title: Tox4 cKO ser5p CUT&Tag rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters, and subsequently aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: mm10 for mouse.
Supplementary files format and content: BigWig files contains normalized read count (CPM, in 50-bp bins) for merged replicates.
Library strategy: CUT&Tag

source_name: DP thymocytes

extract_protocol:
CUT&Tag experiments were performed as previously described with minor modifications(Kaya-Okur, H.S. et al. ). Briefly, 250,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.

value: DP thymocytes

tag: antibody


title: 35SALKBH10B_m6_3_C_0hr

status: Public on Sep 08 2023

type: SRA

city: Philadelphia

first: Brian

middle: D

last: Gregory

state: PA

address: 433 South University Avenue

department: Biology

country: USA

institute: University of Pennsylvania

description: PolyA, m6AIP

library_source: transcriptomic

data_processing:
In order to call m6A peaks reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR. All non-unique reads were discarded from downstream analysis. Mapped read coverage was split into + and minus strand fractions and macs2 callpeak was then used to call m6A peaks on each strand, respectively, using parameters --nomodel --extsize 50 genome size was set to ½ the transcriptome using -g 32542107 and with an FDR cutoff of < 0.05. m6A peaks are provided in bedgraph format in supplementary excel file.
Assembly: TAIR10
Supplementary files format and content: m6A peak are presented in narrowPeak format with respect to treatment.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 14 day old seedling

growth_protocol: for 14 day old and 4wk old plants 16 h light/8 h dark, average lighting of 120 µmol/m2/s, 20°C day/18°C night, 60% hygrometry.

extract_protocol:
Following control or treatement, leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Qiazol (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo).
Paired end libraries used TRueSEq RNA sample prep kit, standard illumina protocols

treatment_protocol: For 14day old flg22 treated: One day before treatment, liquid medium (same medium without agar) was added to the plates under sterile conditions, and plates were transferred onto the bench. Seedlings were treated with a final concentration of 1 μM flg22 for 0 min (no treatment), 30 min or 4 h. Seedlings were finally harvested, rapidly dried with paper, ﬂash-frozen in liquid nitrogen, and stored at -80°C. For 4 week old pst treated: Four week-old plant leaves were infiltrated with bacteria at a concentration of 106 cfu/ml using a needleless syringe.

tag: tissue

value: 14 day old whole seedling

tag: treatment

value: untreated

tag: genotype


title: wt_1.1_un_biol_repB

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

data_processing:
Sequence reads were trimmed with TrimGalore, in single-end mode, clipping 10 bases at the 5’ of each read to remove sequencing bias, and filtering out all low-quality bases from reads (<30 Phred score).
Trimmed sequence reads were mapped to GRCh38/hg38 using HISAT2, with --dta in additional to default parameters.
Aligned sequence reads were sorted by coordinates and indexed using samtools.
Indexed sequence reads were annotated using featureCounts.
Read count normalization was performed with DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: comma-separated values (.csv) file includes normalized counts for each Sample (normalization by median of ratios method).

organism: Homo sapiens

source_name: HAP1 cells

extract_protocol:
Total RNA was purified with Allprep DNA/RNA/Protein Mini Kit (Cat. No. / ID: 80004), according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HAP1 cells

value: wt

value: media


title: HT1080 KDAC6H216A 4

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.4.5 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.26.1
Read count statistical analysis was performed using DESeq2 v1.38.2
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output for all conditions and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

value: Connective tissue

tag: cell type

value: fibrosarcoma


title: COL_m6_1_F_4hr

description: PolyA, m6AIP

value: 1uM flg22 peptide 4 hours


title: 35SALKBH10B_m6_2_F_4hr

description: PolyA, m6AIP


title: HT1080 wild-type 3

value: WT


title: Tox4 cKO ser5p CUT&Tag rep1

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: wt_1.1_un_biol_repA


title: HT1080 wild-type 2


title: wt_1.3_bso_biol_repA

value: BSO


title: Humanized vasculitis mice

city: Rochester

first: Yuki

last: Sato

state: MN

address: 200 1st ST SW

department: Rheumatology

institute: Mayo Clinic

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The single cell fastq data is processed using Cell Ranger pipeline version 6.1.2 (10x Genomics) mapped on GRCh38 v.3.0.0 reference. The downstream analysis was performed using R package Seurat v.4.3.0 for quality control (QC), normalization, scaling, dimensionality reduction, clustering, differential expression, and visualization.
In brief we have retained genes expressed in >3 cells. While cells express between 200 to 4000 genes along with <10% mitochondria percentage cutoff were retained. We have also removed doublets cells using DoubletFinder.
Further we have extracted T cells based on the expression level of CD3 and CD4 and performed the downstream reanalysis using Seurat. The raw counts were normalized, and variable genes were identified using NormalizeData and FindVariableFeatures function in Seurat respectively.
The variable genes were used for dimensionality reduction followed by clustering using graph-based clustering approach via Louvian algorithm. We have performed imputation of gene expression using MAGIC.
Assembly: GRCh38 v3.0.0
Supplementary files format and content: Tab-separated matrix file

source_name: vasculature

extract_protocol:
Freshly collected CD4 T cells from humanized vasculitis mice used for scRNAseq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: CD4 T cells

value: vasculature

tag: strain

value: NGG mice

tag: age

value: 10-12 weeks old


title: Tox4 WT ser5p CUT&Tag rep2


title: wt_1.1_un


title: 35SALKBH10B_m6_1_F_4hr

description: PolyA, m6AIP


title: Tox4 WT ser5p CUT&Tag rep1


title: wt_1.1_bso_biol_repB


title: 22Rv1_CRISPRi_clone3_Tigger3a_H3K27ac_rep2

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 2

data_processing:
For Cut&Run, data is first trimmed for adapters with trimmomatic-0.36 then mapped with bowtie2 with following parameter " -q -I 10 -X 700  --local --very-sensitive-local --no-mixed --no-discordant --no-unal --phred33". Peak calling is done with SEACR q <= 0.05
For ChIP-Seq data, ENCODE ChIP-Seq pipeline was followed with default parameters with bowtie2 aligner, macs2 peak caller.
Assembly: hg38
Supplementary files format and content: narrowPeak, bedgraphs
Library strategy: Cut&Run

source_name: CRISPRi 22Rv1

growth_protocol: DU145 cells were cultivated in DMEM 10% FBS and 1x penicillin/streptomycin, while CRISPRi 22Rv1 clonal cell lines were grown in RPMI 10% FBS, 1x penicillin/streptomycin, Blasticidin 6ug/ml

extract_protocol:
For ChIP-seq cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300. For Cut&Run cells were incubated with concanavalinA beads, followed by incubation with antibody with digitonin-containing buffer. After washing, samples were incubated with G-protein coupled with MNase and exposed DNA was digested by activating MNase with CaCl2 for 30 min in ice bath.
ChIP-seq and Cut&Run libraries were prepared using the Takara Thruplex Library Preparation Kit. 10 ul of  eluted DNA was used as starting material for input and/or IP samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: CRISPRi 22Rv1

value: prostate cancer

tag: chip antibody

value: nucleofection Tigger3a guides combo


title: HT1080 wild-type 1


title: 22Rv1_CRISPRi_clone3_Tigger3a_H3K27ac_rep1

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 1


title: 35SALKBH10B_m6_1_C_0hr

description: PolyA, m6AIP

value: 14 day old whole seedling


title: MTA_3_F

value: mta


title: 18395X1 SVF male normal chow diet (8 weeks)

city: salt lake city

first: Sihem

last: Boudina

state: Utah

department: Nutrition and Integrative Physiology

institute: University of Utah

data_processing:
The Fastq files were aligned to the  human or mouse 3.0.0 references from 10X genomics using cellranger count version 3.1.0 with 10000 expected cells.
The filtered gene barcode matrices were loaded into the Seurat package in R and merged into a single matrix.
Low quality cells with high mitochondrial reads were removed and counts were normalized using the sctransform method.
Assembly: mm10 or hg38
Supplementary files format and content: Filtered feature barcode matrices from cellranger

source_name: periovarian fat

extract_protocol:
Freshly isolated stroval vascular fractions (SVFs) were collected after collagenase digestion of omental fat samples (humans) or gonadal fat samples (mice) and subjected to scRNA-seq
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: periovarian fat

tag: Sex

value: male

tag: diet

value: normal chow


title: wt_1.1_bso_biol_repA

value: HAP1 cells

value: wt


title: wt_1.1_bso


title: MTA_3_C

value: untreated


title: 22Rv1_CRISPRi_clone2_Tigger3a_H3K27ac_rep2

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 2


title: 18303X2 SVF female high fat diet (8 weeks)

source_name: epididymal fat

value: epididymal fat

value: female

value: high fat diet


title: 35SALKBH10B_m6_2_C_0hr

description: PolyA, m6AIP


title: Prostate cancer tissue PCa44889-benign

description: For this ChIP-seq sample (patient data) we need controlled access for the raw fastq files, hence only processed data is being submitted for this sample.

data_processing:
For Cut&Run, data is first trimmed for adapters with trimmomatic-0.36 then mapped with bowtie2 with following parameter " -q -I 10 -X 700  --local --very-sensitive-local --no-mixed --no-discordant --no-unal --phred33". Peak calling is done with SEACR q <= 0.05
For ChIP-Seq data, ENCODE ChIP-Seq pipeline was followed with default parameters with bowtie2 aligner, macs2 peak caller.
Assembly: hg38
Supplementary files format and content: narrowPeak, bedgraphs

source_name: Prostate cancer tissue

value: Prostate cancer tissue


title: 22Rv1_CRISPRi_clone2_Tigger3a_H3K27ac_rep1

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 1


title: MTA_2_F

value: 1uM flg22 peptide 4 hours


title: 18303X1 SVF male high fat diet (8 weeks)


title: 22Rv1_CRISPRi_clone1_Tigger3a_H3K27ac_rep2

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 2


title: Prostate cancer tissue PCa40436-benign


title: MTA_2_C


title: 18395X2 SVF female normal chow diet (8 weeks)


title: Prostate cancer tissue PCa39987-benign


title: 22Rv1_CRISPRi_clone1_Tigger3a_H3K27ac_rep1

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 1


title: KO2

city: Wuhan

first: Mingrui

last: Xiong

address: Hangkong Road 13

institute: School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（ensembl_mus_musculus_grcm38_p6_gca_000001635_8） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

source_name: kidney

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 2°C).

