title: Pipetting speed 50, Biological replicates 2, Technical replicates 3

city: Tsukuba

first: Shodai

last: Taguchi

state: Ibaraki

address: #307 Health and Medical Science Innovation Laboratory, Tennohday, 1-1-1

department: Faculty of Medicine

institute: University of Tsukuba

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version: 0.23.2, parameters: -q 15 -n 10 -t 1 -T 1 -l 20 -w 16 -A)
STAR（version: 2.7.10a, parameters: --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate)
Trimmed sequence reads were mapped to Saccharomyces cerevisiae W303 genomes which is originally constructed by RSEM using STAR (version: 2.7.10a, parameters: --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using RSEM （version: v1.3.1, parameters: rsem-calculate-expression --alignments --paired-end --strandedness reverse --estimate-rspd)
Assembly: W303_SGD_2015_JRIU00000000
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes TPM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: Two biological replicates cells were inoculated in 3 mL YPD liquid and incubated in a water bath at 30 degC and 200 rpm for 16 hr. And then, the cultures are re-inoculated in 20 mL of fresh YPD liquid and incubated in a shaker at 30 degC and 200 rpm.

extract_protocol:
The sampled cultures were pelletted by centrifugication. And then the pelletes/cells were lysed with 500 uL of ISOGEN and Zirconia/Silica Beads
RNA was harvested using a Poly-T column kit (E7490, NEB). 100 ng of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, NEB) following manufacturer's protocols. Finally, 1.5 pM pooled library DNA was sequenced (36 nt paired-end reads) using Illumina NextSeq 500 System (SY-415-1001; Illumina) with NextSeq 500 High-Output v2 Kit (FC-505-2005; Illumina).

treatment_protocol: No chemical treetments were performed. The cultures were experienced four different speeds of pipetting during sampling for RNA-seq and performing spot assays.

value: WT


title: Pipetting speed 130, Biological replicates 2, Technical replicates 3

status: Public on May 07 2025

type: SRA

country: Japan

library_source: transcriptomic

molecule: polyA RNA

tag: cell line

tag: genotype


title: MPC cells, PTX resistance rep2

city: Shanghai

first: Wenshuai

last: Liu

state: Shanghai

address: Fenglin road 180

department: General Surgery

country: China

institute: Zhongshan Hospital Fudan University

description:
Library name: MPC-PTX2
PTX resistance rep2

data_processing:
The original data in FASTQ format (raw data) was generated from the sequencing platform. The fastp (0.22.0) was used to filter the raw date to get high quality sequence for further study.
Assembly: The reference genome and gene annotation files were downloaded from genome website.
Supplementary files format and content: tab-delimited text file includeds raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: MPC-PTX

growth_protocol: The MPC and MPC-PTX were maintained in RPMI 1640 medium (Gibco, 61870036) supplemented with 10% FBS (Gibco, A5669701) and 1% antibiotics (Gibco, 15070063). The cells were maintained in a humidified incubator with 5% CO2 at 37℃.

extract_protocol:
The concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). 3μg of RNA were used as input material for the RNA sequencing.
Firstly, mRNA was purified by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First and second strand cDNA was synthesized using random oligonucleotides with Super Script II and DNA Polymerase I with RNase H, respectively. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: The MPC-PTX cells received over 30 cycles of PTX treatment

value: MPC-PTX

tag: cell type

value: mouse gastric adenocarcinoma

tag: treatment

value: PTX treated over 30 cycles

tag: batch


title: Blood, Healthy Control, F

city: Leeds

first: Sinisa

last: Savic

address: St James's University Hospital

country: United Kingdom

institute: University of Leeds

data_processing:
Data was trimmed and QC using Cutadapt and FastQC
Trimmed Data was aligned to hg38 using STAR
Duplicates were marked with Picard
Reads were quantified using Featurecounts
Count data was analyzed using DESeq2 and Enrichr
Assembly: GRCh38
Supplementary files format and content: Excel workbook file of raw gene counts for each sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
PAXgene Blood miRNA Kit
Eukaryotic mRNA PolyA enrichment

tag: tissue

value: Blood

tag: disease state

value: Healthy Control


title: TAB1_20191129_2_T-1_N2

type: RNA

city: Setagaya-ku

first: Nobumasa

last: Watanabe

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 600ng of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a SurePrint G3 Human GE v3 8x60K Microarray (Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

source_name: temporal arterial biopsy

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: fresh biopsy

extract_protocol: tissue homogenized with Tissue-Lyzer (Qiagen) in Trizol reagent and RNA extracted by RNeasy kit (Qiagen)

treatment_protocol: stored at 4°C in All-protect Solution (Qiagen)

value: temporal arterial biopsy

tag: gender

value: Female

tag: diagnosis

value: PMR


title: Fbn1 mgR/mgR mice, scRNAseq

city: New Haven

first: Fu

last: Gao

state: CT

address: 55 Prospect Street

country: USA

institute: Yale University

description:
Library name: mgR/mgR
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the cellranger-7.1.0.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: mitral valve

extract_protocol:
Single cells were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
Library was performed according to the manufacturer’s instructions (scRNA seq 3’ v3 protocol, 10x Genomics).

value: mitral valve


title: TAB1_20191129_3_T-3_G1

value: GCA


title: Blood, AOSD, Still118

value: AOSD


title: Blood, Healthy Control, H


title: RH4.veh.8, rep 1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Control Software v4.0.2.7, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the hg38 human assembly with the gencode version 43 annotation using the nf-core/rnaseq workflow revision 3.12.0 (Alexander Peltzer et al. 2024). The genomic target included the LexogenSIRVData spike-in reference. Gene level summaries were prepared from the star_salmon quantitation using tximport version 1.28.0.
Assembly: hg38 human assembly with gencode43 annotation and Lexogen SIRV spike-in transcrips.
Supplementary files format and content: 230925Koe_MOLT4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_MOLT4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_PSN1_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_PSN1_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_RH4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_RH4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.

growth_protocol: Cell lines were maintained at 5% CO2 at 37oC. Cells were cultured  in RPMI 1640 (Thermo Fisher Scientific, 11875093) + 10% fatal bovine serum (FBS). Cell lines were tested intermittently throughout studies using MycoAlert Mycoplasma Detection Kit (Lonza, Cat#LT07-418), generally a few days after thawing and immediately before significant studies (e.g. Proteomics, RNA-seq experiments).

extract_protocol:
Follwing treatment, cells were immediately lysed in lysis buffer (from PerkinElmer’s chemagic RNA Tissue 360 H96, VD200615) supplemented with BME flash frozen and stored at -80c. After all biological replicates were collected, samples were thawed in deep 96-well plates. An equal amount (~30pg) of Lexogen’s ERCC spike-in mix (SIRV-3) were added at this point following manufacturer’s recommendations. The PerkinElmer’s Chemagic 360 was used for bead-based RNA extraction following manufacturer’s standard protocol.
RNA was quantified using an Agilent Fragment Analyzer, purified using 2X RNA SPRI beads, and 1ng of total RNA was used for Illumina library preparation. Libraries were prepared using a reduced volume version of SMART-seq2 performed on an SPT Mosquito HV using 10 cycles of amplification for cDNA generation and 16 cycles for library generation using NexteraXT (Illumina).

treatment_protocol: 1000 cells were seeded and treated with treated with KB-0742, KI-CDK9d-32, or DMSO and cultured to the appropriate endpoint (2, 4, or 8 hours after treatment)

value: rhabdomyosarcoma

value: DMSO

tag: time

value: 8 hr


title: MPC cells, control rep3

description:
Library name: MPC3
control rep3

source_name: MPC

value: MPC

value: control


title: TAB1_20191129_1_N-1_N1

value: Male

value: MPA


title: Blood, Healthy Control, E


title: PSN1.deg.8, rep 4

value: pancreatic adenocarcinoma


title: MPC cells, control rep2

description:
Library name: MPC2
control rep2

value: mouse gastric adenocarcinoma


title: Pipetting speed 290, Biological replicates 2, Technical replicates 3

value: WT


title: PSN1.inh.4, rep 4

value: 4 hr


title: MPC cells, control rep1

description:
Library name: MPC1
control rep1


title: Pipetting speed 50, Biological replicates 1, Technical replicates 3


title: Blood, Healthy Control, C

value: Blood

value: Healthy Control


title: Pipetting speed 130, Biological replicates 1, Technical replicates 3


title: PSN1.veh.4, rep 4


title: C671,ZEB1LysMDel,24h,Il-4

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

country: Germany

description: Library name: R306

data_processing:
The preprocessing of raw RNA-seq data (FASTQ files) was performed using the nf-core RNA-seq pipeline v.3.8.11. In particular, reads were adapter- and quality-trimmed using Trim Galore v.0.6.7 (https://github.com/FelixKrueger/TrimGalore). The reads were then mapped to the Ensembl mouse genome assembly GRCm39 (release 107) using STAR v.2.7.10a.
For transcript-level read counting, Salmon v.1.5.2 was employed, relying on the Ensembl gene annotation file release 107. To generate gene-level counts, Salmon's transcript-level quantification files were processed using the R-package tximport v.1.22 within R v.4.0.3.
Differential expression analysis for the RNA-seq data was performed using the DESeq2 package v.1.34.0 101. As DESeq2 design formula ~litter + group was utilized, where the group factor was created by merging together genotype and treatment (LPS/IL-4). Fold change shrinkage was performed relying on the “ashr” method, made available within the DESeq2 package.
Assembly: GRCm39 (release 107)
Supplementary files format and content: BMDM_DESeq2_normalized_counts.xlsx; Excel file; normalized counts
Supplementary files format and content: BMDM_DESeq2_vst_batch_corr_counts.xlsx; Excel file; batch-corrected counts

source_name: bone-marrow

extract_protocol:
For RNA isolation, BMDMs were washed with PBS and lysed with 350 μl RLT Plus from the RNeasy Plus Mini Kit (QIAGEN, 74136) and RNA was isolated following the manufacturer´s instructions
Bulk RNA sequencing of BMDM RNA (n=3 per condition) was performed by Novogene using poly(A) enrichment library preparation protocol and paired-end sequencing (PE150).

