title: Col_H3_set2_Rep1

description: ChIP


title: sir4∆_wtpromoter_Sua7FLAG ChIP rep1

status: Public on May 09 2023

type: SRA

city: Berkeley

first: Eliana

middle: Rose

last: Bondra

state: California

address: 440 Barker Hall

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

library_source: genomic

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site where applicable, and mat∆hmr∆ or hml∆mat∆, using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
PCR duplicates were removed using, sequentially, SAMtools -fixmate -sort -markdup
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication. IPs were performed using 5mL mouse monoclonal anti-FLAG® M2 antibody (MilliporeSigma, product no F1804) and 50uL DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D).   DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

tag: tissue

value: Saccharomyces cerevisiae

tag: cell line

tag: genotype

value: ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; SUA7-3xFLAG-Kanmx

tag: treatment

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: Vps15LKO_rep1

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

library_source: transcriptomic

data_processing:
Raw reads were filtered following sequencing, using SOAPnuke parameters: -n 0.03 -I 20 -q 0.4 -A 0.28 to obtain clean reads. Roughly forty-one million clean reads were obtained per sample (Beijing Genomics Institute, China).
FASTQ files were mapped to the ENSEMBL [Mouse GRCm38/mm10] reference using HISAT2 and counted by featureCounts from the Subread R package
Read count normalizations and groups comparisons were performed by three independent and complementary statistical methods: Deseq2, edgeR, LimmaVoom.
Flags were computed from counts normalized to the mean coverage. All normalized counts <20 were considered as background (flag 0) and >=20 as signal (flag=1). P50 lists used for the statistical analysis regroup the genes showing flag=1 for at least half of the compared samples. Direct comparisons were made between WT and Vps15LKO animals to generate lists of differentially expressed genes

molecule: total RNA

organism: Mus musculus

source_name: Liver, Vps15LKO

extract_protocol:
Total RNA was isolated from liver tissue using RNAeasy Lipid Tissue Mini Kit (Qiagen)
Oligo dT beds enriched polyA taail and mRNA fragmented before cDNA synthesis with random primers. Adaptors ligated to 3' adenylted cDNA fragments and digested the U-labeled second-strand templae with Uracil-DNA-Glycosylase (UDG) prior to PCR amplification. Library amplified and circularized into DNA nanoball (DNB)

value: liver


title: ZH11_R_H3K18Ace_1_IP

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

data_processing:
Sequencing reads were mapped to rice reference genome (MSU7) using Bowtie2. ChIP-seq peaks and the signal tracks were generated by MACS2.
Assembly: MSU7
Supplementary files format and content: ChIP-seq signal tracks in bigWig format.

organism: Oryza sativa Japonica Group

source_name: 4-leaf stage seedling

growth_protocol: The rice seeds were sinked in water in the dark for 2-3 days at 37°C, and then 10 days in the hydroculture.

extract_protocol:
The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by anti-H3K18Ac (A7257, ABclonal). The ChIP DNA was eluted, purified, and dissolved in ddH2O.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

value: 4-leaf stage seedling

tag: chip-seq antibody

value: anti-H3K18Ac (A7257, ABclonal)

value: Normal


title: Non-Tfh cells_day 14_rep1

city: Birmingham

first: Fangming

last: Zhu

state: AL

address: 845 19th Street South

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Low quality reads and sequencing adapters were removed using Trim Galore! (v.0.4.4).
Trimmed reads were aligned to the mouse genome mm10 using Bowtie2 (v.2.3.3).
PCR duplicates were removed using Picard (v.2.20.0).
Peak calling was performed using MACS v2 (FDR q-value 0.01).
IDR (v.2.0.3) software was used to find reproducible peaks between sample replicates.
For each experiment, we combined peaks of all samples to create a union peak list and merged overlapping peaks with BedTools (v.2.28.0) merge.
Raw read counts were normalized using the Bioconductor package DESeq2 (v.1.28.1).
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Comma-Separated Values File with normalized counts of indicated sample.

source_name: mediastinal lymph node

extract_protocol:
5 × 105 cells were sorted into 1.5 ml tubes for library construction.
library was prepared as described (Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-21 29 29 (2015)).

tag: cell type

value: PR8-OVA flu infected ex vivo OT-II T cells

tag: strain

value: mediastinal lymph node

value: PR8-OVA flu infection day 14


title: Non-Tfh cells_day 14_rep2


title: m331_R_H3K18Ace_2_IP


title: Col_H2AZ9_Rep2

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

description: ChIP

data_processing:
For alignment and quality check of sequenced samples, bedtools v2.27.1 was used to convert the raw BAM files to fastq.
FastQC v0.11.8 (Andrews 2010) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to generate quality reports for all sequencing data.
Reads were trimmed using trim_galore v0.6.5 (DOI:10.5281/zenodo.5127898.)
Reads were aligned to the TAIR10 Arabidopsis genome using Bowtie2 (Langmead and Steven L Salzberg 2013) with default settings
Picard v2.22.8 (broadinstitute.github.io/picard/) was used to mark  duplicated reads.
The bamCompare function from Deeptools was used to normalize ChIP samples to Input or H3. log2 ratio (ChIP/ (Input or H3)) bigwig files.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: 4-5 week old Leaves

growth_protocol: Col-0 wild type (WT) and ddm1(-/-) Arabidopsis thaliana seeds were stratified at 4˚C in the dark for three days. Seeds were sown in soil in the growth chamber under long day (LD) conditions (21˚C; 16 h light/8 h dark). After 4-5 week leaves tissue was freshly harvested.

extract_protocol:
Freshly harvested tissues (0.3 g of tissue was used for each immunoprecipitation) were fixed with 1% formaldehyde for 15 min and the cross-linking reaction was stopped by the addition of 125 mM glycine. . Crosslinked tissues were frozen and ground with a mortar and pestle in liquid nitrogen to obtain a fine powder. Ground tissues were resuspended in M1 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM 2-mercaptoethanol, and protease inhibitor (Roche)), and the suspension was filtered through miracloth. Nuclei were precipitated by centrifugation and washed six times with M2 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM MgCl2, 0.5% Triton X-100, 10 mM 2-mercaptoethanol, and protease inhibitor), and then further washed once with M3 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 10 mM 2-mercaptoethanol, and protease inhibitor). Nuclei pellets were rinsed and resuspended in a sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitor) and sonicated with a Covaris E220 High Performance Focused Ultrasonicator for 15 min at 4˚C (Duty factor 5.0; PIP 140.0; Cycles per Burst 200) in 1 ml Covaris milliTUBE. After chromatin shearing, the debris were removed by centrifugation and the solutions containing chromatin fragments were diluted with three times the volume of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, and protease inhibitor). After dilution, protein A/G magnetic beads (50 µl for one gram of tissue; Thermo Fisher Scientific) were added to sheared chromatin and incubated at 4˚C for 1 hour with rotation. Pre-cleared samples were collected and incubated with 5 µg of anti-H3 (Abcam, ab1791), anti-H2A.X.3/5, anti-H2A.13, anti-H2A.2, anti-H2A.Z.9, anti-H2A.Z.11, anti-H2A.W.6, anti-H2A.W.7, anti-H1, anti-H3K36me3 (Abcam, ab9050), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me3 (Abcam, ab8580), anti-H3K4me1 (Abcam, ab8895), anti-H3K27me1 (Millipore 17-643), anti-H4K20me1 (Abcam, ab9051), anti-H3K9me1 (Abcam, ab8896) or anti-H3K9me2 (Abcam, ab1220) antibodies at 4˚C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A/G magnetic beads, incubated at 4˚C for 3 hours with rotation, washed twice with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL® CA-630, and 0.1% deoxycholic acid), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted by adding 500 µl of elution buffer (1% SDS and 0.1 M NaHCO3), incubated at 65˚C for 15 min, and mixed with 51 µl of reverse crosslink buffer (40 mM Tris-HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg/ml proteinase K (Thermo Fisher Scientific)). The reaction mixture was then incubated at 45˚C for 3 hours and subsequently at 65˚C for 16 hours. After crosslink reversal, DNA was treated with 10 µg of RNaseA (Thermo Fisher Scientific), incubated at room temperature for 30 min, and purified with a MinElute PCR purification kit (Qiagen).
For ChIP-seq, libraries were prepared either with  NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with an Illumina Hiseq 2500 to generate single-end 50 bp reads.

value: WT

value: 4-5 week old Leaves

tag: chip antibody


title: WT_rep2

source_name: Liver, WT


title: WT_rep3


title: sir4∆_mutpromoter_Taf1FLAG ChIP rep1

value: , hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; matdelta::k.l.LEU2


title: naïve T cells_rep2

source_name: spleen

value: naive OT-II T cells

value: spleen

value: no treatment


title: WT_rep1


title: m331_R_H3K18Ace_1_IP


title: IP

status: Public on May 08 2023

first: Liqing

last: Lu

address: No.1 of Shizishan street, Hongshan District

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Raw reads would be processed to get high quality clean reads according to three stringent filtering standards: i  Removing reads containing adapters;  ii  Removing reads containing more than 10% of unknown nucleotides (N); iii  Removing low quality reads containing more than 40% of low quality (Q-value≤10) bases.
Bowtie2 was used to align the clean reads from each sample against the reference genome. All reads from transcriptional initiation site (TSS) to transcriptional termination site (TES) interval and upstream and downstream 2k interval were counted by deepTools software
MACS2 v2.1.2 was designed to identify read-enriched regions from DAP-seq data. Dynamic Poisson Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when q-value<0.05.
Peak related genes were annotated by the ChIPseeker R package. According to the genomic location information and gene annotation information of peak, peak related genes can be confirmed Besides, the distribution of peak on different genome regions, such as intergenic, introns, downstream, upstream and exons was performed
MEME and DREME were used to detect the sequence motif, which determined to detect long and short consensus sequence
Assembly: Citrus sinensis 1.0 (http://citrus.hzau.edu.cn/download.php)
Supplementary files format and content: bw(bigwig)
Library strategy: DAP-seq

organism: Citrus reticulata

source_name: ovary

extract_protocol:
After DAP DNA was extracted, the enriched DNAs were fragmented into short fragments by ultrasonic.
The DNA fragments were end repaired, 3’A added, and ligated to Illumina sequencing adapters. DNA fragments with proper size (usually 100-300bp, including adapter sequence) were selected for PCR amplified. Finally we got qualified library for sequencing

tag: cultivar

value: Ponkan

value: ovary


title: input


title: Col_H2AZ9_Rep1

description: ChIP


title: naïve T cells_rep1


title: Tigit-CXCR5+ T cells_day 14_rep1


title: c-12-1

city: Beijing

first: Xiaolan

last: Liu

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
FastQC v0.11.5
trimmomatic v0.39
Hisat2 v2.1.0
Stringtie v1.3.3
DEseq2 v1.16.1
Assembly: Neurospora crassa OR74A
Supplementary files format and content: tpm TPM of all strains

molecule: polyA RNA

organism: Neurospora crassa OR74A

extract_protocol:
The purity of the sample was determined by NanoPhotometer ® (IMPLEN, CA, USA)；The concentration and integrity of RNA samples were detected by Agilent 2100 RNA nano 6000 assay kit (Agilent Technologies, CA, USA).
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02) (Annoroad Gene Technology Co., Ltd, Beijing)  following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cpc-1 knock out

value: 2% glucose with 12mM 3-aminotria in constant light  at 25°C , 18h


title: WT-12-3


title: c-01

value: 2% glucose in constant light  at 25°C , 18h


title: WT-12-1


title: c-02


title: WT-03


title: c-12-3


title: c-12-2


title: WT-02


title: WT-01


title: ESC-derived lung epithelium and iPSC-derived lung mesenchyme after proximal co-culture