extract_protocol:
Total RNA from each sample was extracted using RNAiso Plus (Takara Biotech), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were anesthetized and underwent midline abdominal incisions with both kidneys were clamped to block blood flow for 30 minutes.  Reperfusion was recovered by removing the clamps. Wounds in abdomens were sutured. Mice were euthanized at day 3 to harvest blood, injured kidney and non-injured kidney.

value: kidney

tag: developmental stage

value: adult

value: C57BL/6 x 129S4/SvJae


title: MTA_1_F


title: 22Rv1_CRISPRi_clone3_Ctrl_H3K27ac_rep2

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 2

value: CRISPRi 22Rv1

value: prostate cancer

value: nucleofection Ctrl guides combo


title: Prostate cancer tissue PCa31234-benign


title: WT2


title: Prostate cancer tissue PCa27967-benign


title: 22Rv1_CRISPRi_clone3_Ctrl_H3K27ac_rep1

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 1


title: KO1


title: Prostate cancer tissue PCa27303-benign


title: WT1


title: COL_3_F

value: 14 day old whole seedling


title: LM-2000-oocyte-2_L1

city: Qingdao

first: Li

last: Hui

address: 72 Binhai Road, Jimo District, Qingdao, Shandong

institute: Shandong University

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences at the 3' end were removed using Cutadapt v1.15 with the parameter: -a ATCTCGTATGCCGTCTTCTGCTT.
After filtering, the LACE-seq reads were aligned to mouse pre-rRNA by bowtie with default parameters.
The unmapped reads to mouse pre-rRNA were then aligned to the mm9 reference genome.
Assembly: mm9
Supplementary files format and content: Bigwig files were created using bedtools genomecov v2.28.0 and bedGraphToBigWig v4 software.

source_name: Ovary

extract_protocol:
The crosslinked 2000 oocytes were lysed and LSM14B antibody was used to specifically pull-down protein–RNA complexes from the cell lysate. The RNA was extracted as described in ’experimental design‘.
The LACE-seq library was single-end sequenced using Illumina NovaSeq 6000.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six hours later, they were euthanized, and their 2000 oocytes were collected and irradiated with ultraviolet C (UV-C) light to crosslink RBPs and their interacting RNAs.

value: Ovary

value: oocyte

value: WT

value: UV-crosslink


title: COL_3_C

value: untreated


title: Prostate cancer tissue PCa67319


title: 22Rv1_CRISPRi_clone2_Ctrl_H3K27ac_rep2

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 2


title: COL_2_F


title: 22Rv1_CRISPRi_clone1_Ctrl_H3K27ac_rep2

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 2


title: 22Rv1_CRISPRi_clone2_Ctrl_H3K27ac_rep1

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 1


title: MTA_1_C

value: mta


title: Prostate cancer tissue PCa58751


title: COL_1_C


title: LM-2000-oocyte-1_L1


title: Prostate cancer tissue PCa58298-T1


title: Prostate cancer tissue PCa59187-T1


title: 22Rv1_CRISPRi_clone3_Tigger3a_Cas9_rep1

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 1

value: nucleofection Tigger3a guides combo


title: COL_2_C


title: Prostate cancer tissue PCa58966-T2


title: FGOs, KO3

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
The cell was lysed and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later, they were euthanized, and their  20 oocytes were collected  in 0.5ul lysis buffer to release all RNAs.

value: Lsm14b KO

value: GV-stage fully-grown oocytes


title: COL_1_F

value: 1uM flg22 peptide 4 hours


title: FGOs, WT2


title: FGOs, KO2


title: 22Rv1_CRISPRi_clone1_Ctrl_H3K27ac_rep1

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 1


title: 22Rv1_CRISPRi_clone3_Tigger3a_Cas9_rep2

description: CRISPRi 22Rv1 clone3, dCas9, bio rep 2


title: FGOs, KO1


title: Prostate cancer tissue PCa58583

value: Prostate cancer tissue


title: 35SALKBH10B_2_C


title: 35SALKBH10B_3_F


title: FGOs, WT3


title: 35SALKBH10B_3_C


title: Prostate cancer tissue PCa58215


title: 35SALKBH10B_1_F


title: 35SALKBH10B_2_F


title: 22Rv1_CRISPRi_clone2_Tigger3a_Cas9_rep2

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 2


title: Prostate cancer tissue PCa58191


title: Prostate cancer tissue PCa57794


title: Tox4 WT TT-seq rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Clean reads were aligned using STAR v2.7.9a.
Fragment count were obtained using featureCounts v1.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.
TTchem-seq

treatment_protocol: cells were transferred to fresh antibiotics-free medium and cultured for 0.5 hr before 4-thiouridine (4sU) treatment.


title: Prostate cancer tissue PCa57497


title: Tox4 cKO TT-seq rep1


title: LNCaP, input

description:
LNCaP_H3K27ac_Rep1_R1.srt.nodup_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed
LNCaP_H3K27ac_Rep2_R1.srt.nodup_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed

source_name: LNCaP

value: LNCaP


title: 35SALKBH10B_1_C


title: Pst_MTA_mRNA_24_R3

source_name: 4 week old plant leaves

value: 4 week old leaves


title: FGOs, WT1


title: Prostate cancer tissue PCa57294


title: 22Rv1_CRISPRi_clone1_Tigger3a_Cas9_rep1

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 1

value: CRISPRi 22Rv1


title: Tox4 cKO TT-seq rep2


title: Tox4 WT TT-seq rep1


title: Prostate cancer tissue PCa57238

value: prostate cancer


title: 22Rv1_CRISPRi_clone1_Tigger3a_Cas9_rep2

description: CRISPRi 22Rv1 clone1, dCas9, bio rep 2


title: 22Rv1_CRISPRi_clone2_Tigger3a_Cas9_rep1

description: CRISPRi 22Rv1 clone2, dCas9, bio rep 1


title: Pst_MTA_mRNA_24_R2


title: Tox4 cKO scRNA-seq rep2

data_processing:
Data was then processed using the Cell ranger (10X Genomics, v.6.1.1) for alignment of sequencing reads to the mouse mm10 transcriptome and creation of feature-barcode matrices
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files are the outputs of cellranger  for filtered feature-barcode matrix. See the content of each file in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

source_name: thymocytes

extract_protocol:
Thymocytes in a single cell suspension were counted after being passed through a 70-μm nylon mesh filter. Single cells were captured in droplet emulsions using a Chromium Controller (10X Genomics).
scRNA-seq libraries were constructed with the 10X Genomics protocol using a Chromium Single Cell 3ʹ Reagent Kits v3.

tag: cell tnype

value: thymocytes


title: patient UTH8, tissue with chr1q mosaic gain

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
mRNA, single nucleus
UTH8

data_processing:
FASTQs were generated using cellranger (v6.0.0) mkfastq with default parameters.
Raw counts were generated by aligning FASTQs to a combined custom reference using cellranger (v6.0.0) count with default parameters.
Assembly: made using cellranger mkref with default parameters using GRCh38
Supplementary files format and content: Raw counts are provided in sparse matrices and were generated by aligning FASTQs using cellranger (v6.0.0) count with default parameters.

molecule: polyA RNA

source_name: seizure-affected brain, left parietal lobe

extract_protocol:
Frozen brain tissue was dissociated by mechanical disruption using a dounce homogenizer. Nuclei were washed and stained with Hoechst 33342 dye, filtered through a 30 um mesh filter, and resuspended in PBS for analysis on a BigFoot cell sorter (Thermo Fisher). Samples were gated on Hoechst-positive nuclei, debris was excluded using forward and side scatter pulse area parameters (FSC-A and SSC-A), and then aggregates were excluded using pulse width (FSC-W and SSC-W). Purified nuclei were sorted directly into 10x Genomics reaction buffer and processed according to the manufacturer protocol for 10x Genomics Chromium Next GEM Single-Cell 3’-Reagent Kit v.3.1.
10x Genomics Chromium Single Cell 3' v3.1 single-index or dual-index kit was used according to the manufacturer's protocol.
Sequencing using the following read configuration for single index: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) and for dual index: 28 (R1), 10 (i7), 10 (i5), 90 (R2)

tag: 3'v3.1 kit_used

value: dual index

value: male

tag: age at_surgery_(years)

tag: chr1q gain_detected?

value: yes

tag: pathology diagnosis

value: focal cortical dysplasia 1


title: patient UTH3, tissue with chr1q mosaic gain

description:
mRNA, single nucleus
UTH3

source_name: seizure-affected brain, right temporal lobe


title: Pst_MTA_mRNA_24_R1


title: Prostate cancer tissue PCa57054


title: Tox4 cKO scRNA-seq rep1


title: patient JLE43, tissue without chr1q mosaic gain

description:
mRNA, single nucleus
JLE43_D

source_name: seizure-affected brain, parahippocampus

value: single index

value: seizure-affected brain, parahippocampus

value: no


title: patient JLE43, tissue with chr1q mosaic gain

description:
mRNA, single nucleus
JLE43_B2

source_name: seizure-affected brain, frontoparietal operculum


title: Tox4 WT scRNA-seq rep2


title: Prostate cancer tissue PCa56112


title: patient JLE32, tissue with chr1q mosaic gain

description:
mRNA, single nucleus
JLE32_B

source_name: seizure-affected brain, right frontal

value: seizure-affected brain, right frontal

value: female


title: Pst_MTA_mRNA_00_R2

value: untreated

value: mta


title: patient JLE16, tissue without chr1q mosaic gain

description:
mRNA, single nucleus
JLE16_C1

source_name: seizure-affected brain, right temporal lobe lateral cortex


title: Prostate cancer tissue PCa52947

value: Prostate cancer tissue


title: Tox4 cKO p-SPT5 CUT&Tag rep2

data_processing:
Library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters, and subsequently aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for merged replicates.