value: bone-marrow

value: BMDM


title: PSN1.veh.8, rep 4


title: C671,ZEB1LysMDel,24h,LPS

description: Library name: R305

value: LPS


title: Blood, Healthy Control, A


title: PSN1.inh.8, rep 4


title: Pipetting speed 210, Biological replicates 2, Technical replicates 3


title: Pipetting speed 210, Biological replicates 1, Technical replicates 3


title: Pipetting speed 50, Biological replicates 2, Technical replicates 2


title: PSN1.deg.4, rep 4


title: C666,ZEB1LysMCtrl,24h,Il-4

description: Library name: R303


title: 23. 3702E PBS control 24 hours

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

description:
experiment: 2
23_T02A_3_PBS

data_processing:
Data processing and quality control were performed using the RNAseq PE snakemake pipeline [https://github.com/mgildea87/RNAseq_PE].
Quality control of sequencing reads was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Reads were trimmed using fastp (v.0.20.1), and mapped to human reference genome hg38 using STAR (v.2.7.7a).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: CD34+ cells

growth_protocol: CD34+ cells were maintained in StemSpan™ Serum-Free Expansion Medium II (SFEMII) supplemented with 50 ng/mL recombinant human thrombopoietin (TPO), 25 ng/mL recombinant human stem cell factor (SCF, until Day 5), 100 U/ml penicillin and 100 μg/ml streptomycin (PS) and cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep columns (Zymo Research).
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries were sequenced single end (51bp) on an Illumina NovaSeq 6000 at the Genome Technology Center at NYU Langone.

treatment_protocol: On day 11, cells were treated with 100 µM aspirin (reconstituted in PBS), 5 µM P2Y12 inhibitor AZD1283 (reconstituted in 0.025% DMSO), or both drugs simultaneously for 24 hours. 0.025% DMSO or PBS were vehicle controls.

value: CD34+ cells

value: Hematopoietic Stem and Progenitor Cells

tag: Sex

value: M

tag: donor

value: PBS


title: 20. 3824E PBS control 24 hours

description:
experiment: 2
20_T24A_2_PBS


title: PSN1.veh.2, rep 3

value: DMSO

value: 2 hr


title: 17. 3819E PBS control 24 hours

description:
experiment: 2
17_T19A_1_PBS

value: F


title: Blood, Healthy Control, D


title: Pipetting speed 130, Biological replicates 2, Technical replicates 2


title: PSN1.deg.4, rep 3


title: Pipetting speed 210, Biological replicates 2, Technical replicates 2


title: Blood, Healthy Control, B


title: 16. 3702D Aspirin + AZD1283 treatment 24 hours

description:
experiment: 1
16_3702D_4_Aspirin_AZD1283


title: Pipetting speed 290, Biological replicates 2, Technical replicates 2


title: PSN1.veh.4, rep 3


title: Pipetting speed 290, Biological replicates 1, Technical replicates 3


title: C671,ZEB1LysMDel,24h,M0

description: Library name: R304


title: PSN1.inh.4, rep 3


title: B119,ZEB1LysMDel,24h,LPS

description: Library name: R215


title: Pipetting speed 130, Biological replicates 1, Technical replicates 2


title: B119,ZEB1LysMDel,24h,Il-4

description: Library name: R216


title: 15. 3702C AZD1283 treatment 24 hours

description:
experiment: 1
15_3702C_4_AZD1283


title: 13. 3702A DMSO control 24 hours

description:
experiment: 1
13_3702A_4_DMSO


title: 14. 3702B Aspirin treatment 24 hours

description:
experiment: 1
14_3702B_4_Aspirin

value: Aspirin


title: PSN1.deg.2, rep 3

value: pancreatic adenocarcinoma


title: B119,ZEB1LysMDel,24h,M0

description: Library name: R214


title: Pipetting speed 50, Biological replicates 1, Technical replicates 2


title: B116,ZEB1LysMCtrl,24h,Il-4

description: Library name: R213


title: Pipetting speed 210, Biological replicates 1, Technical replicates 2


title: 12. 3824D Aspirin + AZD1283 treatment 24 hours

description:
experiment: 1
12_3824D_3_Aspirin_AZD1283


title: 8181,ZEB1LysMCtrl,24h,LPS

description: Library name: R105


title: PSN1.veh.8, rep 3

value: 8 hr


title: PSN1.deg.2, rep 2


title: PSN1.inh.8, rep 3


title: C666,ZEB1LysMCtrl,24h,LPS

description: Library name: R302


title: 11. 3824C AZD1283 treatment 24 hours

description:
experiment: 1
11_3824C_3_AZD1283


title: 10. 3824B Aspirin treatment 24 hours

description:
experiment: 1
10_3824B_3_Aspirin


title: B116,ZEB1LysMCtrl,24h,M0

description: Library name: R211


title: PSN1.deg.8, rep 3


title: C666,ZEB1LysMCtrl,24h,M0

description: Library name: R301


title: Pipetting speed 50, Biological replicates 2, Technical replicates 1

value: WT


title: Pipetting speed 290, Biological replicates 1, Technical replicates 2


title: B109,ZEB1LysMDel,24h,Il-4

description: Library name: R210


title: PSN1.deg.4, rep 2

value: 4 hr


title: Pipetting speed 210, Biological replicates 2, Technical replicates 1


title: PSN1.veh.2, rep 2


title: 7. 3819C AZD1283 treatment 24 hours

description:
experiment: 1
7_3819C_2_AZD1283


title: 9. 3824A DMSO control 24 hours

description:
experiment: 1
9_3824A_3_DMSO


title: B109,ZEB1LysMDel,24h,LPS

description: Library name: R209


title: B106,ZEB1LysMCtrl,24h,Il-4

description: Library name: R207


title: B106,ZEB1LysMCtrl,24h,LPS

description: Library name: R206


title: 6. 3819B Aspirin treatment 24 hours

description:
experiment: 1
6_3819B_2_Aspirin


title: PSN1.deg.4, rep 1


title: PSN1.inh.4, rep 2


title: B109,ZEB1LysMDel,24h,M0

description: Library name: R208


title: Pipetting speed 130, Biological replicates 1, Technical replicates 1


title: Pipetting speed 290, Biological replicates 2, Technical replicates 1


title: PSN1.inh.4, rep 1


title: A196,ZEB1LysMCtrl,24h,M0

description: Library name: R159


title: PSN1.veh.4, rep 2


title: Pipetting speed 50, Biological replicates 1, Technical replicates 1


title: Pipetting speed 130, Biological replicates 2, Technical replicates 1


title: Pipetting speed 290, Biological replicates 1, Technical replicates 1


title: 4. 3817D Aspirin + AZD1283 treatment 24 hours

description:
experiment: 1
4_3817D_1_Aspirin_AZD1283


title: Pipetting speed 210, Biological replicates 1, Technical replicates 1


title: BRB sequencing from gastruloids grown from different cell seeding numbers

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

description: Library name: BRB-seq.Gastruloid.size.120h

data_processing:
Reads were assigned to genes and to samples using STAR Solo version 2.7.10b (--soloStrand Forward --soloType CB UMI Simple --soloCellFilter None --soloFeatures Gene). The GTF file used for gene annotation is available on Zenodo (https://zenodo.org/records/10079673). All counts were aggregated into a single matrix, and a second matrix was generated where the counts were normalized to the million reads.
Only protein-coding genes were considered for the diferential gene expression analysis computed with DESeq2 using the Wald test. A gene was considered diferentially expressed if the adjusted p-value was below 0.05 and the fold-change was above 1.5 (or below 0.67).
Assembly: mm10
Supplementary files format and content: all_counts.txt.gz: a matrix with genes as row and samples as columns containing the UMI counts from STAR solo.
Supplementary files format and content: all_counts_pm.txt.gz: same as above but counts were normalized per million reads asigned to genes.
Supplementary files format and content: BRBseq_barcodes_samples.csv: comma separated text file with for each Well (first column), the corresponding barcode (second column) and the sample name (third column).
Supplementary files format and content: DESeq2_summary.txt: tabular separated text file where each row is a gene and columns indicates log2FC, padj and weather it was significant in each of the analysis
Supplementary files format and content: DESeq2_summary_long.txt: tabular separated text file where each row is a gene in a DESeq2 comparison. This format is more compatible with ggplot2.
Library strategy: BRB-seq

source_name: Gastruloids

growth_protocol: Gastruloids seeded from diferent cell numbers (50, 100, 300, 600, 1200, 1800 cells with the regular Chiron treatment and 300 cells without the addition of Chiron) were grown until 120h.

extract_protocol:
For each replicate (three in total), 60 gastruloids from each condition were collected in a 1.7ml Eppendorf tube and washed once with PBS, pelleted and kept in -80°C until all samples were collected. Each sample were then thawed and extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s recommendation with on-column DNase digestion.
Libraries were performed using Alithea Genomics Mercurius protocol v.0.2.2 and sequenced on Novaseq 6000 in a PE run with 28, 8i, 90 configuration.