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: me-prox

library_source: transcriptomic single cell

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38 with GFP and dsRed
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the cell ranger count pipeline:

source_name: Nkx2-1mCherry and Tbx4-LERGFP

growth_protocol:
Separate directed differentiation towards lung epithelial and mesenchymal progenitors, followed by co-culture in proximal differentiation medium for 7 days
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single-Cell 30 Library Kit (10X Genomics) and loaded on a NextSeq2000 (Illumina) with a custom sequencing setting to obtain a sequencing depth of ~40k reads/cell

treatment_protocol: All samples were sorted for live cells and Epcam+/mCherry+ (epithelium) and/or GFP+ (mesenchyme) prior to extract preparation

value: Nkx2-1mCherry and Tbx4-LERGFP

value: ESC-derived proximal lung epithelium and iPSC-derived lung mesenchyme


title: ESC-derived lung epithelium and iPSC-derived lung mesenchyme after distal co-culture

description: me-dist

growth_protocol:
Separate directed differentiation towards lung epithelial and mesenchymal progenitors, followed by co-culture in distal differentiation medium for 7 days
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

value: ESC-derived distal lung epithelium and iPSC-derived lung mesenchyme


title: ESC-derived lung epithelium after distal culture

description: e-dist

growth_protocol:
Directed differentiation toward lung epithelial progenitors, followed by culture in distal differentiation medium for 7 days
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

value: ESC-derived distal lung epithelium


title: iPSC-derived lung mesenchyme before co-culture

description: m-pre

growth_protocol:
Directed differentiation toward lung mesenchymal progenitors
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

value: iPSC-derived lung mesenchymal progenitor


title: ESC-derived lung epithelium before co-culture

description: e-pre

growth_protocol:
Directed differentiation toward lung epithelial progenitors
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

value: ESC-derived lung epithelial progenitor


title: 6morc/ddr4_AT5TE48725_region2_bspcr

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to TAIR10 reference genome using BSMAP v2.90  under default settings (-v 2, allowing up to 2 mismatches; -w 1, report the best hit; -n 1, aligning to both strands). Reads with more than three consecutive methylated CHH were removed as described previously. The methratio.py script from the BSMAP package was used to extract the number of methylated cytosine at single base pair resolution.
Assembly: TAIR10
Supplementary files format and content: The processed data is generated  by the BSMAP methratio.py script.

source_name: seedling

extract_protocol: 10-day-old seedlings were collected for DNA extraction using a CTAB-based method. 400 ng DNA was used for bisulfite conversion with the EZ DNA methylation-lighting kit

value: seedling

tag: time

value: DAY 10


title: 6morc/ddr4_AT5TE48725_region1_bspcr


title: 6morc/ddr4_AT4TE09845_region1_bspcr


title: 6morc/ddr4_AT5G35490_region2_bspcr


title: 6morc/ddr4_AT4TE09845_region2_bspcr


title: 6morc/ddr4_AT3G29639_region1_bspcr


title: 6morc/ddr4_AT3G29639_region2_bspcr


title: 6morc/ddr4_AT5TE46150_region2_bspcr


title: 6morc/ddr4_AT5G35490_region3_bspcr


title: 6morc/ddr4_AT1G06993_region2_bspcr


title: 6morc/ddr4_AT1G06993_region1_bspcr


title: c-03


title: WT-12-2

value: WT


title: 6morc_AT5TE48725_region1_bspcr


title: 6morc_AT5TE48725_region2_bspcr


title: 6morc_AT4TE09845_region1_bspcr


title: 6morc_AT5G35490_region3_bspcr


title: 6morc_AT5TE46150_region2_bspcr


title: ESC-derived lung epithelium after proximal culture

description: e-prox

growth_protocol:
Directed differentiation toward lung epithelial progenitors, followed by culture in proximal differentiation medium for 7 days
Cells were differentiated towards the lung epithelial progenitor state using our previously published protocol (Serra et al, Development 2015) or towards the lung mesenchymal progenitor state using our directed lung mesenchymal protocol (Alber et al., bioRXiv 2022). For subsequent distal differentiation, lung epithelial progenitor cells were cultured in serum-free medium supplemented with 200 ng/ml rmWNT3A, 100 ng/ml rhFGF2, and 100 ng/ml rhFGF10 either alone or with iPSC-derived lung mesenchymal cells. For proximal differentiation lung epithelial progenitor cells were cultured in serum-free medium supplemented with 100 ng/ml rhFGF2, 100 ng/ml rhFGF10, 100 ng/ml Heparin Salt, and 10 μM Y-27632 either alone or with iPSC-derived lung mesenchymal cells.

value: ESC-derived proximal lung epithelium


title: 6morc_AT3G29639_region1_bspcr


title: 6morc_AT5G35490_region2_bspcr


title: 6morc_AT3G29639_region2_bspcr


title: 6wt_AT5TE48725_region2_bspcr


title: 6morc_AT1G06993_region2_bspcr


title: 6wt_AT5TE48725_region1_bspcr


title: 6morc_AT1G06993_region1_bspcr


title: 6wt_AT5TE46150_region2_bspcr


title: 6morc/ddr4_AT3G29639_region3_bspcr


title: 6wt_AT4TE09845_region2_bspcr


title: 6wt_AT4TE09845_region1_bspcr


title: 6wt_AT3G29639_region3_bspcr


title: 6wt_AT5G35490_region3_bspcr


title: 6wt_AT3G29639_region2_bspcr


title: 6wt_AT1G06993_region1_bspcr


title: 6morc_AT3G29639_region3_bspcr


title: 6wt_AT5G35490_region2_bspcr


title: DDR4-ZF/chr11/17, region2, rep2, bspcr

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to TAIR10 reference genome using BSMAP v2.90  under default settings (-v 2, allowing up to 2 mismatches; -w 1, report the best hit; -n 1, aligning to both strands). Reads with more than three consecutive methylated CHH were removed as described previously. The methratio.py script from the BSMAP package was used to extract the number of methylated cytosine at single base pair resolution. A sequencing depth cut-off of >20 was applied followed by calculation of the percentage of DNA methylation using equation #C/(#C+#T). The results were visualized using scripts developed by Gallego-Bartolomé et al., and plotted independently for the two selected regions upstream the TSS of FWA and SDC.
Assembly: TAIR10
Supplementary files format and content: The processed data is generated  by the BSMAP methratio.py script.

value: ZF-DDR4/chr11/17 mutant


title: DDR4-ZF/chr11/17, region1, rep2, bspcr


title: DDR4-ZF/chr11/17, region2, rep1, bspcr


title: DDR4-ZF/chr11/17, region1, rep1, bspcr


title: DDR4-ZF, region1, rep2, bspcr

value: ZF-DDR4 mutant


title: DDR4-ZF, region2, rep1, bspcr


title: DDR4-ZF, region1, rep1, bspcr


title: 6morc_AT4TE09845_region2_bspcr


title: met1, region1, bspcr

value: met1 mutant


title: Col0, region2, bspcr

value: wt


title: Col0, region1, bspcr


title: GFP-drm2/cmt3/ddr4, region2, bspcr

value: drm2/cmt3/ddr4 mutant


title: GFP-drm2/cmt3, region2, bspcr

value: drm2/cmt3 mutant


title: GFP-drm2/cmt3/ddr4, region1, bspcr


title: GFP-morc1/ddr4, region2, bspcr

value: morc/ddr4 mutant


title: GFP-morc1/ddr4, region1, bspcr


title: GFP-morc1, region2, bspcr

value: morc1 mutant


title: 6wt_AT1G06993_region2_bspcr


title: 6wt_AT3G29639_region1_bspcr


title: GFP-morc1, region1, bspcr


title: GFP-wt, region2, bspcr


title: GFP-wt, region1, bspcr


title: Mut-2

city: Chapel Hill

first: Wei

last: Shi

state: NC

address: 221 Fordham Hall

department: Biology

institute: UNC-Chapel Hill

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_ID feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Heart

extract_protocol:
Hearts were dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: developmental stage


title: Mut-3


title: DDR4-ZF, region2, rep2, bspcr


title: Mut-4


title: WT-3


title: 2_14_ITD_D835Y_Co2

city: Tokyo

first: Kotoko

last: Yamatani

address: Building A 6F, Hongo Bunkyo-ku 2-1-1

country: Japan

institute: Juntendo University

data_processing:
The sequenced reads were processed according to the MOIRAI pipeline [PMID: 24884663]. Mapping was performed using tophat-2.0.14 with parameters -i 50 -I 500000 -r 300 on the reference genome hg19.
Counts Per Million reads (CPM) were caluculated for the reference CAGE peaks (mm9.cage_peak_phase1and2combined_coord.bed brovided by RIKEN) using edgeR 3.24.3.
The reference CAGE peak dataset was retrieved from http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: pro-B cell

growth_protocol: Ba/F3 cells were culture in RPMI-1640 medium supplemented with 10% heat -inactivated FBS, 100 U/ml penicilin and 100 μg/mL streptmycin

extract_protocol:
Total RNA was extracted from cells with the Rneasy Mini Kit
nAnt-iCAGE [PMID: 24927836]

value: Pro B cells

value: BALB/c (B cell); BALB/c (myeloma)

tag: gene mutation


title: 2_15_ITD_D835Y_Co3


title: 2_13_ITD_D835Y_Co1


title: Mut-1


title: WT-1


title: WT-2


title: met1, region2, bspcr


title: 2_8_ITDmCo2


title: 2_7_ITDmCo1


title: GFP-drm2/cmt3, region1, bspcr


title: 2_9_ITDmCo3


title: C14

city: London

first: Michael

last: Boffa

state: ON

address: 1151 Richmond Street North

department: Biochemistry

country: Canada

institute: The University of Western Ontario

data_processing:
Partek Flow v10.0.22
fastq files were aligned to hg19 using Star 2.7.3a and annotated with RefSeq Transcripts 100 - 2021-11-01
Features were excluded if maximum reads <= 36.0
Reads were normalized using SESeq2 (mediancounts)
Fold changes and p-values were caluclated using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text file including fold change and statistical significance value for each gene

organism: Homo sapiens

source_name: THP-1 macrophages, apo(a)

growth_protocol: 24-well plates were seeded with 1 mL/well of 80,000 cells/mL THP-1 cells in RPMI-1640 medium supplemented with 100 nM phorbol-12-myristrate-13-acetate (PMA) . After 36 hours, cells were supplied with fresh PMA-supplemented medium. After a further 36 hours, this medium was replaced with serum-free complete medium and incubated for 16 hours (starvation conditions).