source_name: DP thymocytes

value: DP thymocytes

tag: antibody


title: Tox4 WT scRNA-seq rep1


title: Prostate cancer tissue PCa53687

tag: tissue


title: Prostate cancer tissue PCa51852


title: Pst_Col_mRNA_24_R3

value: 4 week old leaves

tag: treatment

value: 1uM flg22 peptide 4 hours


title: Pst_Col_mRNA_24_R2

tag: genotype


title: Tox4 cKO p-SPT5 CUT&Tag rep1


title: patient JLE16, tissue with chr1q mosaic gain

description:
mRNA, single nucleus
JLE16_B1

source_name: seizure-affected brain, right inferior posterior frontal gyrus


title: Prostate cancer tissue PCa49047-T1

value: prostate cancer


title: PANC-1 cells shALKBH5 3

city: Jinan

first: Liu

last: Xiaoyan

address: 247 Beiyuan Street,

institute: The Second Hospital of Shandong University

data_processing:
Raw Reads uses Trimmomatic software for data filtering.
Trimmomatic software were used to remove adapter and low quality reads.
Quality distribution plot and base content distribution were generated by FASTQC.
STAR is used to align clean reads to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: PANC-1 cells with ALKBH5 knockdown or  control cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using TRIzol from the PANC-1 cells
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The PANC-1 cell lines were cultured under hypoxia for 48 h.

tag: cell line

value: Pancreatic cancer ductal cells

value: ALKBH5 knockdown

value: hypoxia(1% oxygen )

tag: time


title: Tox4 WT p-SPT5 CUT&Tag rep1

tag: cell type


title: Prostate cancer tissue PCa56594


title: PANC-1 cells shALKBH5 2


title: Prostate cancer tissue PCa47048


title: Pst_Col_mRNA_24_R1


title: Pst_MTA_mRNA_00_R3


title: PANC-1 cells shALKBH5 1


title: Prostate cancer tissue PCa44889


title: Pst_Col_mRNA_00_R3


title: Tox4 cKO SPT5 CUT&Tag rep1


title: PANC-1 cells shControl 3

value: WT


title: Pst_Col_mRNA_00_R2


title: Tox4 cKO SPT5 CUT&Tag rep2


title: Prostate cancer tissue PCa41892-T2


title: Pst_MTA_mRNA_00_R1


title: PANC-1 cells shControl 2


title: Prostate cancer tissue PCa40892-T2


title: Tox4 WT SPT5 CUT&Tag rep2


title: PANC-1 cells shControl 1


title: Prostate cancer tissue PCa40507


title: Pst_MTA_m6A_pls_00_R3

description: PolyA, m6AIP


title: Pst_Col_mRNA_00_R1


title: Tox4 WT SPT5 CUT&Tag rep1


title: Tox4 cKO TOX4 CUT&Tag rep2


title: Pst_MTA_m6A_pls_00_R2

description: PolyA, m6AIP


title: Prostate cancer tissue PCa4044


title: Tox4 WT p-SPT5 CUT&Tag rep2


title: 19357X1 SVF lean female 2

source_name: omental fat

value: omental fat

tag: phenotype

value: lean


title: 19314X4 SVF obese male 2

value: male

value: obese


title: Pst_MTA_m6A_pls_00_R1

description: PolyA, m6AIP


title: Prostate cancer tissue PCa40436

tag: chip antibody


title: Tox4 WT TOX4 CUT&Tag rep2


title: Tox4 cKO TOX4 CUT&Tag rep1


title: 19314X3 SVF obese female 3

tag: Sex


title: Pst_Col_m6A_pls_24_R3

description: PolyA, m6AIP


title: 19314X2 SVF obese female 2


title: Prostate cancer tissue PCa39987


title: Tox4 WT TOX4 CUT&Tag rep1


title: Pst_Col_m6A_pls_24_R1

description: PolyA, m6AIP


title: 19314X1 SVF lean male 2


title: Prostate cancer tissue PCa33947


title: Prostate cancer tissue PCa33173


title: Pst_Col_m6A_pls_00_R3

description: PolyA, m6AIP


title: 18124X2 SVF obese female 1


title: Prostate cancer tissue PCa31234


title: 18124X1 SVF lean female 1


title: Pst_Col_m6A_pls_00_R2

description: PolyA, m6AIP


title: Tox4 WT ser2p CUT&Tag rep2


title: Tox4 cKO ser2p CUT&Tag rep1


title: Pst_Col_m6A_pls_00_R1

description: PolyA, m6AIP


title: Tox4 WT ser2p CUT&Tag rep1


title: 17697X2 SVF obese male1


title: 17697X1 SVF lean male 1


title: Tox4 cKO Pol II CUT&Tag rep2

value: Pol II


title: Prostate cancer tissue PCa28666


title: Prostate cancer tissue PCa27967


title: Pst_Col_m6A_pls_24_R2

description: PolyA, m6AIP


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 3

city: Singapore

first: Wee Kiat Jeremy

last: Ng

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

description: 10x Genomics

data_processing:
library strategy: scTCR-sequencing
The demultiplexing, barcoded processing, contig assembly and annotation were performed using CellRanger V3.
Assembly: hg38
Supplementary files format and content: XLS file with contig annotation from CellRanger

source_name: gamma-delta T-cells

growth_protocol: Purified GDT cells were mixed with feeder cells consisting of irradiated normal human PBMCs and EBV-LCLs at 1:50:100 ratio in RPMI (Gibco) supplemented with 10% FBS plus 170 U/mL recombinant human interleukin-2 (rhIL-2), 25U/ml rhIL-15 as well as 0.7U/ml rhIL-21 for 2 weeks. At weekly interval, total number of γδ T in culture was enumerated, with the supplementation of irradiated PBMCs and EBV-LCLs at the ratio of 1:10:20, respectively.

extract_protocol: The purified cells were stained with a panel of TotalSeq-C antibodies (Supp. Table M3) according to manufacturer’s protocol and processed according to 10X Genomics’ standard workflow for Chromium Single Cell V(D)J with Feature Barcoding technology for Cell Surface Protein to generate the transcriptome (5’GEX) and featured barcode library. To generate the TCRγδ V(D)J library, a 2-steps target enrichment PCRs were adopted from previously published protocol.

value: gamma-delta T-cells

tag: donor

value: Donor 2

value: Day 14


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 2

description: 10x Genomics


title: Prostate cancer tissue PCa26325

value: Prostate cancer tissue


title: Tox4 cKO Pol II CUT&Tag rep1

value: DP thymocytes


title: Prostate cancer tissue PCa27303


title: Tox4 WT Pol II CUT&Tag rep2


title: Prostate cancer tissue PCa25204


title: Tox4 WT Pol II CUT&Tag rep1


title: Antigen challenged EBV-LCL cultured cells

description: 10x Genomics

value: Donor 1

value: Day 15


title: Day 14, EBV-LCL cultured gamma-delta-T-cells

description: 10x Genomics


title: Tox4 cKO ser2p CUT&Tag rep2


title: Prostate cancer tissue PCa22283

value: prostate cancer


title: Tox4 cKO CD8 ATAC-seq rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
Normalized read aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized insertion count (CPM, in 50-bp bins)

source_name: Lymphatic CD8+ T cell

extract_protocol: After nuclei preparation, tagmentation, termination and DNA purification, samples were amplified by PCR with one universal forward primer and different indexed reverse primers.

value: Lymphatic CD8+ T cell


title: Day 7, EBV-LCL cultured gamma-delta T-cells

description: 10x Genomics

value: Day 7


title: Tox4 cKO CD8 ATAC-seq rep1


title: Prostate cancer tissue PCa19983

source_name: Prostate cancer tissue


title: Prostate cancer tissue PCa28807


title: Prostate cancer tissue PCa19121


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 3 [5GEX]

description:
GDT3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v3
Further processing was done with Seurat v3.0.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

value: Donor 3


title: Prostate cancer tissue PCa18361


title: Prostate cancer tissue PCa18146


title: Tox4 WT CD8 ATAC-seq rep2


title: Tox4 cKO DP ATAC-seq rep2


title: Tox4 cKO DP ATAC-seq rep1


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 2 [5GEX]

description:
GDT1
10x Genomics


title: Prostate cancer tissue PCa14121


title: Day 7, EBV-LCL cultured gamma-delta T-cells [5GEX]

description:
D7
10x Genomics


title: Prostate cancer tissue PCa13266


title: Tox4 WT DP ATAC-seq rep1


title: Day 14, EBV-LCL cultured gamma-delta-T-cells [5GEX]

description:
D14
10x Genomics


title: Antigen challenged EBV-LCL cultured cells [5GEX]

description:
D15
10x Genomics


title: N63.Dataset [204551090032_R02C01]

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: age

tag: confidenceinageestimate

value: Liver

tag: female

tag: specieslatinname

value: Mus musculus

tag: agedetailed

value: m

tag: tissuecolor

value: brown

tag: predictedfemale

tag: predictedtissue

tag: tissues

value: Adipose / Aorta / Astrocyte / Blood / BoneMarrow / Brain / BrainTumor / Cerebellum / Cortex / Crypts / DifferentiatedBloodCells / Ear / ES / Fibroblast / Gut / Heart / Heart.Atrium / Heart.Teratoma / Heart.Ventricle / HematopoieticStem.Progenitor.LSK / HematopoieticStemCells / Hippocampus / Hypothalamus / iPSC / Kidney / Liver / Lung / MacrophageBoneMarrow / MacrophagePeritoneal / Muscle / Pancreas / Pituitary / Placenta / Retina / Serum / Skin / Spleen / Striatum / SVZ / Tail / Villi / WholeBrain


title: Prostate cancer tissue PCa1394

tag: tissue


title: Tox4 WT DP ATAC-seq rep2

tag: genotype


title: Prostate cancer tissue PCa12764


title: Tox4 cKO RNA-seq rep3

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Fragment count were obtained using featureCounts v1.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.


