep3

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

data_processing:
Basecalls performed using CASAVA.
Trimmomatic (version 0.39) was used to filter the raw data.
Reads were mapped to the genome by HISAT2 (version 2.2.1)
Transcripts were assembled and quantitated using StringTie (version 2.1.5).
DESeq2 (version1.32.0) was used to analyze the data.
Assembly: Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa
Supplementary files format and content: Matrix table of normalized data

source_name: whole larvae

growth_protocol: All the stocks are incubated at 25 degree

extract_protocol:
The sequencing library was constructed by removing ribosomal RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: third-instar larvae

value: whole larvae

tag: Sex


title: 45.L-Thyronine


title: 47.L-Thyronine


title: Iswi male, rep2

tag: tissue


title: Iswi male, rep1


title: brain cortex, Adult replicate1

description: brain cortex single cells


title: ParticleL3

city: Nanjing

first: Chen

last: Zhao

state: Jiangsu

address: 22nd Hankou Road

institute: Nanjing University

data_processing:
SOAPnuke software was used to filter reads, including removing reads with sequencing adapters to filter sequencing data, removing reads with a base quality less than 5, and removing reads with an unknown base ratio of more than 5%. The FASTQ format was used to store clean reads. HISAT2 was used to map clean reads to the reference genome, Bowtie2 was used to align clean reads to the reference coding genome, RSEM was used to calculate gene expression levels, and finally, differential expression analysis was performed by DESeq2.
Supplementary files format and content: TPM values for each sample
Assembly: GCF_000001635.26_GRCm38.p6

source_name: lung

extract_protocol:
Total RNA of whole lung was extracted using the RNAeasy™ Animal RNA Isolation Kit with Spin Column (Beyotime, Shanghai, China) according to the manufacturer’s guidelines.
mRNA was purified by magnetic beads with Oligo(dT), and then the purified mRNA was fragmented using fragmentation buffer at the appropriate temperature. The first-strand cDNA was then generated by PCR in the First Strand reaction system, and the same operation was performed for the second-strand cDNA. The PCR product was purified with magnetic beads and incubated with A-Tailing Mix and RNA Index Adaptors to complete the repair process. cDNA fragments with adapters were amplified using PCR and purified using Ampure XP Beads. An Agilent 2100 Bioanalyzer was used to assess the quality and quantity of the library, followed by DSN processing. Finally, it was sequenced and analyzed on the BGI DNBSEQ platform (BGI-Shenzhen, China).

treatment_protocol: Mice were exposed to PM2.5 particulate matter by intranasal instillation at a dose of 10 mg/kg. For short-term exposure, a total of 1 time was administered. For long-term exposure, intranasal instillation was performed once every three days for a total of 6 times was administered.

value: lung

value: BALB/c

value: WT

value: long-term exposure to PM2.5 particulate matter


title: 40.Levothyrox

value: male

value: Levothyrox


title: 42.Levothyrox

value: SBAD2 iPS cells


title: ParticleS3

data_processing:
SOAPnuke software was used to filter reads, including removing reads with sequencing adapters to filter sequencing data, removing reads with a base quality less than 5, and removing reads with an unknown base ratio of more than 5%. The FASTQ format was used to store clean reads. HISAT2 was used to map clean reads to the reference genome, Bowtie2 was used to align clean reads to the reference coding genome, RSEM was used to calculate gene expression levels, and finally, differential expression analysis was performed by DESeq2.
Supplementary files format and content: TPM values for each sampl

value: short-term exposure to PM2.5 particulate matter


title: 41.Levothyrox


title: ParticleL1


title: 43.L-Thyronine


title: 12.Atrovastatin

value: Atrovastatin


title: 37.Levothyrox


title: 10.Atrovastatin


title: 38.Levothyrox


title: 11.Atrovastatin


title: 39.Levothyrox


title: Iswi female, rep2

value: female


title: Iswi female, rep3


title: ParticleS1


title: ERCC_RNA_rep1

organism: unidentified

source_name: ERCC RNA Spike-In Mix & GFP

tag: sample type

value: control


title: 8.Atrovastatin


title: ParticleS2

tag: genotype


title: PBS3

tag: treatment

value: long-term exposure to PBS


title: PBS2


title: PBS1


title: Iswi female, rep1


title: 6.Dmso

value: Dmso


title: 9.Atrovastatin


title: ParticleL2


title: 7.Atrovastatin


title: Control male, rep2


title: Control male, rep3


title: Control female, rep3


title: Control female, rep2


title: Control female, rep1


title: Control male, rep1


title: 4.Dmso


title: 5.Dmso


title: 32.Valproic

value: Valproic


title: HEK,  AS1sh2-MK-S9

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Genome_build: hg38
Supplementary_files_format_and_content: IER3_IER3_AS1_KD.cnt.gz (tab-delimited text file includes count values for each Sample analyzed)

extract_protocol:
Cells were collected 48 hours post-transfection and Total RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat # RS-122-2201). mRNA sequencing on 100PE of DNBseq platform

treatment_protocol: HeLa and HEK293 cells were routinely cultured in DMEM media supplemented with 10% FBS. Stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

value: Kidney,Embryo

value: IER3-AS1 shRNA2

value: IER3-AS1 knockdown


title: HEK,  AS1sh2-MK-S10


title: 35.Valproic


title: K.6.A_(miRNA-4-0)_healthy

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

hyb_protocol: The procedure was performed according to the manufacturer's instructions

scan_protocol: GeneChips were scanned using the affymetrix GeneChip2 Scanner 3000 7G.