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol. Total RNA samples were quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific). Quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) and the RNA 6000 Nano kit (Caliper Life Sciences). Samples were then processed using the Vazyme VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme) which includes ribosomal RNA reduction. Samples were depleted and fragmented prior to cDNA synthesis, then cDNA was indexed, cleaned-up and amplified via polymerase chain reaction. Biological replicate libraries were pooled into one library.
The pooled library size distribution was assessed on an Agilent High Sensitivity DNA Bioanalyzer chip (Agilent Technologies Inc.), and quantified using the Qubit 2.0 Fluorometer. The library was sequenced as a single end run, 1 x76 bp, using a High Output v2 kit (75 cycles). Fastq data files were downloaded from BaseSpace and analyzed using Partek Flow.

treatment_protocol: Following starvation, the medium was replaced with fresh serum-free medium supplemented with 250 nM Lp(a) or 17K apo(a) or no supplement. Each of the aforementioned treatments was performed in duplicate. This represented a single biological replicate for each treatment. Cells were incubated with the treatments for 6 hours, after which

value: THP-1 monocytic leukemia

value: macrophage-like (differentiated for 72 hr with 100 nM PMA

value: 250 nM Purified recombinant 17-kringle apo(a)


title: PBP1 knockout cells in YPL media, biological replicate 2

city: Dallas

first: Benjamin

last: Tu

state: TEXAS

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: 10x Genomics

data_processing:
Read quality assessment and trimming were done using FastQC  and TrimGalore, respectively. Reads with Phred quality score less than 35 were removed.
Indexes were built and paired-end clean reads were aligned to the reference genome (S288C, R64-1-1) using STAR (2.7.3a).
Uniquely mapped reads were quantified per gene using featureCounts from the Subread package (v1.6.3).
Differential expression analysis was performed using the DESeq2 R package (v3.16).
p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
Assembly: R64-1-1(Saccharomyces cerevisiae S288C assembly)
Supplementary files format and content: One tab-delimited text file with normalized read counts per gene for each sample

source_name: yeast cells

extract_protocol:
RNA was extracted using the Masterpure Yeast RNA extraction kit (Lucigen).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. This was followed by fragmentation, first strand cDNA synthesis using random hexamer primers, and second strand cDNA synthesis. End repair, A-tailing, adapter ligation, size selection, amplification, and purification were then performed to generate the library, which was subsequently checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Libraries were sequenced on Illumina platform.

value: yeast cells

value: PBP1 knockout

value: YPL


title: C9

source_name: THP-1 macrophages, Lp(a)

value: 250 nM Purified plasma-derived Lp(a)


title: C5

source_name: THP-1 macrophages, vehicle

value: vehicle (PBS)


title: B2


title: PBP1 knockout cells in YPD media, biological replicate 2

description: 10x Genomics

value: YPD


title: B9


title: PBP1 knockout cells in YPD media, biological replicate 1

description: 10x Genomics


title: A14


title: WT-4

value: WT


title: WT cells in YPL media for 3 hrs, biological replicate 1

description: 10x Genomics


title: WT cells in YPD media, biological replicate 1

description: 10x Genomics


title: A1


title: WT cells in YPD media, biological replicate 2

description: 10x Genomics


title: transgene_MtallGAGAPRE1and2_H3K27me3_rep1

city: Bethesda

first: J.

middle: Lesley

last: Brown

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: NIH

data_processing:
ChIP-seq analysis was carried out on the Galaxy Platform (The Galaxy Community, 2022). ChIP-seq reads were aligned to the reference genome [dm6. BDGP (Berkley Drosophila Genome Project), version 6] using Bowtie2 v2.4.2 with default parameters (Langmead and Salzberg 2012).
PCR duplicates for each dataset were removed using the rmdup function of SAMtools v1.1.3 (Li et al. 2009).
Bam files were converted to tdf files using the igvtools for visualization in IGV (Integrative Genomics Viewer) (Thorvaldsdottir et al. 2013).
Assembly: Dm6
Supplementary files format and content: bam files

organism: Drosophila melanogaster

source_name: 3rd instar larval CNS and imaginal discs

growth_protocol: fly stocks were maintained at 25oC

extract_protocol:
ChIP was performed on larval discs and brains from 3rd instar larvae. The method is as described in Langlais et al. (2012) with the following changes. Action buffer was replaced with: 50mM Tris/HCl pH8.0, 50mM NaCl, 1mM EDTA, 0.1%SDS, 1% Triton X-100, 0.1% deoxycholate plus Roche Complete Protease Inhibitor Cocktail (EDTA free). Sonication was carried out using a Q Sonica (Model Q800R3), at 70% amplitude with 30 seconds on, 30 seconds off for a total time of 22 minutes. Protein A SepharoseTM Fast Flow (Cytiva), was used in place of the Protein G agarose/salmon sperm DNA beads. ChIP was carried out with 1:100 dilutions of anti-Ph (Buchenau et al. 1998), anti-E(z) (Brown et al., 2018), anti-Spps (Brown and Kassis, 2010), anti-Pho (Brown et al., 2003), anti-Sfmbt (Erokhin et al. 2015), anti-H3K27me3 (Millipore 17-622) or (Invitrogen MA5-11198).
DNA concentrations of ChIP samples were measured using a Qubit 3.0 fluorimeter (Invitrogen). 1.5ng of starting material was used to prepare each library. Libraries samples were made using either (H3K27me3 samples only), the NEBNext UltraTM II DNA library preparation kit and single index kit (New England Biolabs), or (all other samples), the Thruplex DNA-seq and single index kits (Takara). Libraries were made following the manufacturer’s directions.

tag: antibody

value: H3K27me3 (Millipore 17-622)


title: transgene_MtallGAGAPRE1and2_input_rep2

value: 3rd instar larval CNS and imaginal discs


title: transgene_MtallGAGAPRE1and2_H3K27me3_rep2


title: transgene_PhoKOPRE1and2_H3K27me3_rep2


title: transgene_WTPRE1and2_H3K27me3_rep1

value: transgene WTPRE1+2


title: transgene_PhoKOPRE1and2_input_rep1


title: transgene_PhoKOPRE1and2_input_rep2


title: transgene_WTPRE1and2_H3K27me3_rep2


title: transgene_WTPRE1and2_input_rep2


title: transgene_WTPRE1and2_input_rep1


title: PBP1 knockout cells in YPL media, biological replicate 1

description: 10x Genomics


title: B13


title: transgene_control_input_rep2

value: transgene control


title: transgene_control_H3K27me3_rep2


title: transgene_control_H3K27me3_rep1


title: A6


title: transgene_control_input_rep1


title: Crisper_MutPhoPRE2_Spps_rep2

value: Spps


title: Crispr_MtPhoPRE2_Ph_rep2

value: Ph


title: Crisper_MutPhoPRE2_Spps_rep1


title: WT cells in YPL media for 3 hrs, biological replicate 2

description: 10x Genomics


title: Crispr_MtPhoPRE2_Ph_rep1


title: Crispr_MtPhoPRE2_Pho_rep2

value: Pho


title: Crispr_MtPhoPRE2_Pho_rep1


title: Crispr_MtPhoPRE1and2_Spps_rep2

value: Crispr mtPhoPRE1+2


title: Crispr_MtPhoPRE2_input_rep1


title: transgene_MtallGAGAPRE1and2_input_rep1


title: Crispr_MtPhoPRE1and2_Spps_rep1


title: Crispr_MtPhoPRE1and2_Ez_rep1

value: Ez


title: Crispr_MtPhoPRE1and2_Sfmbt_rep2

value: Sfmbt


title: Crispr_MtPhoPRE1and2_Sfmbt_rep1


title: Crispr_MtPhoPRE1and2_Ph_rep2


title: Crispr_MtPhoPRE1and2_Pho_rep2


title: Crispr_MtPhoPRE1and2_Pho_rep1


title: Crispr_MtPhoPRE1and2_input_rep2


title: Crispr_MtPhoPRE1and2_Ph_rep1


title: Crispr_WTPRE1and2_Spps_rep2

value: Crispr WTPRE1+2


title: transgene_PhoKOPRE1and2_H3K27me3_rep1


title: Crispr_WTPRE1and2_Spps_rep1


title: Crispr_WTPRE1and2_Ez_rep1


title: Crispr_WTPRE1and2_Ez_rep2


title: Crispr_WTPRE1and2_Ph_rep2


title: Crispr_WTPRE1and2_Sfmbt_rep1


title: Crispr_WTPRE1and2_Pho_rep2


title: Crispr_WTPRE1and2_Sfmbt_rep2


title: Crispr_WTPRE1and2_input_rep2


title: Crispr_WTPRE1and2_Pho_rep1


title: Crispr_MtPhoPRE2_input_rep2


title: endel1_5_Pho_rep1


title: endel1_5_Pho_rep2


title: Crispr_MtPhoPRE1and2_Ez_rep2


title: endel1_5input_rep1


title: 2_6_D835mAML_6

data_processing:
The sequenced reads were processed according to the MOIRAI pipeline [PMID: 24884663]. Mapping was performed using tophat-2.0.14 with parameters -i 50 -I 500000 -r 300 on the reference genome mm9.
Counts Per Million reads (CPM) were caluculated for the reference CAGE peaks (FANTOM_CAT.lv2_permissive.CAGE_cluster.bed provided by RIKEN) using edgeR 3.24.3.
The reference CAGE peak dataset was retrieved from https://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/data/assembly/lv2_permissive/.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: leukemia cells

extract_protocol:
Peripheral blood or bone marrow were obtained from AML patients and ficol-hypaque density gradient centrifugation was used to separetae mononuclear cells.Then RNA was extracted from cells
nAnt-iCAGE [PMID: 24927836]

value: AML patient-derived leukemia cells


title: Crispr_WTPRE1and2_input_rep1


title: 2_5_D835pAML_9


title: 2_4_D835pAML_8


title: 2_3_D835pAML_7


title: Crispr_MtPhoPRE1and2_input_rep1


title: Crispr_WTPRE1and2_Ph_rep1


title: 2_2_D835pAPL_2.


title: BxPC3-FR054-GEM, rep1

city: Milan

first: Ferdinando

last: Chiaradonna

address: Piazza della Scienza 2

department: Biotechnology and Biosciences

country: Italy

institute: University of Milano Bicocca

data_processing:
Libraries were quantified and quality checked on an Agilent 4200 TapeStation system (High Sensitivity D1000), and then sequenced on an Illumina NovaSeq 6000 platform with paired-end reads 150bp long, with a depth of 30 million cluster/sample.
Fastq reads were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for overall and per-base read quality and presence of adaptor sequences. Paired reads were subsequently aligned to the human reference genome (GRCh38/hg38) using the splice-aware aligner STAR v 2.5.0c (Dobin, Davis et al. 2013) and indexed with Samtools (Li, Handsaker et al. 2009). Per-gene read counts were generated using the STAR quantMode geneCounts option.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data normalised counts.xlsx

growth_protocol: MiaPaca2 and BxPC3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Qiagen RNeasy Kit starting from 5x10^6 cells/sample
Total RNA was quantified with a spectrophotometer method and RNA integrity was evaluated with Agilent 4200 TapeStation analysis.  RNA stranded libraries were generated starting from 500ng total RNA and mRNA was selected with poly-T oligo attached magnetic beads using Illumina TruSeq® Stranded mRNA Library Prep kit (Catalog #: 20020594).

treatment_protocol: 1uM gemcitabine, and 0.5mM FR054 in the presence of 10% FBS until day 2.

