title: GCSFR Pmel, scRNA-seq

city: Stanford

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: 10 X Genomics

data_processing:
The fastq files were generated and demultiplexed by cellranger mkfastq from 10x Genomics, and primary data analysis was performed with Cell Ranger
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: tumor

growth_protocol: tumor infiltrating T cells

extract_protocol:
C57BL/6 mice were inoculated s.c. with B16F10 tumor cells (1 × 106), sublethally lymphodepleted by irradiation on day 7, and received i.v. adoptive transfer of 3 × 106 Pmel T cells (either untransduced or transduced with mo2R, mo4R, mo20R, mo22R, or moGCSFR) on day 8 post tumor followed by i.p. administration of MSA-oIL-2 (2.5 × 104 unit per day) or PBS control every other day until day 16. On day 17, mice were sacrificed, tumors were minced and dissociated using a mouse tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (Cytiva), and then stained with surface markers and DAPI (Thermo Fisher Scientific). Thy1.1+CD8+ or Thy1.1+CD8+ YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for Single cell RNA sequencing.
10x 3' Gene Expression v3.1

treatment_protocol: mouse orthogonal IL2

value: tumor

value: primary cells

value: Pmel-1 TCR transgenic T cells

value: TCR for gp100, orthogonal mouse IL-GCSFR

value: mouse orthogonal IL-2


title: TWGBS batch_C_Col_0,rep1

status: Public on Jun 14 2025

type: SRA

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

country: Austria

institute: GMI

description: Library name: TWGBS_batch_C_Col_0_rep1

library_source: genomic

data_processing:
Libraries for cdca7α/β and ddm1 mutants (Fig. 2, 3) were randomly subsampled to 30 million reads to improve depth homogeneity, since there were up to 2-fold more reads in some samples. The data were analyzed with the nfcore methylseq pipeline v2.3.0 (https://nf-co.re/methylseq) (Ewels et al., 2020) with Nextflow (v22.10.7). Cytosine positions covered by fewer than 3 reads (--meth_cutoff 3) were excluded. Tagmentation creates gaps in the double-stranded DNA which are later filled by unmethylated cytosines during gap repair. These nucleotides were excluded from the analysis by trimming reads with the "clip" and "ignore" options, using M-bias plots to ensure the removal of unmethylated fragment ends. The parameters were as follow: --meth_cutoff 4 --comprehensive --cytosine_report --clip_r1 14 --three_prime_clip_r1 4 --three_prime_clip_r2 2 --ignore_3prime_r2 17. Note that the unmethylated cytosines are incorporated at the 5' end of read 2, while the options mentioned above suggest we ignored the 3' end of read 2 instead, but methylseq v2.3.0 had an issue which made it clip the wrong end of read 2 (see https://github.com/nf-core/methylseq/issues/299). Using M-bias plots, we noticed a 5' bias on read 1 that resembled the Tn5 sequence bias (Wolpe et al. 2023), and removed it by clipping 14 nucleotides at the 5' end of read 1. We also excluded additional small methylation biases at the 3' end of read 1 and read 2.
Assembly: TAIR10
Supplementary files format and content: methylation ratios provided for CG, CHG and CHH as bigwig files

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 31-day-old rosette leaves

growth_protocol: grown in soil in long days at 21°C in a climatic chamber

extract_protocol:
Genomic DNA was extracted from rosette leaves with the DNeasy Plant Pro kit (Qiagen, reference 69206), following the manufacturer’s instructions.
Illumina libraries of sodium bisulfite-converted DNA were prepared with a tagmentation-based approach (Wang et al. 2013) with modifications (Montgomery and Berger, 2023, bioRxiv). Briefly, we tagmented 50 ng of DNA with Tn5 (Molecular Biology Services, IMP, Vienna, Austria). Tagmented DNA was purified with the Zymo DNA Clean and Concentrator kit (Zymo Research) instead of SPRI beads. After oligonucleotide replacement, gap repair, and purification, we used the entirety of the eluted DNA for bisulfite conversion, which was performed with the EZ DNA Methylation-Gold Kit from Zymo (reference D5006). The rest of the protocol was performed as indicated by Wang et al (2013). Directional libraries were amplified with Nextera-compatible unique dual indices and sequenced on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.

tag: tissue

value: 31-day-old rosette leaves

tag: genotype

tag: batch

value: C


title: 22R Pmel TILs, scRNA-seq

country: USA

description: 10 X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

value: TCR for gp100, orthogonal mouse IL-22R

tag: treatment


title: L1EID2100339-KD3.R1.raw.fastq.gz

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: blood

growth_protocol: LP-1 were cultured in RPMI-1640 medium with 15% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using short-hairpin RNA (shRNA) depleted RNF5 expression in LP-1 cells

value: blood

value: tumor cell

value: RNF5 KD


title: L1EID2100338-KD2.R1.raw.fastq.gz


title: MEF PUS10KO small RNA-seq #1

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
The raw sequence data were trimmed the 3’ adaptor sequence (TGGAATTCTCGGGTGCCAAGG) by cutadapt v2.9 with parameter -m set to 23. The sequence reads were aligned to an rRNA reference using Bowtie v.1.2.2.
The unaligned reads were collected and the rRNA alignments were discarded to reduce rRNA contamination.
For tRNA analysis, Bowtie was used to map the reads to tRNA sequences from GtRNAdb2. The data was quantified using samtools idxstats and read counts generated for each tRNA isoacceptor were combined.
For tRNA fragments (tRFs) analysis, the reads were annotated using MINTmap software (Loher et al., 2017). Each fragment sequence was grouped according to tRNA isoacceptor, origin (5′, 3′ or internal) and length (fragment or half) according to MINTmap annotation. DESeq2 was used to determine differentially expressed tRFs in WT and PUS10-KO cells.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for tRFs

source_name: Mouse embryonic fibroblasts

extract_protocol:
Total DNA-free RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). Following, RNA quality assessment by Bioanalyzer RNA 6000 Nano assay (Agilent).
Libraries were prepared using NEXTFLEX®Small RNA-Seq Kit v4 (Perkin-Elmer) according to manufacturer’s instructions. Library quality was verified by Bioanalyzer High Sensitivity DNA Analysis (Agilent). Sequencing was carried out on the Illumina NextSeq 500 System in a single-read approach.

value: Mouse embryonic fibroblasts

value: PUS10 KO


title: Acinar_ATF3-/-KRAS_repl 3

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

description: Batch acini2

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mouse genome mm10 and sorted by coordinate using STAR 2.7.9a
Gene counts were generated using the featureCounts function of the Subread aligner v2.0.3
Subsequent differential expression analysis was performed using the DESeq2 v1.38.3
Assembly: mm10
Supplementary files format and content: tab delimited format (txt) includes raw counts for each sample.

source_name: Pancreas

extract_protocol:
RNA was isolated from pancreatic tissue and isolated acinar cells 22 days after initial TX gavage using Trizol (ThermoFisher Scientific, 15596018) and the PureLink RNA mini kit (ThermoFisher Scientific, 12183018A). RNA from organoids was isolated using RNeasy Mini Kit (Qiagen, cat #74104).
Illumina NextSeq High Output 150 cycle sequencing kit was used for library making following rRNA reduction.

value: Pancreas

value: Tamoxifen oral gavage


title: MEF control small RNA-seq #4

value: WT


title: TWGBS batch_C_cdca7ab_1_G8,rep2

description: Library name: TWGBS_batch_C_cdca7ab_1_G8_rep2


title: TWGBS batch_C_cdca7ab_1_G8,rep1

description: Library name: TWGBS_batch_C_cdca7ab_1_G8_rep1


title: MEF PUS10KO small RNA-seq #2


title: 20R Pmel TILs, scRNA-seq

description: 10 X Genomics

value: TCR for gp100, orthogonal mouse IL-20R


title: MEF control small RNA-seq #3


title: 4R Pmel TILs, scRNA-seq

description: 10 X Genomics

value: tumor

value: TCR for gp100, orthogonal mouse IL-4R


title: Pmel TILs, scRNA-seq

description: 10 X Genomics

value: primary cells

value: Pmel-1 TCR transgenic T cells

value: TCR for gp100


title: MEF control small RNA-seq #2


title: TWGBS batch_C_cdca7ab_1_G3,rep1

description: Library name: TWGBS_batch_C_cdca7ab_1_G3_rep1

value: 31-day-old rosette leaves


title: TWGBS batch_C_cdca7ab_1_G3,rep2

description: Library name: TWGBS_batch_C_cdca7ab_1_G3_rep2

value: C


title: MEF control small RNA-seq #1


title: PU 3

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

institute: Haijun Tu

data_processing:
The image data measured by the high-throughput sequencer is converted into sequence data (reads) by Casava base recognition.
It mainly includes the removal of reads with adapter, the removal of reads containing n (n indicates that the base information cannot be determined), and the removal of low-quality reads (the base number with qphred < =20 accounts for more than 50% of the whole read length).
The raw gene expression matrix was imported into the R environment for further processing and analysis. Genes with low read counts (less than 50 reads in all eight libraries) were filtered out.
Reads were mapped to the worm reference genome (Wbcel235) using HISAT2. Uniquely mapped reads were summarised to Worm Base annotated genes using feature Counts.
Assembly: Wbcel235
Supplementary files format and content: ON-1_1.fq, ON-1_2.fq, ON-2_1.fq, ON-2_2.fq, ON-3_1.fq and ON-3_2.fq files include complete raw data for one sample.
Supplementary files format and content: processed data files for unc-17 text file include RPKM values for all samples

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Transferring L4 stage worms, which were maintained in NGM plate at 20C, to new plate  at  25C.

extract_protocol:
RNA was harvested using TransZol  Up Plus RNA Kit(Thermo Fisher).
>=1ug total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Using pathogenic bacterial PA14 to infect the WT N2 and unc-17(e245) mutant worms.

value: whole body

value: Hermaphrodite

value: PA14 infection


title: C57BL/6JJcl, Sorbitol5, Day0

city: Minato ku

first: Yun-Gi

last: Kim

country: Japan

institute: Kitasato University

description: Library name: Sorbitol5

data_processing:
Primary analysis: Raw sequencing data were mapped to murine reference genomes using HISAT2, followed by adapter trimming and quality assessment using Trim Galore.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text files containing gene expression values (FPKM/TPM) with gene IDs and corresponding expression levels for each sample.
Supplementary files format and content: Differential expression analysis results including log2 fold changes, p-values, and adjusted p-values for significantly expressed genes.

source_name: Colon

growth_protocol: Mice were housed under standard laboratory conditions with ad libitum access to food and water. Environmental conditions were maintained at 22±2°C with a 12-hour light/dark cycle.

extract_protocol:
The harvested colon was immersed in RNAlater solution (Invitrogen) and stored at 4°C. For RNA extraction, the colon tissue was processed using PureLink™ RNA mini Kit (Invitrogen) according to the manufacturer's instructions.
RNA sequencing library preparation and sequencing were performed at BGI (Japan) following standard protocols for RNA-seq library construction.