title: DU145, input

description:
DU145_H3K27ac_Rep1_R1.srt.nodup_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed
DU145_H3K27ac_Rep2_R1.srt.nodup_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed

tag: cell line


title: Tox4 cKO RNA-seq rep1

tag: cell type


title: Tox4 cKO RNA-seq rep2


title: LNCaP, H3K27ac, bol rep 2

description:
LNCaP_H3K27ac_Rep2_R1.srt.nodup_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed

value: LNCaP


title: Day 0 uncultured gamma-delta T-cells

description: 10x Genomics

value: gamma-delta T-cells

tag: time

value: Day 0

tag: treatment


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 2 [FB]

description: 10x Genomics

data_processing:
library strategy: 10X FB-seq
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v3
Downstream analysis was performed with Seurat
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

value: Donor 2

value: Day 14


title: Day 14, EBV-LCL cultured gamma-delta-T-cells, Donor 3 [FB]

description: 10x Genomics


title: Tox4 WT RNA-seq rep3

value: DP thymocytes


title: Antigen challenged EBV-LCL cultured cells [FB]

description: 10x Genomics

value: Donor 1


title: Tox4 WT CD8 ATAC-seq rep1


title: Day 14, EBV-LCL cultured gamma-delta-T-cells [FB]

description: 10x Genomics


title: Tox4 WT RNA-seq rep2


title: DU145, H3K27ac, biol rep 1

description:
DU145_H3K27ac_Rep1_R1.srt.nodup_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed

tag: chip antibody


title: Tox4 WT RNA-seq rep1


title: Tp53_Trim28_rep16

status: Public on Sep 07 2023

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v.2011.1 and SeSAMe

label: Cy5 and Cy3

source_name: genomic DNA from 10 days old mouse ear clips

label_protocol: Standard Illumina Infinium HD Assay Methylation Protocol document #15019519 v01

growth_protocol: Ear punch biopsies were collected at 10 days and placed in 20 µl reaction mix composed of genomic DNA lysis buffer (100 mM Tris-HCl pH 8.5, 5 mM EDTA, 0.2% SDS, 100 mM NaCl) supplemented with 20 mg proteinase K (Thermo Scientific, EO0491).

extract_protocol: We used the DNeasy Blood & Tissue Kit (QIAGEN, 69504) for DNA extraction

treatment_protocol: Digestion was carried out overnight in a Thermocycler under the following conditions: 55C for 16 hours, 95C for 10 minutes, 4C hold (lid at 105C). After lysis, the lysate was diluted by adding 160 µl of nuclease-free water (Invitrogen, AM9938) to the same tube (180 µl final volume).

tag: Sex

value: male

value: ear

tag: developmental stage

value: 10 days

tag: phenotype

tag: batch


title: Day 7, EBV-LCL cultured gamma-delta T-cells [FB]

description: 10x Genomics

tag: donor

value: Day 7


title: LNCaP, H3K27ac, biol rep 1

description:
LNCaP_H3K27ac_Rep1_R1.srt.nodup_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_LNCaP__1_-_Input_S5_L001_R1_001.merged.narrowPeak.sorted.qval0.05.bed

value: prostate cancer


title: Tp53_Trim28_rep15


title: Day 0 uncultured gamma-delta T-cells [5GEX]

description:
D0
10x Genomics


title: Tp53_Trim28_rep13


title: Tp53_Trim28_rep12


title: Tp53_Trim28_rep14


title: Tp53_Trim28_rep9


title: Tp53_Trim28_rep8


title: Tp53_Trim28_rep6


title: Tp53_Trim28_rep5


title: Tp53_Trim28_rep7


title: Tp53_Trim28_rep3


title: Tp53_Trim28_rep2


title: Tp53_Trim28_rep4


title: Tp53_Trim28_rep1


title: DU145, H3K27ac, biol rep 2

description:
DU145_H3K27ac_Rep2_R1.srt.nodup_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed
rep.pooled_x_DU145_input_Rep1_R1.narrowPeak.sorted.qval0.05.bed


title: Tp53_rep8


title: Tp53_rep11


title: Tp53_rep9


title: Tp53_rep10


title: Tp53_rep7


title: STAR_21: D28-12w2

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

data_processing:
NovaSeq 6000
Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. Only the reads derived from xenograft samples were separated human and rat reads using Xenome (v1.0.0). Reads classified as human were mapped to the hg38 reference with STAR (v2.7.2a) and gene count matrix was generated with featureCounts (v1.6.4).
Raw counts were normalized with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_1-4-13-18-19-21.txt is a raw counts file and tpm-normalized_counts_vivo3m.csv is a transcripts per million (TPM) normalized count file

organism:
Homo sapiens
Rattus norvegicus

source_name: human induced pluripotent stem cell-derived cardiomyocyte in rat heart

growth_protocol: Undifferentiated human induced pluripotent stem cells reached 90% confluency, E8 medium was supplied with 1 uM of Wnt activator CHIR99201 (Sigma-Aldrich). The next day (day 0), E8 medium was changed to the cardiac differentiation medium (RPMI 1640 with B27 supplement minus insulin (Gibco) plus L-glutamine adding activin A (100 ng/mL, R&D) and Matrigel. On day1, bone morphologic protein 4 (BMP4; 10 ng/mL, R&D) and CHIR99201, followed by addition of Wnt inhibitor XAV939 (1 uM Sigma-Aldrich) on day 3-4. After day 7, medium was changed to RPMI 1640 with B27 supplement (Gibco) every other day. The cells were heat-shocked at 43ºC for 30 minutes and cryopreserved on day 28 or 56.

extract_protocol:
For sample 1-2, total RNA was isolated using the RNeasy Mini Kit (Qiagen), in accordance with the manufacturer’s protocol including DNase treatment.  For sample 5-8, rat hearts of each time points were collected and immediately embedded in an OCT-embedding compound and kept in -80℃. Tissues were sectioned at a thickness of 10 µm using a cryostat (Leica). The graft areas were captured using laser microdissection system (Leica) from unstained unfixed specimens attached on the membrane coated slides (Leica 11600289). Total RNA was extracted by Arcturus PicoPure RNA Isolation Kit (Thermo).
cDNA was synthesized by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa). Library preparations were conducted using Nextera DNA Library Prep Kit

treatment_protocol: 2 x 10^7 human induced pluripotent stem cell-derived cardiomyocytes were directly injected to rat hearts (sample 5-8)

value: 253G1, F344/Ncjcl-rnu/rnu

value: Cardiomyocytes

tag: dev stage

value: differentiation day 112


title: STAR_19: D56-12w1

value: differentiation day 140


title: Day 0 uncultured gamma-delta T-cells [FB]

description: 10x Genomics


title: Tp53_Trim28_rep11


title: Tp53_rep4


title: Tp53_rep6


title: Tp53_Trim28_rep10


title: DRM3_3

first: Wenfang

last: Peng

address: No.368 Youyi Avenue

institute: Hubei University

data_processing:
Bcl2fastq (v2.17.1.14)
Quality assessment was performed using FastQC (v0.12.1), and based on the results, the paired FASTQ files were further subjected to quality trimming and adapter removal using Trim Galore (v0.6.10) tool.
Alignment of sequencing data was performed using hisat2(v2.2.1), followed by conversion between SAM and BAM files using samtools(v1.9)
featureCounts(v2.0.1) was used to generate counts
Performing data normalization and FPKM value conversion using the R programming language
Assembly: The reference sequence is from the Genebank database under NCBI, with the unique identifier sequence being AE008692
Supplementary files format and content: Displaying count values in matrix format
Supplementary files format and content: Displaying FPKM values in matrix format

organism: Zymomonas mobilis

source_name: microbial cells

growth_protocol: Cells were cultured in a standard RMG2 medium for Zymomonas mobilis

extract_protocol:
Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer, NanoDrop and 1% agrose gel. 1μg total RNA was used for following library preparation
Generation sequencing library preparations were constructed according to the manufacturer’s protocol

treatment_protocol: No special treatment was included.

value: microbial cells

value: whole cell

value: wt

value: grown to log phase


title: DRM3_2


title: STAR_13: D28-12w1


title: STAR_18: D56-12w2


title: Tp53_rep5


title: Tp53_rep3


title: Tp53_rep2


title: KO_Cocl2_Rep1

city: Beiing

first: TAO

last: XING

state: Beiing

address: Beiing

institute: Peking University Cancer Hospital

data_processing:
Read mapping was performed to GRCh38/hg38 using Bowtie2
Apparent PCR duplicates were removed using samtools
MACS2 peak calling algorithm was used to identify enrichment peaks.
bigWig files were generated using deeptools
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

organism: Homo

source_name: liver cancer

extract_protocol:
CUT&RUN experiments were performed using the CUT&RUN Assay Kit(#86652; Cell Signaling)
DNA Library Prep Kit for Illumina®(#56795 Cell Signaling ) was using Constructed NG-Sequencing Library then sequenced on Illumina NovaSeq 6000

value: liver cancer

tag: antibody

value: KO

value: Cobalt Chloride(CoCl2)


title: Trim28_heavy_rep15

value: heavy


title: Trim28_heavy_rep14

value: male


title: KO_Cocl2_Rep2


title: Tp53_rep1

value: ear


title: Trim28_heavy_rep12

value: 10 days


title: WT_Cocl2_Rep2

value: WT


title: WT_Cocl2_Rep1


title: Trim28_heavy_rep13


title: KO_Rep2

value: normal


title: Trim28_heavy_rep10


title: WT_Rep2


title: Trim28_heavy_rep11


title: KO_Rep1


title: ARID1A_Rep2

value: ARID1A (#12354; Cell Signaling)


title: Trim28_heavy_rep7


title: Trim28_heavy_rep5


title: Trim28_heavy_rep4


title: WT_Rep1


title: Trim28_heavy_rep8


title: Trim28_heavy_rep6


title: DRM3_1


title: Trim28_heavy_rep3


title: Trim28_heavy_rep1


title: Trim28_heavy_rep2


title: ARID1A_Rep1


title: Trim28_light_rep7

value: light


title: Trim28_light_rep6


title: Trim28_light_rep4


title: Trim28_light_rep5


title: Trim28_light_rep3


title: WT_rep7


title: Trim28_light_rep1


title: WT_rep6


title: Trim28_heavy_rep9


title: WT_rep4


title: WT_rep1


title: WT_rep3


title: WT_rep2


title: Trim28_light_rep8


title: Trim28_light_rep2


title: germinal vesical oocytes,high-fat diet,rep4

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina high-throughput sequencing results are converted into original sequencing sequences by bcl2fastq software and stored in FASTQ file format.
Clean Reads of high quality were obtained after the original sequences were filtered. The filtered sequencing sequences of each sample were compared with the reference genome Mus_musculus.GRCm38.90.chr to locate the genome.
FPKM (Fragments per Kilobase per Million Mapped Fragments) method was used to obtain differentially expressed genes that could be directly used to compare different samples.
Assembly: ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/Mus_musculus.GRCm38.90.gtf.gz
Supplementary files format and content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: oocytes

growth_protocol: The embryos were cultured in KSOM in vitro.