value: pancreatic cancer cells

value: WT K-ras

value: FR054 and Gemcitabine


title: BxPC3-FR054-GEM, rep2


title: BxPC3-GEM, rep1

value: Gemcitabine


title: BxPC3-FR054, rep2

value: FR054, HBP inhbition


title: BxPC3-GEM, rep2


title: BxPC3-NT control, rep2

value: Untreated cells


title: 24_D835mAPL_1


title: 23_D835pAMOL_1


title: BxPC3-FR054, rep1


title: BxPC3-NT control, rep1


title: CTLi.RNAseq_2

city: San Diego

first: George

last: Sen

address: 9452 Medical Ctr Dr, La Jolla, CA 92037

department: Department of Dermatology

institute: University of California San Diego

data_processing:
NovaSeq S4PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Assembly: hg19

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
PureLinkTMRNA mini kit (Thermo Fisher Scientific; 12183025)
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: ARID1A siRNA knockdown

tag: timepoints

value: 24 hr

value: PolyIC induced for  24hr


title: ARID1Ai.RNAseq_3


title: ARID1Ai.RNAseq_1


title: CTLi.RNAseq_1


title: CTLi.RNAseq_3


title: 20_D835mAML_5


title: ARID1Ai.RNAseq_2


title: endel1_5input_rep2

value: 3rd instar larval CNS and imaginal discs


title: MIA-PACA-FR054-GEM, rep2

value: mutated K-ras


title: MIA-PACA-GEM, rep1


title: MIA-PACA-GEM, rep2


title: 19_D835mAML_4


title: MIA-PACA-FR054-GEM, rep1


title: 18_D835mAMML_5


title: MIA-PACA-FR054, rep2


title: 17_D835mAML_3


title: MIA-PACA-NT control, rep2


title: MIA-PACA-FR054, rep1


title: 2_1_D835pAPL_1


title: MIA-PACA-NT control, rep1


title: 16_D835mAMML_4


title: 12_D835mAMML_3


title: PanIN_A2b-3

city: Baltimore

first: Emily

last: Lo

address: 733 N Broadway

institute: Johns Hopkins

data_processing:
Adapter sequences were computationally trimmed with Trim Galore using default parameters for libraries prepared with NEBNext. For libraries prepared with Accel-NGS, an additional 10 bp were trimmed from the 3’ end of R1 and 10 bp from the 5’ end of R2 to account for the low complexity polynucleotide tail added by the Adaptase enzyme.
Bisulfite-aware alignment of the trimmed reads to the hg19 genome was performed using Bismark with default parameters. Samtools was used to merge individual bam files corresponding to fastq file pairs and to name sort the merged bam file. Methylation bias (mbias) plots were generated using Bismark’s methylation extractor in --mbias_only mode. Bismark was then used to deduplicate merged, name-sorted bam files. Position-sorted and indexed bam files were then created using samtools.
Bismark methylation_extractor was used to create CpG_report files. CpG report files were read into R using Bioconductor package bsseq, smoothed using default parameters, and coverage-filtered with a cutoff of 2X for each biological replicate. Smoothed, coverage-filtered bsseq object was saved as a .rda (RData) file.
Assembly: hg19
Supplementary files format and content: lcm_wbgs_bsseq_smoothed_coverage_filtered_geo.rda: Rdata file containing smoothed and coverage-filtered bsseq object (with CpG reports from all samples)

source_name: Pancreas

extract_protocol:
Frozen tissue samples were cryo-sectioned at 5 - 9 uM thick onto PEN membrane slides and stored at -80°C. Slides were fixed briefly in 70% ethanol, then stained with cresyl violet acetate or hematoxylin and eosin. Immediately following staining, laser-capture microdissection for the appropriate cell compartment targeted was performed using Zeiss PALM Microbeam on 10X or 20X magnification. The number of pooled cuts per cell type needed to reach a desired input of 20-50 ng DNA for WGBS varied for each sample. Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen cat. #56304) according to manufacturer’s instructions for the “Isolation of Genomic DNA from Laser-Microdissected Tissues” protocol, with carrier RNA inclusion. To increase final DNA yield, samples were eluted twice, using the eluate from the first elution for the second, incubating for 5 min each before centrifugation.
Genomic DNA samples were quantified by Qubit dsDNA HS assay (ThermoFisher Scientific, cat# Q32851). 1% unmethylated Lambda DNA (Promega cat. #D1521) was spiked into genomic DNA to monitor bisulfite conversion efficiency. For WGBS library preparation, either NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. #E7370L) or Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences cat. #30024, now xGen Methyl-Seq, IDT cat. #10009860) were used.  For the modified NEBNext Ultra DNA Library Prep Kit, genomic DNA (39–119 ng) was fragmented to a target peak of 300-400 bp using the Covaris S2 Focused-ultrasonicator in a 50 μl volume according to the manufacturer’s instructions. The fragmented DNA was converted to end-repaired, adenylated DNA using NEBNext Ultra End Repair/dA-Tailing Module (New England BioLabs, cat. #7442L). Methylated adaptors (NEBNext Multiplex Oligos for Illumina; New England BioLabs, cat. #E7535L) were ligated to the product from the preceding step using  NEBNext Ultra Ligation Module (New England BioLabs, cat. #7445L). The resulting product was size-selected as described in the manufacturer’s protocol by employing modified AMPure XP bead ratios of 0.4X and 0.2X to select for an insert size of 300–400 bp. After size-selection, the samples were bisulfite converted and purified using the EZ DNAm-Lightning Kit (Zymo Research, cat. #D5030). Bisulfite converted libraries were PCR amplified and indexed using primers from the NEBNext Multiplex Oligos for Illumina module (New England BioLabs, cat. #E7535L) and the Kapa HiFi Uracil+ PCR system (Kapa Biosystems, cat. #KK2801). PCR enrichment was performed with the following cycling parameters: 98°C for 45 sec followed by 10 - 11 cycles at 98°C for 15 sec, 65°C for 30 sec, 72°C for 30 sec and a final extension at 72°C for 1 min. The PCR enriched product was cleaned up using 0.9X AMPure XP beads (Beckman Coulter, cat. #A63881).   For the Accel-NGS Methyl-Seq DNA Library Kit, genomic DNA (11–25 ng) was fragmented to a target peak of 300-400 bp using the Covaris S2 Focused-ultrasonicator in a 50 μl volume according to the manufacturer’s instructions. The fragmented genomic DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research, cat# D5005) following the manufacturer’s instructions. Methyl-seq libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, cat# 30024) according to the manufacturer’s instructions and the resulting libraries were amplified for 7 PCR cycles using unique dual indexing primers (Swift Bioscience, cat# X9096-PLATE).
The resulting WGBS libraries were evaluated on a 2100 Bioanalyzer using the Agilent High-Sensitivity DNA Kit (Agilent Technologies, cat. #5067-4626) and quantified via qPCR using the KAPA Library Quantification Kit (KAPA Biosystems, cat. #KK4824). NEBNext Ultra DNA libraries were sequenced on the Illumina HiSeq 4000 system at a 2 × 151 bp read length with 8% PhiX spike-in. Accel-NGS Methyl-Seq DNA libraries were pooled and sequenced on an Illumina NovaSeq 6000 system at a 2 × 150 bp read length with 7% spike-in of a balanced library.

value: Pancreas

value: PanIN lesion

tag: disease state

value: Non-invasive neoplasia


title: PanIN_A1-1


title: PanIN_A2a-2


title: PanIN_A1-2


title: PanIN_A2a-1


title: 15_D835mAML_2


title: 14_D835mAMOL_2


title: PanIN_A2a-3


title: 10_D835mAMML_2


title: PanIN_A1-3


title: 9_D835mAMML_1


title: 11_D835mAML_1


title: Duct_A2

value: Ducts

value: Normal


title: Jejunum-03

city: Kobe

first: Hijiri

last: Fujioka

address: 6-7-5, Minatojimaminamimachi, Chuouku,

institute: NBI

data_processing:
Illumina Real-Time Analysis (RTA) v2.7.7 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using STAR aligner.
After filtering out duplicate reads, RNA quantification and normarization with Trimmed mean of M-values (TMM) or Transcripts per million (TPM)  were done by using Strand NGS 3.4 (Strand Life Sciences).
Assembly: GRCh38
Supplementary files format and content: Matrix table with TMM or TPM-normalized gene counts for every gene and every sample

source_name: Jejunum

extract_protocol:
RNA was harvested using QIAzol reagent.Illumina TruSeq stranded totalRNA (#20020596) was used total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted and purified by using an RNeasy Mini kit (QIAGEN) according to manufacturer’s standard protocol. RNA quality was evaluated in the same way as the biopsy samples using the BioAnalyzer (Agilent Technologies).

value: non

value: Jejunum

tag: sampling region

value: non-inflammatory area

tag: age

tag: Sex

value: male

tag: race

value: Japanese


title: 8_D835mAMOL_1

value: AML patient-derived leukemia cells


title: Duct_A0

tag: tissue


title: Ileum-11

source_name: Ileum

value: IBD

value: Ileum


title: 6_D835pAML_6


title: Colon-21

source_name: Colon

value: Colon


title: Acinar_A0

value: Acini


title: Acinar_A1


title: Acinar_A2


title: Jejunum-02


title: Colon-20


title: 5_D835pAML_5


title: PanIN_A2b-1


title: PanIN_A2b-2


title: 4_D835pAML_4


title: Duct_A1


title: Jejunum-01


title: Colon-01


title: 3_D835pAML_3


title: 2_D835pAML_2


title: Ileum-01


title: Colon-16

value: female


title: Colon-18


title: Colon-15


title: 1_D835pAML_1


title: Colon-19


title: Colon-17


title: Ileum-10


title: Rectum-05

source_name: Rectum

value: Rectum


title: NAc_Male_Water_4

first: Mahashweta

last: Basu

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

data_processing:
Samples were sequenced on an Illumina HiSeq 4000 with a 75 bp paired-end read.
An averageof 64–100million reads were obtained for each sample.
Reads were aligned to the mousegenome (Mus_musculus.GRCm38) usingTopHat(version 2.0.8; maximum number ofmismatches = 2; segment length = 30; maximum multi-hits per read = 25; maximum intronlength = 50,000).
The number of reads that aligned to the predicted coding regions wasdetermined using HTSeq.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Raw counts file (without normalization)
Supplementary files format and content: File is in text format with first column as gene ensemble IDs and second its counts.

source_name: Nucleus accumbens

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and the MicroElute Total RNA kit (Omega) with a Dnase step (Qiagen, Germantown, MD)
Librarieswere prepared from10ng of RNAusing theSmart-Seq v4 kit(Takara).

value: Nucleus accumbens

value: Male

tag: genotype

value: Wildtype

tag: treatment

value: Water


title: NAc_Male_Water_5


title: Colon-23


title: Colon-11


title: NAc_Male_Water_3


title: NAc_Male_Water_2


title: Ileum-09


title: Colon-22


title: NAc_Male_Water_1


title: Ileum-07


title: Rectum-03


title: Colon-12


title: Ileum-08


title: NAc_Male_Fentanyl_4

value: Fentanyl


title: Colon-09


title: Duodenum-11

source_name: Duodenum

value: Duodenum


title: NAc_Male_Fentanyl_5


title: Ileum-06


title: Duodenum-07


title: NAc_Male_Fentanyl_3


title: Colon-13

value: non


title: Ileum-05

value: non-inflammatory area


title: Duodenum-12

value: male


title: Colon-08

value: Japanese


title: NAc_Male_Fentanyl_1


title: Colon-07


title: Colon-14


title: NAc_Female_Water_5

value: Female


title: NAc_Male_Fentanyl_2


title: NAc_Female_Water_4


title: Duodenum-09


title: Duodenum-10


title: Rectum-04


title: Duodenum-06


title: NAc_Female_Water_3


title: Duodenum-05


title: NAc_Female_Water_2


title: NRI1_RNA

city: Grand Rapids

first: Ronald

middle: L

last: Chandler

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned hg38 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 49’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for reverse-strand (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Assembly: hg38indexed to GENCODE (vM16) GFF3 annotation
Supplementary files format and content: Tabular text files including gene counts (STAR output) for each sample.