value: Gastruloids

tag: Stage

tag: background


title: PSN1.veh.4, rep 1


title: 3. 3817C AZD1283 treatment 24 hours

description:
experiment: 1
3_3817C_1_AZD1283


title: PSN1.deg.2, rep 1


title: 8. 3819D Aspirin + AZD1283 treatment 24 hours

description:
experiment: 1
8_3819D_2_Aspirin_AZD1283


title: NES5

city: Yangling

first: Lutong

last: Zhang

state: shannxi

institute: northwestern A&F university

description: Library name: Sample 11

data_processing:
Clean Data (fastq format ) Remove low quality reads and adapter (cutadapt, FASTQC)
Mapping (bam format) map the reads of each sample to the reference genome (hisat2)
Back splicing identify (bam format) Map the unmapped reads of each sample to the reference genome (tophat_fusion)
CireRNA identify(gtf format) idenltify circRNAs in each sample and merged an unique gtf (CIRCExplorer, CIRI)
Experssion profiles of circRNAs
Assembly: Sscrofa11.1
Supplementary files format and content: The matrix files contains the RNA counts and normalized values for each sample.

organism: Sus scrofa

source_name: ovary

extract_protocol:
Total RNA was extracted from each ovary using the Trizol method.
Constructing strand-specific libraries using the rRNA depletion method (rRNA depletion, RNA fragmentation, Random primer RT, dUTP incorporation, Adenosine tailing with A, Adapter ligation, Strand degradation, PCR)

value: ovary


title: 2. 3817B Aspirin treatment 24 hours

description:
experiment: 1
2_3817B_1_Aspirin


title: NES4

description: Library name: Sample 10


title: PSN1.veh.2, rep 1


title: CMO multiplexing library of Gastruloids of various size at 144h rep1

description: Library name: 144h_size_rep1_CMO

library_source: other

data_processing:
Single-cell analysis was performed as previously described (Mayran et al. 2023). Fastq files containing the sample information (cell multiplexing oligo) were processed with CITE-seq-Count version 1.4.4 using the following arguments: --cell_barcode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 --expected_cells 24000 --whitelist ’cellranger_barcodes_3M-february-2018.txt’ The barcodes were then translated (8th and 9th base were changed to their complementary bases) to match the barcode cells of the Gene Expression part. The reads containing the expression part were processed with STARSolo version 2.7.10b using: --sjdbOverhang 100 --sjdbGTFfile ’input.gtf’ --soloType CB_UMI_Simple --soloCBwhitelist ’cellranger_barcodes_3M-february-2018.txt’ --soloUMIlen 12 --soloUMIdedup 1MM_CR --soloUMIfiltering - --soloCellFilter None --outSAMmapqUnique 60 The GTF file is available at https://zenodo.org/records/10079673. Barcodes associated with empty droplets were filtered with DropletUtils using the EmptyDrops method with a lower-bound threshold of 100 and a false discovery rate (FDR) threshold of 0.01. Matrices were then processed with Seurat version 4.3.0 in R version 4.3.0, following the methods described in Mayran et al. (2023). Barcodes with fewer than 200 identified genes and genes detected in fewer than three cells were filtered out. For CMO libraries, demultiplexing was performed in R using counts from CITE-seq-Counts. Cell barcodes with fewer than 5 CMO UMIs or absent in the Seurat object were discarded. Sample attribution was performed using demuxmix with the total number of UMIs per cell. Cells classified as non-singlets (negative, unsure, or doublets) were excluded. Low-quality cells and potential doublets were removed based on the mean UMI content and mitochondrial percentage. Barcodes with fewer than 0.4 times or more than 2.5 times the mean UMI, and those outside of 0.05% to 8% mitochondrial UMIs, were excluded. The matrices were normalized, and the cell cycle score (using the 2019 updated gene list from Seurat) was computed. Samples were merged using the merge command in Seurat. The combined object was normalized, 2000 variable features were identified, and the data was scaled and regressed by cell cycle score and mitochondrial percentage. Principal components were computed using variable genes within the 5th and 80th percentiles of expression to limit batch effects. UMAP and k-nearest neighbors were computed with 25 principal components, and the clustering resolution (0.6) was optimized to avoid duplicate or missing clusters. Cluster annotation was performed manually using marker genes. Genes from the module analysis of the BRB-seq experiment were scaled across the dataset and split to display each seeding number in Fig. 4E. The list of genes within each module was scored using the addModuleScore command in Seurat, and a custom featurePlot visualization was used as described in Mayran et al. 2023.
Assembly: mm10
Supplementary files format and content: metadata.csv: a comma separated table where each row is a cell and columns are metadata associated to each cell as well as the coordinates on the UMAP.
Supplementary files format and content: tar.gz: output of STARsolo or CITE-seq-Counts (translated) as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)
Supplementary files format and content: RDS: R object with everything to redo the plots
Supplementary files format and content: CMO.Samples.csv.gz: comma separated text file with for each Library (first column), the different samples (second column), with their barcodes (third column).

molecule: other

extract_protocol:
Gastruloids seeded from different cell numbers (100, 300, 600, 1800, 5400 cells) were grown until 120 h and 144 h across two independent replicates. For each condition the number of gastruloids used was chosen to unsure that a minimum of 200 000 cells were obtained for each sample and a minimum of 24 gastruloids were collected for each sample to limit the impact of gastruloids-to-gastruloids variation. Gastruloids were collected and washed in 1ml of PBS in a 1.7 ml Eppendorf tube and dissociated using 100μl of Accutase (Stempro) for 5 minutes at 37°C. Full dissociation was verified to ensure absence of doublets and if necessary, it was completed using mechanical dissociation by pipetting. All centrifugation were done at 400 g for 5 minutes. Conditions were multiplex using the CellPlex procedure according to manufacturer’s recommendations. Cells were incubated in 50μl of cell multiplexing oligos (3’ CellPlex Kit Set A, PN-1000261) for 5 minutes at room temperature. They were then thoroughly washed three times with 1 ml PBS 1% BSA ensuring to remove as much as possible of the supernatant each time to prevent sample-to-sample contamination. Each sample was then counted and viability was assessed using a Countess 3 automated cell counter (Invitrogen) and viability was above 90% in all cases. Samples were then pooled in desired proportion to ensure proper representation of each experimental condition and the pooled cell suspension was filtered using a 40 μm cell strainer (Flowmi, BAH136800040). The final count was performed and 24 000 cells were targeted for recovery using the 10x Genomics approach following their recommendations since multiplexing allows for the resolution of more doublet cells, yielding on average 15000 singlet cells that can be used for analysis.
The pool of cells was counted and subjected to single cell RNA-seq following manufacturer’s recommendation (protocol CG000388 Rev A). We aimed for a recovery of c.a. 24000 cells per sample as a large number of  doublet droplets can be resolved with this method. cDNA preparations were performed according to 10x Genomics recommendations, amplified for 10–12 cycles and verified on fragment analyser. Both cell multiplexing oligo, and gene expression libraries were sequenced on a Novaseq (Illumina protocol #1000000106351 v03) with the cbot2 chemistry.

tag: multiplexing

value: CellPlex

tag: library type

value: CMO


title: Multiplexed scRNA-seq from Gastruloids of various size at 144h rep2

description: Library name: 144h_size_rep2_GEX

value: GEX


title: 1. 3817A DMSO control 24 hours

description:
experiment: 1
1_3817A_1_DMSO

value: CD34+ cells


title: CMC-iPSC-009_Z_rep2

city: Gyeonggi-do

first: Taemook

last: Kim

address: Dongtancheomdansaneop 1-ro

country: South Korea

institute: Deargen Inc.

data_processing:
The sequenced reads were aligned to the human reference genome (hg19) using the RNA-Seq by Expectation Maximization (RSEM) software [BMC Bioinformatics. 2011; 12:323].
The rsem-calculate-expression in RSEM was utilized to quantify the count of aligned reads and transcription per million (TPM) of genes.
Differentially expressed genes (DEGs) were investigated using the R package, DESeq2, (adjusted P-value <0.05 and log2 FC > |1|) and visualized as heatmaps and volcano plots.
Gene ontology (GO) analysis of DEGs was performed using the Enrichr online web tool [DOI: 10.1186/1471-2105-14-128]. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed using GSEA software (version 4.2.3) with default values for other parameters [ Proc. Natl. Acad. Sci. USA 106, 13820–13825 (2009)].
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: cord blood derived iPSC

growth_protocol: CMC-iPSC-009 cell lines were cultured at 5% CO2, 37℃ using mTeSR plus media on vitronectin plate, ultra low attachment plate or polymer coated plates.

extract_protocol:
10 ug of total RNA was extracted using TRIzol Reagent (Invitrogen).
Library construction and sequencing were performed at Novogene.

treatment_protocol: The mTeSR plus medium was continuously used to maintain the pluripotency of CMC-iPSC-009 cells.