treatment_protocol: Mice were subjected to dietary intervention (ad libitum feeding conditions). Colon samples were collected at specified time points for RNA extraction.

value: Colon


title: MEFs iPUS10 rep 2, iCLIP

data_processing:
The reads were classified into samples according to sample-specific barcodes. The barcodes and UMIs, 5nucleotide unique sequence identifiers introduced during RT step, were removed and appended to the read name using UMI-tools.
The sequences were trimmed the 3’ adaptor sequence (AGATCGGAAGAGCGGTTCAG) by cutadapt v2.9 (Martin M 2011) with parameter -m set to 18 and mapped to mouse genome mm10 using STAR v2.5.2b (Dobin A et al. 2013) with the following parameters: --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 (unique mapping) or --outFilterMultimapNmax 100 (multiple mapping).
PCR duplicates were removed based on UMIs using UMI-tools.
Peak identification was performed using Piranha v1.2.1. Peaks were annotated using Gencode, miRBase and GtRNAdb2.
Assembly: mm10
Supplementary files format and content: bigwig files

extract_protocol:
Cells were harvested and lysed in iCLIP lysis buffer, sonicated, then extracts were treated with RNase I and TURBO Dnase. Lysates were cooled down on ice, centrifuged and supernatants were collected. Supernatants were incubated with pre-washed anti-FLAG magnetic beads. Lysis buffer was applied to the samples. RNA digestion was performed.
Membrane’s fragments containing protein-RNA complexes were excised and incubated with PK buffer for 30 minutes at 37oC shaking at 1100 rpm. Reactions were stopped by adding an equal amount of PK buffer supplemented with 7 M urea. RNA was extracted using Phase Lock Gel Heavy tube (VWR) and ethanol-precipitation. cDNA synthesis was performed using Superscript III (Thermo Fisher). cDNA was circularized using CircLigase II (Epicenter), annealed with 0.25 μM Cut oligo and digested with BamHI (Thermo Fisher). Digested cDNA was ethanol-precipitated and resuspended in 21 μL of water. 1 μL of cDNA was used for PCR amplification using Accuprime Supermix I with 18-21 PCR cycles. Sequencing was carried out on the Illumina NextSeq 500 System in a single-read approach.

value: Mouse embryonic fibroblasts


title: PU 2


title: C57BL/6JJcl, Sorbitol4, Day0

description: Library name: Sorbitol4


title: PU 1


title: PN 3

value: OP50 fed


title: MEFs iPUS10 rep 1, iCLIP


title: C57BL/6JJcl, Sorbitol3, Day0

description: Library name: Sorbitol3


title: MEFs PUS10 KO, iCLIP

value: PUS10 KO


title: MEF PUS10KO RNA-seq #4

data_processing:
RNA-seq datasets were aligned to the mm10 annotation ofmouse genomeusing STAR v2.7.8a with the parameter outFilterMultimapNmax set to 1
Bioconductorpackage DESeq2 was used to analyzedifferential gene expression.
Gene expression levels, log2of normalized counts by DESeq2, were used to input into GSEA v4.3.2 for gene set enrichment analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each Sample
Supplementary files format and content: tab-delimited text file includes normalized abundance by DESeq2 for each Sample

growth_protocol: MEF cells were grown in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum (company) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
Total DNA-free RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). RNA quality was assessed by Bioanalyzer RNA 6000 Nano assay (Agilent).
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold (Illumina) according to manufacturer’s instructions. Library quality was verified by Bioanalyzer High Sensitivity DNA Analysis (Agilent). Sequencing was carried out on the Illumina NextSeq 500 System in a paired-end approach.


title: PN 2


title: C57BL/6JJcl, Sorbitol2, Day0

description: Library name: Sorbitol2


title: C57BL/6JJcl, Sorbitol1, Day0

description: Library name: Sorbitol1


title: MI 7d 73

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: C57BL/6  Mouse withMI treated for 7days

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: C57BL/6  Mouse withMI treated for 7days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: 10-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized via an overdose of pentobarbital on days 1, 3, and 7 post-myocardial infarction (MI). Total RNA was extracted from atrial tissues at each time point using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Ten-week-old male C57BL/6 wild-type mice were subjected to ligation of the left anterior descending coronary artery (LAD) and were euthanized on days 1, 3, and 7 post-surgery for further analysis.

tag: strain

tag: gender

value: Male

value: atrial


title: MEF PUS10KO RNA-seq #3


title: C57BL/6JJcl, Sorbitol6, Day0

description: Library name: Sorbitol6


title: MI 3d 33

description: C57BL/6  Mouse withMI treated for 3days

source_name: C57BL/6  Mouse withMI treated for 3days


title: MI 3d 32

description: C57BL/6  Mouse withMI treated for 3days


title: C57BL/6JJcl, Control6, Day0

description: Library name: Control6


title: OU 3


title: MI 7d 72

description: C57BL/6  Mouse withMI treated for 7days


title: MEF PUS10KO RNA-seq #2


title: MI 1d 14

description: C57BL/6  Mouse withMI treated for 1day

source_name: C57BL/6  Mouse withMI treated for 1day


title: MI 7d 71

description: C57BL/6  Mouse withMI treated for 7days


title: MI 3d 31

description: C57BL/6  Mouse withMI treated for 3days


title: MI 3d 34

description: C57BL/6  Mouse withMI treated for 3days


title: MEF PUS10KO RNA-seq #1


title: MI 1d 12

description: C57BL/6  Mouse withMI treated for 1day


title: C57BL/6JJcl, Control4, Day0

description: Library name: Control4


title: OU 1


title: PN 1


title: C57BL/6JJcl, Control3, Day0

description: Library name: Control3


title: ON 3


title: MI 7d 74

description: C57BL/6  Mouse withMI treated for 7days


title: MEF control RNA-seq #4

value: WT


title: MEF control RNA-seq #3


title: ON 2


title: C57BL/6JJcl, Control5, Day0

description: Library name: Control5


title: C57BL/6JJcl, Control2, Day0

description: Library name: Control2


title: MI 1d 11

description: C57BL/6  Mouse withMI treated for 1day


title: MEF control RNA-seq #2


title: OU 2


title: Con2

description: C57BL/6  Mouse with sham surgery

source_name: C57BL/6  Mouse with sham surgery


title: MI 1d 13

description: C57BL/6  Mouse withMI treated for 1day


title: Con3

description: C57BL/6  Mouse with sham surgery


title: C57BL/6JJcl, Control1, Day0

description: Library name: Control1


title: MEF control RNA-seq #1


title: healthy.child_s322

status: Public on Jun 13 2025

city: Fukuoka

first: Itaru

last: Komine

address: 3-1-1 Maidashi Higashi-ku

institute: Kyushu University

description: Library name: sample6

data_processing:
DNBSEQ-G400RS v1.20.0
NextSeq 2000
NextSeq 500
NovaSeq
Assembly: GRCh38.p14 (hg38)
Supplementary files format and content: tab-delimited text files include values for each sample

source_name: dental pulp

extract_protocol:
SHED was frozen and RNA was extracted with Trisol regant.
RNA libraries for RNA-seq were prepared using QIAseq UPX 3' Transcriptome Kit and MGIEasy Universal Library Conversion Kit follwing manufactured protcols.

value: dental pulp

value: SHED

value: mesenchymal stem cell


title: ON 1


title: Down.synd_s719

description: Library name: sample3


title: Down.synd_s109

description: Library name: sample2


title: healthy.child_s312

description: Library name: sample5


title: healthy.child_s082

description: Library name: sample4


title: S370D_2

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Reads that aligned to the mouse genome were then removed and the unaligned reads were mapped to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: mm10
Supplementary files format and content: raw counts in tab-delimited text file

source_name: mouse embryonic fibroblasts with Pten S370D mutation

growth_protocol: MEFs were generated from independent E13.5 embryos and expanded at 3% O2 in DMEM medi-um supplemented with 10% heat-inactivated fetal bovine serum, l-glutamine, nonessential amino acids, ß-mercaptoethanol, gentamicin and sodium pyruvate.

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

value: Pten S370A mutation

value: mouse embryonic fibroblasts


title: S370D_4


title: S370D_3


title: S370A_3

source_name: mouse embryonic fibroblasts with Pten S370A mutation


title: Down.synd_s102

description: Library name: sample1


title: S370A_2


title: S370A_1


title: WT_3

source_name: wildtype mouse embryonic fibroblasts

value: wild type


title: S370D_1


title: S370A_4


title: WT_1


title: Met-3-1126

first: Han

last: Ding

address: No.154 Anshan Road

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping to Rattus norvegicus genomes using miRDeep2's mapper.pl
The differentially expressed miRNA was regarded when∣log2 (fold change)∣＞1 and p value＜0.05 by DEseq2.
Assembly: Genome_build: rn6

organism: Rattus norvegicus

source_name: Spinal cord

growth_protocol: Rat spinal cord neural stem cells were cultured in DMEM/F-12  supplemented with 15 mM HEPES, 1.5% D-glucose, 67 μg/mL penicillin/streptomycin, 2 mM L-glutamine, 20 ng/mL EGF, 20 ng/mL bFGF, 5 μg/mL heparin, 25 μg/mL bovine insulin and TPPS at 37°C and 8.5% CO2.

extract_protocol:
Total RNA in exosomes was extracted by TRIzol.
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction

treatment_protocol: NSCs at the beginning of the proliferating or differentiating stage were treated with 1 μM metformin, collected the conditioned medium and isolated NSC-derived exosomes.

value: Spinal cord

value: Neural stem cell

value: Metformin


title: Met-4-1130


title: Con4

description: C57BL/6  Mouse with sham surgery


title: Met-2-1202


title: control-4-1130

value: No


title: Met-1-1128


title: control-3-1126


title: control-2-1202


title: Con1

description: C57BL/6  Mouse with sham surgery


title: control-1-1128


title: BCPAP_40C

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: Library name: BCPAP_40C

data_processing:
FastQC/MultiQC, Trimmomatic v0.38, mapping with HISHAT2 v2.1.0, quantification using featureCounts v2.0.0
Assembly: GRCh38
Supplementary files format and content: a csv file includes TPM values for each sample

source_name: B-CPAP

growth_protocol: Thyroid cancer cell lines TPC-1 and B-CPAP were grown in T25 flasks submerged at 37 or 40 degrees Celsius for 15 minutes.