data_processing: RNA was analyzed using GeneChip miRNA 4.0 (Affymetrix), detecting all noncoding and mi- nor RNA from miRBase database, including mature miRNA and pre-miRNA. CEL files were processed using the oligo R package in the default mode to obtain the normalized expression values.

label_protocol: biotin

extract_protocol: Isolation of RNA from 200 µl of each plasma specimen was carried out using miRNeasy Serum/Plasma Kit (Qiagen) according to the instruction.

treatment_protocol: Blood was collected in S-Monovette EDTA-KE tubes, 8 ml (Sarstedt). Plasma was separated by 2-step  centrifugation on a 5810R centrifuge (Eppendorf) at ambient temperature. Step 1 centrifugation was carried out at 2000g for 1 min at medium acceleration  and inhibition velocity. The upper liquid phase was then transferred into a new tube and step 2 centrifugation was carried out at 4000g, after which plasma was  carefully collected, only 10% volume was left at the bottom of the tube.

value: healthy

tag: age

tag: gleason

tag: tnm

tag: psa

tag: group

value: Control


title: HEK,  AS1sh1-MK-S8

value: IER3-AS1 shRNA1


title: 30.Methorexate

tag: gender

tag: cell type

value: Methorexate


title: P.133_(miRNA-4-0)_prostate-cancer_N0M0

tag: disease state

value: prostate cancer

value: High risk


title: 34.Valproic

value: male

value: SBAD2 iPS cells


title: K.1.A_(miRNA-4-0)_healthy


title: 33.Valproic


title: K.2.A_(miRNA-4-0)_healthy


title: 31.Valproic


title: K.4.A_(miRNA-4-0)_healthy


title: CX-4945_5μM_H295R_24hr_3

city: Fukuoka

first: Kenji

last: Ohe

state: Fukuoka

address: 8-19-1, Jyonan-ku, nanakuma

department: Faculty of Pharmaceutical Sciences

institute: Fukuoka University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: cell line