value: cord blood derived iPSC

value: human induced pluripotent stem cell

value: maintenance of pluripotency, polymer coated plate


title: Multiplexed scRNA-seq from Gastruloids of various size at 144h rep1

description: Library name: 144h_size_rep1_GEX


title: PSN1.deg.8, rep 2


title: NES3

description: Library name: Sample 9


title: 5. 3819A DMSO control 24 hours

description:
experiment: 1
5_3819A_2_DMSO

value: Hematopoietic Stem and Progenitor Cells

value: DMSO


title: PSN1.veh.8, rep 2


title: NES2

description: Library name: Sample 8


title: CMO multiplexing library of Gastruloids of various size at 120h rep2

description: Library name: 120h_size_rep2_CMO


title: PSN1.inh.8, rep 2


title: CMC-iPSC-009_Z_rep1


title: CMC-iPSC-009_U_rep2

value: maintenance of pluripotency, ultra low attachment plate


title: PSN1.deg.8, rep 1


title: CMO multiplexing library of Gastruloids of various size at 144h rep2

description: Library name: 144h_size_rep2_CMO


title: NES1

description: Library name: Sample 7


title: Multiplexed scRNA-seq from Gastruloids of various size at 120h rep2

description: Library name: 120h_size_rep2_GEX


title: CMC-iPSC-009_U_rep1


title: NES6

description: Library name: Sample 12


title: PSN1.inh.8, rep 1


title: CMO multiplexing library of Gastruloids of various size at 120h rep1

description: Library name: 120h_size_rep1_CMO


title: ES6

description: Library name: Sample 6


title: CMC-iPSC-009_T_rep2

value: maintenance of pluripotency, vitronectin plate


title: PSN1.veh.8, rep 1

value: pancreatic adenocarcinoma


title: Multiplexed scRNA-seq from Gastruloids of various size at 120h rep1

description: Library name: 120h_size_rep1_GEX


title: CMC-iPSC-009_T_rep1


title: ES5

description: Library name: Sample 5


title: MOLT4.deg.4, rep 3

value: acute lymphoblastic leukemia


title: ES4

description: Library name: Sample 4


title: Pro-B_Cell_WT3

city: New York

first: Ryan

last: Smolkin

state: NY

address: 408 E 69th St

institute: MSKCC

data_processing:
Files were converted to Sam Format and Illumina adapters were marked (GATK v4.1.9.0)
Low quality reads were trimmed (GATK v4.1.9.0 -QT10)
Reads were aligned (STAR v2.7.7a with standard options) to mm10
Duplicate reads were removed (GATK v 4.1.9.0)
Combined reads were counted against gencode.vM25 using featureCounts (-t exon -g gene_id)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: Pro-B Cell

extract_protocol:
Total RNA was extracted from CD25-sufficient and -deficient cells by standard Trizol purification
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Pro-B Cell

value: WT


title: priary HASMC, si-OTUB1 transfected 3

first: Fei

last: Xu

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: aortic smooth muscle cell

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: aortic smooth muscle cell

value: cultured primary cell

value: OTUB1 knockdown

value: PDGF-BB, OTUB1 siRNA


title: MOLT4.inh.4, rep 3

value: 4 hr


title: ES3

description: Library name: Sample 3

value: ovary


title: priary HASMC, si-OTUB1 transfected 2


title: MOLT4.veh.4, rep 3


title: primary HASMC, si-NC transfected 3

value: PDGF-BB, control siRNA


title: Pro-B_Cell_WT1


title: ES2

description: Library name: Sample 2


title: Male 3

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

institute: Weifang University

description:
Library name: M3
M3

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were obtained by filtering the low-quality reads through processing the raw reads with fastq format using FASTQ preprocessor, and then mapped to the reference genome database of A. pernyi (https://bigd.big.ac.cn/gwh/, accession number: GWHABGR00000000) using HISAT2.
The FPKM measure was used to calculate expression of each gene of which read counts were determined by HTSeq-count. The biological duplication of samples was evaluated by principal component analysis (PCA) with R (v 3.2.0).
Assembly: A. pernyi (https://ngdc.cncb.ac.cn/gwh/Assembly/875/show), accession number: GWHABGR00000000.
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Antheraea pernyi

source_name: antennae

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: antennae

value: Male


title: Pro-B_Cell_WT2


title: priary HASMC, si-OTUB1 transfected 1


title: primary HASMC, si-NC transfected 2


title: MOLT4.veh.8, rep 3

value: 8 hr


title: Male 2

description:
Library name: M2
M2


title: ES1

description: Library name: Sample 1


title: MOLT4.inh.8, rep 3


title: Pro-B_Cell_KO4


title: primary HASMC, si-NC transfected 1


title: MOLT4.deg.2, rep 3

value: 2 hr


title: Pro-B_Cell_KO2


title: Pro-B_Cell_KO3


title: Male 1

description:
Library name: M1
M1


title: Pro-B_Cell_WT4


title: Jurkat cells,Simulated microgravity,replicate 3

city: Beijing

first: Li

last: Nuomin

address: No.5 Yard，Zhong Guan Cun South Street Haidian District，Beijing

institute: Beijing Institute of Technology

library_source: genomic

data_processing:
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA or Bowtie,and only uniquely mapped reads were kept, Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Assembly: hg38
Supplementary files format and content: bed

molecule: genomic DNA

source_name: Jurkat cells

growth_protocol: RPMI1640 medium containing 10% fetal bovine serum（FBS） and 1%  penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The samples were purified by MinElute PCR Purification kit(Qiagen, Frederick, MD) according to the instruction.
Following purification, the samples were PCR-amplified using NEBNext High-Fidelity PCR master mix and 0.25μl PCR primer. The quality of the tagmented libraries was visualized by Agilent D1000 ScreenTape on 2100 TapeStation system.

treatment_protocol:
To prepare nuclei, 50000 cells were collected and suspended in 50ul ice-cold lysis buffer(10mM Tris-HCl pH7.4, 10mM NaCl , 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) for 3min. 1ml elution buffer(10mM Tris-HCl pH7.4, 10mM NaCl , 3mM MgCl2, 0.1% Tween-20)was added and the samples were centrifuged at 500×g for 10min. The pellet was suspended in the transposon reaction mix(2x TD buffer, Transposase, 0.01% Digitonin and 0.1% Tween-20).
To simulate the microgravity environment, the nuclei was placed in a  random positional machine  (angular velocity of the rotation is at a speed of 30°/s) for 30 minutes at 37°C.The transposition reaction was carried out for 30 minutes at 37 °C.

value: Jurkat cells

value: Human Jurkat T Lymphocytes

value: Simulated microgravity


title: Pro-B_Cell_KO1


title: Female 3

description:
Library name: F3
F3

value: Female


title: Jurkat cells,Simulated microgravity,replicate 2


title: MOLT4.inh.2, rep 3

value: acute lymphoblastic leukemia


title: Female 2

description:
Library name: F2
F2


title: MOLT4.veh.2, rep 3

value: DMSO


title: MOLT4.deg.2, rep 2


title: C4

first: Baichao

last: Yu

address: NO.130,  Dong'an Road , Xuhui District

institute: Fudan University

description: 10x Genomics

data_processing:
Genome alignment, quantification, single cell matrix generation, and clustering were performed using Cell Ranger 6.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
Assembly: mm10
Supplementary files format and content: tap-separated value files and matrix files

source_name: mediastinal lymph node

extract_protocol:
Total cells were sorted from MedLNs of C4-treated or -untreated OVA-induced asthma model. The single cells were obtained by the method of grinding through a 70 μm cell strainer. For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM.
Library construction was performed according to the manufacture's protocol(Single Cell 3′ library and Gel Bead Kit v.3).Briefly, GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: mediastinal lymph node

value: WT

tag: strain


title: OVA

description: 10x Genomics


title: MOLT4.deg.8, rep 3

tag: cell line


title: Jurkat cells,Simulated microgravity,replicate 1


title: Female 1

description:
Library name: F1
F1


title: Jurkat cells,Normal gravity, replicate 3

value: Normal gravity


title: MOLT4.inh.2, rep 2


title: KO3_input

first: Qianqian

last: Feng

address: 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: sample 12
ko_3_input

data_processing:
Quality control, low-quality filtering and read de-adaptor functions were performed with the fastp tool to obtain clean reads. The clean reads were subsequently aligned to the mouse reference genome (mm39, with gene annotations from the Ensembl database v108) via HISAT2 software. Finally, the m6A RNA methylation peaks were identified by using the exomePeak2 R package.
Assembly: mm39
Supplementary files format and content: diff_peaks.txt

source_name: right ventricle and outflow tract on embryonic day 10.5-11.5

extract_protocol:
The Nano UMI MeRIP experiment, high-throughput sequencing and data analysis were conducted by Seqhealth Technology Co., Ltd. (Wuhan, China). The right ventricle and outflow tract tissues from E10.5-11.5 Mettl3-CV KO and control embryos were isolated. Each group consisted of two biological duplicate samples and each sample contained tissues from 20 embryos. The RNA was extracted using TRIzol reagent. Total RNA (5 μg) was fragmented into approximately 200 nt fragments and used for the MeRIP experiment. A specific anti-m6A antibody (Synaptic Systems, 202003) was used for m6A immunoprecipitation.
The stranded RNA sequencing library was constructed by using the KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd., China) with five PCR cycles. The kit eliminates duplication bias in PCR and sequencing steps by using a unique molecular identifier (UMI) of 8 random bases to label the preamplified cDNA molecules. Then, ribosomal cDNA was removed with a SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian, 634413, Takara/Clontech, Japan), and ten PCR cycles were added. The library products of 200-500 bp were enriched, quantified and finally sequenced on a PE150 model DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China).