extract_protocol:
RNA from cell lysates was extracted using RNeasy Plus Kits (QIAGEN)
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2

value: B-CPAP

value: T25 flasks submerged at 40 degrees Celsius for 24 h


title: TPC1_40C

description: Library name: TPC1_40C


title: BCPAP_37C

description: Library name: BCPAP_37C

value: T25 flasks submerged at 37 degrees Celsius for 24 h


title: TPC1_37C

description: Library name: TPC1_37C


title: HCT116 dTag-CLNS1A Knock-In, DMSO-treated, Rep 4

city: Cambridge

first: Colin

middle: Emory

last: Fowler

state: MA

address: 500 Main Street

department: Biology

institute: Massachusetts Institute of Technology

description: Library name: 239092

data_processing:
To generate counts for alternative splicing analysis, raw reads were mapped to the human GRCh38 genome using STAR (--runMode alignReads --runThreadN 16 --sjdbOverhang 149 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic) and Bowtie (-n 1 -l 30 -e 70 -t -p 4 -m 1 -X 500 -S).
Mapped reads were filtered using Bedtools to remove reads overlapping expressed repeats from the UCSC genome browser RNA repeats and Gencode hg38 and coding exons annotated in the Gencode hg38 annotations. Alternative and constitutive classifications were performed using custom Python scripts and are agnostic to existing annotations other than known gene boundaries. All three cell lines were run in parallel to ensure consistency between annotations. Alternative splicing events were quantified using DEXSeq.
Assembly: Gencode GRCh38 v33 and Gencode GRCm38 vM24
Supplementary files format and content: genes.results files are outputted raw count files from RSEM for each gene.
Supplementary files format and content: isoform.results files are outputted raw count files from RSEM for each isoform (Consensus/Coding or DI).
Supplementary files format and content: DEXSeq files are outputted exon count files from DEXSeq.
Supplementary files format and content: Supplementary files are gff files needed for DEXSeq alternative splicing analysis.

molecule: polyA RNA

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s media (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Η23 cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Cells were routinely tested for mycoplasma and were found to be negative.

extract_protocol:
For whole cell lysates, following 3-day treatment with either DMSO (vehicle), PRMT5i, or dTag-13, cells were harvested by scraping. RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) according to manufacturer’s instructions, including the optional DNaseI addition to remove contaminating gDNA (Qiagen, 79254). For fractionated cells, after 3 days in drug, cells were harvested via trypsinization, pelleted, and separated into nuclear and cytoplasmic fractions. Briefly, cell pellets were resuspended in cytoplasmic lysis buffer [0.15% (v/v) NP40, 10 mM Tris (pH7), 150 mM NaCl] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then incubated on ice for 5 minutes. Cell lysate was layered on top of sucrose buffer [0 mM Tris (pH7), 150 mM NaCl, 25% (w/v) sucrose] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then centrifuged at 16,000 x g for 10 minutes at 4 °C. The supernatant contains the cytoplasmic fraction and was harvested for RNA extraction. The remaining pellet contains the nuclear fraction and was washed twice with 800 μL cold PBS, centrifuging at 16,000 x g for 1 minute at 4°C after each wash. The pellet was resuspended in cold RIPA buffer [50 mM Tris (pH 8), 150 mM NaCl, 1% (v/v) NP-40, 0.5% sodium deoxycholate, and 0.1% (w/v) SDS] supplemented with 10 U SUPERase.IN (ThermoFisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Lysate was incubated for 30 minutes on ice, with vortexing every 10 minutes, and then pelleted at 16,000 x g for 10 minutes at 4°C. The supernatant contains the nuclear fraction and was harvested for RNA extraction. The RNA from the nuclear and cytoplasmic fractions were extracted using TRIzol Reagent (Thermo Fisher, 15596026) according to manufacturer’s instructions. Briefly, to each aqueous fraction, 0.5 mL of isopropanol and 1 mL of TRIzol Reagent was added, followed by an incubation on ice for 10 minutes. Samples were then centrifuged for 10 minutes at 12,000 x g at 4 °C, pellets were washed in 1 mL 75% ethanol, and centrifuged again for 5 minutes at 7,500xg at 4 °C. Pellets were air dried for 10 minutes and resuspended in RNase-free water.
RNA-Seq libraries were prepared using the NEB Ultra II Directional RNA Kit with Poly(A) Selection per the manufacturer's protocol.

treatment_protocol: Cells were grown in the presence of PRMT5 inhibitor, dTag-13, or vehicle control.

value: dTag-CLNS1A Knock-In

value: DMSO

tag: time

value: Day 3


title: HCT116 dTag-CLNS1A Knock-In, dTag13-treated, Rep 3

description: Library name: 239095

value: 1 μM dTag-13


title: HCT116 dTag-CLNS1A Knock-In, dTag13-treated, Rep 1

description: Library name: 239093


title: HCT116 dTag-CLNS1A Knock-In, dTag13-treated, Rep 2

description: Library name: 239094


title: HEK293T dTag-CLNS1A Knock-In, dTag13-treated, Rep 3

description: Library name: 239087


title: HCT116 dTag-CLNS1A Knock-In, DMSO-treated, Rep 1

description: Library name: 239089


title: WT_4


title: HCT116 dTag-CLNS1A Knock-In, DMSO-treated, Rep 2

description: Library name: 239090


title: HEK293T dTag-CLNS1A Knock-In, DMSO-treated, Rep 2

description: Library name: 239082


title: HEK293T dTag-CLNS1A Knock-In, DMSO-treated, Rep 4

description: Library name: 239084


title: HEK293T dTag-CLNS1A Knock-In, DMSO-treated, Rep 3

description: Library name: 239083


title: CAL51 dTag-CLNS1A Knock-In, dTag13-treated, Rep 3

description: Library name: 239079


title: CAL51 dTag-CLNS1A Knock-In, dTag13-treated, Rep 4

description: Library name: 239080


title: WT_2


title: HEK293T dTag-CLNS1A Knock-In, dTag13-treated, Rep 1

description: Library name: 239085


title: CAL51 dTag-CLNS1A Knock-In, DMSO-treated, Rep 3

description: Library name: 239075


title: CAL51 dTag-CLNS1A Knock-In, DMSO-treated, Rep 1

description: Library name: 239073


title: HEK293T, JNJ-treated, Rep 4

description: Library name: 239072

value: WT


title: HEK293T, JNJ-treated, Rep 3

description: Library name: 239071


title: CAL51 dTag-CLNS1A Knock-In, dTag13-treated, Rep 2

description: Library name: 239078


title: CAL51 dTag-CLNS1A Knock-In, dTag13-treated, Rep 1

description: Library name: 239077


title: CAL51 dTag-CLNS1A Knock-In, DMSO-treated, Rep 4

description: Library name: 239076


title: CAL51 dTag-CLNS1A Knock-In, DMSO-treated, Rep 2

description: Library name: 239074


title: HEK293T, DMSO-treated, Rep 3

description: Library name: 239067


title: HEK293T, JNJ-treated, Rep 2

description: Library name: 239070


title: HEK293T, DMSO-treated, Rep 4

description: Library name: 239068


title: HEK293T, DMSO-treated, Rep 1

description: Library name: 239065


title: CAL51, JNJ-treated, Rep 4

description: Library name: 239064


title: HEK293T, DMSO-treated, Rep 2

description: Library name: 239066


title: HEK293T dTag-CLNS1A Knock-In, dTag13-treated, Rep 2

description: Library name: 239086


title: CAL51, JNJ-treated, Rep 3

description: Library name: 239063


title: CAL51, DMSO-treated, Rep 2

description: Library name: 239058


title: CAL51, JNJ-treated, Rep 1

description: Library name: 239061


title: U87, cytoplasmic fraction, DMSO-treated, Rep 3

description: Library name: 239051

value: DMSO, cytoplasmic fraction


title: U87, cytoplasmic fraction, JNJ-treated, Rep 4

description: Library name: 239056

value: 10 nM JNJ-64619178, cytoplasmic fraction


title: U87, cytoplasmic fraction, JNJ-treated, Rep 1

description: Library name: 239053


title: CAL51, DMSO-treated, Rep 3

description: Library name: 239059


title: HEK293T, JNJ-treated, Rep 1

description: Library name: 239069


title: U87, nuclear fraction, JNJ-treated, Rep 3

description: Library name: 239047

value: 10 nM JNJ-64619178, nuclear fraction


title: U87, cytoplasmic fraction, DMSO-treated, Rep 2

description: Library name: 239050


title: U87, nuclear fraction, JNJ-treated, Rep 2

description: Library name: 239046


title: U87, cytoplasmic fraction, JNJ-treated, Rep 3

description: Library name: 239055


title: U87, cytoplasmic fraction, DMSO-treated, Rep 4

description: Library name: 239052


title: U87, nuclear fraction, DMSO-treated, Rep 4

description: Library name: 239044

value: DMSO, nuclear fraction


title: U87, nuclear fraction, DMSO-treated, Rep 2

description: Library name: 239042


title: U87, nuclear fraction, DMSO-treated, Rep 1

description: Library name: 239041


title: U87, nuclear fraction, DMSO-treated, Rep 3

description: Library name: 239043


title: U87, nuclear fraction, JNJ-treated, Rep 1

description: Library name: 239045


title: U87, cytoplasmic fraction, DMSO-treated, Rep 1

description: Library name: 239049


title: RPE, JNJ-treated, Rep 4

description: Library name: 239040


title: RPE, JNJ-treated, Rep 1

description: Library name: 239037


title: U87, nuclear fraction, JNJ-treated, Rep 4

description: Library name: 239048


title: U87, cytoplasmic fraction, JNJ-treated, Rep 2

description: Library name: 239054


title: RPE, DMSO-treated, Rep 4

description: Library name: 239036


title: CAL51, DMSO-treated, Rep 1

description: Library name: 239057


title: CAL51, DMSO-treated, Rep 4

description: Library name: 239060


title: CAL51, JNJ-treated, Rep 2

description: Library name: 239062


title: RPE, JNJ-treated, Rep 2

description: Library name: 239038


title: RPE, DMSO-treated, Rep 2

description: Library name: 239034


title: H23, JNJ-treated, Rep 1

description: Library name: 239029


title: H23, JNJ-treated, Rep 2

description: Library name: 239030


title: RPE, DMSO-treated, Rep 3

description: Library name: 239035


title: H23, JNJ-treated, Rep 3

description: Library name: 239031


title: RPE, DMSO-treated, Rep 1

description: Library name: 239033


title: H23, DMSO-treated, Rep 4

description: Library name: 239028


title: PANC1, JNJ-treated, Rep 4

description: Library name: 239024


title: PANC1, DMSO-treated, Rep 3

description: Library name: 239019


title: H23, DMSO-treated, Rep 3

description: Library name: 239027


title: PANC1, DMSO-treated, Rep 4

description: Library name: 239020


title: H23, DMSO-treated, Rep 2

description: Library name: 239026


title: H23, DMSO-treated, Rep 1

description: Library name: 239025


title: PANC1, JNJ-treated, Rep 2

description: Library name: 239022


title: PANC1, JNJ-treated, Rep 3

description: Library name: 239023


title: H23, JNJ-treated, Rep 4

description: Library name: 239032


title: RPE, JNJ-treated, Rep 3

description: Library name: 239039


title: PANC1, DMSO-treated, Rep 2

description: Library name: 239018


title: PANC1, DMSO-treated, Rep 1

description: Library name: 239017


title: HCT116, JNJ-treated, Rep 1

description: Library name: 239013


title: HCT116, JNJ-treated, Rep 2

description: Library name: 239014


title: HCT116, DMSO-treated, Rep 4

description: Library name: 239012


title: HCT116, JNJ-treated, Rep 4

description: Library name: 239016


title: HCT116, DMSO-treated, Rep 2

description: Library name: 239010


title: U87, JNJ-treated, Rep 4

description: Library name: 239008


title: HCT116, DMSO-treated, Rep 1

description: Library name: 239009


title: U87, JNJ-treated, Rep 3

description: Library name: 239007


title: U87, DMSO-treated, Rep 4

description: Library name: 239004


title: U87, DMSO-treated, Rep 3

description: Library name: 239003


title: HCT116, DMSO-treated, Rep 3

description: Library name: 239011


title: U87, JNJ-treated, Rep 2

description: Library name: 239006


title: PANC1, JNJ-treated, Rep 1

description: Library name: 239021


title: U87, DMSO-treated, Rep 2

description: Library name: 239002


title: U87, DMSO-treated, Rep 1

description: Library name: 239001


title: K562, IgG, replicate 2, CUT&Tag

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: Library name: CT_K562_IgG_rep2