value: H295R adrenocortical cancer cell line

tag: agent


title: 36.Valproic


title: P.34.A_(miRNA-4-0)_prostate-cancer_NxM0


title: P.134_(miRNA-4-0)_prostate-cancer_N0M0

value: Low risk


title: 29.Methorexate


title: K.3.A_(miRNA-4-0)_healthy


title: P.132_(miRNA-4-0)_prostate-cancer_N0M0


title: CX-4945_5μM_H295R_24hr_1


title: P.131_(miRNA-4-0)_prostate-cancer_N0M0


title: CX-4945_5μM_H295R_24hr_2


title: DMSO_H295R_24hr_2

value: DMSO


title: HEK,  AS1sh1-MK-S7


title: DMSO_H295R_24hr_3


title: DMSO_H295R_24hr_1


title: HEK,  sh2-MK-S5

value: IER3 shRNA2

value: IER3 knockdown


title: HEK,  sh1-MK-S4

value: IER3 shRNA1


title: HEK,  sh2-MK-S6

value: Kidney,Embryo


title: HEK,  sh1-MK-S3


title: HEK,  csh-MK-S2

value: control shRNA

value: control


title: 28.Methorexate


title: P.127_(miRNA-4-0)_prostate-cancer_NxM0_GIST_thyroid_pancreatic-cancer


title: HEK,  csh-MK-S1


title: 27..Methorexate


title: P.130_(miRNA-4-0)_prostate-cancer_N0M0


title: P.129_(miRNA-4-0)_prostate-cancer_N0M0


title: P.128_(miRNA-4-0)_prostate-cancer_N0M0


title: P.126_(miRNA-4-0)_prostate-cancer_N0M0


title: 26.Methorexate


title: P.115_(miRNA-4-0)_prostate-cancer_N1-4M0


title: P.120_(miRNA-4-0)_prostate-cancer_N0M0

value: Intermediate risk


title: P.121_(miRNA-4-0)_prostate-cancer_N0M0


title: P.116_(miRNA-4-0)_prostate-cancer_N0M0


title: 24.Paroxetine

value: Paroxetine


title: HeLa, consh_B_2

source_name: HeLa

value: HeLa

value: Cervix, Uterus


title: P.118_(miRNA-4-0)_prostate-cancer_N0M0

value: prostate cancer


title: 25.Methorexate

value: Methorexate


title: 23.Paroxetine

value: male


title: 22.Paroxetine

value: SBAD2 iPS cells


title: 21.Paroxetine


title: __P.119_(miRNA-4-0)_prostate-cancer_N1-4M0

value: High risk


title: P.109_(miRNA-4-0)_prostate-cancer_N1-4M0


title: P.111_(miRNA-4-0)_prostate-cancer_N1-4M0


title: __P.112_(miRNA-4-0)_prostate-cancer_N0M0


title: HeLa, consh_A_1


title: HeLa, IER3sh2_A-9


title: HeLa, IER3sh1_B_8


title: HeLa, IER3sh1_A_7


title: 20.Paroxetine


title: P.104_(miRNA-4-0)_prostate-cancer_N0M0


title: HeLa, IER3_AS1sh2_2

value: IER3-AS1 shRNA2

value: IER3-AS1 knockdown


title: P.106_(miRNA-4-0)_prostate-cancer_N1-4M0


title: 18.Isotretinoin

value: Isotretinoin


title: HeLa, IER3_AS1sh2_1


title: P.107_(miRNA-4-0)_prostate-cancer_N0M0

value: Low risk


title: P.102_(miRNA-4-0)_prostate-cancer_N0M0


title: P.100_(miRNA-4-0)_prostate-cancer_N0M0


title: 17.Isotretinoin


title: P.101_(miRNA-4-0)_prostate-cancer_NxM0


title: P.99_(miRNA-4-0)_prostate-cancer_N0M0


title: P.108_(miRNA-4-0)_prostate-cancer_N0M0


title: P.96_(miRNA-4-0)_prostate-cancer_N0M0


title: P.97_(miRNA-4-0)_prostate-cancer_N1-4M0


title: P.98_(miRNA-4-0)_prostate-cancer_N1-4M0


title: 15.Isotretinoin


title: 19.Paroxetine


title: P.88_(miRNA-4-0)_prostate-cancer_N0M0


title: 14.Isotretinoin


title: P.93_(miRNA-4-0)_prostate-cancer_N0M0


title: 16.Isotretinoin


title: HeLa, IER3_AS1sh1_2

value: IER3-AS1 shRNA1


title: P.87_(miRNA-4-0)_prostate-cancer_N0M0


title: P.86_(miRNA-4-0)_prostate-cancer_N0M0_lung-cancer


title: P.89_(miRNA-4-0)_prostate-cancer_N1-4M0


title: HeLa, IER3_AS1sh1_1


title: HeLa, consh_2


title: HeLa, consh_1


title: P.82_(miRNA-4-0)_prostate-cancer_N0M0


title: 12.Thalidomide

value: Thalidomide


title: P.95_(miRNA-4-0)_prostate-cancer_N1-4M0


title: P.76_(miRNA-4-0)_prostate-cancer_N0M0


title: P.84_(miRNA-4-0)_prostate-cancer_N0M0


title: P.81_(miRNA-4-0)_prostate-cancer_N0M0


title: 13.Isotretinoin


title: P.78_(miRNA-4-0)_prostate-cancer_N0M0


title: P.69_(miRNA-4-0)_prostate-cancer_N0M0


title: P.67_(miRNA-4-0)_prostate-cancer_NxM0


title: P.79_(miRNA-4-0)_prostate-cancer_NxM0


title: 8.Thalidomide


title: 11.Thalidomide


title: 60.Dmso

value: Dmso


title: P.58.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.61_(miRNA-4-0)_prostate-cancer_N0M0


title: 9.Thalidomide


title: 10.Thalidomide


title: __P.65_(miRNA-4-0)_prostate-cancer_N0M0


title: P.56.A_(miRNA-4-0)_prostate-cancer_N0M0_bladder-cancer


title: 7.Thalidomide


title: 59.Dmso


title: P.73_(miRNA-4-0)_prostate-cancer_NxM0


title: P.70_(miRNA-4-0)_prostate-cancer_N0M0


title: 54.Famot

value: Famot


title: P.51.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.50.A_(miRNA-4-0)_prostate-cancer_N0M0


title: phod1-3

city: Shanghai

first: Mingguang

last: Lei

address: No. 3888, Chenhua Road

institute: Shanghai Center for Plant Stress Biology

data_processing:
Basecalls performed using CASAVA version 1.4
low quality sequences were trimmed using the bbduk.sh script in the bbmap suite of tools
Clean reads were mapped to the TAIR10 genome using the STAR aligner and gene abundances were estimated with StringTie.
Assembly: TAIR10
Supplementary files format and content: Excel sheet with differentially expressed genes between mutant and wild-type shoot.

growth_protocol: The shoot of 8-day-old wild-type and phod1 mutant grown under 1/2 MS conditions were collected in triplicate.

extract_protocol:
Total RNA was extracted via the RNeasy Plant Kit (Qiagen) and DNase was added to digest contaminating genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Murashige and Skoog (1/2 MS) agar medium with 1.0% (w/v) sucrose and 1.1% (w/v) agar under 16 h/8 h light/dark cycle at 23 0C

value: phod1 Mutant


title: P.57.A_(miRNA-4-0)_prostate-cancer_NxM0


title: phod1-2


title: P.54.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.55.A_(miRNA-4-0)_prostate-cancer_N0M0_kidney-cancer


title: phod1-1


title: 58.Dmso


title: WT-1

value: Wild type


title: 52.Famot


title: P.42.A_(miRNA-4-0)_prostate-cancer_N0M0


title: 51.Famot


title: P.38.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.33.A_(miRNA-4-0)_prostate-cancer_N0M0


title: 50.Famot


title: __P.9.A_(miRNA-4-0)_prostate-cancer_N0M0


title: 48.Busp

value: Busp


title: P.35.A_(miRNA-4-0)_prostate-cancer_N0M0


title: 49.Famot


title: P.36.A_(miRNA-4-0)_prostate-cancer_N0M0

value: Intermediate risk


title: P.25.A_(miRNA-4-0)_prostate-cancer_N0M0

value: prostate cancer


title: WT-2


title: WT-3


title: P.37.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.24.A_(miRNA-4-0)_prostate-cancer_N0M0


title: 53.Famot


title: P.22.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.7.A_(miRNA-4-0)_prostate-cancer_N0M0


title: P.2.A+B_(miRNA-4-0)_prostate-cancer_N0M0


title: HeLa, IER3sh2_B_10

value: HeLa

value: Cervix, Uterus

value: IER3 shRNA2

value: IER3 knockdown


title: L1CAM-negative 28 [A732T130]