tag: genotype

value: Tagln-Cre; Mettl3flox/flox


title: Jurkat cells,Normal gravity, replicate 2

tag: cell type


title: KO3_ip

description:
Library name: sample 11
ko_3_ip

value: right ventricle and outflow tract on embryonic day 10.5-11.5


title: Adult HdrR skin & scales, run2

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Alignment and generation of the count matrix were performed using the Cell Ranger (version 7.1.0) pipeline against the medaka genome (GCA_002234675.1) and using Ensemble gene annotation version ASM223467v1.110, the number of cells for the first experiment was 4671 cells and for the second 614 cells.
Assembly: medaka genome (GCA_002234675.1) and using Ensemble gene annotation version ASM223467v1.110
Supplementary files format and content: tsv files with features, count matrix and cell barcodes

organism: Oryzias latipes

source_name: skin & scales

extract_protocol:
Fish were anesthetized with Tricaine and euthanized on ice. Skin and scales were removed using tweezers and immersed in TrypLE Express (Invitrogen, 12604039). The sample was incubated at 37°C and shaken at 300 rpm for 1 hr, followed by mechanical disruption with a the isolated cells were incubated with Draq5 (Thermo Scientific™, Cat. 62251) to mark the nuclei for 10 min prior to FACS. Cells were analyzed and sorted using a BD FACSAria II Special Order Research Product (SORP) Cell Sorter with a 100 µM nozzle. Cells were counted and diluted to a final concentration in PBS supplemented with 0.04% BSA. Cellular suspension was loaded onto Next GEM Chip G targeting first experiment 10,000 cells and second experiment 1,000 cells, then ran on a Chromium X instrument to generate gel beads in emulsion (GEMs, 10x Genomics).
Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3.1 Chemistry). : Single-cell 3’ RNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~25,000 reads per cell. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina) with the following read length: 28 bp Read1, 10 bp I7 Index, 10 bp I5 Index and 90 bp Read2.
Single-cell 3’ RNA-seq

value: skin & scales

value: skin and scale cells

value: HdrR medaka. Southern phenotype

tag: treatment

value: Male and female adult WT fish


title: Adult HdrR skin & scales, run1


title: KO2_input

description:
Library name: sample 10
ko_2_input


title: 10_C6758 PV patient

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: Genomic DNA was bisulfite converted and analyzed with the Illumina human methylation 450k BeadChip array for PBMCs

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium Methylation 450k BeadChips (Illumina) according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing: pOOBAH using sesame

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Standard Illumina protocol

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifucation (Ficoll) of 4 patients diagnosed with Post-PV-MF, 4 patients diagnosed with PV and 4 healthy donors.

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit.

value: Male

tag: age

tag: allele burden

value: PBMC


title: MOLT4.inh.2, rep 4

value: 2 hr


title: fibrotic liver

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

description: 10 × Genomics

data_processing:
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v2.3.0) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Assembly: FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38.
Supplementary files format and content: Matrix table with raw gene counts and transcript counts for every gene and every sample.

source_name: liver

extract_protocol:
Mice were perfused through portal vein cannulation by normal saline solution. Liver tissues were removed and minced with ophthalmic scissors in DMEM medium, and enzymatically digested using the liver dissociation kit (Miltenyi Biotech , 130-105-807). Cell suspensions were filtered through a 100 μm nylon mesh, centrifuged at 50 g for 3 min  at 4 ºC, and the supernatants were further centrifuged at 320 g for 8 min to obtain non-parenchymal liver cells. Isolation of hepatic immune cells were performed through a 30% Percoll (GE Healthcare, 17-0891-01) . Primary CD45+ non-parenchymal liver cells  were further sorted by staining with antibodies antibody  for mouse CD45 (Biolegend, 103112). Cells were sorted using FACSAria (Becton, Dickinson).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

tag: tissue

value: liver


title: 1_C126 PV patient


title: MOLT4.veh.2, rep 4


title: MOLT4.veh.2, rep 2


title: Jurkat cells,Normal gravity, replicate 1

value: Jurkat cells

value: Human Jurkat T Lymphocytes


title: MOLT4.deg.2, rep 4

value: acute lymphoblastic leukemia


title: MOLT4.deg.4, rep 2

value: 4 hr


title: KO1_input

description:
Library name: sample 8
ko_1_input


title: 3_C2759 PV patient


title: KO1_ip

description:
Library name: sample 7
ko_1_ip


title: MOLT4.inh.4, rep 2


title: WT3_input

description:
Library name: sample 6
wt_3_input


title: 6_C4752 PV patient


title: MOLT4.deg.4, rep 4


title: 5_C4296 Post-PV-MF patient

value: Female


title: MOLT4.inh.4, rep 4


title: WT3_ip

description:
Library name: sample 5
wt_3_ip


title: 11_C7388 Post-PV-MF patient


title: WT2_input

description:
Library name: sample 4
wt_2_input


title: MOLT4.veh.4, rep 4

value: DMSO


title: KO2_ip

description:
Library name: sample 9
ko_2_ip


title: WT2_ip

description:
Library name: sample 3
wt_2_ip


title: 2_C2484 Post-PV-MF patient


title: MOLT4.deg.8, rep 2

value: 8 hr


title: WT1_input

description:
Library name: sample 2
wt_1_input


title: 4_C4017 Post-PV-MF patient


title: 3a_healthy control samples


title: MOLT4.inh.8, rep 2


title: WT1_ip

description:
Library name: sample 1
wt_1_ip


title: MOLT4.veh.8, rep 2


title: Salivary_glands_Infection_3

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

data_processing:
We used two rounds of krakenuniq (i.e. against a database built using EuPathDB and then malariae reads against a database build using genomes from Anopheles gambiae complex and the P. malariae genome) to decontaminate reads and extract potential P.malariae reads (2x150bp)
We used sortmerna to remove rRNA reads
We used hisat2 –very-sensitive to perform alignment
samtools view and Picard’s MarkDuplicates to remove duplication, samtools view and the perl expression “perl -nle 'if (/^@/){ print } else {@ar=split(/\t/); ($n)= $ar[5] =~ /(\d{3,}M)/; if (defined($1)) { print }}'” to filter out reads that did not aligned at least 100 bp
The software coco to perform read counting and quantification.
Assembly: PmUG01
Supplementary files format and content: DESEQ2 to obtain TPM counts and Differentially Expressed Genes subset of genes that are significant (FDR < 0.05) for the comparison between tissues

organism: Anopheles gambiae

source_name: Salivary glands

extract_protocol:
Mosquitoes were maintained under standard insectary conditions (27 ± 2 °C, 80 ± 5% relative humidity, 12:12 LD). Females were fed through membrane feeders on blood containing gametocytes of P. malariae, prepared according to standard protocols. Thereafter the mosquitoes were given access to a solution of 5% glucose/ 0.05% 4-aminobenzoic acid ad libitum
Immediately after dissection, tissues were stored in TRIzol (Invitrogen) and frozen at -80ºC until subsequent processing. Total RNA was extracted from a pool of midguts and salivary glands from ~10 mosquitoes using the TRIzol manufacturer protocol. RNA concentration was quantified using a Qubit® 2.0 Fluorometer, and RNA integrity was determined with an Agilent 2100 Bioanalyzer. We used the Ovation® Universal RNA-seq System (Nugen Technologies) for RNA-seq library construction following the manufacturer’s instructions

value: Salivary glands

value: P. malariae-infection 18 days

tag: replicate


title: iPSC patient 3  JAK2 V617F homozygous

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

label: Cy3 and Cy5

source_name: iPSC

growth_protocol: Induced pluripotent stem cells (iPSC) were generated from PBMCs of three PV patients with varying JAK2 V617F allele burdens (37 %, 96 %, and 25 %) in a previous work as described before (Boehnke et al., 2021; Flosdorf et al., 2024; Satoh et al., 2021). Using CRISPR/Cas9 genome editing, additional genotypes (wild type, heterozygous, and homozygous) were generated for each patient derived clones. In the Human Pluripotent Stem Cell Registry, these iPSCs are listed as: patient 1 WT (UKAi002-A), heterozygous (UKAi002-B) and homozygous JAK2 V617F clone (UKAi002-B3); patient 2 WT (UKAi003-A1), heterozygous (UKAi003-A2) and homozygous clones (UKAi003-A); patient 3 WT (UKAi013-A), heterozygous (UKAi013-B) and homozygous clones (UKAi013-B1).

extract_protocol: Genomic DNA was isolated using the Macherey Nagel Tissue kit.

treatment_protocol: For hematopoietic differentiation, iPSCs were cultured in micro-contact printed plates with StemMACS iPS Brew XF medium (Miltenyi Biotec) and 10 μM Y-27632 (Abcam) to form embryonic bodies (EB) at 37°C / 5% CO2. Self-detachment of EBs was observed after 6 to 9 days, depending on the clone, and they were then resuspended in serum-free medium containing 50% IMDM, 50% Ham’s F12, 1% chemically defined lipid concentrate, 2 mM GlutaMAX (all Thermo Fisher Scientific), 0.5% Albiomin (Unifols), 400 μM 1-thioglycerol, 50 μg/mL L-ascorbic acid, and 6 μg/mL holo transferrin (all Sigma Aldrich) supplemented with 10 ng/mL FGF-2 (Peprotech) and 10 ng/mL BMP-4 (Miltenyi Biotec). Approximately 30 to 50 EBs were distributed per well on a gelatin coated 6-well plate. From day 2 to day 7, cells were cultured in serum-free medium supplemented with 10 ng/mL FGF 2, 10 ng/mL BMP-4, 50 ng/mL SCF, 10 ng/mL VEGF-A (all Peprotech), and 10 U/mL penicillin/streptomycin (Thermo Fisher Scientific). From day 8 to day 16, serum-free medium was supplemented with 10 ng/mL FGF 2 and 50 ng/mL SCF only. Cells were harvested on day 16 and their phenotype was analyzed by flow cytometry. Further cells were collected for DNA methylation analysis.

value: iPSC

tag: patient

value: patient 3

value: JAK2 V617F homozygous

tag: genetic modification

value: CRISPR/Cas9 mutated

tag: hpsc registry id

value: male


title: 1a_healthy control samples

tag: Sex

value: PBMC


title: iPSC patient 3  JAK2 V617F heterozygous

value: JAK2 V617F heterozygous

value: Reprogramming


title: MOLT4.deg.8, rep 4

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Control Software v4.0.2.7, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the hg38 human assembly with the gencode version 43 annotation using the nf-core/rnaseq workflow revision 3.12.0 (Alexander Peltzer et al. 2024). The genomic target included the LexogenSIRVData spike-in reference. Gene level summaries were prepared from the star_salmon quantitation using tximport version 1.28.0.
Assembly: hg38 human assembly with gencode43 annotation and Lexogen SIRV spike-in transcrips.
Supplementary files format and content: 230925Koe_MOLT4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_MOLT4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_PSN1_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_PSN1_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_RH4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_RH4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.