data_processing:
Reads were aligned using bowtie2 and quantification was performed using deepTools.
Assembly: hg38
Supplementary files format and content: bigwig files normalised as RPKM
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed on 100,000 K562 cells using the CUTANA CUT&Tag kit (EpiCypher) following the manufacturer's instructions.
CUT&Tag

value: Wild-type

value: IgG (EpiCypher, #13-0042)


title: K562, H1.4 KO, H1.4, CUT&Tag

description: Library name: CT_K562_H1.4_KO_H1.4

value: H1.4 KO


title: HCT116, JNJ-treated, Rep 3

description: Library name: 239015


title: K562, H1.5, replicate 2, CUT&Tag

description: Library name: CT_K562_H1.5_rep2


title: K562, H3K9me3, CUT&Tag

description: Library name: CT_K562_H3K9me3

value: H3K9me3 (Abcam, #ab8898)


title: K562, H1.5 KO, H1.5, CUT&Tag

description: Library name: CT_K562_H1.5_KO_H1.5

value: H1.5 KO


title: K562, H1.4, replicate 3, CUT&Tag

description: Library name: CT_K562_H1.4_rep3


title: K562, H1.3, replicate 2, CUT&Tag

description: Library name: CT_K562_H1.3_rep2


title: K562, H1.4, replicate 2, CUT&Tag

description: Library name: CT_K562_H1.4_rep2


title: V5, replicate 2, CUT&RUN

description: Library name: CR_K562_V5_rep2

data_processing:
Reads were aligned using bowtie2 and quantification was performed using deepTools.
Assembly: hg38
Supplementary files format and content: bigwig files normalised as RPKM
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed on 500,000 K562 cells using the CUTANA CUT&RUN kit (EpiCypher) following the manufacturer's instructions.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina


title: K562, H1.2, replicate 2, CUT&Tag

description: Library name: CT_K562_H1.2_rep2


title: K562, H1.3 KO, H1.3, CUT&Tag

description: Library name: CT_K562_H1.3_KO_H1.3

value: H1.3 KO


title: V5-CRAMP1dDomII CUT&RUN

description: Library name: CR_K562_V5-dDomII

value: Wild-type expressing V5-CRAMP1dDomII


title: V5-CRAMP1dSANT, CUT&RUN

description: Library name: CR_K562_V5-dSANT

value: Wild-type expressing V5-CRAMP1dSANT


title: K562, H1.2 KO, H1.2, CUT&Tag

description: Library name: CT_K562_H1.2_KO_H1.2

value: H1.2 KO


title: V5-CRAMP1, replicate 2, CUT&RUN

description: Library name: CR_K562_V5-CRAMP1_rep2

value: Wild-type expressing V5-CRAMP1


title: V5-CRAMP1dUBL CUT&RUN

description: Library name: CR_K562_V5-dUBL

value: Wild-type expressing V5-CRAMP1dUBL


title: U87, JNJ-treated, Rep 1

description: Library name: 239005

value: Day 3


title: H358_MEKi_Replicate1

city: Salt Lake City

first: Gabriela

last: Fort

state: UT

address: 2000 Circle of Hope Drive

institute: Huntsman Cancer Institute, University of Utah

description: RNAseq

data_processing:
Optical duplicates were removed from Fastq files using Clumpify v38.34.
Adaptor sequences were trimmed using Cutadapt v3.5 with a minimum overlap of 6 bp and minimum trimmed read length of 20.
Reads were aligned to the reference using STAR v2.7.6a in two pass basic mode.
Mapped reads were assigned to annotated genes using featureCounts v1.6.3 in paired-end mode.
Raw counts were filtered to remove features with zero counts and features with five or fewer reads in every sample.
Assembly: mm10; for murine 1027B and 3311 MEKi experiments, and 3154 Hnf4a deletion experiments
Assembly: mm39; for murine 3154 MRTX1133 +/- Hnf4a experiment
Assembly: hg38; for all human samples
Supplementary files format and content: tab-delimited text files with raw counts for each experiment

growth_protocol: Organoid cultures were grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013). H358 cells were cultured in RPMI/10% FBS. H1651 cells were cultured in Advanced DMEM F-12/10% FBS/10mM HEPES. 3311 cells were cultured in DMEM/10% FBS.

extract_protocol:
RNA was isolated via Trizol-chloroform extraction followed by column-based purification. The aqueous phase was brought to a final concentration of 35% ethanol, and RNA was purified using the PureLink RNA Mini kit according to the manufacturer’s instructions (ThermoFisher Scientific).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA isolation. Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: For Hnf4a deletion RNA-seq, 3154 organoids were treated with 2mM 4OHT (or ethanol) for 2 days to delete Hnf4a, and RNA was harvested 2 weeks later. For H1651 RNA-seq, H1651 cells harboring lentiviral HNF4α overexpression construct were treated with 1μg/mL doxycycline for 7 days. For MEKi RNA-seq, 3311 cells were treated with 50nM Trametinib for 48h, 1027B organoids were treated with 10nM Trametinib or 20nM MRTX1133 for 48h, H358 cells and H1651 cells were treated with 20nM Trametinib for 48h. For 3154 MEKi/Hnf4a deletion RNA-seq, 3154 organoids were treated with 3nM MRTX1133 and/or 4OHT to delete Hnf4a for 48 hours.

value: LUAD Cell Line

value: Trametinib


title: H358_MEKi_Replicate2

description: RNAseq


title: H358_Control_Replicate1

description: RNAseq

value: Control


title: H1651_MEKi_Replicate2

description: RNAseq


title: H1651_Control_Replicate2

description: RNAseq


title: H358_Control_Replicate2

description: RNAseq


title: H1651_Control_Replicate1

description: RNAseq


title: K562, CRAMP1 KO, H1.4, CUT&Tag

description: Library name: CT_K562_CRAMP1_KO_H1.4

value: CRAMP1 KO


title: H1651_Dox_Replicate2

description: RNAseq

value: HNF4a Overexpression

value: Doxycycline


title: H1651_MEKi_Replicate1

description: RNAseq


title: H1651_Dox_Replicate1

description: RNAseq


title: H1651_NoDox_Replicate2

description: RNAseq


title: H1651_NoDox_Replicate1

description: RNAseq


title: H358_MEKi_NKX2-1_Replicate2

description:
ChIPseq
25591X8

data_processing:
Fastq alignments were pre-processed with the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts) to associate the UMI sequence, provided as a third Fastq file, into the read comment.
Reads were aligned using Bowtie2 v2.2.9 to the standard chromosomes of the mouse genome (version mm10) or the human genome (version hg38).
Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 v2.2.7 with a significance of q-value < 0.01.
Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: mm10; for murine samples
Assembly: hg38; for human samples
Supplementary files format and content: bigwig, BED files (except for Input samples)

growth_protocol: Organoid cultures grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013). H358 cells were cultured in RPMI/10% FBS. H1651 cells were cultured in Advanced DMEM F-12/10% FBS/10mM HEPES. 3311 cells were cultured in DMEM/10% FBS.

extract_protocol:
For cell line ChIP-seq, ~1 x 107 cells were collected per ChIP experiment. For organoid ChIP-seq, ~4 x 106 cells were collected per ChIP experiment. For ChIP-re-ChIP, ~3 x 107 cells were collected per ChIP experiment. For organoid ChIP experiments, organoids were first collected in Cell Recovery Solution and incubated on ice for 30 mins. Organoids were then washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). 2D adherent cell lines were washed 2X in cold PBS, then cells were scraped and collected and washed once more. Cell/organoid pellets were then resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) containing 40μL of 0.25 M disuccinimidyl glutarate (DSG) (Thermo Fisher Scientific) and rotated at room temperature for 35 min. Methanol-free formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was quenched with the addition of glycine to a final concentration of 125mM. Cells were washed with cold PBS, then the cell pellet was snap frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed on ice for 5 minutes then lysed in 1 mL of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) with Pierce Protease Inhibitor (PPI, ThermoFisher Scientific, A32959). Samples were centrifuged at 4°C (1000G) then resuspended in 1mL of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) with PPI. Chromatin was sonicated with a QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 minutes; amplitude: 70%). After sonication, samples were centrifuged at 17,000 x g for 15 minutes and an input was collected from each sample of sheared chromatin. Chromatin from each sample was then immunoprecipitated overnight with 5ug of the following antibodies (per sample) premixed with Protein G Dynabeads (for mouse antibodies; ThermoFisher Scientific, 10004D) or Protein A Dynabeads (for rabbit antibodies; ThermoFisher Scientific, 10002D): HNF4α (Perseus Proteomics PPH1415), NKX2-1 (Abcam ab133737), FoxA1 (Abcam, ab170933), FoxA2 (CST 8186). The next day, bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). At this point, ChIP-re-ChIP samples were subjected to an extra processing step: samples were resuspended in 10mM DTT and incubated with agitation at 37°C for 40 minutes. DTT was diluted by adding 1mL RIPA buffer with PPI, and diluted chromatin was immunoprecipitated for a second time overnight with the reciprocal antibody (either FoxA1 or HNF4α). For all samples, crosslinks were reversed by incubating samples in IP Elution Buffer (1% SDS, 0.1% NaHCO3) overnight at 65°C. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit (Zymo, D5205).
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: For Hnf4a deletion ChIP-seq, 3154 organoids were treated with 2mM 4OHT (or ethanol) for 6 days to delete Hnf4a. For H1651 ChIP-seq, H1651 cells harboring lentiviral HNF4α overexpression construct were treated with 1μg/mL doxycycline for 7 days. For MEKi ChIP-seq, 3311 cells were treated with 50nM Trametinib for 48h, and 1027B organoids and H358 cells were treated with 20nM Trametinib for 48h.