extract_protocol:
The single-cell samples were collected in tubes with lysis component and ribonuclease inhibitor. Then we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection.Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.
RNA libraries were prepared foe sequencing using standard Illumina protocols.

treatment_protocol: The transcript of siAcox1 group  were deleted by small-interfering-RNA(siRNA) microinjection into mouse zygotes.

value: oocytes

value: germinal vesical oocytes

value: oocyte maturation

value: high-fat diet


title: 2-cell,high-fat diet,rep6

source_name: embryos

value: embryos

value: embryonic development


title: 2-cell,high-fat diet,rep8


title: germinal vesical oocytes,high-fat diet,rep3


title: 2-cell,high-fat diet,rep2


title: 2-cell,normal diet,rep1

value: wild type


title: 2-cell,high-fat diet,rep5


title: 2-cell,high-fat diet,rep1


title: 2-cell,high-fat diet,rep7


title: WT_rep5


title: germinal vesical oocytes,high-fat diet,rep2


title: metaphase II oocytes,normal diet,rep4

value: metaphase II oocytes


title: metaphase II oocytes,normal diet,rep5


title: metaphase II oocytes,normal diet,rep6


title: germinal vesical oocytes,high-fat diet,rep1


title: 2-cell,normal diet,rep3


title: 2-cell,normal diet,rep2


title: metaphase II oocytes,normal diet,rep2


title: Zygote,normal diet,rep3

value: Zygote


title: 2-cell,high-fat diet,rep4


title: metaphase II oocytes,normal diet,rep3


title: 2-cell,high-fat diet,rep3


title: germinal vesical oocytes,normal diet,rep3


title: germinal vesical oocytes,normal diet,rep2


title: germinal vesical oocytes,normal diet,rep1


title: Zygote,normal diet,rep2


title: Trim28_light_rep9


title: Zygote,normal diet,rep1


title: 2-cell embryos, siAcox1 injection, rep1

value: 2-cell embryos

value: gene knockdown


title: 2-cell embryos, siAcox1 injection, rep2


title: 2-cell embryos, siAbcd3 injection, rep2


title: 2-cell embryos, siAbcd3 injection, rep1


title: 2-cell embryos, siAcox1 injection, rep3


title: MUC14088, HFHS diet, CCK, IP

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

description: HTSeq quantification of transcript expression

data_processing:
BCL files were converted to FASTQ using Bcl2fastq v.2.20. The alignment was done 739 using STAR v.7.2a and was mapped to the mouse reference genome GRCm38 (mm10). The 740 counts and FPKM were generated using HTSeq v0.11.2
These transcript abundances were then imported into R (v4.0.3, R Core Team, 2019), and summarized with tixmeta (Love et al., 2020). Employing DESeq2 (Love et al., 2014), gene expression levels were normalized with median ratio method, and principal components were calculated on variance stabilizing transformed counts.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text file report un-normalized counts

source_name: Brain

growth_protocol: Mice were housed in groups under a 12-h light/12-h dark cycle at 22 +/- 2°C. All animals had free access to water and food.

extract_protocol:
2 hours post-injection, hypothalami were dissected , snap frozen and pooled together (2-3 mice per sample) for downstream affinity purification of HA-tagged ribosomes.
The libraries were sequenced in paired-end mode (2x150bases) in the Novaseq 6000 at a depth of ≥ 40 million paired reads per sample.

treatment_protocol: Adult male mice (4-6 months) were either fed SC diet or HFHS diet for 3 months. On the day of experiment, food was removed for 3h prior to injection to normalize gastric content. Mice received either vehicle or CCK (20 ug/kg BW i.p.) at dark onset

value: Brain

value: Neurons

tag: strain

tag: age

value: 4-6 months old

value: male

tag: diet

value: High-fat high-sugar (HFHS) diet

value: CCK (20 ug/kg BW; BW)

value: 2 hours post-injection

tag: fraction

value: immunoprecipitate (IP)


title: 2-cell embryos, siAbcd3 injection, rep3

tag: tissue

tag: genotype


title: 2-cell embryos, rep2

tag: cell type


title: MUC14087, HFHS diet, CCK, IP

tag: time


title: 2-cell embryos, rep3

tag: treatment


title: MUC14085, HFHS diet, CCK, IP


title: MUC14086, HFHS diet, CCK, IP


title: metaphase II oocytes,normal diet,rep1

value: oocytes

value: oocyte maturation


title: MUC14084, HFHS diet, vehicle, IP

value: vehicle


title: MUC14082, HFHS diet, vehicle, IP


title: germinal vesical oocytes,normal diet,rep4

value: embryos

value: germinal vesical oocytes


title: MUC13134, SC diet, CCK, IP

value: Standard chow (SC) diet


title: MUC13138, SC diet, vehicle, IP


title: MUC13139, SC diet, vehicle, IP


title: MUC13136, SC diet, CCK, IP


title: MUC14083, HFHS diet, vehicle, IP


title: MUC13137, SC diet, vehicle, IP


title: MUC13133, SC diet, CCK, IP


title: MUC13131, SC diet, vehicle, input

value: input


title: MUC13140, SC diet, vehicle, IP


title: MUC14081, HFHS diet, vehicle, IP


title: MUC13130, SC diet, vehicle, input


title: MUC13129, SC diet, vehicle, input


title: MUC13132, SC diet, vehicle, input


title: MUC13127, SC diet, CCK, input


title: MUC13128, SC diet, CCK, input


title: 2-cell embryos, rep1

value: 2-cell embryos

value: wild type

value: embryonic development


title: MUC13125, SC diet, CCK, input

value: Brain

value: Neurons


title: MUC13126, SC diet, CCK, input

value: 4-6 months old

value: male


title: HepG2 cells FN3K KO, sample 3

city: Athens

first: Natarajan

last: Kannan

address: 120 E. Green Street

department: Department of biochemistry and molecular biology

institute: University of Georgia

data_processing:
"new tuxedo suite" of HISAT2, StringTie and Ballgown
Sequence reads were trimmed for adapters and low quality sequences.
Trimmed sequence reads were mapped to the GRCh38.p5 using HISAT2 (default parameters)
Transcripts were then assembled using StringTie v2.0.6
Then, differential expression analysis was performed using Ballgown v2.26.
Assembly: GRCh38.p5
Supplementary files format and content: tab delimited file contains the FPKM values for each sample.

source_name: Liver

growth_protocol: HepG2 (WT and KO) cells were cultured on 6 am plates in triplicate to 70-80% confluency in Eagle’s Minimum Essential Media (EMEM, ATCC) containing 10% Fetal Bovine Serum.

extract_protocol:
After cell lysis, impurities removal, and inhibition of RNAse activity, total RNA was extracted by using phase separation method from cell debris, and was precipitated by ethanol. Then Agilent bioanalyzer 2100 were used to check RNA integrity and concentration.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. The quality control of library consists of three steps: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

value: Liver

tag: cell line

value: FN3K KO


title: OPCs, Bmal1 KO, ZT18, rep 3

city: Palo Alto

first: Erin

middle: M

last: Gibson

address: 3165 Porter Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

data_processing:
Raw reads of fastq format were firstly processed through fastp software. In this step, clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file of a matrix containing raw counts for each Sample.

source_name: Forebrain

growth_protocol: Mice were housed in group cages, according to standard guidelines with ad libitum access to food and water under a 12::12 hr light/dark cycle. Both sexes were equally used in all experiments. NG2::Cre were bred with Bmal1fl/fl mice (The Jackson Laboratory 008533 and 007668) to produce NG2::Cre;Bmal1fl/fl conditional constitutive knock out model. OPCs were isolated from postnatal day (P)6-7 NG2::Cre-;Bmal1fl/fl (OPC-Bmal1-WT) and NG2::Cre+;Bmal1fl/fl (OPC-Bmal1-KO) mice at 6-hr intervals for 24 hrs. OPCs were isolated at 4 different zeitgeber times: ZT0 (lights on), ZT6, ZT12 (lights off), and ZT18.

extract_protocol:
OPCs were purified using immunopanning through 2 negative selection plates for microglia and endothelial cells with BSL1 (Vector Laboratories L1100) and one positive selection plate with an anti-PDGFRα antibody (rat anti-mouse CD140A, BD Pharmingen 558774). One million OPCs were immediately lysed using QIAzol Lysis Reagent. RNA extraction was performed following manufacturer’s instructions and RNA purity, integrity and concentration were assessed using a Bioanalyzer.
Library prep and Bulk RNA sequencing was performed using Novogene Co., Ltd. sequencing service. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using NEBNext Ultra II RNA Library Prep kit. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on NovaSeq 6000 S4 system and paired-end reads were generated. All libraries had > 80 million reads.