extract_protocol:
Follwing treatment, cells were immediately lysed in lysis buffer (from PerkinElmer’s chemagic RNA Tissue 360 H96, VD200615) supplemented with BME flash frozen and stored at -80c. After all biological replicates were collected, samples were thawed in deep 96-well plates. An equal amount (~30pg) of Lexogen’s ERCC spike-in mix (SIRV-3) were added at this point following manufacturer’s recommendations. The PerkinElmer’s Chemagic 360 was used for bead-based RNA extraction following manufacturer’s standard protocol.
RNA was quantified using an Agilent Fragment Analyzer, purified using 2X RNA SPRI beads, and 1ng of total RNA was used for Illumina library preparation. Libraries were prepared using a reduced volume version of SMART-seq2 performed on an SPT Mosquito HV using 10 cycles of amplification for cDNA generation and 16 cycles for library generation using NexteraXT (Illumina).

tag: time


title: Salivary_glands_Infection_2

value: P. malariae-infection 16 days


title: AC13-2_healthy control samples


title: MOLT4.inh.8, rep 4


title: MOLT4.veh.8, rep 4


title: APOE-KO mice，control8，16 weeks

city: shanghai

first: yang

last: xiaobo

address: 上海市浦东新区松涛路647弄四孵产业园

data_processing:
Illumina Casava software used for basecalling
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mus musclus 103
Supplementary files format and content: tab-delimited text files include FPKM values for Sample1-Sample16
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. llumina TruSeg RNA SamplePrep Kit was used with 1ug oftotal RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard lllumina protocols

value: liver

value: hepatocyte


title: iPSC patient 3 JAK2 wild type

value: JAK2 wild type


title: Salivary_glands_Infection_1


title: iPSC patient 2  JAK2 V617F homozygous

value: patient 2


title: MOLT4.deg.2, rep 1

first: Charles

last: Whittaker

value: acute lymphoblastic leukemia

value: 2 hr


title: 2a_healthy control samples

value: Male


title: Midguts_Infection_1

source_name: Midguts

value: Midguts


title: APOE-KO mice，control7，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: iPSC patient 2  JAK2 V617F heterozygous

value: iPSC

value: CRISPR/Cas9 repair


title: MOLT4.inh.2, rep 1


title: APOE-KO mice，control6，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: vrn1 FRI, cold, bio_rep4

city: Norwich

first: Miguel

last: Montez

address: Norwich Research Park, Colney Ln

department: Department of Cell and Developmental Biology

institute: John Innes Centre

description:
PE150
MN-1W-8

data_processing:
Demultiplexed FASTQ data was obtained from BGI. Illumina adaptor sequences were trimmed with fastp. Paired-end reads were aligned to the Arabidopsis TAIR10 reference genome using Bowtie2 --end-to-end --no-unal (version 2.4.1). Samtools (version 1.5) was used to convert the SAM files into BAM files and sort reads by genomic coordinate, and then to split the sorted BAM files into files containing only reads mapped to FLC locus. At this step, reads with a base quality under 10 were discarded. Further analyses were performed using in-house scripts (available on https://github.com/Miguel-Montez/Targeted-MNase-seq-analysis) using RStudio (version 4.2.3).
Assembly: TAIR10
Supplementary files format and content: Tab-separated text file with FLC-specific data including genotype, treatment, biological replicate, DNA leftmost coordinate, DNA rightmost coordinate, DNA fragment length, and DNA fragment frequency.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis Columbia (Col-0) with an active FRIGIDA allele introgressed from the ecotype San Feliu-2 was used as wild-type (WT FRI), and vrn1-4 FRI as mutant. Seeds were surface-sterilized with chlorine gas, sown on plates with full-strength Murashige & Skoog (MS) medium including vitamins (Duchefa, M0222) plus 1% agar, and stratified for 3 days at 4°C. Seedlings were grown at 22°C, 16h light/8h dark for 10 days (warm) and subject to 1 week at 5°C (cold).

extract_protocol:
1.5 g of seedlings per replicate was ground with liquid nitrogen to a fine powder Nuclei were isolated and purified on a Percoll gradient. 65 mg of purified nuclei were treated with 10 U of MNase (Worthington) for 30 min at 37°C. DNA was extracted with phenol-chloroform and treated with RNase A for 20 min at 37°C. Mono- and sub-nucleosomal DNA fragments were purified with AMPure XP beads (Beckman Coulter), recovering all fragments < 200 bp and excluding all fragments > 300 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645) following the manufacturer’s instructions. After adaptor ligation, DNA was purified with AMPure XP beads, recovering all fragments > 200 bp. Illumina indexing PCR was performed with 8 cycles. Libraries were pooled and enriched for target loci in one reaction using myBaits Custom Kit (Daicel Arbor Biosciences) following the manufacturer’s instructions for high sensitivity hybridization capture for targeted NGS.

treatment_protocol: Seedlings grown at ambient temperature (warm) and subject to 5°C for 1 week (cold).

value: whole seedling

value: vrn1-4 with an active FRIGIDA allele

value: 1 week cold


title: MOLT4.veh.2, rep 1

value: DMSO


title: iPSC patient 1  JAK2 V617F homozygous

value: patient 1

value: JAK2 V617F homozygous

value: CRISPR/Cas9 mutated

value: female


title: vrn1 FRI, cold, bio_rep3

description:
PE150
MN-1W-7


title: APOE-KO mice，control5，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园

value: liver

value: hepatocyte


title: MOLT4.deg.4, rep 1

value: 4 hr


title: APOE-KO mice，control4，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: iPSC patient 1  JAK2 V617F heterozygous

value: JAK2 V617F heterozygous

value: Reprogramming


title: APOE-KO mice，control3，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: vrn1 FRI, cold, bio_rep1

description:
PE150
MN-1W-5


title: MOLT4.deg.8, rep 1

value: acute lymphoblastic leukemia

value: 8 hr


title: vrn1 FRI, cold, bio_rep2

description:
PE150
MN-1W-6


title: WT FRI, cold, bio_rep3

description:
PE150
MN-1W-3

value: Col-0 with an active FRIGIDA allele


title: iPSC derived hematopoietic stem and progenitor cells patient 3  JAK2 V617F homozygous

value: patient 3


title: MOLT4.inh.4, rep 1


title: iPSC patient 2 JAK2 wild type

value: iPSC

value: patient 2

value: JAK2 wild type

value: CRISPR/Cas9 repair

value: male


title: MOLT4.veh.4, rep 1

value: DMSO


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh8，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: APOE-KO mice，control2，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: Midguts_Infection_2

value: Midguts

value: P. malariae-infection 16 days


title: MOLT4.inh.8, rep 1


title: APOE-KO mice，control1，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园

value: liver


title: iPSC derived hematopoietic stem and progenitor cells patient 3  JAK2 V617F heterozygous


title: WT FRI, cold, bio_rep4

description:
PE150
MN-1W-4

value: whole seedling

value: 1 week cold


title: WT FRI, cold, bio_rep2

description:
PE150
MN-1W-2


title: iPSC derived hematopoietic stem and progenitor cells patient 3 JAK2 wild type


title: MOLT4.veh.8, rep 1


title: 1833-sgACBP-with oil acid3

city: Houston

last: Ma

state: Texas

address: MD Anderson Cancer Center, Zayed Building, Z7.2036, 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

data_processing:
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome with hisat2(v2.1.0). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2).
Assembly: human hg38 genome
Supplementary files format and content: RNASeq: Deseq2 normalized read count and differential expression result in csv file.

source_name: breast

growth_protocol: BoM-1833 cells cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% and 10,000 U/mL of penicillin-streptomycin. All cells were cultured in a 37 °C incubator in a humidified, 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated by using the RNeasy Mini kit (Qiagen, 74104) and was treated with DNase I (Qiagen, 79254). RNA-seq libraries were prepared from 3 μg of total RNA by using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020594) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer’s instructions.  Sample preparation for ribosome profiling was conducted according to the manufacturer’s specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina). ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer’s instructions.

treatment_protocol: sample with oli acid we culture cells in the present of oleic acid.

value: breast

value: Breast invasive carcinoma

value: ACBP-knockout


title: vrn1 FRI, warm, bio_rep3

description:
PE150
MN-NV-6

value: vrn1-4 with an active FRIGIDA allele

value: ambient temperature


title: iPSC derived hematopoietic stem and progenitor cells patient 1  JAK2 V617F homozygous

value: patient 1

value: JAK2 V617F homozygous


title: iPSC derived hematopoietic stem and progenitor cells patient 2  JAK2 V617F heterozygous

value: patient 2

value: JAK2 V617F heterozygous


title: 1833-CON-with oil acid3

value: control


title: iPSC derived hematopoietic stem and progenitor cells patient 2 JAK2 wild type

value: JAK2 wild type


title: vrn1 FRI, warm, bio_rep2

description:
PE150
MN-NV-5


title: iPSC derived hematopoietic stem and progenitor cells patient 2  JAK2 V617F homozygous


title: 1833-sgACBP-with oil acid2


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh5，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园

value: hepatocyte


title: WT FRI, cold, bio_rep1

description:
PE150
MN-1W-1

value: Col-0 with an active FRIGIDA allele


title: 1833-sgACBP-with oil acid1


title: vrn1 FRI, warm, bio_rep1

description:
PE150
MN-NV-4


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh3，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh6，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh4，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: WT FRI, warm, bio_rep3

description:
PE150
MN-NV-3


title: Cord blood from newborns without GDM1

city: Shanghai, China

first: Yang

last: Lily

address: No.1239, Siping Road, Yangpu District, Shanghai

institute: Tongji University

hyb_protocol: DNA samples were hybridized to Illumina HumanMethylation850 BeadChip following standard protocol

scan_protocol: BeadChips were scanned using Illumina iScan system

data_processing: Raw IDAT files were processed using minfi R package. Background correction and normalization were performed using SWAN method.