value: LUAD cell line

tag: chip antibody


title: H358_MEKi_Input_Replicate1

description:
ChIPseq
25591X2

value: No antibody


title: H358_MEKi_NKX2-1_Replicate1

description:
ChIPseq
25591X4


title: H358_MEKi_Input_Replicate2

description:
ChIPseq
25591X6


title: H358_Control_NKX2-1_Replicate1

description:
ChIPseq
25591X3


title: H358_Control_Input_Replicate2

description:
ChIPseq
25591X5


title: H358_Control_Input_Replicate1

description:
ChIPseq
25591X1


title: H1651_FoxA1_Replicate1

description:
ChIPseq
20701X5

value: FoxA1 (Abcam, ab170933)


title: H1651_FoxA1_Replicate2

description:
ChIPseq
20788X7


title: H1651_NKX2-1_Replicate2

description:
ChIPseq
20701X4


title: H1651_NKX2-1_Replicate1

description:
ChIPseq
20701X2


title: UY7 [ATAC-Seq]

city: Palo Alto

first: Rebeca

last: Arroyo Hornero

state: California

address: Campus Drive

institute: Stanford

data_processing:
Reads were analyzed for quality control, trimmed, aligned, and filtered, and normalizedusing nfatac (https://nf-co.re/atacseq/2.1.2) on Stanford’s Sherlock computing cluster. Reads were aligned to hg19.Narrow peak-calling and consensus peak generation wasperformed using nfatac. Peak tracks were visuzlied using Integrative Genomics Viewer. Differential peak analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: bigwig files with ATAC-seq profiles

source_name: Blood

extract_protocol:
pDCs were FACS-sorted from 6 adult (20-40 years old) and 6 elderly (>65 years old). DNA extraction and library preparation was performed by the Stanford Functional Genomics Core. DNA was stored at -20C post transposase reaction until all samples had been collected. Samples were sequenced on a NovaSeq 6000.
DNA was extracted and library preparation was performed using the Omni-ATAC protocol (Nature Methods 2017).

value: Blood

tag: group

value: young

value: plasmacytoid dendritic cell

tag: Sex

value: Female


title: UY6 [ATAC-Seq]


title: UY4 [ATAC-Seq]


title: UY5 [ATAC-Seq]

value: Male


title: UY1 [ATAC-Seq]


title: H1651_HNF4a_Replicate1

description:
ChIPseq
20701X8

value: HNF4a (Perseus Proteomics PPH1415)


title: H1651_HNF4a_Replicate2

description:
ChIPseq
21231X2


title: Ue6 [ATAC-Seq]

value: elderly


title: H1651_Input_Replicate2

description:
ChIPseq
20701X3


title: Ue7 [ATAC-Seq]


title: Ue3 [ATAC-Seq]


title: Ue5 [ATAC-Seq]


title: shSUZ12,  ATAC-seq, replicate2

data_processing:
Read files were processed using the nf-core ATAC-seq pipeline.
Assembly: hg38
Supplementary files format and content: Tab-delimited file showing raw counts for consensus peaks.

extract_protocol: ATAC-seq was performed using the Diagenode ATAC-seq kit according to the manufacturer's instructions.


title: shSUZ12,  ATAC-seq, replicate1


title: Ue4 [ATAC-Seq]


title: UY2 [ATAC-Seq]


title: H358_Control_NKX2-1_Replicate2

description:
ChIPseq
25591X7


title: shControl, ATAC-seq, replicate2

value: shControl


title: Ue2 [ATAC-Seq]


title: shSUZ12, H3K27me3, CUT&Tag

extract_protocol: CUT&Tag was performed on 100,000 K562 cells using the CUTANA CUT&Tag kit (EpiCypher) following the manufacturer's instructions.

tag: antibody


title: H1651_Input_Replicate1

description:
ChIPseq
20701X1


title: shCRAMP1, SUZ12, CUT&Tag

value: SUZ12 (Proteintech, #20366-1-AP)


title: shControl, ATAC-seq, replicate1


title: shCRAMP1, H3K27me3, CUT&Tag


title: shControl, IgG, CUT&Tag

value: IgG (EpiCypher, #13-0042)


title: shCRAMP1,  ATAC-seq, replicate1


title: shControl, SUZ12, CUT&Tag


title: shSUZ12, IgG, CUT&RUN


title: shControl, H3K27me3, CUT&Tag


title: shSUZ12, SUZ12, CUT&RUN


title: shCRAMP1, IgG, CUT&RUN


title: shCRAMP1, H3K27me3, CUT&RUN

value: H3K27me3 (Merck Millipore, #07-449)


title: shCRAMP1, SUZ12, CUT&RUN


title: shControl, IgG, CUT&RUN


title: shSUZ12, H3K27me3, CUT&RUN


title: shControl, SUZ12, CUT&RUN


title: shControl, H3K27me3, CUT&RUN


title: shCRAMP1,  ATAC-seq, replicate2


title: SUZ12-KO2

data_processing:
Reads were trimmed with cutadapt and aligned using bowtie2. Further analysis was performed in SeqMonk using the RNA-seq pipeline.
Assembly: hg38
Supplementary files format and content: Tab-delimited file showing normalised and log2-transformed RPKM values for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (QIAGEN) and treated with DNaseI (QIAGEN). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit v2 (NEB).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer's instructions.

value: SUZ12 KO


title: SUZ12-KO1


title: shSUZ12, SUZ12, CUT&Tag


title: Wild-type, replicate2

value: Wild-type


title: CRAMP1-KO2

value: CRAMP1 KO


title: CRAMP1-KO3


title: Wild-type, replicate1


title: Wild-type, replicate3


title: Jurkat, IgG, CUT&Tag

source_name: Jurkat

value: Jurkat


title: Jurkat, H3K27me3, CUT&Tag


title: Jurkat, H1.5, CUT&Tag


title: Jurkat, H1.2, CUT&Tag


title: RPE-1, H3K27me3, CUT&Tag

source_name: hTERT RPE-1

value: hTERT RPE-1


title: RPE-1, IgG, CUT&Tag


title: RPE-1, H1.4, CUT&Tag


title: RPE-1, H1.3, CUT&Tag


title: RPE-1, H1.2, CUT&Tag


title: HCT116, H3K27me3, CUT&Tag


title: HCT116, H1.5, CUT&Tag


title: HCT116, H1.4, CUT&Tag


title: HCT116, H1.2, CUT&Tag


title: K562, FLAG-H1.5, CUT&Tag

value: Wild-type, expressing FLAG-H1.5

value: FLAG (Merck, #F1804)


title: K562, FLAG, CUT&Tag


title: K562, FLAG-H1.4, CUT&Tag

value: Wild-type, expressing FLAG-H1.4


title: CRAMP1-KO1


title: K562, FLAG-H1.3, CUT&Tag

value: Wild-type, expressing FLAG-H1.3


title: K562, FLAG-H1.2, CUT&Tag

value: Wild-type, expressing FLAG-H1.2


title: K562, H3K27me3, CUT&Tag


title: K562, H1.3, CUT&Tag


title: K562, IgG, CUT&Tag


title: K562, H1.5, CUT&Tag


title: Jurkat, H1.4, CUT&Tag


title: K562, H1.2, CUT&Tag


title: shSUZ12, replicate2


title: shSUZ12, replicate3


title: shSUZ12, replicate1


title: shCRAMP1, replicate3


title: RPE-1, H1.5, CUT&Tag


title: shCRAMP1, replicate2


title: shCRAMP1, replicate1


title: shControl, replicate3


title: shControl, replicate1


title: V5 control, CUT&RUN


title: shControl, replicate2


title: HCT116, IgG, CUT&Tag


title: V5-CRAMP1, CUT&RUN

value: Wild-type expressing V5-CRAMP1


title: IgG, CUT&RUN


title: CRAMP1, CUT&RUN

value: CRAMP1 (Bethyl Laboratories, #A304-094A)


title: Liver cancer stem cells, siControl_3

city: Guangzhou

first: changgui

last: zhong

state: Guangdong

address: Guangzhou University Town, Panyu District, Guangzhou

institute: South China University of Technology

data_processing:
we used Fastp (version 0.23.1) to perform basic statistics on the quality of the raw reads.
Discard a paired reads if either one read contains adapter contamination
Discard a paired reads if more than 10% of bases are uncertain in either one read
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using HiScript III RT SuperMix for qPCR(+gDNA wiper) (Vazyme). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations

value: Liver

value: Liver cancer stem cells

value: WT


title: Liver cancer stem cells, shICAM1_3

value: ICAM1 knockdown


title: K562, H1.4, CUT&Tag


title: Liver cancer stem cells, siControl_1


title: BMP4-treated_micropatterned_hPSCs_42h_rep2

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
BCL Convert Conversion Software v4 (Illumina)
Fastq files were processed with the count function of Cell Ranger v6.0.0 against reference GRCh38-2020-A and further cell filtering to include cells with 12k to 50k reads, mitochodrial expression between 150 and 900 (as measured in scprep) and genes expressed in more than 10 cells
per cell counts were normalized to 1e4, log1p transcformed, integrated with SCVI (regressing out cell cycle), clustered with Leiden, and visualized with Phate.
Assembly: GRCh38-2020-A
Supplementary files format and content: hd5 file from cellranger count (see 10x website for format)
Supplementary files format and content: Cluster_Annotation.csv contains cluster assignment for each cell
Supplementary files format and content: Counts.csv files contain the counts matrix after filtering

growth_protocol: Human pluripotent stem cells were grown in defined pluripotency maintenance media mTeSR1 at low density with 0.1% ROCK inhibitor in an incubator at 37C and 5% CO2

extract_protocol:
Samples were collected using accutase and resuspended in ice cold PBS. Cells were barcoded using the 10x Genomics Chromium system (part numbers 1000268, 1000120, 1000215). For quality control cDNA was quantified by Qubit High Sensitivity DNA assay and Agilent TapeStation
The University of Michigan Advanced Genomics Core performed library preparation.

treatment_protocol: To differentiate cells for 2D gastruloids by micropatterning, cells were pre-incubated for 24 hours in mTeSR before adding the 50ng/ml BMP4 treatment by a full medium change. Full media changes with 50ng/ml BMP4 were performed every 24 hours.