treatment_protocol: No pharmacological treatment was applied prior to OPC isolation.

value: Forebrain

value: Oligodendrocyte precursor cells

tag: devleopmental stage


title: OPCs, Bmal1 KO, ZT18, rep 2


title: HepG2 cells FN3K KO, sample 2


title: OPCs, Bmal1 KO, ZT12, rep 2


title: OPCs, Bmal1 KO, ZT18, rep 4


title: OPCs, Bmal1 KO, ZT12, rep 3


title: OPCs, Bmal1 KO, ZT18, rep 1


title: OPCs, Bmal1 KO, ZT12, rep 4


title: HepG2 cells WT, sample 3

value: WT


title: OPCs, Bmal1 KO, ZT6, rep 7


title: OPCs, Bmal1 KO, ZT12, rep 1


title: OPCs, Bmal1 KO, ZT6, rep 5


title: OPCs, Bmal1 KO, ZT6, rep 6


title: HepG2 cells WT, sample 1


title: HepG2 cells WT, sample 2


title: OPM2-scRNAseq-2hours_All_samples_multiplexed

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Cell Ranger reads were aligned to the reference genome; cellular barcodes were demultiplexed, and unique molecular identifiers and antibody capture (HTO) were quantified using 10x Genomics’ Cell Ranger software (version 3.1.0).
Cell barcodes containing RNA or antibody counts from cells from more than one sample (intersample doublets) were identified using Seurat’s HTODemux function.
Gene expression and HTO count matrices were processed in R (version 3.6.1) using the Seurat R package (version 3.1.0).
RNA transcript counts for barcodes identified as cells by Cell Ranger were normalized using sctransform via Seurat’s SCTransform function. The counts were first transformed with no covariates in the sctransform model; then, cell cycle phase scores were estimated using Seurat’s CellCycleScoring function.
The sctransform normalization was then rerun with the cell cycle phase scores and the percentage of raw RNA counts belonging to mitochondrial genes for each cell as variables to be regressed out in the model. ADT counts were normalised using centred log ratio transformation.
Supplementary files format and content: Filtered list of gene features detected for each sample in gzipped tsv file (features.tsv.gz) produced by Cell Ranger.
Supplementary files format and content: Filtered list of cell barcodes for each sample in gzipped tsv file (barcode.tsv.gz) produced by Cell Ranger
Supplementary files format and content: Filtered count matrix for each sample in gziped matrix file (matrix.mtx.gz) produced by Cell Ranger.

source_name: Hematopoietic

growth_protocol: OPM2 cells were cultured in vitor under standard culture conditions.

extract_protocol:
Cells were harvested, pelleted by centrifugation, and resuspended in FACS buffer (2% FCS in PBS) then incubated with Cell Hashing antibodies (BioLegend) for 20 minutes on ice. Next, cells were thrice washed in FACS buffer followed by resuspension in PBS supplemented with 0.04% BSA at a concentration of 1500 cells/µL, and then each of the treatment conditions were pooled together into a single tube.
Cells were loaded onto the 10x Chromium instrument (10x Genomics) to generate single-cell gel beads in emulsion and barcode cells.
For 5′ multiomics 5′ hashtag oligos (HTO) was prepared using the Chromium Single Cell 5′ Feature Barcode Library Kit and indexed using the Chromium i7 Multiplex Kit N, Set A.

treatment_protocol: OPM2 cells were treated in vitro with JQ1, BKM120, 18DS, or DMSO vehicle control for 2 hours.

value: Hematopoietic

value: Plasma cell myeloma

value: 2 hours treatment


title: OPCs, Bmal1 KO, ZT6, rep 3


title: OPCs, Bmal1 KO, ZT6, rep 4


title: DPP9-KO-3

city: Shanghai

first: Xuanzhi

last: Zhang

address: Dong'an Road NO.130

institute: Fudan University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and processed Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Read Counts for each gene in each sample was counted by HTSeq v0.6.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each Sample.

source_name: clear cell renal cell carcinoma

growth_protocol: 786-O cells were maintained in RPMI‐1640 media (Gibco, Thermo Fisher Scientific, Inc.).

extract_protocol:
Total RNA was extracted by TRIzol reagent (Tiangen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

value: Clear cell renal cell carcinoma

value: DPP9 Knock-out


title: DPP9-NC-3


title: DPP9-KO-2


title: DPP9-KO-1


title: OPCs, Bmal1 KO, ZT6, rep 2


title: OPCs, Bmal1 KO, ZT0, rep 4


title: DPP9-NC-2


title: OPCs, Bmal1 KO, ZT0, rep 3


title: OPCs, Bmal1 KO, ZT6, rep 1


title: DPP9-NC-1


title: HepG2 cells FN3K KO, sample 1


title: OPCs, Bmal1 KO, ZT0, rep 2


title: ATAC, PML knockdown, MDA231 rep 2

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description: shPML.bw

data_processing:
Reads were trimmed using BBDuk from BBTools suite version 37.36 with suggested settings (ktrim=r k=23 mink=11 hdist=1).
Reads were aligned to the UCSC hg38 genome using BWA-MEM version 0.7.12-r1039 . Uniquely mapped reads were selected with MarkDuplicates from Picard Tools version 1.104
Filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist and regions flagged as not primary alignment or with mapping quality score less than 15.
Peaks were detected using MACS2 v2.2.7.1
Assembly: bigWig files were generated using bamCoverage from Deeptools.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: Nextera XT DNA Library Prep kit (Illumina)

treatment_protocol: Silencing of PML was performed via lentiviral shRNA

value: Human breast cancer

value: PML silenced


title: OPCs, Bmal1 KO, ZT0, rep 1


title: ATAC, PML knockdown, MDA231 rep 1

description: shPML.bw


title: ATAC, control, MDA231 rep 1

description: shCT.bw

value: control


title: OPCs, Bmal1 WT, ZT18, rep 4


title: OPCs, Bmal1 WT, ZT18, rep 3


title: ATAC, control, MDA231 rep 2

description: shCT.bw


title: serotonin neurons, FOXA2 knockout

first: Ting

last: Xu

address: 1239 Siping Road

institute: Tongji University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger , version 7.0)
Assembly: homo_sapiens GRCh38 V101
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
At day42 of the differentiation of TPH2-EGFP reporter hPSCs towards serotonin neurons, cells were dissociated by accutase and filtered through cell strainer (40 µm) to obtain single cells. Highly purified EGFP-labeled SNs were then derived by fluorescence-activated cell sorting (FACS).
cDNA amplification and library construction were performed according to standard protocols.  Breifly, Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3). Gel beads containing barcode information were bound to a mixture of cells and enzymes and then encapsulated by droplets of oil surfactant located in a microfluidic system to form gel bead-in-emulsions (GEMs). After GEMs flowing into a reservoir and being collected, the gel beads were lysed to release the barcode sequence. Then the cDNA fragment were reverse transcribed and the cells were labeled. The products of all GEMs were mixed and a standard sequencing library was constructed.

value: serotonin neurons

value: TPH2-EGFP knockin  and FOXA2 knockout

value: induced serotonin neuron differentiation, FOXA2 knockout


title: Patient LIMET325 multiplexed fluorescent in situ RNA hybridization ROI D2_1

type: other

city: Milano

first: Renato

last: Ostuni

address: Via Olgettina 58

institute: San Raffaele Telethon Institute for Gene Therapy

description: Raw data files include tab-separated values files containing x-y-z location for each transcript (txt format) and staining images of DAPI and KRT19 (tiff format).Processed data include output from segmentation with Baysor.

hyb_protocol: Briefly, 10-µm PDAC tissue sections were hybridized at 37°C for 24 hours with oligonucleotides probes specific for the selected target genes, designed using Resolve’s proprietary algorithm.

scan_protocol: Probe binding was revealed with fluorescent tags in a multi-step automated imaging process, repeating color development, imaging and decolorization for a total of 8 cycles on a Zeiss Celldiscoverer 7 instrument, using a 50x water immersion objective.

data_processing: We segmented cell nuclei in the DAPI image with Cellpose (v. 2.2) using the pre-trained nuclei model, with automated estimation of diameter parameter. Subsequently, cells were segmented on transcript coordinates with Baysor (v. 0.5.0) using DAPI segments as prior.

molecule: other

source_name: Primary tumor

value: Primary tumor

tag: disease state

value: PDAC

tag: individual

value: Patient LIMET325


title: 449 R2 T21

data_processing:
The sgRNA reads were mapped to sgRNA sequence with Bowtie2
FeatureCounts (v1.5.0) was used to count the reads numbers mapped to each gene.
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) algorithm was used to generate a ranked list of fitness genes
Assembly: tkov3_guide_sequence.fasta

growth_protocol: HCC cell lines were cultured in DMEM with 10% FBS and 1% Penicillin / streptomycin at 37 °C supplied with 5% CO2.

extract_protocol:
Genomic DNA was isolated using the TIANamp Genomic DNA Kit (#DP304; TIANGEN) as the manufacturer’s instructions.
PCR was used to amplify sgRNA barcodes (#M0544S; New England Biolabs), and deep sequencing was then performed to assess the sgRNA sequences.