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.6.1a_08-27 with default paramters and --outFilterMismatchNoverLmax 0.04.
Gene expression values (FPKM=fragments per kilobase per million reads) were computed by Cufflinks v2.2.146
Normalization between samples was done using quantile normalization (R/Bioconductor package LIMMA)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM normalized values for each sample

source_name: adrenal

growth_protocol: Described in Sriha et al. (submitted)

extract_protocol:
Total RNA was extracted from frozen cells using the NucleoSpin RNA kit (Macherey-Nagel)
RNA sequencing libraries were prepared from 500 ng of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit

value: adrenal

value: Postnatal day 5 (P5)

value: non-adrenergic

tag: strain

value: Sphere culture 8 day


title: P.6.A_(miRNA-4-0)_prostate-cancer_N0M0

value: Low risk


title: P.3.A_(miRNA-4-0)_prostate-cancer_N1-4M0

value: High risk


title: P.124_(miRNA-4-0)_prostate-cancer_M1


title: 46.Busp

value: male

value: SBAD2 iPS cells


title: P.1.A_(miRNA-4-0)_prostate-cancer_N1-4M0


title: 47.Busp


title: L1CAM-positive 31 [A732T128]

value: chromaffin cell

value: Sphere culture 5 day


title: L1CAM-positive 25 [A732T126]

value: Sphere culture  8 day


title: N3 Control

city: HONGO, BUNKYO-KU

first: Taku

last: Saito

state: TOKYO

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

data_processing:
DNBseq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The filtered data were aligned against the human reference genome (GRCh38.p12).
Genome_build: GRCh38.p12

source_name: yellow ligament

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Kit (#R2062, Zymo Research, CA, USA) in accordance with the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard BGI protocols

value: Control


title: P.91_(miRNA-4-0)_prostate-cancer_M1

value: prostate cancer


title: 44.Busp

data_processing: All analyses were conducted using the statistical software R, version 4.0.5. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

value: Busp


title: C3 Chondrogenesis

value: Chondrogenesis


title: 41.Choloph

value: Choloph


title: 43.Busp


title: 42.Choloph


title: L1CAM-negative 31 [A732T129]


title: C2 Chondrogenesis


title: L1CAM-negative 25 [A732T127]


title: IndRTexp5rep3_YM115_DMSOReadsPerGene

city: Heidelberg

first: Lukas

last: Mathur

address: Meyerhofstraße 1

department: Genome Biology

institute: EMBL

description:
Cells were treted with drug combinations or single drugs and processed in plates, 3 replicates for each treatment conditions
bulk_CombiSeq_screen_matrix

data_processing:
CASANA software was used for basecalling
Read1 (Barcode) was used to demultiplex read 2 according to treatment conditions using Je Debarcode version 2.0.beta allowing a maximum of 6 mismatches per barcode sequence,
Sequences were aligned to Homo_sapiens.GRCh38.84. using STAR version 2.4.2a
Created matrix with all alignments (treatment conditions) and remove genes with 0 read counts in all samples
Supplementary files format and content: Matrix containing read counts for all samples and replicate

source_name: K562 cells

growth_protocol: K562 cells were cultures in DMEM media supplemented with 10% BSA and 1% Penicillin Streptomycin

extract_protocol:
Cells were lysed and the released mRNA was reversed transcribed using barcoded poly-dT primers.
Biotin on the poly-dT primer was used to purify cDNA. Priming sites introduced over the poly-dT primers and the template switching oligonucleotide were used to amplify the cDNA. Subsequently, cDNA was fragmented using a hyperactive Tn5 transposase.

treatment_protocol: Cells were encapsulated into picoliter sized droplts along with 420 unique combinatorial treatment conditions. Droplets with cells were incubated for 12h/24h at 37 degrees Celsius

value: Myelogenous leukemia cells

value: bcr:abl fusion gene

value: Cells were treated with 9 different combinations out of Imatinib, trametinib, YM155 or DMSO in 6 well plates


title: IndRTexp5rep3_DMSO_DMSOReadsPerGene


title: 40.Choloph

first: Jan

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

extract_protocol: The cells were homogenised with TRIzol lysis reagent (Thermo Fisher Scientific, Germany), and the total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.