value: hESCs

value: BMP4 50ng/ml


title: COVIM-94 healthy adult Bcells

city: Berlin

first: Lev

last: Petrov

address: Charitépl. 1

department: BIH Translational Immunology

country: Germany

institute: Charite, BIH

description:
single cell RNA
COVIM-94_98_103_439_50177_66_76_94_B

data_processing:
Raw sequencing data were processed with CellRanger’s (v5) multi workflow and aligned against the GRCh38 reference, including TotalSeq C hashtag barcodes and VDJ data. Common variants from the 1000Genomes project were scored with cellsnp-lite (v1.2.0).
Assembly: GRCh38
Supplementary files format and content: H5 file, count matrices as cell ranger output
Supplementary files format and content: CSV, TCR contig annotation cell ranger output
Supplementary files format and content: CSV, BCR contig annotation cell ranger output
Supplementary files format and content: CSV, BCR contig annotation cell ranger output
Supplementary files format and content: TSV, donor ID SNP demultiplexing output

source_name: blood

extract_protocol:
Human peripheral blood mononuclear cells (PBMCs) were isolated from heparinized whole blood by density gradient centrifugation over Pancoll (density: 1,077g /ml, PAN-Biotech, Germany). Subsequently, the cells were counted, frozen and stored in liquid nitrogen. On the day of the experiment, the frozen PBMCs were thawed in pre-warmed thawing medium (RPMI 1640, Gibco; 2% FCS, Sigma; 0,01% Pierce Universal Nuclease, Thermo Fisher, USA).
PBMCs were resuspended in staining buffer (DPBS, Gibco; 0,5% BSA, Miltenyi Biotec, Germany; 2 mM EDTA, Gibco, Thermo Fisher Scientific, USA) and hashtagged with 0.5 μg Total-Seq-C™ Hashtag antibodies for 30 min at 4°C. After the incubation, the PBMCs were washed three times, resuspended in DPBS, filtered through a 40 μm mesh (Flowmi™ Cell Strainer, Merck, Germany) and counted using the C-Chip hemocytometer (NanoEntek, South Korea). Subsequently, up to seven different samples were pooled equally. The cell suspension was super-loaded with 40000 - 50,000 cells per lane, in the Chromium™ Controller for partitioning single-cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). In order to achieve a high enough cell number for each population on interest, the process above was repeated twice for each PBMC pool and additionally, B cells were enriched using untouched human B Cell Isolation Kit II (Miltenyi Biotec, Germany) and loaded separately with approximately 20000 cells per lane. The Chromium Next GEM Single Cell 5′ v.2 Dual Index kit was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (10x Genomics, USA). For additional VDJ and hashtag libraries the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell and Human B Cell (10x Genomics, USA), as well as the Chromium Single Cell 5’ Feature Barcode Library Kit (10x Genomics, USA) were used. All libraries were prepared following the detailed protocols provided by 10x Genomics, quantified by Qubit Flex Fluorometer (Thermo Fisher, USA) and quality was checked using 4150 TapeStation automated electrophoresis system (Agilent, USA). Sequencing was performed in paired-end mode with a S1 and S2 flow cell using NovaSeq 6000 sequencer (Illumina, USA).

tag: disease phase

tag: severity group

value: healthy adult

tag: donor group

value: HC

tag: donor id

value: blood

value: Bcells

tag: multiplex sample_tag

value: magnetic negative enrichment


title: COVIM-94 healthy adult PBMC rep2

description:
single cell RNA
COVIM-94_98_103_439_50177_66_76_94_P2

tag: tissue

value: PBMC

value: Ficoll


title: COVIM-76 healthy adult Bcells

description:
single cell RNA
COVIM-76_98_103_439_50177_66_76_94_B


title: COVIM-76 healthy adult PBMC rep2

description:
single cell RNA
COVIM-76_98_103_439_50177_66_76_94_P2


title: COVIM-76 healthy adult PBMC rep1

description:
single cell RNA
COVIM-76_98_103_439_50177_66_76_94_P1


title: COVIM-66 healthy adult Bcells

description:
single cell RNA
COVIM-66_98_103_439_50177_66_76_94_B


title: COVIM-66 healthy adult PBMC rep2

description:
single cell RNA
COVIM-66_98_103_439_50177_66_76_94_P2


title: COVIM-66 healthy adult PBMC rep1

description:
single cell RNA
COVIM-66_98_103_439_50177_66_76_94_P1


title: C19-CB-439 healthy child Bcells

description:
single cell RNA
C19-CB-439_98_103_439_50177_66_76_94_B

value: healthy child


title: C19-CB-50177 asymptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50177_98_103_439_50177_66_76_94_P1

value: acute

value: asymptomatic child


title: C19-CB-50177 asymptomatic child Bcells

description:
single cell RNA
C19-CB-50177_98_103_439_50177_66_76_94_B


title: Liver cancer stem cells, shICAM1_2

tag: genotype


title: C19-CB-50177 asymptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50177_98_103_439_50177_66_76_94_P2


title: Liver cancer stem cells, shICAM1_1


title: C19-CB-439 healthy child PBMC rep1

description:
single cell RNA
C19-CB-439_98_103_439_50177_66_76_94_P1


title: C19-CB-103 severe adult PBMC rep1

description:
single cell RNA
C19-CB-103_98_103_439_50177_66_76_94_P1

value: severe adult


title: C19-CB-103 severe adult PBMC rep2

description:
single cell RNA
C19-CB-103_98_103_439_50177_66_76_94_P2


title: C19-CB-103 severe adult Bcells

description:
single cell RNA
C19-CB-103_98_103_439_50177_66_76_94_B


title: C19-CB-98 severe adult Bcells

description:
single cell RNA
C19-CB-98_98_103_439_50177_66_76_94_B


title: C19-CB-98 severe adult Bcells rep2

description:
single cell RNA
C19-CB-98_98_103_439_50177_66_76_94_P2


title: C19-CB-439 healthy child PBMC rep2

description:
single cell RNA
C19-CB-439_98_103_439_50177_66_76_94_P2


title: C19-CB-50114 healthy adult Bcells

description:
single cell RNA
C19-CB-50114_548_128_76_150_50114_B


title: Liver cancer stem cells, siControl_2

value: Liver


title: C19-CB-50114 healthy adult PBMC rep2

description:
single cell RNA
C19-CB-50114_548_128_76_150_50114_P2


title: C19-CB-50114 healthy adult PBMC rep1

description:
single cell RNA
C19-CB-50114_548_128_76_150_50114_P1


title: COVIM-94 healthy adult PBMC rep1

description:
single cell RNA
COVIM-94_98_103_439_50177_66_76_94_P1


title: C19-CB-0150 severe adult Bcells

description:
single cell RNA
C19-CB-0150_548_128_76_150_50114_B


title: C19-CB-0150 severe adult PBMC rep2

description:
single cell RNA
C19-CB-0150_548_128_76_150_50114_P2


title: C19-CB-98 severe adult PBMC rep1

description:
single cell RNA
C19-CB-98_98_103_439_50177_66_76_94_P1


title: C19-CB-0128 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0128_548_128_76_150_50114_B

value: IFNa severe adult


title: C19-CB-0076 severe adult PBMC rep1

description:
single cell RNA
C19-CB-0076_548_128_76_150_50114_P1


title: C19-CB-0128 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0128_548_128_76_150_50114_P1


title: C19-CB-0128 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0128_548_128_76_150_50114_P2


title: C19-CB-0076 severe adult PBMC rep2

description:
single cell RNA
C19-CB-0076_548_128_76_150_50114_P2


title: C19-CB-0548 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0548_548_128_76_150_50114_B


title: C19-CB-0548 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0548_548_128_76_150_50114_P1


title: C19-CB-0548 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0548_548_128_76_150_50114_P2


title: C19-CB-50138 mild adult Bcells

description:
single cell RNA
C19-CB-50138_160_310_61_82_50138_B

value: mild adult


title: C19-CB-0082 severe adult Bcells

description:
single cell RNA
C19-CB-0082_160_310_61_82_50138_B


title: C19-CB-0076 severe adult Bcells

description:
single cell RNA
C19-CB-0076_548_128_76_150_50114_B


title: C19-CB-50138 mild adult PBMC rep2

description:
single cell RNA
C19-CB-50138_160_310_61_82_50138_P2


title: C19-CB-0082 severe adult PBMC rep1

description:
single cell RNA
C19-CB-0082_160_310_61_82_50138_P1


title: C19-CB-0310 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0310_160_310_61_82_50138_B


title: C19-CB-0310 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0310_160_310_61_82_50138_P2


title: C19-CB-0061 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0061_160_310_61_82_50138_P1


title: C19-CB-0160 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0160_160_310_61_82_50138_B


title: C19-CB-0150 severe adult PBMC rep1

description:
single cell RNA
C19-CB-0150_548_128_76_150_50114_P1


title: C19-CB-0160 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0160_160_310_61_82_50138_P1


title: COVIM-28 healthy adult PBMC rep2

description:
single cell RNA
COVIM-28_83_224_409_50006_50090_50178_28_P2


title: C19-CB-0160 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0160_160_310_61_82_50138_P2


title: COVIM-28 healthy adult Bcells

description:
single cell RNA
COVIM-28_83_224_409_50006_50090_50178_28_B


title: C19-CB-50178 symptomatic child Bcells

description:
single cell RNA
C19-CB-50178_83_224_409_50006_50090_50178_28_B

value: symptomatic child


title: COVIM-28 healthy adult PBMC rep1

description:
single cell RNA
COVIM-28_83_224_409_50006_50090_50178_28_P1


title: C19-CB-50138 mild adult PBMC rep1

description:
single cell RNA
C19-CB-50138_160_310_61_82_50138_P1


title: C19-CB-50178 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50178_83_224_409_50006_50090_50178_28_P2


title: C19-CB-50006 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50006_83_224_409_50006_50090_50178_28_P1


title: C19-CB-50090 asymptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50090_83_224_409_50006_50090_50178_28_P2


title: C19-CB-0082 severe adult PBMC rep2

description:
single cell RNA
C19-CB-0082_160_310_61_82_50138_P2


title: C19-CB-0224 mild adult Bcells

description:
single cell RNA
C19-CB-0224_83_224_409_50006_50090_50178_28_B


title: C19-CB-50006 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50006_83_224_409_50006_50090_50178_28_P2


title: C19-CB-50090 asymptomatic child Bcells

description:
single cell RNA
C19-CB-50090_83_224_409_50006_50090_50178_28_B


title: C19-CB-0409 healthy child PBMC rep1

description:
single cell RNA
C19-CB-0409_83_224_409_50006_50090_50178_28_P1


title: C19-CB-50178 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50178_83_224_409_50006_50090_50178_28_P1


title: C19-CB-50090 asymptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50090_83_224_409_50006_50090_50178_28_P1


title: C19-CB-0224 mild adult PBMC rep2

description:
single cell RNA
C19-CB-0224_83_224_409_50006_50090_50178_28_P2


title: C19-CB-50006 symptomatic child Bcells

description:
single cell RNA
C19-CB-50006_83_224_409_50006_50090_50178_28_B


title: C19-CB-0409 healthy child Bcells

description:
single cell RNA
C19-CB-0409_83_224_409_50006_50090_50178_28_B


title: C19-CB-0409 healthy child PBMC rep2

description:
single cell RNA
C19-CB-0409_83_224_409_50006_50090_50178_28_P2


title: C19-CB-50141 healthy adult Bcells

description:
single cell RNA
C19-CB-50141_57_115_351_514_50088_50130_50141_B


title: C19-CB-0083 severe adult Bcells

description:
single cell RNA
C19-CB-0083_83_224_409_50006_50090_50178_28_B


title: C19-CB-0083 severe adult PBMC rep1

description:
single cell RNA
C19-CB-0083_83_224_409_50006_50090_50178_28_P1


title: C19-CB-0083 severe adult PBMC rep2

description:
single cell RNA
C19-CB-0083_83_224_409_50006_50090_50178_28_P2


title: C19-CB-50130 symptomatic child Bcells

description:
single cell RNA
C19-CB-50130_57_115_351_514_50088_50130_50141_B


title: C19-CB-50141 healthy adult PBMC rep2

description:
single cell RNA
C19-CB-50141_57_115_351_514_50088_50130_50141_P2


title: C19-CB-50141 healthy adult PBMC rep1

description:
single cell RNA
C19-CB-50141_57_115_351_514_50088_50130_50141_P1


title: C19-CB-50130 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50130_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0310 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0310_160_310_61_82_50138_P1