growth_protocol: 12Z cells were grown in DMEM/F12 + 10% FBS, 1% pen/strep, 1% L-glutamine

extract_protocol:
24 hours after insulin or vehicle treatment, RNA was prepared using the Quick-RNA Miniprep Kit (Zymo Research).
Libraries were prepared from 500 ng of total RNA using the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA).

treatment_protocol: Cells were transfected with siRNAs using Lipofectamine RNAiMax reagent. 24 hours after siRNA transfection, cells were transfected with pBabe vector containing PIK3CA*H1047R or pBabe empty vector using the FuGene HD transfection reagent (Promega). Media was replaced after 4 hours. 24 hours after plasmid transfection, cells were serum starved for 4 hours, and then treated with serum-free media containing 100 nM insulin or vehicle.

tag: cell line

tag: cell type

value: Epithelia

value: Non-targeting siRNA, PIK3CA*H1047R vector, insulin treatment


title: NAc_Female_Water_1


title: NRI3_RNA


title: NRI2_RNA


title: NRV3_RNA

value: Non-targeting siRNA, PIK3CA*H1047R vector, vehicle treatment


title: NRV2_RNA


title: NRV1_RNA


title: NBI3_RNA

value: Non-targeting siRNA, pBabe control vector, insulin treatment


title: NBI2_RNA


title: NAc_Female_Fentanyl_4


title: NAc_Female_Fentanyl_5


title: NBV3_RNA

value: Non-targeting siRNA, pBabe control vector, vehicle treatment


title: NAc_Female_Fentanyl_3


title: NAc_Female_Fentanyl_1


title: NBV2_RNA


title: NBV1_RNA


title: VI3_RNA

treatment_protocol: Cells were transfected with pCAG vector containing Viperin or pBabe empty vector using the FuGene HD transfection reagent (Promega). Media was replaced after 4 hours. 24 hours after plasmid transfection, cells were serum starved for 4 hours, and then treated with serum-free media containing 100 nM insulin or vehicle.

value: pCAG Viperin plasmid, 100 nM insulin treatment


title: VI2_RNA


title: PrL_Male_Water_5

source_name: Prrelimbic cortex

value: Prrelimbic cortex


title: VI1_RNA


title: VV1_RNA

value: pCAG Viperin plasmid, vehicle treatment


title: PrL_Male_Water_4

value: Male

value: Wildtype


title: FI2_RNA

value: pCAG empty vector, 100 nM insulin treatment


title: VV2_RNA


title: FI3_RNA


title: PrL_Male_Water_3

value: Water


title: NAc_Female_Fentanyl_2

value: Nucleus accumbens

value: Fentanyl


title: FI1_RNA


title: FV3_RNA

value: pCAG empty vector, vehicle treatment


title: FV2_RNA


title: PrL_Male_Water_1


title: PrL_Male_Water_2


title: SRI3_RNA

value: RSAD2 siRNA, PIK3CA*H1047R vector, insulin treatment


title: FV1_RNA


title: NBI1_RNA


title: PrL_Male_Fentanyl_5


title: SRI1_RNA


title: SRI2_RNA


title: PrL_Male_Fentanyl_4


title: SRV2_RNA

value: RSAD2 siRNA, PIK3CA*H1047R vector, vehicle treatment


title: PrL_Male_Fentanyl_3


title: SRV1_RNA

value: Epithelia


title: SBI3_RNA

value: RSAD2 siRNA, pBabe control vector, insulin treatment


title: SRV3_RNA


title: VV3_RNA


title: PrL_Male_Fentanyl_2


title: SBI1_RNA


title: PrL_Male_Fentanyl_1


title: SBV2_RNA

value: RSAD2 siRNA, pBabe control vector, vehicle treatment


title: SBI2_RNA


title: PrL_Female_Water_5

value: Female


title: SBV1_RNA


title: PrL_Female_Water_4


title: PrL_Female_Water_3


title: NBV4_RNA

value: Non-targeting siRNA, pBabe control vector, vehicle treatment


title: NBV6_RNA


title: NBV5_RNA


title: PrL_Female_Water_2


title: PrL_Female_Water_1


title: batch_11, BCR

city: Hangzhou

first: Jian

last: Chen

address: Jiefang Road

department: Department of Gastrointestinal Surgery of the Second Affiliated Hospital

institute: Zhejiang University School of Medicine

description:
batch_11_BCR
multiplexed
batch_11_DBEC_MolsPerCell.csv
batch_11_Sample_Tag_Calls.csv

data_processing:
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers (UMIs). R2 reads were aligned to the human reference genome (GRCh38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts.
Quality control and downstream analysis of gene expression matrix were performed using Seurat v4.03. The UMI counts given by expression metrics were log normalized and scaled.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Spreadsheet and matrix files

source_name: stomach

extract_protocol:
Paired, fresh tumor and adjacent normal tissue samples were surgically removed from patients and immersed in MACS tissue storage solution (Miltenyi Biotec) immediately and kept ice-cold until the next step. Fresh samples were then washed with ice-cold phosphate-buffered saline (PBS) and then minced with the Iris scissor into small pieces, resuspended with digestion buffer consisting of RPMI-1640, DNase I (0.5 mg/ml, Sigma), collagenase II (1 mg/ml, Worthington) and collagenase IV (1 mg/ml, Diamond), incubated in 37 ℃ and gently piped until there were no obvious clumps. The cell suspension was further filtered through 70-µm nylon mesh to remove residues and cell aggregates, centrifuged at 300 rcf for 10 min, sediment was washed with wash buffer (RPMI-1640 with 10% FBS) and resuspended in 2 ml wash buffer. Density gradient centrifugation based on 20%-40%-70% Percoll gradient was performed for further purification of leukocytes. Purified cells were collected from the 40%-70% Percoll interface, and washed with ice-cold PBS. Red blood cells were excluded from the cell suspension using 1X Red Blood Cell Lysis Buffer (Invitrogen). Then the single-cell suspension was stained with anti-CD45 antibody (BD Biosciences) and Fixable Viability Dye eFluor (Biolegend) for the following cell sorting performed with SONY SH800 to obtain single alive immune cells.
Single cells were carefully washed with BD Pharmingen Stain Buffer and labeled with distinctive sample tags following the manual of BDTM Human Single-Cell Multiplexing Kit. After incubation, labeled cells were then stained with viability markers (Calcein AM and Draq7), counted and pooled together at an equal ratio of all samples to obtain a total number of 40,000 live cells at most in 650 µl cold Sample Buffer. Mixed cells were loaded into primed and treated BD Rhapsody Cartridge fixed upon Express instrument, incubated at room temperature for 15 min to ensure the cells were randomly distributed into > 200,000 microwells of Rhapsody Cartridge. Cell Load Scan was performed with BD RhapsodyTM Scanner. Supersaturated Cell Capture Beads labeled with oligonucleotide barcodes were then loaded into the cartridge, incubated at room temperature for 3 min to capture the loaded cells. Cell-lysis was performed by incubation with freshly prepared Lysis Buffer, making for RNA fragments hybridized to the beads. Beads captured with mRNA were retrieved and washed with magnet and cold Bead Wash Buffer as soon as possible, following reverse transcription and then Exonuclease I incubation. To ensure that the intact V(D)J sequence can be read, optimal steps including template switching, denaturation, self-hybridization, and Klenow extension were needed before exonuclease treatment. Exonuclease I-treated beads were taken into libraries preparation following the BD Rhapsody system V(D)J CDR3 and Sample Tag library protocol. In brief, all beads were amplified in PCR1 with a targeted mRNA primer panel (including 399 immune-specific targets), sample tag primers, and TCR/BCR primers. The products were purified by AMPure beads for double-sided size selection and divided into shorter Sample Tag PCR1 products and longer targeted mRNA/TCR/BCR PCR1 products. Purified PCR1 products were then applied into separated PCR2 reactions with respective primers (targeted mRNA, sample tag, TCR, BCR). All the four PCR2 products were purified with AMPure beads for the following index PCR to label the sequences with distinct indexes. After another AMPure beads purification, the indexed products were the final sequencing libraries named targeted mRNA libraries, TCR libraries, BCR libraries, and Sample Tag libraries. Qubit Fluorometer was used to estimate the concentration of each library, and Agilent Bioanalyzer and qPCR were performed for quality control. Targeted mRNA libraries and Sample Tag libraries were sequenced by PE 150 (50,000 read pairs/cell, 600 read pairs/cell), while TCR libraries and BCR libraries were sequenced by PE 250 (1,000 read pairs/cell).

value: stomach

value: immune cell


title: batch_11, targeted mRNA

description:
batch_11_tmR
multiplexed
batch_11_DBEC_MolsPerCell.csv
batch_11_Sample_Tag_Calls.csv


title: batch_10, BCR

description:
batch_10_BCR
multiplexed
batch_10_DBEC_MolsPerCell.csv
batch_10_Sample_Tag_Calls.csv


title: batch_10, TCR

description:
batch_10_TCR
multiplexed
batch_10_DBEC_MolsPerCell.csv
batch_10_Sample_Tag_Calls.csv


title: batch_11, sample tag

description:
batch_11_ST
multiplexed
batch_11_DBEC_MolsPerCell.csv
batch_11_Sample_Tag_Calls.csv


title: batch_10, targeted mRNA

description:
batch_10_tmR
multiplexed
batch_10_DBEC_MolsPerCell.csv
batch_10_Sample_Tag_Calls.csv


title: batch_11, TCR

description:
batch_11_TCR
multiplexed
batch_11_DBEC_MolsPerCell.csv
batch_11_Sample_Tag_Calls.csv


title: PrL_Female_Fentanyl_5

value: Prrelimbic cortex


title: batch_10, sample tag

description:
batch_10_ST
multiplexed
batch_10_DBEC_MolsPerCell.csv
batch_10_Sample_Tag_Calls.csv


title: PrL_Female_Fentanyl_4


title: batch_9, TCR

description:
batch_9_TCR
multiplexed
batch_9_DBEC_MolsPerCell.csv
batch_9_Sample_Tag_Calls.csv


title: PrL_Female_Fentanyl_3


title: SBV3_RNA


title: batch_9, sample tag

description:
batch_9_ST
multiplexed
batch_9_DBEC_MolsPerCell.csv
batch_9_Sample_Tag_Calls.csv


title: PrL_Female_Fentanyl_2


title: batch_9, BCR

description:
batch_9_BCR
multiplexed
batch_9_DBEC_MolsPerCell.csv
batch_9_Sample_Tag_Calls.csv


title: batch_9, targeted mRNA

description:
batch_9_tmR
multiplexed
batch_9_DBEC_MolsPerCell.csv
batch_9_Sample_Tag_Calls.csv