source_name: umbilical cord blood

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Standard DNA extraction from cord blood using QIAamp DNA Blood Mini Kit

treatment_protocol: No experimental treatments were administered. Samples were collected following standard clinical procedures.

value: umbilical cord blood


title: Cord blood from newborns of GDM5


title: iPSC derived hematopoietic stem and progenitor cells patient 1  JAK2 V617F heterozygous


title: Cord blood from newborns without GDM5


title: 1833-CON-with oil acid2


title: Cord blood from newborns without GDM4


title: 1833-CON-with oil acid1


title: whole_blood_derived_DNAm_30

status: Public on May 06 2025

city: London

first: Paula

last: Longhi

address: Charterhouse Square

department: William Harvey Research Institute

institute: Queen Mary University of London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridised to Human Infinium MethylationEPIC beadchip (Illumina) using standard Illumina protocol

scan_protocol: Array were imaged using Illumina iScan System and standard recommended Illumina Scanner settings

data_processing:
meffil (v1.1.1) package in R environment (v3.6.1)
Processed data file norm_beta.csv.gz represents Average Beta.

source_name: whole blood

extract_protocol: Genomic DNA was extracted from whole blood using the QIAamp DNA blood mini kit (Qiagen) (catalogue number: 51104)

value: Male

value: whole blood

value: N


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh1，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园

value: liver


title: whole_blood_derived_DNAm_32

value: Ex


title: WT FRI, warm, bio_rep1

description:
PE150
MN-NV-1

value: whole seedling


title: whole_blood_derived_DNAm_29


title: whole_blood_derived_DNAm_31


title: whole_blood_derived_DNAm_27

value: Female


title: whole_blood_derived_DNAm_28

value: Y


title: whole_blood_derived_DNAm_25


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh2，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: Cord blood from newborns of GDM3


title: WT FRI, warm, bio_rep2

description:
PE150
MN-NV-2

value: ambient temperature


title: iPSC derived hematopoietic stem and progenitor cells patient 1 JAK2 wild type

value: patient 1


title: whole_blood_derived_DNAm_26


title: whole_blood_derived_DNAm_24


title: whole_blood_derived_DNAm_22


title: whole_blood_derived_DNAm_23


title: Cord blood from newborns of GDM4


title: Cord blood from newborns without GDM3


title: whole_blood_derived_DNAm_21


title: Cord blood from newborns of GDM2


title: Cord blood from newborns without GDM2


title: whole_blood_derived_DNAm_20


title: Cord blood from newborns of GDM1


title: whole_blood_derived_DNAm_19


title: whole_blood_derived_DNAm_18


title: whole_blood_derived_DNAm_17


title: whole_blood_derived_DNAm_16


title: whole_blood_derived_DNAm_11


title: whole_blood_derived_DNAm_10


title: APOE-KO mice，SAA (20 mg/kg) or PBS daily sh7，16 weeks

address: 上海市浦东新区松涛路647弄四孵产业园


title: whole_blood_derived_DNAm_15


title: whole_blood_derived_DNAm_13


title: whole_blood_derived_DNAm_9


title: whole_blood_derived_DNAm_8


title: whole_blood_derived_DNAm_7


title: whole_blood_derived_DNAm_4


title: whole_blood_derived_DNAm_5


title: whole_blood_derived_DNAm_6


title: whole_blood_derived_DNAm_3


title: whole_blood_derived_DNAm_1


title: iPSC patient 1 JAK2 wild type

value: iPSC

value: Reprogramming

value: female


title: whole_blood_derived_DNAm_14


title: whole_blood_derived_DNAm_12


title: whole_blood_derived_DNAm_2


title: HEK293T STORM-seq

city: Grand Rapids

first: Benjamin

middle: K

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description:
Library name: Sample2
STORM-seq with UMIs in HEK293T

data_processing:
Unmapped Smart-seq3xpress (SS3x) HEK293T and K-562 BAM files were demultiplexed to individual cell FASTQ files by extracting reads assigned to expected cell barcodes in the CB BAM tag (concatenation of i5 and i7 indices, yielding a 20 bp barcode) and appending conserved sequences to delineate internal and 5’ UMI containing reads. Briefly, to reconstruct the expected 4 FASTQs per cell file structure, cell barcodes (CB BAM tag) were added to index 1 and index 2 FASTQ files, and respective read 1 and read 2 reads to separate FASTQ files. If the UB BAM tag (UMI) was populated, the conserved ‘ATTGCGCAATG’ sequence motif was added, then the UMI (UB tag), followed by the ‘GGG’ motif. Internal and 5’ UMI containing reads from SS3x were separated as previously described, using the conserved ‘ATTGCGCAATG’ sequence motif at the start of read 1 to delineate 5’ UMI reads. VASA-seq data were demultiplexed to single cell FASTQ files using provided scripts from https://github.com/hemberg-lab/VASAseq_2022. Scripts for STORM-seq de-multiplexing from GEO/SRA/ENA FASTQs can be found at https://github.com/biobenkj/stormseq_protocols/tree/main/analysis/stormseq_manuscript/demux_storm.
VASA-seq data were pre-processed and trimmed using cutadapt (v4.4) through provided scripts at https://github.com/hemberg-lab/VASAseq_2022. After trimming, the UMI and cell barcode were appended to the 5’ end of the read. Importantly, in the provided concatenator.py, a conversion error occurs when extracting and appending the UMI and cell barcode where a base quality score of 14 (ASCII character ‘/’) is unintentionally converted to a base quality score of 46 (ASCII character ‘O’). As a result, during the addition of the UMI and cell barcode to the 5’ end of the read, these base qualities were reverted to their original value.
All subsampling was performed using seqtk (v1.4-r122) sample on pre-processed/trimmed reads across technologies, setting the random seed to 100, unless specified otherwise.
STORM-seq HEK293T, K-562, and RMG-2 reads were mapped and quantified at the gene and transcript isoform level using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) and kb_python (v0.28.2) with the -x STORM-seq preset. For transcript isoform quantification, kb_python was called with the --tcc option enabled to output transcript compatibility counts (TCC). TCCs were quantified using kallisto quant-tcc to produce transcript isoform level counts. Further, fragment length bias was accounted for in quant-tcc as well as including at least 50 bootstraps for gene/transcript isoform quantification. Per-cell mapping rates were extracted from the log files.
Passage matched (for direct comparison to STORM-seq) K-562 and HEK293T VASA-seq data generated by Single Cell Discoveries were mapped and quantified against Ensembl 101 using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) following the kb_python analysis toolchain, with modifications to support this data type. Briefly, kallisto bus was used with default parameters and 1) -x 0,6,8:0,0,6:0,14,0, 2) --fr-stranded. Next, bus files were sorted (bustools sort), inspected (bustools inspect), and counted (bustools count). For bustools count, default parameters were used with the following modifications, 1) --multimapping, 2) --umi-gene. Next, kallisto quant-tcc was used to quantify transcript abundance with default parameters and 1) -t 8, 2) -l 550, 3) -s 300, 4) -b 50, and 5) --matrix-to-files. The average fragment length and standard deviation parameters were specified based on VASA-seq bioanalyzer traces provided (Supp. Fig. 19). Per-cell mapping rates were extracted from the log files.
HEK293T and K-562 pre-processed SS3x FASTQs were mapped and quantified using a similar strategy as VASA-seq, using kallisto|bustools. Briefly, per-cell 5’ UMI reads and internal reads were extracted as described above, prior to subsampling and mapping/quantification. Next, for gene/transcript quantification, kallisto bus was used with 5’ UMI reads with default parameters and the following modifications, 1) -x 0,0,0,1,0,0:2,0,21:2,24,0,3,0,0, 2) --tag ATTGCGCAATG, 3) --paired, 4) --fr-stranded, and 5) -t 8. Transcript abundance quantification was performed using kallisto quant-tcc with default parameters and the following modifications 1) -b 50 and 2) --matrix-to-files.
Assembly: GRCh38 (Ensembl 101)
Supplementary files format and content: Text file STORM-seq metadata for demultiplexing
Supplementary files format and content: Text files of raw UMI counts with multimappers from kallisto|bustools using Ensembl 101 annotations

growth_protocol: The K-562 cell line was purchased from ATCC (CCL-243). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/Streptomycin (Gibco). HEK293T cells were purchased from the American Type Culture Collection (ATCC; CRL-3216) and cultured in DMEM medium supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin/Streptomycin (Gibco). RMG-2 cells were purchased from the JCRB Cell Bank and Seikiusi XenoTech, LLC. RMG-2 cells were maintained in DMEM/F12, supplemented with 10% FBS and sub-cultured at 1:3-1:5 every 7-9 days. Fresh media was added every 2-3 days between sub-culturing.