title: C19-CB-0061 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0061_160_310_61_82_50138_P2


title: C19-CB-50130 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50130_57_115_351_514_50088_50130_50141_P1


title: C19-CB-50088 asymptomatic child Bcells

description:
single cell RNA
C19-CB-50088_57_115_351_514_50088_50130_50141_B


title: C19-CB-0061 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0061_160_310_61_82_50138_B


title: C19-CB-50088 asymptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50088_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0224 mild adult PBMC rep1

description:
single cell RNA
C19-CB-0224_83_224_409_50006_50090_50178_28_P1


title: C19-CB-50088 asymptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50088_57_115_351_514_50088_50130_50141_P1


title: C19-CB-0514 symptomatic child Bcells

description:
single cell RNA
C19-CB-0514_57_115_351_514_50088_50130_50141_B


title: C19-CB-0514 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-0514_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0351 healthy child PBMC rep2

description:
single cell RNA
C19-CB-0351_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0514 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-0514_57_115_351_514_50088_50130_50141_P1


title: C19-CB-0351 healthy child PBMC rep1

description:
single cell RNA
C19-CB-0351_57_115_351_514_50088_50130_50141_P1


title: C19-CB-50113 healthy adult Bcells

description:
single cell RNA
C19-CB-50113_16_70_336_483_50019_50068_50113_B


title: C19-CB-0115 mild adult PBMC rep1

description:
single cell RNA
C19-CB-0115_57_115_351_514_50088_50130_50141_P1


title: C19-CB-0057 severe adult PBMC rep2

description:
single cell RNA
C19-CB-0057_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0351 healthy child Bcells

description:
single cell RNA
C19-CB-0351_57_115_351_514_50088_50130_50141_B


title: C19-CB-0057 severe adult Bcells

description:
single cell RNA
C19-CB-0057_57_115_351_514_50088_50130_50141_B


title: C19-CB-0115 mild adult Bcells

description:
single cell RNA
C19-CB-0115_57_115_351_514_50088_50130_50141_B


title: C19-CB-0057 severe adult PBMC rep1

description:
single cell RNA
C19-CB-0057_57_115_351_514_50088_50130_50141_P1


title: C19-CB-50113 healthy adult PBMC rep2

description:
single cell RNA
C19-CB-50113_16_70_336_483_50019_50068_50113_P2


title: C19-CB-50068 asymptomatic child Bcells

description:
single cell RNA
C19-CB-50068_16_70_336_483_50019_50068_50113_B


title: C19-CB-50113 healthy adult PBMC rep1

description:
single cell RNA
C19-CB-50113_16_70_336_483_50019_50068_50113_P1


title: C19-CB-50019 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50019_16_70_336_483_50019_50068_50113_P2


title: C19-CB-50019 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50019_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0483 symptomatic child Bcells

description:
single cell RNA
C19-CB-0483_16_70_336_483_50019_50068_50113_B


title: C19-CB-50068 asymptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50068_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0483 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-0483_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0336 healthy child PBMC rep2

description:
single cell RNA
C19-CB-0336_16_70_336_483_50019_50068_50113_P2


title: C19-CB-50068 asymptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50068_16_70_336_483_50019_50068_50113_P2


title: C19-CB-0336 healthy child Bcells

description:
single cell RNA
C19-CB-0336_16_70_336_483_50019_50068_50113_B


title: C19-CB-0336 healthy child PBMC rep1

description:
single cell RNA
C19-CB-0336_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0070 mild adult Bcells

description:
single cell RNA
C19-CB-0070_16_70_336_483_50019_50068_50113_B


title: C19-CB-0483 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-0483_16_70_336_483_50019_50068_50113_P2


title: C19-CB-0070 mild adult PBMC rep2

description:
single cell RNA
C19-CB-0070_16_70_336_483_50019_50068_50113_P2


title: C19-CB-0016 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0016_16_70_336_483_50019_50068_50113_B


title: C19-CB-0115 mild adult PBMC rep2

description:
single cell RNA
C19-CB-0115_57_115_351_514_50088_50130_50141_P2


title: C19-CB-0070 mild adult PBMC rep1

description:
single cell RNA
C19-CB-0070_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0016 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0016_16_70_336_483_50019_50068_50113_P1


title: C19-CB-0016 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0016_16_70_336_483_50019_50068_50113_P2


title: C19-CB-50001 symptomatic child Bcells

description:
single cell RNA
C19-CB-50001_13_49_335_389_447_50001_50051_B


title: C19-CB-50001 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50001_13_49_335_389_447_50001_50051_P2


title: C19-CB-50051 asymptomatic child Bcells

description:
single cell RNA
C19-CB-50051_13_49_335_389_447_50001_50051_B


title: C19-CB-50051 asymptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50051_13_49_335_389_447_50001_50051_P1


title: C19-CB-0477 symptomatic child Bcells

description:
single cell RNA
C19-CB-0477_13_49_335_389_447_50001_50051_B


title: C19-CB-50051 asymptomatic child PBMC rep2

description:
single cell RNA
C19-CB-50051_13_49_335_389_447_50001_50051_P2


title: C19-CB-0389 healthy adult Bcells

description:
single cell RNA
C19-CB-0389_13_49_335_389_447_50001_50051_B


title: C19-CB-50001 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-50001_13_49_335_389_447_50001_50051_P1


title: C19-CB-0389 healthy adult PBMC rep2

description:
single cell RNA
C19-CB-0389_13_49_335_389_447_50001_50051_P2


title: C19-CB-0477 symptomatic child PBMC rep2

description:
single cell RNA
C19-CB-0477_13_49_335_389_447_50001_50051_P2


title: C19-CB-0335 healthy child Bcells

description:
single cell RNA
C19-CB-0335_13_49_335_389_447_50001_50051_B


title: C19-CB-50019 symptomatic child Bcells

description:
single cell RNA
C19-CB-50019_16_70_336_483_50019_50068_50113_B


title: PRRSV group-3

city: Wuhan

first: Deshi

last: shi

address: hongshanqu

institute: Huazhong Agriculture University Department of Veterinary Medicine

description:
Library name: PRRSV3
PRRSV group-3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (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 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.
Assembly: ensembl_110_sus_scrofa_sscrofa11_1_toplevel
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Sus scrofa

source_name: lung

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306）following manufacturer's protocols.

value: lung

tag: cell line

value: porcine alveolar macrophages

value: primary cell

value: PRRSV infection


title: C19-CB-0335 healthy child PBMC rep1

description:
single cell RNA
C19-CB-0335_13_49_335_389_447_50001_50051_P1

value: HC

value: blood

tag: cell type


title: C19-CB-0049 mild adult PBMC rep1

description:
single cell RNA
C19-CB-0049_13_49_335_389_447_50001_50051_P1

tag: treatment


title: C19-CB-0049 mild adult PBMC rep2

description:
single cell RNA
C19-CB-0049_13_49_335_389_447_50001_50051_P2


title: PRRSV group-2

description:
Library name: PRRSV2
PRRSV group-2


title: BNPP treatment group-4

description:
Library name: BNPP4
BNPP treatment group-4

value: BNPP treatment


title: C19-CB-0335 healthy child PBMC rep2

description:
single cell RNA
C19-CB-0335_13_49_335_389_447_50001_50051_P2

value: PBMC


title: PRRSV group-1

description:
Library name: PRRSV1
PRRSV group-1


title: BNPP treatment group-3

description:
Library name: BNPP3
BNPP treatment group-3


title: C19-CB-0477 symptomatic child PBMC rep1

description:
single cell RNA
C19-CB-0477_13_49_335_389_447_50001_50051_P1

value: Ficoll


title: BNPP treatment group-2

description:
Library name: BNPP2
BNPP treatment group-2


title: C19-CB-0013 IFNa severe adult PBMC rep2

description:
single cell RNA
C19-CB-0013_13_49_335_389_447_50001_50051_P2


title: BNPP treatment group-1

description:
Library name: BNPP1
BNPP treatment group-1


title: control group-2

description:
Library name: C2
control group-2

value: control


title: control group-3

description:
Library name: C3
control group-3


title: Ue7

data_processing:
Reads were aligned using STAR to hg19 on Stanford’s Sherlock computing cluster. Counts were generated using featureCounts. Differential gene expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: RNAseq.counts.txt. Gene read counts matrix in .txt format generated by featureCounts

extract_protocol:
pDCs were FACS-sorted from 6 adult (20-40 years old) and 6 elderly (>65 years old) donors directly into Qiazol lysis buffer (Quiagen) and frozen at -80C for RNA sequencing. RNA extraction and library preparation were performed by the Stanford Functional Genomics Core.
Library preparation was performed by the Stanford Functional Genomics Core. Amplification and qPCR were performed simultaneously after all samples were collected. Quality control was conducted using the Bioanalyzer analysis through the Stanford Functional Genomics Core. Samples were barcoded and pooled for sequencing. Samples were sequenced on a NovaSeq 6000 through the Stanford Functional Genomics Core.

value: Blood

value: plasmacytoid dendritic cell

value: Female

tag: developmental stage

value: elderly


title: control group-1

description:
Library name: C1
control group-1


title: C19-CB-0389 healthy adult PBMC rep1

description:
single cell RNA
C19-CB-0389_13_49_335_389_447_50001_50051_P1

value: healthy adult


title: anti-CD3 NOD mouse islets 6

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

institute: University of Manitoba

data_processing:
Sequence reads were trimmed to remove possible adaptor sequences and poor quality using Trimmomatic v.0.36.
Trimmed reads were mapped to Mus musculus reference genome GRCm38 using STAR aligner v.2.5.2b
Unique hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads falling within exon regions were counted
DESeq2 was used to compute differential gene expression between IgG control and anti-CD3 groups with padj < 0.05 and log2 fold-change > 0.59
Assembly: mm10
Supplementary files format and content: tab delimited raw counts file shows for each sample
Supplementary files format and content: tab delimited total differential gene expression file shows normalized transcript counts for each sample for each gene id

source_name: Endocrine pancreas

growth_protocol: Pancreatic islets were isolated with collagenase P via bile duct cannulation and processed for RNA extraction immediately

extract_protocol:
Total RNA was extracted from islets using a commercial Trizol based kit (Zymogen total RNA microprep kit)
Poly(A) RNA was selected, mRNA fragmented and random primers were used to make first and second strand cDNA. Standard end-repair, 5'phosphorylation and dA-tailing was done. Adaptor ligation and PCR enrichment was used prior to library sequencing

treatment_protocol: Islets were not treated prior to collection.