title: P.68_(miRNA-4-0)_prostate-cancer_M1


title: P.85_(miRNA-4-0)_prostate-cancer_M1


title: P.80_(miRNA-4-0)_prostate-cancer_M1


title: P.52.A_(miRNA-4-0)_prostate-cancer_M1


title: P.75_(miRNA-4-0)_prostate-cancer_M1


title: P.77_(miRNA-4-0)_prostate-cancer_M1


title: P.83_(miRNA-4-0)_prostate-cancer_M1_penis-cancer


title: 39.Choloph


title: 37.Choloph


title: 45.Busp


title: P.71_(miRNA-4-0)_prostate-cancer_M1


title: PolyA5_YM155_DMSO_CGTCGCNNNNNNNNNN_countsPerGene

description:
3 replicates for each treatment condition
Combi_PolyA_bulk_matrix

value: 4 different drug treatments


title: PolyA5_Trametinib_YM155_TGGGCCNNNNNNNNNN_countsPerGene


title: N2 Control


title: C1 Chondrogenesis


title: N1 Control


title: IndRTexp5rep3_Imatinib_DMSOReadsPerGene


title: IndRTexp5rep2_YM115_DMSOReadsPerGene


title: PolyA5_Trametinib_DMSO_GGACATNNNNNNNNNN_countsPerGene


title: PolyA5_DMSO_DMSO_TAAAACNNNNNNNNNN_countsPerGene


title: P.46_(miRNA-4-0)_prostate-cancer_M1


title: IndRTexp5rep1_Imatinib_YM115ReadsPerGene


title: 38.Choloph


title: PolyA3_YM155_DMSO_CGTCGCNNNNNNNNNN_countsPerGene


title: IndRTexp5rep2_Imatinib_DMSOReadsPerGene


title: IndRTexp5rep1_Imatinib_DMSOReadsPerGene


title: 36.Ampicilin

value: Ampicilin


title: P.45_(miRNA-4-0)_prostate-cancer_M1


title: IndRTexp5rep2_Trametinib_DMSOReadsPerGene


title: IndRTexp5rep3_Trametinib_YM115ReadsPerGene


title: P.49_(miRNA-4-0)_prostate-cancer_M1


title: 33.Ampicilin


title: IndRTexp5rep2_Trametinib_YM115ReadsPerGene


title: P.48_(miRNA-4-0)_prostate-cancer_M1


title: P.66_(miRNA-4-0)_prostate-cancer_N0M0


title: 35.Ampicilin


title: P.40.B_(miRNA-4-0)_prostate-cancer_M1


title: 34.Ampicilin


title: 32.Ampicilin


title: P.43.A_(miRNA-4-0)_prostate-cancer_M1


title: P.31.A_(miRNA-4-0)_prostate-cancer_M1


title: PolyA3_DMSO_DMSO_TAAAACNNNNNNNNNN_countsPerGene


title: IndRTexp5rep1_Imatinib_TrametinibReadsPerGene


title: IndRTexp5rep2_DMSO_DMSOReadsPerGene


title: PolyA3_Trametinib_YM155_TGGGCCNNNNNNNNNN_countsPerGene


title: IndRTexp5rep1_DMSO_DMSOReadsPerGene


title: P.47_(miRNA-4-0)_prostate-cancer_N0M0


title: PolyA1_Trametinib_YM155_TGGGCCNNNNNNNNNN_countsPerGene


title: IndRTexp5rep1_Trametinib_DMSOReadsPerGene


title: 31.Ampicilin


title: IndRTexp5rep2_Imatinib_YM115ReadsPerGene


title: P.44_(miRNA-4-0)_prostate-cancer_M1


title: 27.Methicilin

value: Methicilin


title: Combi5_Trametinib_YM155_AATTCCCAGGGCGGCTCACTGATAG_countsPerGene


title: PolyA3_Trametinib_DMSO_GGACATNNNNNNNNNN_countsPerGene


title: 26.Methicilin


title: 30.Methicilin


title: Combi5_Trametinib_DMSO_AATTCCCAGGGCGGCAGATTCGGCT_countsPerGene


title: 25.Methicilin


title: IndRTexp5rep3_Imatinib_ImatinibReadsPerGene


title: P.30.A_(miRNA-4-0)_prostate-cancer_M1

value: High risk


title: PolyA1_YM155_DMSO_CGTCGCNNNNNNNNNN_countsPerGene


title: P.21.A_(miRNA-4-0)_prostate-cancer_M1


title: 23.Ascorbic

value: male

value: Ascorbic


title: 24.Ascorbic

value: SBAD2 iPS cells


title: P.17.A_(miRNA-4-0)_prostate-cancer_M1


title: 29.Methicilin


title: IndRTexp5rep2_Imatinib_ImatinibReadsPerGene


title: P.16.A_(miRNA-4-0)_prostate-cancer_M1


title: P.18.A_(miRNA-4-0)_prostate-cancer_M1


title: PolyA1_Trametinib_DMSO_GGACATNNNNNNNNNN_countsPerGene


title: P.20.B_(miRNA-4-0)_prostate-cancer_M1


title: Combi5_DMSO_DMSO_CCAATATGTGGCGGCCAGTTCCACC_countsPerGene


title: 22.Ascorbic


title: PolyA1_DMSO_DMSO_TAAAACNNNNNNNNNN_countsPerGene


title: P.15.A_(miRNA-4-0)_prostate-cancer_M1


title: IndRTexp5rep3_Imatinib_TrametinibReadsPerGene


title: Combi5_YM155_DMSO_CGTCTAACGAGCGGCTCACTGATAG_countsPerGene


title: IndRTexp5rep1_YM115_DMSOReadsPerGene


title: 28.Methicilin


title: Combi4_YM155_DMSO_CGTCTAACGAGCGGCTCACTGATAG_countsPerGene


title: IndRTexp5rep2_Imatinib_TrametinibReadsPerGene


title: Combi4_Trametinib_YM155_AATTCCCAGGGCGGCTCACTGATAG_countsPerGene


title: IndRTexp5rep1_Imatinib_ImatinibReadsPerGene


title: P.5.A_(miRNA-4-0)_prostate-cancer_M1


title: untreated_Run1_BCABCO_Rep3_YM155_ReadsPerGene

description:
Droplets with drug (treated) were mixed with DMSO droplets (untreated) to test "leackage" of the drugs to the DMSO droplets. 14 drugs with corresponding DMSO controls, 3 replicates each, plus 3 additional separate DMSO controls.
drug_exchage_matrix