extract_protocol:
Single cells were deposited in a 384-well plate using a BD FACSymphony S6 equipped with a 130 um nozzle at 14 psi. Single cells were lysed in their respective lysis buffer (e.g., STORM-seq, VASA-seq, or Smart-seq3xpress). Passage matched K-562 and HEK293T cells were deposited same day for both STORM-seq and VASA-seq.
Libraries were constructed as previously described for Smart-seq3xpress (https://doi.org/10.1038/s41587-022-01311-4) or by Single Cell Discoveries following the VASA-seq protocol (https://www.scdiscoveries.com/services/vasa-seq/; https://doi.org/10.1038/s41587-022-01361-8). For STORM-seq, libraries were constructed following https://doi.org/10.5281/zenodo.15178455.


title: RMG-2 STORM-seq

description:
Library name: Sample3
STORM-seq with UMIs in RMG-2


title: OVCAR4, shRNA#2-MPZL3, replicate 3

city: Pittsburgh

first: Nadine

last: Hempel

state: PA

address: 5051 Centre Ave

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

description: Library name: OV4_3087_N3

data_processing:
Raw data (raw reads) in fastq format were processed through in-house perl scripts (Novogene). 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 were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built 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. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab delimited text file contains raw counts for each sample
Supplementary files format and content: tab delimited text file contains fpkm data for each sample

growth_protocol: OVCAR4 cells were maintained in RPMI-1640 (Gibco, 11875) supplemented with 2 mM glutamine (Gibco, 25030081), 10% FBS (Avantor Seradigm, 1500-500), 0.25 U/mL insulin (Gibco, 12585014)

extract_protocol:
Total RNA was extracted from cells using Direct-zol RNA Miniprep kit (Zymo Research, R2052).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dTTP, end repair, A-tailing, adapter ligation, size selection, amplification, and purification for non-directional library preparation. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Ovarian serous adenocarcinoma

value: MPZL3 knock-down


title: K-562 STORM-seq

description:
Library name: Sample1
STORM-seq with UMIs in K-562


title: OVCAR4, shRNA#2-MPZL3, replicate 2

description: Library name: OV4_3087_N2


title: OVCAR4, shRNA#2-MPZL3, replicate 1

description: Library name: OV4_3087_N1


title: OVCAR4, shRNA#1-MPZL3, replicate 2

description: Library name: OV4_304_N2


title: OVCAR4, shRNA#1-MPZL3, replicate 3

description: Library name: OV4_304_N3


title: OVCAR4, shRNA#1-MPZL3, replicate 1

description: Library name: OV4_304_N1


title: OVCAR4, shRNA scramble Control vector, replicate 3

description: Library name: OV4_SCR_N3

value: WT


title: OVCAR4, shRNA scramble Control vector, replicate 2

description: Library name: OV4_SCR_N2


title: OVCAR4, shRNA scramble Control vector, replicate 1

description: Library name: OV4_SCR_N1


title: OVCA433, shRNA#3-MPZL3, replicate C

description: Library name: C3

growth_protocol: Human ovarian cancer OVCA433 cells were maintained in RPMI 1640 medium (Corning,10-040-CV) supplemented with 10% FBS


title: OVCA433, shRNA#3-MPZL3, replicate B

description: Library name: B3


title: OVCA433, shRNA#3-MPZL3, replicate A

description: Library name: A3


title: OVCA433, shRNA#1-MPZL3, replicate C

description: Library name: C2


title: OVCA433, shRNA#1-MPZL3, replicate B

description: Library name: B2


title: OVCA433, shRNA#1-MPZL3, replicate A

description: Library name: A2


title: OVCA433, shRNA Control vector, replicate C

description: Library name: C1


title: OVCA433, shRNA Control vector, replicate A

description: Library name: A1


title: Renal Microvascular Endothelial Cells, H/R+Fuc-pPGC-1α-GVs+US, HR6

city: Hangzhou

first: Yuxian

last: Kuai

state: Zhejiang

address: No. 88 Jiefang Road, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: sample 6

data_processing:
Reads mapping: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Expression analysis: We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM（Fragments Per Kilo bases per Million fragments） / TPM（Transcripts per Million） to standardize the expression.
Differential expression analysis: Then difference expression of genes was analyzed by DESeq2 (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used ComplexHeatmap (v2.16.0) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Enrichment analysis: We mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using ClusterProfiler (v4.6.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value < 0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes.  ClusterProfiler (v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value < 0.05.
GSEA(Gene Set EnrichmentAnalysis): ClusterProfiler (v4.6.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn.
Assembly: GRCh38.p13
Supplementary files format and content: .tar.gz

source_name: Renal Microvascular Endothelial Cells

extract_protocol:
RNA extraction and detection Reagent kit: InvitrogenTRIzol reagent Operation steps: 1. Homogenization treatment Take the sample in a 2ml grinding tube and thoroughly grind it using a grinder at 60Hz for 60 seconds. Then take 2-4 samples each time, add 1ml TRIzol reagent to the ground powder and mix immediately (the sample needs to be kept at low temperature before adding TRIzol). After adding all the samples to TRIzol, wet beat at 55Hz for 30 seconds and incubate at room temperature for 5 minutes to facilitate complete separation of nuclear protein bodies in the homogenized sample. Centrifuge at 12000rpm for 5 minutes and take the supernatant (a 1.5ml centrifuge tube can be prepared during centrifugation to hold the supernatant). 2. Phase separation Add 0.2ml chloroform to the supernatant, shake the tube vigorously for 30 seconds, and incubate at room temperature for 2-3 minutes. Centrifuge at 4 ° C and 12000rpm for 15 minutes (during centrifugation, prepare a 1.5ml centrifuge tube and write the sample name and number). The mixture separates into a red lower layer (phenol chloroform phase), an intermediate phase, and an upper colorless aqueous phase. RNA exists in the aqueous phase. 3. RNA precipitation Transfer 400 μ l of aqueous phase to a 1.5ml final tube, add 500 μ l of isopropanol, invert and mix well (about 30 times). Incubate the sample at room temperature for 10 minutes. Centrifuge at 4 ° C and 12000rpm for 10 minutes. 4. RNA washing Discard the supernatant and add 1ml of 75% ethanol to wash the precipitate (try to resuspend the precipitate as much as possible). Centrifuge at 4 ° C and 12000rpm for 5 minutes. 5. Dissolve RNA again At the end of the process, briefly centrifuge and extract ethanol, then add an appropriate amount of RNase free water-soluble sample directly. Do not vacuum centrifuge RNA. It is important not to let the RNA precipitate completely dry, as this will greatly reduce its solubility.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

value: Renal Microvascular Endothelial Cells


title: Renal Microvascular Endothelial Cells, H/R+Fuc-pPGC-1α-GVs+US, HR5

description: Library name: sample 5


title: OVCA433, shRNA Control vector, replicate B

description: Library name: B1


title: Renal Microvascular Endothelial Cells, H/R+Fuc-pPGC-1α-GVs+US, HR4

description: Library name: sample 4


title: RA_11_2

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description: Library name: Sample18

data_processing:
The scRNA-seq data was analyzed using our previously established workflow. Briefly, raw FASTQ files generated by 10× Genomics were aligned and quantified using Cell Ranger (v4.3.0) against the GRCh38 human reference genome (v6.1.2). The Read10X function of the Seurat package was used to read the output of Cell Ranger. Doublets were identified and removed using the scrublet tool in Python, with an expected doublet rate of 0.1. Next, to facilitate downstream analyses, cells were distinctly labeled using the RenameCells function and integrated into a single aggregate object using the Merge function. To ensure data quality, stringent filtering parameters were applied to weed out any empty oil beads, mortality, and doublet cells, excluding cells with fewer than 200 or more than 4,000 detected genes, or with mitochondrial content exceeding 15%. Global scaling normalization was performed using the ‘LogNormalize’ method with a scaling factor of 10,000 to equalize overall gene expression across cells. The FindVariableFeatures function identified the top 2,000 highly variable genes, which were used for dimensionality reduction via principal component analysis (PCA). The first 30 principal components were selected, and the ScaleData function was applied to regress out undesired sources of variation. Sample batch effect correction was performed using the RunFastMNN function, which is based on a multi-canonical correlation analysis algorithm. For clustering, the FindNeighbors and FindClusters functions with the built-in Louvain method were applied. Clusters were visualized using uniform manifold approximation and projection (UMAP). Cluster-specific marker genes were identified using the non-parametric Wilcoxon rank-sum test with Bonferroni correction (adjusted p-value < 0.05; PCT > 0.25) implemented in the FindAllMarkers function. Cell populations were annotated based on canonical marker genes from published literature. Due to the inherent instability of neutrophils during processing and their predominant origin from a small number of samples, this cell type was excluded from subsequent analyses to mitigate technical bias. The proportion of each cluster was estimated by dividing the count of cells within each cluster by the total cell count in the respective sample. These ratios were statistically compared across treatment groups to assess significant differences in cell composition.
Assembly: GRCh38
Supplementary files format and content: rds file

source_name: Synovial fluid

extract_protocol:
The patient’s knee joint synovial fluid was extracted under aseptic conditions. Hyaluronidase (20426ES60, Yeasen) was added to the fresh SF sample obtained at a final concentration of 100 U/ml and incubated at 37°C for 30 min. SF samples from each RA patient were obtained from the same joint longitudinal to avoid potential bias.
The cell suspension was placed into 30 (v3) chemistry-equipped Chromium microfluidic chips, and a 10 × Chromium Controller (10×Genomics) was used to barcode the samples. Next, using components from a Chromium Single Cell 30 v3 reagent kit (10×Genomics), sequencing libraries were created using RNA from the barcoded cells after reverse transcription, in accordance with the manufacturer’s instructions.

value: Synovial fluid

value: Adalimumab


title: Renal Microvascular Endothelial Cells, hypoxia/reoxygenation, HR1

description: Library name: sample 1

value: hypoxia/reoxygenation (H/R)