title: batch_8, BCR

description:
batch_8_BCR
multiplexed
batch 8_DBEC_MolsPerCell.csv
batch_8_Sample_Tag_Calls.csv


title: batch_8, TCR

description:
batch_8_TCR
multiplexed
batch 8_DBEC_MolsPerCell.csv
batch_8_Sample_Tag_Calls.csv


title: batch_8, sample tag

description:
batch_8_ST
multiplexed
batch 8_DBEC_MolsPerCell.csv
batch_8_Sample_Tag_Calls.csv


title: batch_7, targeted mRNA

description:
batch_7_tmR
multiplexed
batch_7_DBEC_MolsPerCell.csv
batch_7_Sample_Tag_Calls.csv


title: S1_Male_Water_5

source_name: Somatosensory cortex S1

value: Somatosensory cortex S1

value: Male


title: batch_7, sample tag

description:
batch_7_ST
multiplexed
batch_7_DBEC_MolsPerCell.csv
batch_7_Sample_Tag_Calls.csv


title: batch_6, BCR

description:
batch_6_BCR
multiplexed
batch_6_DBEC_MolsPerCell.csv
batch_6_Sample_Tag_Calls.csv


title: batch_7, BCR

description:
batch_7_BCR
multiplexed
batch_7_DBEC_MolsPerCell.csv
batch_7_Sample_Tag_Calls.csv


title: batch_7, TCR

description:
batch_7_TCR
multiplexed
batch_7_DBEC_MolsPerCell.csv
batch_7_Sample_Tag_Calls.csv


title: batch_5, BCR

description:
batch_5_BCR
multiplexed
batch_5_DBEC_MolsPerCell.csv
batch_5_Sample_Tag_Calls.csv


title: batch_6, targeted mRNA

description:
batch_6_tmR
multiplexed
batch_6_DBEC_MolsPerCell.csv
batch_6_Sample_Tag_Calls.csv


title: batch_6, TCR

description:
batch_6_TCR
multiplexed
batch_6_DBEC_MolsPerCell.csv
batch_6_Sample_Tag_Calls.csv


title: batch_6, sample tag

description:
batch_6_ST
multiplexed
batch_6_DBEC_MolsPerCell.csv
batch_6_Sample_Tag_Calls.csv


title: batch_4, BCR

description:
batch_4_BCR
multiplexed
batch 4_DBEC_MolsPerCell.csv
batch_4_Sample_Tag_Calls.csv


title: batch_3, BCR

description:
batch_3_BCR
multiplexed
batch_3_DBEC_MolsPerCell.csv
batch_3_Sample_Tag_Calls.csv


title: batch_5, sample tag

description:
batch_5_ST
multiplexed
batch_5_DBEC_MolsPerCell.csv
batch_5_Sample_Tag_Calls.csv


title: batch_5, targeted mRNA

description:
batch_5_tmR
multiplexed
batch_5_DBEC_MolsPerCell.csv
batch_5_Sample_Tag_Calls.csv


title: batch_3, TCR

description:
batch_3_TCR
multiplexed
batch_3_DBEC_MolsPerCell.csv
batch_3_Sample_Tag_Calls.csv


title: S1_Male_Water_1

value: Wildtype


title: S1_Male_Fentanyl_2


title: PrL_Female_Fentanyl_1


title: S1_Male_Water_3

value: Water


title: S1_Male_Water_4


title: batch_4, TCR

description:
batch_4_TCR
multiplexed
batch 4_DBEC_MolsPerCell.csv
batch_4_Sample_Tag_Calls.csv


title: batch_8, targeted mRNA

description:
batch_8_tmR
multiplexed
batch 8_DBEC_MolsPerCell.csv
batch_8_Sample_Tag_Calls.csv


title: batch_4, targeted mRNA

description:
batch_4_tmR
multiplexed
batch 4_DBEC_MolsPerCell.csv
batch_4_Sample_Tag_Calls.csv


title: batch_3, targeted mRNA

description:
batch_3_tmR
multiplexed
batch_3_DBEC_MolsPerCell.csv
batch_3_Sample_Tag_Calls.csv


title: batch_3, sample tag

description:
batch_3_ST
multiplexed
batch_3_DBEC_MolsPerCell.csv
batch_3_Sample_Tag_Calls.csv


title: S1_Female_Water_4


title: S1_Male_Fentanyl_5


title: batch_2, BCR

description:
batch_2_BCR
multiplexed
batch_2_DBEC_MolsPerCell.csv
batch_2_Sample_Tag_Calls.csv


title: batch_2, TCR

description:
batch_2_TCR
multiplexed
batch_2_DBEC_MolsPerCell.csv
batch_2_Sample_Tag_Calls.csv


title: batch_4, sample tag

description:
batch_4_ST
multiplexed
batch 4_DBEC_MolsPerCell.csv
batch_4_Sample_Tag_Calls.csv


title: S1_Male_Fentanyl_1


title: batch_2, targeted mRNA

description:
batch_2_tmR
multiplexed
batch_2_DBEC_MolsPerCell.csv
batch_2_Sample_Tag_Calls.csv


title: batch_2, sample tag

description:
batch_2_ST
multiplexed
batch_2_DBEC_MolsPerCell.csv
batch_2_Sample_Tag_Calls.csv


title: batch_5, TCR

description:
batch_5_TCR
multiplexed
batch_5_DBEC_MolsPerCell.csv
batch_5_Sample_Tag_Calls.csv


title: S1_Male_Fentanyl_3


title: batch_1, BCR

description:
batch_1_BCR
multiplexed
batch_1_DBEC_MolsPerCell.csv
batch_1_Sample_Tag_Calls.csv


title: S1_Female_Water_2


title: S1_Male_Fentanyl_4


title: S1_Female_Water_1


title: S1_Female_Fentanyl_4


title: batch_1, targeted mRNA

description:
batch_1_tmR
multiplexed
batch_1_DBEC_MolsPerCell.csv
batch_1_Sample_Tag_Calls.csv


title: iPSC-neurons, Untreated, rep3

city: Philadelphia

first: Jennine

middle: M

last: Dawicki-McKenna

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

description:
Unt_3
SAMPLE_1

data_processing:
For differential gene expression analysis, RNA-seq libraries were demultiplexed, and adapter sequences were removed with Cutadapt v1.18.
Transcriptome indices were prepared for Salmon v1.5.2 using a decoy-aware transcriptome file (gencode.v38.transcripts.fa with GRCh38.primary_assembly.genome.fa genome as decoy). Transcripts were quantified from paired-end reads in mapping-based mode (selective alignment, --libType ISR --gcBias --validateMappings).
Salmon transcript counts were imported into R and aggregated to the gene level using the tximeta (Love et al., 2020) and SummarizedExperiment (Martin Morgan et al., 2021) packages in Bioconductor.
For splicing analysis, demultiplexed, paired-end reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa) with STAR v2.7.1a in two-pass mode. For first-pass alignment, GENCODE basic gene annotation (gencode.v38.basic.annotation.gtf) was used (--outSAMstrandField intronMotif --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --scoreGenomicLengthLog2scale 0). The output splice junction files were concatenated and filtered (to remove junctions on chrM, non-canonical junctions, junctions supported by multi-mappers or by too few reads) then used in on-the-fly second-pass alignment (--outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --scoreGenomicLengthLog2scale 0 --quantMode TranscriptomeSAM GeneCounts).
Alignments were filtered with samtools v0.1.19 to remove unmapped reads and reads mapping to 10 or more locations.
Differential splicing analysis was performed using rMATS v4.1.1 with bam files as input (group 1 Untreated, group 2 PTBP2 KD). Prep and post steps were run (--gtf gencode.v38.primary_assembly.annotation.gtf -t paired --libType fr-firststrand --readLength 151 --variable-read-length --novelSS --allow-clipping) followed by the statistical model (--cstat 0.01).
Bigwig files were prepared using Yeo lab’s makebigwigfiles [https://github.com/YeoLab/makebigwigfiles].
Assembly: hg38
Supplementary files format and content: summarizedExperiment counts: tab-delimited text file includes gene-summarized counts for each sample
Supplementary files format and content: salmon_quant tar: entire sample output directory from Salmon
Supplementary files format and content: rMATS output: entire output directory from rMATS, sample information specified in README.txt

growth_protocol: For generation of mature iPSC-neurons, we used a protocol, modified from a combination of previous studies (Telezhkin et al., 2016; Yan et al., 2013). Experiments were performed when neurons matured to day 40-50 of differentiation.

extract_protocol:
iPSC-derived neurons were lysed with TRIzol Reagent (Invitrogen 15596-026). Chloroform was added to the lysate, and samples were centrifuged at 4°C to separate phases. After addition of ethanol, the aqueous phase was applied to an RNeasy Mini column (Qiagen #74104). On-column DNAse treatment was performed using Qiagen DNAse Set (Qiagen #79254) at room temperature for 15 minutes.
Purified total RNA was analyzed on Agilent TapeStation systems, using D1000 Screen Tape & Reagents, and then quantified with a Qubit BR kit (Thermo Fisher #Q10210). Poly(A)+ RNA transcript was isolated from 1 ug purified total RNA (RNA integrity number >9.0) with NEBNext poly(A) mRNA magnetic isolation module (New England Biolabs #E7490). RNA-seq libraries were prepared with NEBNext Ultra Directional RNA library preparation kit for Illumina (New England Biolabs #E7420S) according to the manufacturer's instruction.

treatment_protocol: LNA gapmer treatments in mature iPSC-neurons were performed by gymnotic delivery of the gapmer for 7 days.

value: iPSC-neurons

value: WT

value: Untreated


title: iPSC-neurons, 5 µM PTBP2 gapmer, rep1

description:
PTBP2_1
SAMPLE_2

value: 5 microM PTBP2 LNA gapmer


title: batch_1, sample tag

description:
batch_1_ST
multiplexed
batch_1_DBEC_MolsPerCell.csv
batch_1_Sample_Tag_Calls.csv


title: iPSC-neurons, 5 µM PTBP2 gapmer, rep2

description:
PTBP2_2
SAMPLE_2


title: S1_Female_Water_5


title: iPSC-neurons, 5 µM PTBP2 gapmer, rep3

description:
PTBP2_3
SAMPLE_2


title: S1_Female_Fentanyl_3

value: Fentanyl


title: iPSC-neurons, Untreated, rep1

description:
Unt_1
SAMPLE_1


title: iPSC-neurons, Untreated, rep2

description:
Unt_2
SAMPLE_1


title: S1_Female_Water_3


title: iPSC-neurons, 5 µM NegA, rep3

value: 5 microM NegA LNA gapmer


title: iPSC-neurons, 5 µM NegA, rep2


title: S1_Female_Fentanyl_1


title: iPSC-neurons, 5 µM NegA, rep1


title: S1_Female_Fentanyl_2


title: experiment 2: TVA stimulated 2 hr, biol rep2

city: Chicago

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

description: Column "O" is catenated, columns "P" and "Q" are individual component files

data_processing:
Sequence reads from two separate Illumina sequencing runs were catenated
First, the fastqc (0.11.9) and trim-galore (0.6.7) packages were used for (i) quality control and (ii) to remove low-qualified bases and adapter-containing reads from raw KAS-seq data, respectively. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome using bowtie2 (2.4.4) under default parameters.
Bed files were converted to bedGraph files using bedtools (2.30.0). Bedgraph files were then normalized to total read counts using the normalize_KAS-seq script (KAS-pipe) and normalized bedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Differential analysis was then performed using the diff_KAS-seq script (KAS-pipe: which applies DESeq2 (1.26.0) differential analysis)
Assembly: hg19/mm10
Supplementary files format and content: bigWig, read density