value: liver cancer


title: Patient LIMET325 multiplexed fluorescent in situ RNA hybridization ROI D2_2


title: Patient LIMET165 multiplexed fluorescent in situ RNA hybridization ROI B1_2

value: Patient LIMET165


title: Patient LIMET165 multiplexed fluorescent in situ RNA hybridization ROI B1_1


title: serotonin neurons, widetype

description: 10x Genomics

value: TPH2-EGFP knockin

value: induced serotonin neuron differentiation


title: OPCs, Bmal1 WT, ZT18, rep 1

value: Forebrain

value: Oligodendrocyte precursor cells


title: OPCs, Bmal1 WT, ZT12, rep 6


title: OPCs, Bmal1 WT, ZT12, rep 5


title: Patient LIMET163 multiplexed fluorescent in situ RNA hybridization ROI C2_1

value: Patient LIMET163


title: 449 R1-T0

value: WT


title: Patient LIMET163 multiplexed fluorescent in situ RNA hybridization ROI C2_2


title: 449 R2 T0


title: Patient LIMET49 multiplexed fluorescent in situ RNA hybridization ROI A2

value: Patient LIMET49


title: Patient LIMET10 multiplexed fluorescent in situ RNA hybridization ROI C1

value: Patient LIMET10


title: OPCs, Bmal1 WT, ZT18, rep 2


title: Patient LPDAC30 multiplexed fluorescent in situ RNA hybridization ROI D2

value: Patient LPDAC30


title: 449 R1 T21


title: OPCs, Bmal1 WT, ZT12, rep 2


title: Patient LPDAC30 multiplexed fluorescent in situ RNA hybridization ROI C2


title: OPCs, Bmal1 WT, ZT12, rep 1


title: HepG2 KO Rep2 T21

value: KO


title: Bulk ATAC-seq on HepG2

city: Leuven

first: Carmen

last: Bravo Gonzalez-Blas

address: Herestraat 49

country: Belgium

institute: VIB-KU Leuven Center for Brain & Disease Research

data_processing:
Adapters were removed with fastq-mcf (ea-utils v1.12), cleaned reads were mapped to the hg19 (HepG2) or mm10 (AML12 and Hepa16) genome  using Bowtie2 (v2.3.5.1) and and bigwig files were generated using deepTools bamCoverage function (v3.5.0, with --normalizeUsing CPM --binSize 1 as parameters). Coverage heatmaps were done using deepTools (v3.5.0).
Assembly: hg19 for HepG2 and mm10 for AML12 and Hepa16
Supplementary files format and content: CLE__e257b6__27092021_HepG2wt_OmniATAC_S4_q4_sorted.bw: Bigwig containing HepG2 ATAC-seq profile. MLV__babe04__OmniATAC_Hepa1-6_S3_q4_sorted.bw: Bigiwg containing Hepa16 ATAC-seq profile. CLE__77d534__27092021_AML12wt_OmniATAC_S3_q4_sorted.bw:  Bigwig containing AML12 ATAC-seq profile.
Library strategy: OmniATAC-seq

extract_protocol:
The HepG2, Hepa1-6 and AML12 cell lines were purchased from ATCC (HB-8065, CRK-1830 and CRL-2254, respectively). HepG2 cells were cultured in Eagle’s Minimum Essential Medium (EMEM, Thermo Fisher Scientific), Hepa1-6 cells were clustered in Dulbecco’s Modified Eagle’s Medium (DMEM), and AML12 in DMEM-F12 medium. All media were supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 50 µg/mL penicillin/streptomycin (Thermo Fisher Scientific).  Cell cultures were kept at 37°C, with 5% CO2.
Omni-assay for transposase-accessible chromatin using sequencing (OmniATAC-seq) was performed as described previously. Briefly, 50,000 cells obtained after FACS were resuspended in 50 µL of cold ATAC-seq resuspension buffer (RSB; 10 mM TrisHCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 µL of transposition mix (25 µL 2x TD buffer, 2.5 µL transposase (Nextera Tn5 transposase, Illumina), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermoblock. Reactions were cleaned-up by MinElute (Qiagen). Transposed DNA was amplified with primers 'i5_Indexing_For’ and ‘i7_Indexing_Rev’ (Supplementary Table 4). Number of PCR cycles was based on quantitative real-time PCR as described previously. All libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2.


title: HOrF Cells, CAL27' EVs, Rep 3

city: Vancouver

first: Rebecca

last: Towle

state: BC

department: Integrative Oncology

institute: British Columbia Cancer Research Centre

description:
column 4 in FPKM matrix
EVCTRL3

data_processing:
Base calls on BaseSpace (Illumina)
Sequencing data was de-multiplexed using Illumina's bcl2fastq2
Reads were aligned using the STAR alignerusing hg19 reference genome
Assembly and differential analysis done by CuffLinks
Assembly: Homo sapiens (UCSC hg19)
Supplementary files format and content: Cufflinks differential analysis results files for each treatment type compared to cells treated with PBS as a control

source_name: oral

growth_protocol: Cells were cultured on coated surfaces using poly-L-lysine (ScienCell™ Research Laboratories Cat #0413) and in complete Fibroblast Medium (ScienCell™ Research Laboratories Cat #2301) containing 2% FBS. The HOrFs were used for no more than passage ten. All cells were cultured in a 37oC, 5% CO2 incubator

extract_protocol:
TRIZol method
NEBNextUltraII Directional RNA Library Prep Kit for Illumina

treatment_protocol: HOrFs were seeded in six well plates with 2 ml of media until reaching 30% confluency. Filtered EVs isolated from oral cancer cell lines and resuspended in PBS (25 µl per well) were added to the culture media (22.6 x 1015 EV particles per well). To the PBS control, 25 µl of PBS was added per well  and to the TGFβ control, 20 ng/well of TGF-beta 1 protein with carrier  (R&D systems, final concentration 10 ng/µl after reconstitution) resuspended in 25 ul PBS was added per well. For samples co-cultured with EVs, the media was replaced with 2 ml/well of EV supplemented fresh media at 24 hours (45.2 x 1015 EV particles per well), and again at 48 hours (45.2 x 1015 EV particles per well) after the first EV incubation. PBS control wells were replaced with 2 ml/well of PBS-supplemented fresh media at the same time points. For the TGFβ control, 20 ng/well TGFβ (final concentration 10 ng/ml) was resuspended in 25 µl PBS and the media was replaced with 2 ml/well of TGFβ-supplemented fresh media at the same time points as HOrFs co-cultured with EVs. EVs, PBS, or TGFβ was thus added three times with 24 hour intervals in between (total time of co-culture: 72 hours).

value: oral

value: HOrF

value: human oral fibroblast (HOrF)

value: CAL27 Evs


title: HOrF Cells, CAL27' EVs, Rep 2

description:
column 3 in FPKM matrix
EVCTRL2


title: HepG2 KO Rep2 T0


title: HOrF Cells, CAL27' EVs, Rep 1

description:
column 2 in FPKM matrix
EVCTRL1


title: Patient LIMET162 multiplexed fluorescent in situ RNA hybridization ROI A1

value: Primary tumor

value: PDAC

value: Patient LIMET162


title: HepG2 KO Rep1 T0

value: liver cancer


title: OPCs, Bmal1 WT, ZT12, rep 4


title: Patient LIMET139 multiplexed fluorescent in situ RNA hybridization ROI B2

value: Patient LIMET139


title: HepG2 KO Rep1 T21


title: HOrF Cells, SCC25 EVs, Rep 3

description:
column 7 in FPKM matrix
SCC25-EV3

value: SCC25 Evs


title: OPCs, Bmal1 WT, ZT6, rep 5

value: Forebrain

value: Oligodendrocyte precursor cells


title: OPCs, Bmal1 WT, ZT12, rep 3


title: HOrF Cells, SCC25 EVs, Rep 2

description:
column 6 in FPKM matrix
SCC25-EV2


title: OPCs, Bmal1 WT, ZT6, rep 4


title: HepG2 T21

value: WT


title: HOrF Cells, SCC25 EVs, Rep 1

description:
column 5 in FPKM matrix
SCC25-EV1


title: OPCs, Bmal1 WT, ZT6, rep 3


title: HOrF Cells, SCC9 Evs, Rep 3

description:
column 10 in FPKM matrix
SCC9-EV3

value: SCC9 Evs


title: HOrF Cells, SCC9 EVs, Rep 2

description:
column 9 in FPKM matrix
SCC9-EV2


title: HOrF Cells, SCC9 EVs, Rep 1

description:
column 8 in FPKM matrix
SCC9-EV1


title: OPCs, Bmal1 WT, ZT6, rep 2


title: HOrF Cells, TGFb, Rep 3

description:
column 13 in FPKM matrix
TGFb3

value: TGFb


title: HepG2 T0


title: Patient LPDAC30 multiplexed fluorescent in situ RNA hybridization ROI B2

value: Patient LPDAC30


title: OPCs, Bmal1 WT, ZT6, rep 1


title: Hep3B T21


title: HOrF Cells, TGFb, Rep 1

description:
column 11 in FPKM matrix
TGFb1


title: HOrF Cells, TGFb, Rep 2

description:
column 12 in FPKM matrix
TGFb2


title: HOrF Cells, PBS, Rep 3

description:
Used as the comparator in the differential analysis in each treatment, each processed data; column 7 in FPKM matrix
PBS3

value: PBS (Control)


title: Hep3B T0


title: HOrF Cells, PBS, Rep 1

description:
Used as the comparator in the differential analysis in each treatment, each processed data; column 5 in FPKM matrix
PBS1

value: oral


title: OPCs, Bmal1 WT, ZT0, rep 3


title: HOrF Cells, PBS, Rep 2

description:
Used as the comparator in the differential analysis in each treatment, each processed data; column 6 in FPKM matrix
PBS2

value: HOrF


title: Hep3B KO Rep2 T21

value: KO


title: OPCs, Bmal1 WT, ZT0, rep 2


title: 12_B6Sst1sBach1KO_Mtb2

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using salmon
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each Sample and Matrix table with raw gene counts for every gene and every sample

source_name: Lung cells

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturers’ recommendation.
Illumina stranded mRNA prep and paired end sequencing.