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: P.11.A_(miRNA-4-0)_prostate-cancer_M1


title: untreated_Run1_BCABCO_Rep3_Wortmannin_ReadsPerGene


title: Combi3_Trametinib_YM155_AATTCCCAGGGCGGCTCACTGATAG_countsPerGene


title: P.123_(miRNA-4-0)_prostate-cancer

value: Intermediate risk


title: 16.Doxylamine

value: Doxylamine


title: 18.Doxylamine


title: 21.Ascorbic


title: P.14.A_(miRNA-4-0)_prostate-cancer_M1

value: prostate cancer


title: IndRTexp5rep3_Imatinib_YM115ReadsPerGene


title: IndRTexp5rep3_Trametinib_DMSOReadsPerGene


title: Combi4_DMSO_DMSO_CCAATATGTGGCGGCCAGTTCCACC_countsPerGene


title: Combi4_Trametinib_DMSO_AATTCCCAGGGCGGCAGATTCGGCT_countsPerGene


title: Combi3_YM155_DMSO_CGTCTAACGAGCGGCTCACTGATAG_countsPerGene


title: IndRTexp5rep1_Trametinib_YM115ReadsPerGene


title: Combi3_Trametinib_DMSO_AATTCCCAGGGCGGCAGATTCGGCT_countsPerGene


title: untreated_Run1_BCABCO_Rep3_TRAMETINIB_ReadsPerGene


title: untreated_Run1_BCABCO_Rep3_Triciribine_ReadsPerGene


title: P.10.A_(miRNA-4-0)_prostate-cancer_M1


title: 15.Doxylamine


title: 19.Ascorbic


title: 20.Ascorbic


title: P.4.A_(miRNA-4-0)_prostate-cancer_M1


title: ur-138_(miRNA-4-0)_prostate-cancer_N0M0

value: Low risk


title: untreated_Run1_BCABCO_Rep3_SB747651_ReadsPerGene


title: 22s000164_DMSO_DMSO_countsPerGene

description:
5 replicates for each sample with different cell numbers
ERCC_spike_in_matrix

value: untreated or Trametinib treated cells with ERCC spike-ins


title: 22s000164_Trametinib_DMSO_countsPerGene


title: ur-142_(miRNA-4-0)_prostate-cancer_N0M0


title: 14.Doxylamine


title: 17.Doxylamine


title: 13.Doxylamine


title: untreated_Run1_BCABCO_Rep3_Sangivamycin_ReadsPerGene


title: ur-143_(miRNA-4-0)_prostate-cancer_N0M0


title: Combi3_DMSO_DMSO_CCAATATGTGGCGGCCAGTTCCACC_countsPerGene


title: 22s000163_Trametinib_DMSO_countsPerGene


title: untreated_Run1_BCABCO_Rep3_NMS1286937_ReadsPerGene


title: 22s000163_DMSO_DMSO_countsPerGene


title: ur-140_(miRNA-4-0)_prostate-cancer_N0M0


title: P.8.A_(miRNA-4-0)_prostate-cancer_M1


title: untreated_Run1_BCABCO_Rep3_Pomalidomide_ReadsPerGene


title: Ketogenic Diet Oligodendrocytes - R5

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

data_processing:
Demultiplexing
FastQC
Trimming based on quality thresholds
Mapping
Counting
Assembly: Mm10, Ensemble Annotation 86
Supplementary files format and content: Tab Separated Text Files - Raw Read Counts

source_name: Brain

extract_protocol:
Cells were isolated from cortex according to the adult brain dissociation protocol (Miltenyi Biotec). Antibody labeling was done according to the Microbead kit protocols using the antibodies specific to markers for the following cell types: oligodendrocytes (O4: 1:40; 130-096-670), astrocytes (ACSA-2: 1:10; 130-097-679), microglia (CD11b: 1:10; 130-093-636) and endothelial cells (CD31: 1:10; 130-091-935). Neurons were isolated by negative selection. The purity of cell populations was routinely determined by qPCR on extracted and reverse-transcribed RNA.
RNA was extracted with the Qiagen Micro-RNeasy Kit (Qiagen, Cat. No. 74004) according to the manufacturer’s protocol. As external control, 1µl of ERCC RNA Spike-In Mix (ThermoFisher, Cat No. 4456740) diluted at 1:5000 was added to the isolated RNA. cDNA was synthesised with the Ovation RNA-Seq system v2 (NuGEN, Cat. No.7102). As input, 100ng of cDNA was used for library preparation using the IonXpress plus gDNA and Amplicon library preparation kit (Thermofischer,cat no: 4471269). To achieve size selection of the library, a 2% E-Gel was used and the samples were barcoded and subsequently amplified. Further quantification for each sample library was performed using the Kapa Library Quantification Kit (Kapa, Cat. No. KK4827). Of each sample, equal amounts were sequenced on an Ion Torrent Proton Sequencer.

treatment_protocol: Each foster mother received 5 male C57BL/6N mice. To maintain normal lactogenesis in dams (Lippert et al., 2020; Sussman et al., 2013), commencing at the age of P10 of pups, dams received liquefied standard chow (65% ssniff V1124 and 35% ssniff E15712-10) on a shelf inaccessible for pubs. At P14, ketogenic (KD, ssniff E15149-30) or normal chow (SD, ssniff V1124) was provided in boxes with small holes making it only accessible for pups. Mice were weaned at P17 and kept on the respective diet. Measurement of blood glucose, ketone bodies and bodyweight were performed between 10-12 a.m. Blood was taken from tail tip and measured using the Freestyle Precision System with respective strips for glucose or 3HB (Abbott Diabetes Care). Analyses were done at indicated ages.