source_name: CD8+ T cells

growth_protocol: Mouse and human CD8+ T cells were maintained in Click's medium supplemented with 10% fetal bovine serum (FBS), 1% glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
After labeling, genomic DNA was isolated using a PureLink Genomic DNA mini kit. 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin. The mixture was shaken at 37 °C for 1.5 h, after which 5 µL RNase A was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. 5% of the sonicated DNA was set aside and saved, and the rest was used for enrichment with 10 µL Dynabeads MyOne Streptavidin C1. The beads were washed with three times with 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were then washed five times in 1× B&W buffer and then were resuspended in 15 uL H2O. Beads were then heated at 95 °C for 10 min to elute DNA; DNA eluate solution was then moved onto ice for library construction.
Sonicated/sheared enriched DNA libraries were constructed using a Accel-NGS Methyl-Seq DNA library kit

treatment_protocol:
After activation with anti-CD3/28, CD8+ T cells were treated with 20 μM TVA for various timepoints, or were untreated as indicated above
To detect ssDNA levels, following TVA stimulation (or no stimulation for unstimulated cells), cells were treated with 5 mM N3-kethoxal in DMSO supplemented into the growth media

value: CD8+ T cells

value: Primary T cell

value: 20 uM TVA

value: 2 hours


title: batch_1, TCR

description:
batch_1_TCR
multiplexed
batch_1_DBEC_MolsPerCell.csv
batch_1_Sample_Tag_Calls.csv

value: stomach


title: experiment 2: TVA stimulated 2 hr, biol rep1


title: VBT_Male_Water_4

source_name: Ventrobasal thalamus

value: Ventrobasal thalamus


title: experiment 2: TVA stimulated 40 min, biol rep1

value: 40 min


title: experiment 2: TVA stimulated 40 min, biol rep2


title: VBT_Male_Water_3


title: H1975 cells, sh-C, 3

first: Daisuke

middle: Jefferson

last: Shibahara

address: 330 Brookline Avenue, E/CLS-0417

department: Oncology

institute: Beth Israel Deaconess Medical Center

description: Control-VS-Sh-C.GeneDiffExp

data_processing:
The sequencing data was filtered by (1) Removing reads with adaptors; (2) Removing reads in which unknown bases are more than 10%; (3) Removing low quality reads.
After filtering, clean reads were stored as FASTQ format. The clean reads were mapped to the reference gene using Bowtie2 and referenced to genome using HISAT.
Gene expression level  was quantified by RSEM.
Differential gene expression was analyzed using EBSeq with foldchange ≥2 and PPEE ≤0.05.
Clustering analysis of gene expression patterns was performed using cluster and javaTreeview software.
Assembly: hg19
Supplementary files format and content: excel files include RPKM values for each sample
Supplementary files format and content: excel files include defferentially expressed genes for each pairwise comparison

growth_protocol: H1975 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using an RNA Isolation Kit (ZYMO, Direct-zol RNA Miniprep Plus).
Total RNA from each sample was treated with Oligo (dT) magnetic beads to select polyA mRNA. Target RNA fragments were reverse transcribed into double-strand cDNA (dscDNA) using N6 random primers. We then performed end repair on dscDNA fragments creating a phosphate at each 5′-end and an ‘A’ single nucleotide overhang at each 3′-end. Next, the adaptor with ‘T’ at 3′ end was ligated to the dscDNA, and ligation products were used for PCR amplification. The PCR products were denatured by heating, and single strand DNA was cyclized using a splint oligo and DNA ligase to format as the final library.

treatment_protocol: Tet-inducible conditional shRNA knockdown were induced by 2-day treatment with 0.5 ug/ml doxycycline.

value: Non-small cell lung cancer

value: KAT5 knockdown

value: Doxycycline


title: S1_Female_Fentanyl_5

value: Somatosensory cortex S1

value: Female

value: Wildtype


title: experiment 2: TVA stimulated 20 min, biol rep2

value: WT

value: 20 min


title: H1975 cells, sh-C, 1

description: Control-VS-Sh-C.GeneDiffExp


title: VBT_Male_Water_2

value: Male

value: Water


title: H1975 cells, sh-B, 4

description: Control-VS-Sh-B.GeneDiffExp


title: VBT_Male_Fentanyl_4

value: Fentanyl


title: VBT_Male_Fentanyl_5


title: H1975 cells, sh-B, 5

description: Control-VS-Sh-B.GeneDiffExp


title: VBT_Male_Water_1


title: experiment 2: unstimulated, biol rep2

value: CD8+ T cells

value: Primary T cell


title: VBT_Male_Water_5


title: VBT_Male_Fentanyl_3


title: experiment 1: TVA stimulated 2 hr, biol rep1

value: 20 uM TVA

value: 2 hours


title: VBT_Male_Fentanyl_2

value: Ventrobasal thalamus


title: experiment 1: TVA stimulated 40 min, biol rep2

value: 40 min


title: experiment 1: TVA stimulated 2 hr, biol rep2


title: H1975 cells, sh-A, 4

description: Control-VS-Sh-A.GeneDiffExp

value: Non-small cell lung cancer


title: H1975 cells, sh-A, 5

description: Control-VS-Sh-A.GeneDiffExp

value: KAT5 knockdown


title: H1975 cells, sh-C, 2

description: Control-VS-Sh-C.GeneDiffExp

value: Doxycycline


title: experiment 1: TVA stimulated 40 min, biol rep1


title: H1975 cells, sh-A, 3

description: Control-VS-Sh-A.GeneDiffExp


title: VBT_Female_Water_5


title: H1975 cells, shControl, 3


title: H1975 cells, shControl, 2


title: experiment 1: TVA stimulated 20 min, biol rep1


title: experiment 2: TVA stimulated 20 min, biol rep1


title: experiment 1: unstimulated, biol rep2


title: experiment 1: TVA stimulated 20 min, biol rep2


title: VBT_Female_Water_3


title: H1975 cells, sh-B, 3

description: Control-VS-Sh-B.GeneDiffExp


title: VBT_Female_Water_2


title: experiment 2: unstimulated, biol rep1


title: experiment 1: unstimulated, biol rep1


title: VBT_Female_Water_1


title: H1975 cells, shControl, 1


title: VBT_Female_Fentanyl_5


title: VBT_Male_Fentanyl_1


title: VBT_Female_Fentanyl_4


title: MDCKII_WT_N2

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Sequenced reads were aligned to the NCBI canis lupus familiaris canFam3.1 genome with STAR v. 2.7.0f.
The reads counts were prepared with HTSeq count v.0.9.1
Assembly: canFam3.1
Supplementary files format and content: Normalized_counts_cpm_project22.xlsx

organism: Canis lupus familiaris

source_name: Kidney

extract_protocol: RNA libraries for RNA-seq were prepared using Illumina TruSeq HT kit following manufacturer's protocols.

value: Kidney

value: MDCKII

value: Epithelial

value: No


title: MDCKII_WT_N3

value: WT


title: MDCKII_WT_N1


title: VBT_Female_Fentanyl_3

value: Female

value: Wildtype


title: VBT_Female_Water_4

value: Water


title: Patient 105

type: RNA

city: Seong-nam

first: Yu Ho

last: Lee

address: 59 Yatap-ro, Bundang-gu

country: South Korea

institute: CHA

hyb_protocol: For analysing of miRNA expression, the digital multiplexed nanoString nCounter human miRNA expression assay (nanoString Technologies) was performed with Human miRNA Panel Kit according to the manufacturer’s protocol.

scan_protocol: Abundances of specific target molecules were quantified on the nCounter Digital Analyzer by counting the individual fluorescent barcodes and assessing the target molecules. For each assay, a high-density scan encompassing 555 fields of view was performed. The data was collected using the nCounter Digital Analyzer after taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera.

data_processing:
To analysis the miRNA data, we used the nSolver(version 4.0) software analysis, freely available from nanoString Technologies.
The miRNA data was normalized using Top100 genes.

label: biotin

source_name: Urinary exosome

label_protocol: NanoString’s nCounter CodeSet chemistry utilizes target-specific Reporter and Capture Probes, collectively referred to as a CodeSet, that directly hybridize to a target of interest. Each probe pair consists of a color-coded Reporter and a Capture Probe to which a  target-specific sequence has been covalently attached.

extract_protocol: Mid-stream, second morning void urine samples were collected, centrifuged at 2,000× g for 20 minutes at room temperature, and the supernatant was transferred into RNA later solution and stored at -80 °C. Urinary exosomal RNA was isolated from 1 mL of urinary supernatant using spin column-based exoRNeasy serum/plasma midi kits (QIAGEN GmbH, Hilden, Germany), as described previously.

tag: urinary exosome

value: urinary exosome

tag: diagnosis

value: NP


title: Patient 106

value: TCMR


title: Patient 108

value: LTGS


title: VBT_Female_Fentanyl_2

value: Ventrobasal thalamus

value: Fentanyl


title: Patient 104


title: VBT_Female_Fentanyl_1


title: Patient 103


title: PM1 strain, SDA 7d, 37℃ [Nanopore_WT_yeast_02(Y2)]

city: Beijing

first: Xueyan

last: Hu

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: Peking University Health Science Center

data_processing:
cut adapter and low quanlity filter (cutadapt for Illumina and porechop for Nanopore)
circRNA identification (CIRI2 for Illumina and CIRI-long for Nanopore)
circRNA merge and quatification (CIRIquant)
linear RNA quantification (HISAT2 + Stringtie)
feature identification (in house scripts)
Assembly: De novo assembly of T. marneffei PM1 (PRJNA967827)
Supplementary files format and content: comma-delimited text files include Counts values for each Sample

organism: Talaromyces marneffei

extract_protocol:
E.Z.N.A. fungal RNA kit (Omega Bio-Tek)
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina and circFL for Nanopore

tag: strain

value: cultured at 37degreeC in SDB for 3 d


title: PM1 strain, SDA 7d, 25℃ [Nanopore_WT_mycelium_02(M2)]

value: cultured at 25degreeC in SDB for 3 d


title: Patient 102


title: PM1 strain, SDA 7d, 25℃ [Nanopore_WT_mycelium_01(M1)]


title: VTA_Male_Water_5

source_name: Ventral tegmental area

value: Ventral tegmental area

value: Male


title: VTA_Male_Water_4


title: CENH3_rep1_control

city: Seeland OT Gatersleben

first: Anne

last: Fiebig

address: Correnstraße 3

department: BIT

country: Germany

institute: IPK Gatersleben

description: The original chromatin DNA was a mixture of chromatin isolated from flowers of Chionographis japonica and leaves of Secale cereale inbred line Lo7, and sonicated to 150-400 bp in length.