value: Endocrine pancreas

value: Pancreatic islets

value: NOD/ShiLtJ wild-type

value: anti-CD3 antibody


title: Ue5


title: anti-CD3 NOD mouse islets 5


title: Ue6


title: PRRSV group-4

description:
Library name: PRRSV4
PRRSV group-4

value: lung

value: porcine alveolar macrophages

value: primary cell


title: anti-CD3 NOD mouse islets 4


title: C19-CB-0049 mild adult Bcells

description:
single cell RNA
C19-CB-0049_13_49_335_389_447_50001_50051_B

value: acute

value: mild adult

value: blood

value: Bcells

value: magnetic negative enrichment


title: Ue4

value: Blood

value: Male


title: anti-CD3 NOD mouse islets 3


title: Ue2

value: plasmacytoid dendritic cell


title: UY7

value: Female

value: adult


title: anti-CD3 NOD mouse islets 2

value: Endocrine pancreas


title: anti-CD3 NOD mouse islets 1

value: Pancreatic islets


title: UY5


title: IgG control NOD mouse islets 6

value: NOD/ShiLtJ wild-type

value: IgG


title: C19-CB-0013 IFNa severe adult Bcells

description:
single cell RNA
C19-CB-0013_13_49_335_389_447_50001_50051_B

value: IFNa severe adult


title: UY6


title: C19-CB-0013 IFNa severe adult PBMC rep1

description:
single cell RNA
C19-CB-0013_13_49_335_389_447_50001_50051_P1

value: PBMC

value: Ficoll


title: UY1


title: IgG control NOD mouse islets 4


title: UY2


title: IgG control NOD mouse islets 3


title: Ue3

value: elderly


title: IgG control NOD mouse islets 5


title: IgG control NOD mouse islets 2


title: ATAC

library_source: genomic single cell

data_processing:
Raw sequencing data were processed following the Cell Ranger ARC pipeline (v2.0.2) and output was uploaded into Seurat and Signac for further processing
Assembly: GRCh38 (hg38)
Supplementary files format and content: atac_fragments.tsv.gz: Count and barcode information for every ATAC fragment observed in the experiment in TSV format. (CellRanger Output)
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. (CellRanger Output)
Supplementary files format and content: gex_molecue_info.h5: Count and barcode information for every GEX molecule observed in the experiment in hdf5 format. (CellRanger Output)

source_name: Blodd

extract_protocol:
Plasmocytoid dendritic cells were magnetically enriched from peripheral blood of a healthy donor, followed by FACS-sorting. Nuclei was extracted from sorted cells according to manufacturer's instructions (protocol CG000365, 10X Genomics)
Single-cell libraries were performed usign Chromium Next GEM Single-Cell Multiome ATAC+ Gene Expression Kit according to the manufacturer's instructions (10X Genomics).

value: Blodd


title: IgG control NOD mouse islets 1


title: 30-day old male flies 3

city: Gießen

first: Sonja

last: Dähn

address: Wilhelmstrasse 20

institute: Justus-Liebig-Universität Gießen

description:
Library name: CML3
column name in fpkm_30day.csv: male 3

data_processing:
data processing was done by  Novogene Co., Ltd (Beijing, China).
Assembly: NCBI 7227
Supplementary files format and content: fpkm_10day.csv: csv file, containing gene counts and fpkm of DEG, of 10-day old flies
Supplementary files format and content: fpkm_30day.csv: csv file, containing gene counts and fpkm of DEG, of 30-day old flies

organism: Drosophila melanogaster

source_name: whole flies

extract_protocol:
for RNA extraction, the Quick-RNA Tissue/Insect kit (Zymo Research, Freiburg, Germany) was used, according to the manufacturer’s instructions.
polyA enrichment library preparation resulting in the construction of 250-300 bp insert cDNA library, done by Novogene Co., Ltd (Beijing, China).

value: whole flies


title: PanDC_ATAC

data_processing:
Raw sequencing data were processed following the Cell Ranger ARC pipeline (v2.0.2) and output was uploaded into Seurat and Signac for further processing
Assembly: GRCh38 (hg38)
Supplementary files format and content: Supplementary files format and content: atac_fragments.tsv.gz: Count and barcode information for every ATAC fragment observed in the experiment in TSV format. (CellRanger Output)
Supplementary files format and content: Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. (CellRanger Output)
Supplementary files format and content: Supplementary files format and content: gex_molecue_info.h5: Count and barcode information for every GEX molecule observed in the experiment in hdf5 format. (CellRanger Output)

value: dendritic cell


title: day4pDC_ATAC

data_processing:
Raw sequencing data were processed following the Cell Ranger ARC pipeline (v2.0.0) and output was uploaded into Seurat and Signac for further processing
Assembly: GRCh38 (hg38)
Supplementary files format and content: Supplementary files format and content: atac_fragments.tsv.gz: Count and barcode information for every ATAC fragment observed in the experiment in TSV format. (CellRanger Output)
Supplementary files format and content: Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. (CellRanger Output)
Supplementary files format and content: Supplementary files format and content: gex_molecue_info.h5: Count and barcode information for every GEX molecule observed in the experiment in hdf5 format. (CellRanger Output)

extract_protocol:
Plasmocytoid dendritic cells isolated from peripheral blood of a healthy donor were cultured with IL-3 and CD40L for 4 days. Nuclei were extracted from sorted live cells according to manufacturer's instructions (protocol CG000365, 10X Genomics)
Single-cell libraries were performed usign Chromium Next GEM Single-Cell Multiome ATAC+ Gene Expression Kit according to the manufacturer's instructions (10X Genomics).


title: 30-day old male flies 2

description:
Library name: CML2
column name in fpkm_30day.csv: male 2


title: 30-day old male flies 1

description:
Library name: CML1
column name in fpkm_30day.csv: male 1


title: Plate8_D04

data_processing:
Data was processed with STAR
Assembly: hg19
Supplementary files format and content: feature_counts.csv (csv file)

extract_protocol:
Plasmocytoid dendritic cells were magnetically enriched from peripheral blood of a healthy donor, cultured with IL-3 and CD40L for two days and single-cell FACS-sorted on a FACS Aria Fusion (BD Biosciences) into Takara Smart-Seq Single Cell kit lysis buffer and frozen at -80C.
The Illumina Nextera XT DNA Library Prep and Unique Dual Index Kits (Illumina) were used for library preparation according to manufacturer's instructions.

value: blood

value: sorted as:day2_icDC2_donor 2


title: 30-day old female flies 3

description:
Library name: CFL3
column name in fpkm_30day.csv: female 3


title: UY4

value: Blood


title: day4pDC_GEX

molecule: nuclear RNA

value: plasmacytoid dendritic cell


title: 30-day old female flies 1

description:
Library name: CFL1
column name in fpkm_30day.csv: female 1


title: Plate8_D03


title: 10-day old male flies 3

description:
Library name: CMS3
column name in fpkm_10day.csv: male 3


title: Plate8_D02


title: Plate8_D01


title: 10-day old male flies 2

description:
Library name: CMS2
column name in fpkm_10day.csv: male 2


title: Plate8_C12


title: 10-day old male flies 1

description:
Library name: CMS1
column name in fpkm_10day.csv: male 1


title: Plate8_C11


title: Plate8_C10


title: 10-day old female flies 3

description:
Library name: CFS3
column name in fpkm_10day.csv: female 3


title: 10-day old female flies 2

description:
Library name: CFS2
column name in fpkm_10day.csv: female 2


title: GEX


title: 10-day old female flies 1

description:
Library name: CFS1
column name in fpkm_10day.csv: female 1


title: KP1233, JNJ-treated, Rep 3

description: Library name: 215006

data_processing:
To generate counts for alternative splicing analysis, raw reads were mapped to the human GRCh38 genome using STAR (--runMode alignReads --runThreadN 16 --sjdbOverhang 149 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic) and Bowtie (-n 1 -l 30 -e 70 -t -p 4 -m 1 -X 500 -S).
Mapped reads were filtered using Bedtools to remove reads overlapping expressed repeats from the UCSC genome browser RNA repeats and Gencode hg38 and coding exons annotated in the Gencode hg38 annotations. Alternative and constitutive classifications were performed using custom Python scripts and are agnostic to existing annotations other than known gene boundaries. All three cell lines were run in parallel to ensure consistency between annotations. Alternative splicing events were quantified using DEXSeq.
Assembly: Gencode GRCh38 v33 and Gencode GRCm38 vM24
Supplementary files format and content: genes.results files are outputted raw count files from RSEM for each gene.
Supplementary files format and content: isoform.results files are outputted raw count files from RSEM for each isoform (Consensus/Coding or DI).
Supplementary files format and content: DEXSeq files are outputted exon count files from DEXSeq.
Supplementary files format and content: Supplementary files are gff files needed for DEXSeq alternative splicing analysis.

extract_protocol:
For whole cell lysates, following 3-day treatment with either DMSO (vehicle), PRMT5i, or dTag-13, cells were harvested by scraping. RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) according to manufacturer’s instructions, including the optional DNaseI addition to remove contaminating gDNA (Qiagen, 79254). For fractionated cells, after 3 days in drug, cells were harvested via trypsinization, pelleted, and separated into nuclear and cytoplasmic fractions. Briefly, cell pellets were resuspended in cytoplasmic lysis buffer [0.15% (v/v) NP40, 10 mM Tris (pH7), 150 mM NaCl] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then incubated on ice for 5 minutes. Cell lysate was layered on top of sucrose buffer [0 mM Tris (pH7), 150 mM NaCl, 25% (w/v) sucrose] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then centrifuged at 16,000 x g for 10 minutes at 4 °C. The supernatant contains the cytoplasmic fraction and was harvested for RNA extraction. The remaining pellet contains the nuclear fraction and was washed twice with 800 μL cold PBS, centrifuging at 16,000 x g for 1 minute at 4°C after each wash. The pellet was resuspended in cold RIPA buffer [50 mM Tris (pH 8), 150 mM NaCl, 1% (v/v) NP-40, 0.5% sodium deoxycholate, and 0.1% (w/v) SDS] supplemented with 10 U SUPERase.IN (ThermoFisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Lysate was incubated for 30 minutes on ice, with vortexing every 10 minutes, and then pelleted at 16,000 x g for 10 minutes at 4°C. The supernatant contains the nuclear fraction and was harvested for RNA extraction. The RNA from the nuclear and cytoplasmic fractions were extracted using TRIzol Reagent (Thermo Fisher, 15596026) according to manufacturer’s instructions. Briefly, to each aqueous fraction, 0.5 mL of isopropanol and 1 mL of TRIzol Reagent was added, followed by an incubation on ice for 10 minutes. Samples were then centrifuged for 10 minutes at 12,000 x g at 4 °C, pellets were washed in 1 mL 75% ethanol, and centrifuged again for 5 minutes at 7,500xg at 4 °C. Pellets were air dried for 10 minutes and resuspended in RNase-free water.
RNA-Seq libraries were prepared using the NEB Ultra II Directional RNA Kit with Poly(A) Selection per the manufacturer's protocol.

value: WT

value: Day 3


title: PanDC_GEX


title: Plate8_C09


title: Plate8_C08


title: KP1233, JNJ-treated, Rep 2

description: Library name: 215005


title: 30-day old female flies 2

description:
Library name: CFL2
column name in fpkm_30day.csv: female 2


title: Plate8_C05


title: Plate8_C06


title: Plate8_C04

value: sorted as:day2_itDC_donor 2


title: KP1233, JNJ-treated, Rep 1

description: Library name: 215004


title: Plate8_C03


title: KP1233, DMSO-treated, Rep 3

description: Library name: 215003

value: DMSO