value: Brain

value: Oligodendrocytes

value: WT

value: Ketogenic Diet


title: Ketogenic Diet Oligodendrocytes - R4


title: untreated_Run1_BCABCO_Rep3_Gemcitabine_ReadsPerGene

value: Myelogenous leukemia cells

value: bcr:abl fusion gene


title: 12.Magnesium

city: Dortmund

last: Hengstler

source_name: SBAD2 iPS cells

value: Magnesium


title: 10.Magnesium


title: ur-134_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-135_(miRNA-4-0)_prostate-cancer_N0M0


title: 9.Magnesium


title: ur-122_(miRNA-4-0)_prostate-cancer


title: ur-126_(miRNA-4-0)_prostate-cancer_N1-4M0

value: High risk


title: untreated_Run1_BCABCO_Rep3_EPIRUBICIN_ReadsPerGene


title: Ketogenic Diet Oligodendrocytes - R3


title: untreated_Run1_BCABCO_Rep3_Dovitinib_ReadsPerGene


title: Ketogenic Diet Oligodendrocytes - R2


title: Ketogenic Diet Oligodendrocytes - R1


title: untreated_Run1_BCABCO_Rep3_Baricitinib_ReadsPerGene


title: untreated_Run1_BCABCO_Rep3_AT9283_ReadsPerGene


title: 11.Magnesium

value: male


title: ur-125_(miRNA-4-0)_prostate-cancer_N0M0


title: Standard Diet Oligodendrocytes - R5

value: Standard Diet


title: untreated_Run1_BCABCO_Rep2_Wortmannin_ReadsPerGene


title: ur-114_(miRNA-4-0)_prostate-cancer_N0M0


title: 8.Magnesium

value: SBAD2 iPS cells


title: untreated_Run1_BCABCO_Rep2_YM155_ReadsPerGene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: 7.Magnesium


title: ur-105_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-112_(miRNA-4-0)_prostate-cancer_N0M0

value: Intermediate risk


title: Standard Diet Oligodendrocytes - R4


title: Standard Diet Oligodendrocytes - R3


title: untreated_Run1_BCABCO_Rep2_Triciribine_ReadsPerGene


title: Standard Diet Oligodendrocytes - R2


title: 6.Folic

value: Folic


title: 4.Folic


title: ur-103_(miRNA-4-0)_prostate-cancer_N0M0

value: prostate cancer


title: WT_Veh_R5

city: Reading

first: Angela

last: Clerk

state: Berkshire

address: Whiteknights Campus

department: School of Biological Sciences

institute: University of Reading

data_processing:
sample demultiplexing and basecalling with bcl2fastq 2.20.0
nf-core/rnaseq pipeline version 3.1 was used to prepare quantified expression matrices with '-- aligner star_rsem'
Raw gene-level counts were imported into R using tximport
DESeq2 version 1.32.0 was used to test for differential expression with a FDR threshold of 1%.
Assembly: GRCm38 reference and Ensembl release-95
Supplementary files format and content: rsem output

source_name: heart

growth_protocol: The Pkn2Het mouse strain (KOMPtm1a) was maintained on a C57Black6J background at Francis Crick Institute, and genotyped by a QPCR method developed by Transnetyx guided by the PCR genotyping method described in Quetier, Marshall et al. Cell Reports 2016. For in vivo basal and AngII-challenge studies, male Pkn2Het and wild-type (WT) littermates (average age 11 weeks) on a C57Bl/6J background were imported into the BioResource Facility at St. George’s University of London and allowed to acclimatise for 7 d.

extract_protocol:
The apex of each of the mouse hearts was ground to powder under liquid N2. Samples (10-15 mg) were homogenised with 1 ml RNA Bee (AMS Biotechnology Ltd). RNA was prepared according to the manufacturer's instructions and dissolved in nuclease-free water. The concentration and purity were assessed from the A260 and A260/A280 values measured using an Implen NanoPhotometer.
polyA KAPA mRNA hyper prep

treatment_protocol: Mice were randomly allocated to each treatment group. Drug delivery used 1007D Alzet osmotic pumps, filled according to the manufacturer’s instructions. Mice received minipumps for delivery of 0.8 mg/kg/d AngII (Merck) or vehicle (acidified PBS) Minipumps were incubated overnight in sterile PBS (37°C), then implanted subcutaneously under continuous inhalation anaesthesia using isoflurane (induction at 5%, maintenance at 2-2.5%) mixed with 2 L/min O2. A 1 cm incision was made in the mid-scapular region and mice were given 0.05 mg/kg (s.c.) buprenorphine (Ceva Animal Health Ltd.) to repress post-surgical discomfort. Minipumps were implanted portal first in a pocket created in the left flank region of the mouse. Wound closure used a simple interrupted suture with polypropylene 4-0 thread (Prolene, Ethicon). Mice were allowed to recover singly and returned to their home cage once fully recovered. Echocardiography was performed on anaesthetised mice using the VEVO2100 imaging system equipped with a MS400 18-38 MHz transducer (Visualsonics). Mice were anaesthetised in an induction chamber with isoflurane (5% flow rate) with 1 l/min O2 then transferred to the heated Vevo Imaging Station. Anaesthesia was maintained with 1.5% isoflurane delivered via a nose cone. Baseline scans were taken prior to experimentation (-7 to -3 days). Cardiac scans of the parasternal long-axis and short-axis were recorded in B mode and M mode, and flow velocity waveforms of the aorta near the aortic valve were obtained with colour Doppler and then placing the pulsed wave Doppler sample gate over the colour Doppler signals. Further scans were taken at intervals following minipump implantation. Each imaging session was completed within 20 min per mouse. Mice were recovered singly and transferred to the home cage once fully recovered. At 7 days after mini-pump introduction, after imaging, mice were euthanized by CO2 inhalation followed by cervical dislocation. Hearts were excised quickly, washed in PBS and blotted to remove excess PBS. The apex of the heart was snap-frozen in liquid N2 and the remainder fixed in 10% buffered formalin for histology.