data_processing:
The adaptor trimmed pair-end illumina reads of ChIPseq and RNAseq in length of 150 bp were mapped to the C. japonica genome assembly using Bowtie2 with default parameters.
The Deeptools bamCompare was used to generate ChIPseq signal tracks of the average of log2-ratio of read counts in IP over input in genome-wide 10 kb windows.
Deeptools multiBigWigSummary and plotCorrelation were used to calculate and plot the Spearman correlation between different ChIPseq and RNAseq targets as a heatmap.
Assembly: GCA_947650365.1
Supplementary files format and content: bigwig

organism:
Secale cereale
Chionographis japonica

source_name: leaf, flower

growth_protocol: Chionographis japonica plants which were grown in a shady greenhouse condition: 16 h light (from 6 AM to 10 PM), day temperature 16 °C, night temperature 12 °C) in IPK Gatersleben. Seeds of Secale cereale (inbred line Lo7) were germinated at room temperature to collect young leaf tissue.

extract_protocol:
Flowers of Chionographis japonica plants and young leaves of Secale cereale were collected, fixed, and used for chromatin preparation. The flower and leaf tissues were ground with liquid nitrogen and isolated nuclei were fixed with 1% PFA. Isolated chromatin DNAs were sonicated into 150-400 bp used for immunoprecipitation.
The ChIP-seq libraries were prepared by using NEBNEXT® UltraTM II DNA Library Prep Kit (New England Biolabs).
Low-pass genome sequencing was performed, generating 2 × 150 bp paired-end (PE) reads using NovaSeq 6000 system (Illumina).

value: leaf, flower

tag: developmental stage

value: flowering stage

tag: replicate

value: Koshiki

tag: chip antibody


title: Patient 101


title: CENH3_rep2_control


title: CENH3_rep2

value: Koshiki and Lo7


title: Patient 107

value: aABMR


title: Patient 99


title: VTA_Male_Water_3

value: Wildtype


title: CENH3_rep1


title: PM1 strain, SDA 7d, 37℃ [Nanopore_WT_yeast_01(Y1)]

value: WT


title: VTA_Male_Water_1

value: Water


title: VTA_Male_Fentanyl_5


title: Patient 96

value: urinary exosome


title: VTA_Male_Fentanyl_3


title: Patient 98

value: TCMR


title: Patient 97

value: LTGS


title: VTA_Male_Fentanyl_4


title: lung, PPARa KO, vehicle, 149

city: Burlinton

first: Arti

last: Sukla

state: VT

address: 89 Beaumont Avenue

department: Pathology and Laboratory Medicine

institute: University of Vermont

description:
Sample column in processed data file:
149_710_504_S22

data_processing:
All samples were sequence in two lanes and on two flow cells. Reads were concatenated by sample into a single fastq.
Poorer quality bases from the 3’ end were trimmed if phred score <20.
Aligned reads were quantified using an Expectation-Maximization model, and translated to genes.
Genes that had fewer than 20 counts were then filtered, retaining 19,366 high count genes.
Differential gene expression was evaluated using the algorithm in DESeq2 v3.5 base on median ratio normalization and the negative binomial distribution of gene signal.
Assembly: Trimmed reads were aligned to the mouse reference genome mm10 using the STAR 2.6 aligner in Partek® Flow®.
Supplementary files format and content: Tab-delimited text file of raw gene counts.

source_name: lung

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). Tissues were disrupted using an Omniprep and homogenized using a QIAshredder column. 6 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using SMARTer Stranded Total RNA-Seq v2 Pico (Takara) following manufacturer's protocols.

treatment_protocol: PFOA or vehicle was administered by drinking water for 14 weeks

value: lung

value: Female

value: PPARa KO

value: vehicle


title: Patient 95


title: VTA_Male_Fentanyl_2

value: Ventral tegmental area

value: Fentanyl


title: lung, PPARa KO, Hi-PFOA, 155

description:
Sample column in processed data file:
155_703_501_S3

value: Hi-PFOA


title: Patient 93

value: NP


title: Patient 94


title: VTA_Male_Fentanyl_1

value: Male


title: Patient 100


title: lung, PPARa KO, vehicle, 137

description:
Sample column in processed data file:
137_707_502_S7


title: lung, PPARa KO, vehicle, 145

description:
Sample column in processed data file:
145_709_504_S21


title: VTA_Female_Water_5


title: Patient 92


title: lung, hPPARa KI, vehicle, 116

description:
Sample column in processed data file:
116_710_502_S10

value: hPPARa KI


title: lung, wildtype, vehicle, 122

description:
Sample column in processed data file:
122_706_503_S18

value: wildtype


title: Patient 91


title: VTA_Female_Water_4

value: Wildtype


title: lung, hPPARa KI, vehicle, 135

description:
Sample column in processed data file:
135_711_504_S23


title: Patient 90


title: lung, PPARa KO, Hi-PFOA, 154

description:
Sample column in processed data file:
154_706_501_S6


title: VTA_Female_Water_3


title: VTA_Female_Water_2


title: lung, wildtype, vehicle, 107

description:
Sample column in processed data file:
107_705_503_S17


title: Patient 89


title: lung, hPPARa KI, vehicle, 102

description:
Sample column in processed data file:
102_702_501_S2


title: Patient 88


title: VTA_Male_Water_2


title: lung, hPPARa KI, Hi-PFOA, 139

description:
Sample column in processed data file:
139_702_504_S26


title: lung, hPPARa KI, Hi-PFOA, 80

description:
Sample column in processed data file:
80_709_502_S9


title: VTA_Female_Fentanyl_5


title: Patient 86


title: Patient 87


title: VTA_Female_Fentanyl_4


title: lung, hPPARa KI, Hi-PFOA, 57

description:
Sample column in processed data file:
57_701_503_S13


title: VTA_Female_Fentanyl_3


title: lung, wildtype, Hi-PFOA, 56

description:
Sample column in processed data file:
56_701_501_S1


title: lung, wildtype, Hi-PFOA, 65

description:
Sample column in processed data file:
65_704_503_S16


title: VTA_Female_Fentanyl_2


title: Patient 84

value: aABMR


title: Patient 83


title: Patient 82


title: VTA_Female_Fentanyl_1


title: lung, wildtype, Hi-PFOA, 50

description:
Sample column in processed data file:
50_712_502_S12


title: lung, PPARa KO, Hi-PFOA, 52

description:
Sample column in processed data file:
52_705_501_S5


title: RCAS-nTva Bulk Tumor ATRX Positive 4

city: Houston

first: Benjamin

last: Whitfield

state: TX

address: 5918 Belrose Dr

institute: MD Anderson/UT Health GSBS

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis
Alignment to mouse mm9 genome was performed using RNASTAR (version 2.7.8a).
Raw transcript counts were generated using HTseq-count tool (version 0.9.1)
Assembly: mm9
Supplementary files format and content: Tab-delimited count file containing counts for all samples

source_name: Brain Tumor

extract_protocol:
Extraction was performed using the Qiagen Rneasy Plus kit according to manufacturer's instructions.
Libraries were generated using Truseq library preparation kits (Illumina)

value: Brain Tumor

value: ATRX-wildtype

value: Tumorigenic RCAS and CRE RCAS


title: RCAS-nTva Bulk Tumor ATRX Positive 3


title: Pelv2

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

country: United Kingdom

institute: The University of Edinburgh

description:
snRNA-seq 10x
pelv2

data_processing:
Supplementary files format and content: Raw sequencing data were aligned to the unmasked ICSASG_v2 reference assembly (Ensembl release 104) of the Atlantic salmon genom
The analysis used just protein coding genes. Mapping of reads to the genome, assignment of reads to cellular barcodes, and collapsing of unique molecular identifiers (UMIs) was performed using STARsolo v2.7.7a
The top 100,000 cell barcodes ranked by UMI number were retained to ensure the capture of transcriptionally quiet nuclei, these are normally lost when using the automated STARsolo filtering algorithm
Assembly: S.salar V2 emsbl
Supplementary files format and content: Tab-separated values files and matrix files

organism: Salmo salar

source_name: skin

extract_protocol:
for libraries S3 and s6 we followed the nuclei extraction protocol of Taylor & Ruiz Daniels 2022
For libraries PElv2 and Skin1 we followed the nuclei extratraction protocol of dx.doi.org/10.17504/protocols.io.261genwm7g47/v2
Nuclei were processed through the 10X Chromium™ Single Cell Platform using the Chromium™ Single Cell 3` Library and Gel Bead Kit v3.1 and Chromium™ Single Cell A Chip Kit (both 10X Genomics) as per the manufacturer’s protocol with the aim of recovery of 7000 nuclei.

value: skin

value: frozen tissue

value: nucleus

value: single nucleus

value: Ruiz Daniels 2023


title: RCAS-nTva Bulk Tumor ATRX Positive 2


title: Patient 81

value: urinary exosome

value: TCMR


title: RCAS-nTva Bulk Tumor ATRX Positive 1


title: Patient 80


title: Patient 79


title: Skin1

description:
snRNA-seq 10x
skin1


title: RCAS-nTva Bulk Tumor ATRX Negative 4

value: ATRX-floxed


title: Patient 78

value: NP


title: RCAS-nTva Bulk Tumor ATRX Negative 3


title: Patient 77


title: Patient 85


title: S3

description:
snRNA-seq 10x
S3

value: Tayor & Ruiz Daniels 2022


title: LLC OVA, Tumor (day16), rep5

first: Lijian

last: Wu

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

institute: 清华大学

data_processing:
STAR v2.6.1d, Salmon v0.13.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to mm10 genome vM25 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.13.1 in its alignment-based mode.
Gene-level raw counts as well as transcript per million (TPM) from quantification files were prepared with tximport v1.22.0.
Normalization of raw counts and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: mm10
Supplementary files format and content: comma-delimited csv files include TPM (Transcripts Per Million) values for each Sample
Supplementary files format and content: comma-delimited csv files include DESeq2 results for comparisons

source_name: LLC

growth_protocol: LLC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. T cell were maintained in RPMI 1640  supplemented with 10% fetal bovine serum (FBS), glutamine, sodium pyruvate, NEAA, HEPES and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LLC cells were either pretreated or left untreated for 200nM BAY-876 for 24 hours, followed by treatment with 20ng/ml TNF or left untreated for 32 hours; 10^6 of LLC-OVA-NGFR cells were subcutaneously injected to Rag1 ko mice. On 9 day, 2*10^6 activated OT1 T cells were transferred by tail vein injection. On day 16, tumors were harvested and tumor and OT1 T cell were sorted.

tag: time

value: LLC

value: lung cancer

value: WT

value: Adoptive cell transfer


title: Patient 76


title: LLC OVA, Tumor (day16), rep4


title: RCAS-nTva Bulk Tumor ATRX Negative 2

value: Brain Tumor


title: RCAS-nTva Bulk Tumor ATRX Negative 1


title: Patient 75

value: aABMR


title: LLC OVA, Tumor (day16), rep3


title: LLC OVA, Tumor (day16), rep2


title: Patient 73


title: RCAS-nTva-derived Cell Line, ATRX Positive Line 1, sample 3

value: Tumor

value: ATRX-wildtype


title: RCAS-nTva-derived Cell Line, ATRX Positive Line 1, sample 2


title: RCAS-nTva-derived Cell Line, ATRX Positive Line 1, sample 1


title: LLC OVA, OT1 (day16), rep5

value: T cell


title: LLC OVA, Tumor (day16), rep1


title: Patient 72


title: RCAS-nTva-derived Cell Line, ATRX Negative Line 1, sample 3

value: ATRX KO


title: Patient 71

value: LTGS


title: LLC OVA, OT1 (day16), rep4