tag: genotyping

value: Sst1s (homozygous) Bach1 KO(homozygous)

tag: timepoint

value: 17 days post-infection

value: Mtb infected

tag: Sex

value: Male

value: single-cell suspension


title: Hep3B KO Rep1 T21

value: liver cancer


title: 14_B6Sst1sBach1KO_Mtb4


title: 10_B6Sst1s_Mtb4


title: OPCs, Bmal1 WT, ZT0, rep 1


title: Hep3B KO Rep2 T0


title: 9_B6Sst1s_Mtb3


title: 8_B6Sst1s_Mtb2


title: 11_B6Sst1sBach1KO_Mtb1


title: 6_B6Sst1sBach1KO_Uni3

value: naive


title: KPC organoid Il1b stimulation 48h single-cell RNA-seq pool

description: 10X Genomics

data_processing:
Fastq files were processed with Cell Ranger (v 4.0.0), using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)

source_name: KPC organoid Il1b stimulation 48h

growth_protocol: KPC organoids were previously established from tumors arising in KPC genetically engineered mouse model (Kras+/LSLG12D Trp53fl/f lp48+/Cre) and were cultured following already published protocols

extract_protocol:
Matrigel domes containing murine KPC organoids were dissolved in Cell Recovery Solution (CRS) (Gibco) for 30 min on ice, manually inverting the tubes every 5 min. After addition of ice-cold basal medium, organoid suspensions was centrifuged and supernatant was removed prior to incubation in TrypLE Express (Gibco) for 20 min on an orbital shaker at 37°C. The resulting cell suspension was collected from the supernatant without interfering with the lower fraction containing larger cellular aggregates, centrifuged, and resuspended in ultrapure BSA [400ug/mL] (Invitrogen).
scRNA-Seq libraries were generated using a microfluidics-based approach on Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v3.1, according to the manufacturers’ instructions.

treatment_protocol: KPC organoids were stimulated with IL-1b (10 ng/mL) for 24 or 48 hours. Controls were left untreated.

value: KPC organoid

value: PDAC

value: Kras+/LSLG12D Trp53fl/f lp48+/Cre

value: IL-1b (10 ng/mL)


title: KPC organoid control 48h single-cell RNA-seq pool

description: 10X Genomics

source_name: KPC organoid control 48h

value: untreated


title: Hep3B KO Rep1 T0


title: 7_B6Sst1s_Mtb1


title: Hep3B_WT_Rep2

data_processing:
Paired-end clean reads were aligned to the reference genome (GRCh38/hg38) using Bowtie2.
Apparent PCR duplicates were removed using samtools
MACS2 peak calling algorithm was used to identify enrichment peaks.
bigWig files were generated using deeptools
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
The unfixed nuclei of these cells were tagged using tn5 transposase (TruePrep DNA Library Prep Kit V2 for Illumina) for 30min at 37 °C
and the resulting library fragments were generated by 10–12 PCR cycles

value: WT


title: 5_B6Sst1sBach1KO_Uni2


title: 4_B6Sst1sBach1KO_Uni1


title: KPC organoid Il1b stimulation 24h single-cell RNA-seq pool

description: 10X Genomics

source_name: KPC organoid Il1b stimulation 24h


title: Hep3B_WT_Rep1


title: KPC organoid control 24h single-cell RNA-seq pool

description: 10X Genomics

source_name: KPC organoid control 24h


title: OPCs, Bmal1 WT, ZT0, rep 4

value: Forebrain

value: Oligodendrocyte precursor cells


title: 3_B6Sst1s_Uni3


title: 2_B6Sst1s_Uni2


title: Hep3B_KO_Rep2

value: ARID1A deficient


title: 1_B6Sst1s_Uni1


title: KPC organoid control 72h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_UT_72h_Sample3
Organoids_KPC_counts_matrix.csv.gz

data_processing:
Reads were aligned using STAR aligner (v STAR_2.5.3a). Read counts matrices were computed using the featureCounts function from Rsubread package (v 2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated counts file (gzipped format)

source_name: KPC organoid control 72h

growth_protocol: KC (DT6606) and KPC (K8484) cell lines were previously established from tumors arising in genetically engineered mouse models carrying the G12D oncogenic mutation in the Kras gene (KrasLSL-G12D/+;Pdx1Cre/WT for KC) and the missense point R720H mutation in the Tpr53 gene (KrasLSL-G12D/+;Tpr53LSL-R270H/+;Pdx1Cre/WT for KPC) and were cultured under standard conditions. KPC organoids were previously established from tumors arising in KPC genetically engineered mouse model (Kras+/LSLG12D Trp53fl/f lp48+/Cre) and were cultured following already published protocols.

extract_protocol:
Total RNA was purified using the ReliaPrep RNA Cell Miniprep System.
RNA-Seq libraries were generated using the Smart-seq2 method with minor modification. Briefly, five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0, assessed for fragment size distribution on an Agilent 4200 TapeStation system.

treatment_protocol: KC and KPC cells were stimulated with IL-1b (10 ng/mL) for 24, 48 or 96 hours. KPC organoids were stimulated with IL-1b (10 ng/mL) for 8, 24, 48 or 72 hours. Controls were left untreated.

value: PDAC tumor organoids


title: KPC organoid control 72h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_UT_72h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: Hep3B_KO_Rep1


title: KPC organoid control 72h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_UT_72h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: 10x multiome (ATAC) on the mouse liver (rep 1)

data_processing:
The generated fastq files were processed with cellranger-arc (v1.0.0) count function, with include introns =True option. Reads were aligned to Mus musculus reference genome (ata-cellranger-arc-mm10-2020-A-2.0.0).
Data was processed as the other multiome samples and combined with the other multiome samples and analyzed using VSN-pipelines (for the snRNA-seq layer) and pycisTopic (for the scATAC-seq layer, using 100 topics).
Assembly: mm10
Supplementary files format and content: TEW__872466__dedf23__Multiome_Liver_CTRL1_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample CTRL1
Supplementary files format and content: TEW__95843a__0f8200__Multiome_Liver_CTRL2_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample CTRL2
Supplementary files format and content: multiome_validation_rna_counts.tsv.gz: tab seperated flat text file containing genes as rows, cells as columns and counts for each gene in each cell as values.
Library strategy: Single-cell Multiome (10X Genomics)

source_name: Liver (P56)

extract_protocol:
We used a modified protocol from the Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (CG000375) from 10x Genomics. Briefly, 100 mg of fresh mouse liver tissue was chopped and transferred to a Dounce homogenizer cylinder containing 1 mL of ice-cold homogenization buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0,1% IGEPAL CA-63, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)). The tissue was homogenized with 5 strokes of pestle A and 10 strokes of pestle B until a homogeneous nuclei suspension was achieved. The resulting homogenate was filtered through a 70-μm cell strainer (Corning). The homogenizer and the filter were rinsed with an additional 0.5 μL of homogenization buffer. The tissue material was spun down at 500 x g for 5 min and the supernatant was discarded. The tissue pellet was resuspended in wash buffer (1% BSA in PBS + 1 U/µlL of Protector RNase inhibitor (Sigma)). Nuclei were stained with 7AAD (Thermo Fisher Scientific) and viability sorted on a BD FACS Fusion into 5 mL low bind Eppendorf tube containing BSA with RNase inhibitor. The sorted nuclei were spun down at 500 x g for 5 min and the supernatant was discarded. Next, the nuclei were permeabilized by resuspending the pellet in 0.1x lysis buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0.1% IGEPAL CA-63, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)) and incubated on ice for 2 min. 1 mL Wash Buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)) was added. The nuclei were spun down at 500 x g for 5 min and the supernatant was discarded. The nuclei pellet was resuspended in diluted nuclei buffer (1x Nuclei buffer Multiome kit (10x Genomics)), 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)).
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. In brief, the single mouse liver nuclei were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanolitre-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 37°C for 45 min, 25°C for 30 min and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). Next quenching reagent (Multiome 10x kit) was used to stop the reaction. After quenching, single-cell droplets were dissolved, and the transposed DNA and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To fill gaps and generate sufficient mass for library construction, the transposed DNA and cDNA were amplified via PCR: 72°C for 5 min; 98°C for 3 min; 7 cycles of 98°C for 20 s, 63°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. The pre-amplified product was used as input for both ATAC library construction and cDNA amplification for gene expression library construction. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 7-9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC-seq library was cleaned up with SPRIselect beads (Beckman Coulter). Barcoded, full-length pre-amplified cDNA was further amplified via PCR: 98°C for 3 min; 6-9 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end- repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 5-16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s. 72°C for 1 min; and hold at 4°C. The sequencing-ready GEX library was cleaned up with SPRIselect beads. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip. All 10x Multiome ATAC libraries were sequenced on NextSeq2000 instruments (Illumina) with the following sequencing parameters: 50 bp read 1 – 8 bp index 1 (i7) – 16 bp index 2 (i5) - 49 bp read 2. All 10x Multiome GEX libraries were sequenced on NovaSeq6000 instruments with the following sequencing parameters: 28 bp read 1 – 10 bp index 1 (i7) – 10 bp index 2 (i5) – 75 bp read 2.

value: Liver (P56)


title: 10x multiome (ATAC) on the mouse liver (rep 2)


title: 10x multiome (RNA) on the mouse liver (rep 1)


title: KPC organoid Il1b stimulation 72h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_IL1B_72h_Sample3
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid Il1b stimulation 72h


title: Bulk ATAC-seq on AML12


title: PML knockdown, MDA231, rep3

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
Sequencing adapters were removed using trimmomatic v0.39.
Trimmed sequence reads were mapped to the human genome assembly GRCh38 (hg38) using the STAR aligner v2.5.3a.
Annotation of genomic features was performed using the featureCounts tool v1.6.4 using the GENCODE v31 Gene transfer format (GTF). Differential gene expression was evaluated in R/BioConductor using the DeSeq2 package.
Assembly: hg38
Supplementary files format and content: tab delimited text of normalized counts

extract_protocol:
RNA was isolated using the RNAeasy mini kit (Qiagen)
RNA libraries were prepared using the TruSeq stranded mRNA protocol (Illumina).

value: Human breast cancer

value: PML knockdown

value: shPML


title: KPC organoid Il1b stimulation 72h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_IL1B_72h_Sample2
Organoids_KPC_counts_matrix.csv.gz