value: heart

value: wild-type

value: vehicle (acidified PBS)


title: untreated_Run1_BCABCO_Rep2_TRAMETINIB_ReadsPerGene


title: 5.Folic

address: Ardeystraße 67


title: ur-91_(miRNA-4-0)_prostate-cancer_N0M0


title: Standard Diet Oligodendrocytes - R1

value: Brain

value: Oligodendrocytes


title: ur-90_(miRNA-4-0)_prostate-cancer_N0M0


title: 1.Folic


title: 2.Folic


title: 3.Folic


title: ur-57_(miRNA-4-0)_prostate-cancer_N0M0


title: WT_Veh_R4


title: untreated_Run1_BCABCO_Rep2_SB747651_ReadsPerGene


title: ur-56_(miRNA-4-0)_prostate-cancer_N0M0


title: WT_Veh_R2


title: WT_Veh_R1


title: WT_Veh_R3


title: Ketogenic Diet Astrocytes - R2

data_processing:
Demultiplexing
FastQC
Trimming based on quality thresholds
Mapping
Counting
Assembly: Mm10, Ensemble Annotation 86
Supplementary files format and content: Tab Separated Text File - Normalised Counts (DESeq2)

value: Astrocytes

value: WT

value: Ketogenic Diet


title: Ketogenic Diet Astrocytes - R1


title: Standard Diet Astrocytes - R4


title: ur-49_(miRNA-4-0)_prostate-cancer_N0M0


title: untreated_Run1_BCABCO_Rep2_Sangivamycin_ReadsPerGene

value: Myelogenous leukemia cells

value: bcr:abl fusion gene


title: ur-55_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-44_(miRNA-4-0)_prostate-cancer_N0M0

value: Low risk


title: untreated_Run1_BCABCO_Rep2_Pomalidomide_ReadsPerGene


title: Standard Diet Astrocytes - R3

value: Standard Diet


title: WT_AngII_R5

value: 0.8 mg/kg/d AngII


title: Ketogenic Diet Astrocytes - R3


title: ur-42_(miRNA-4-0)_prostate-cancer_N0M0


title: untreated_Run1_BCABCO_Rep2_NMS1286937_ReadsPerGene

value: Cells were treated with 14 different drugs in droplets, each treatment has a corresponding DMSO control


title: untreated_Run1_BCABCO_Rep3_Imatininb_ReadsPerGene


title: untreated_Run1_BCABCO_Rep2_Imatininb_ReadsPerGene


title: Ketogenic Diet Astrocytes - R4


title: WT_AngII_R1


title: ur-37_(miRNA-4-0)_prostate-cancer_N0M0


title: Het_Veh_R5


title: untreated_Run1_BCABCO_Rep2_Gemcitabine_ReadsPerGene


title: untreated_Run1_BCABCO_Rep2_AT9283_ReadsPerGene


title: WT_AngII_R3


title: WT_AngII_R2


title: WT_AngII_R4


title: untreated_Run1_BCABCO_Rep2_EPIRUBICIN_ReadsPerGene


title: untreated_Run1_BCABCO_Rep2_Dovitinib_ReadsPerGene


title: untreated_Run1_BCABCO_Rep2_Baricitinib_ReadsPerGene


title: untreated_Run1_BCABCO_Rep1_YM155_ReadsPerGene


title: Standard Diet Astrocytes - R1


title: Het_Veh_R3


title: ur-38_(miRNA-4-0)_prostate-cancer_N0M0


title: Standard Diet Astrocytes - R2


title: Het_Veh_R4


title: untreated_Run1_BCABCO_Rep1_Wortmannin_ReadsPerGene


title: ur-31_(miRNA-4-0)_prostate-cancer_N0M0


title: untreated_Run1_BCABCO_Rep1_Triciribine_ReadsPerGene


title: ur-33_(miRNA-4-0)_prostate-cancer_N0M0

value: High risk


title: ur-36_(miRNA-4-0)_prostate-cancer_N0M0


title: Het_Veh_R1


title: Het_Veh_R2


title: ur-35_(miRNA-4-0)_prostate-cancer_N0M0

value: Intermediate risk


title: untreated_Run1_BCABCO_Rep1_SB747651_ReadsPerGene


title: Het_AngII_R4


title: untreated_Run1_BCABCO_Rep1_TRAMETINIB_ReadsPerGene


title: Het_AngII_R5


title: ur-34_(miRNA-4-0)_prostate-cancer_N0M0

value: prostate cancer


title: untreated_Run1_BCABCO_Rep1_NMS1286937_ReadsPerGene


title: Het_AngII_R2

value: heart


title: ur-27_(miRNA-4-0)_prostate-cancer


title: ur-23_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-24_(miRNA-4-0)_prostate-cancer_N0M0


title: untreated_Run1_BCABCO_Rep1_Sangivamycin_ReadsPerGene


title: ur-17_(miRNA-4-0)_prostate-cancer


title: Het_AngII_R3


title: ur-18_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-19_(miRNA-4-0)_prostate-cancer_N0M0


title: ur-16_(miRNA-4-0)_prostate-cancer_N0M0


title: Het_AngII_R1


title: untreated_Run1_BCABCO_Rep1_Imatininb_ReadsPerGene


title: untreated_Run1_BCABCO_Rep1_Pomalidomide_ReadsPerGene