title: V3036

description: Library name: V3036

value: iPS Cells

value: iPSC


title: Ube2fflox mice-2, male, 8 weeks old, untreated with DSS

status: Public on Mar 04 2026

type: SRA

city: Hangzhou

first: Zhijian

last: Li

address: Kaixuan street number 86

country: China

institute: Zhejiang university

description: Library name: WT_2

library_source: transcriptomic

data_processing:
AcDNAlibrary constructed by technology from the pooled RNA from < colon epithelium > samples of <mouse > was sequenced run with Illumina NovaseqTM X Plus sequence platform. Using the Illumina paired-end RNA seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the < mouse > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. 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). 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 abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: LC-P20250115035_genes_expression.xlsx includes FPK values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Colon

growth_protocol: Normal drinking.

extract_protocol:
Colon epithelial cells were collected from Ube2fflox and Ube2fΔIEC mice. Colons were collected, opened longitudinally, and flushed with cold PBS. The tissue was cut into ~2 mm pieces and incubated in 5 mM EDTA-PBS at 37 °C for 30 min. Following the incubation, the fluid containing cells and residual tissues were filtered through a 40-μm cell strainer and centrifuged at 300 × g for 5 min. Samples were digested with trizol to extract total RNA.
Total RNA was extracted using Trizol reagent (ThermoFisher, 15596018) following the manufacturer’s procedure.The total RNA quantity and purity were analysis of Thermo Fisher Qubit3.0 (ThermoFisher, Q33216) and Agilent 5300 Fragment Analyzer (Agilent, CA, USA, M5311AA), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

treatment_protocol: Mice were untreated with any drugs.

tag: tissue

value: Colon

tag: cell line

value: no

tag: cell type

value: epithelial cells

tag: genotype

value: WT

tag: treatment


title: Ube2fΔIEC mice-2, male, 8 weeks old, untreated with DSS

description: Library name: KO_2

value: KO


title: IgG, Trp53-/-; sgPten

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description: Library name: CUTTag_IgG_1

library_source: genomic

data_processing:
CUT&Tag assays were conducted on chromatin isolated from TP and TPA gastric organoids using antibodies against ARID1A or control IgG. The Illumina NovaSeq X plus platform was employed to perform sequencing. Following quality control by the fastp standard workflow, the Bowtie2 software was utilized to construct an index for the mouse genome (mm10) and align paired-end clean data of 150 bp length using the options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700". The SAMtools program was utilized to convert sam files to sorted bam files. Picard's MarkDuplicates tool was used to remove duplicates with the option "REMOVE_DUPLICATES=true". Normalized bw files were generated using deepTools with the option "bamCoverage -bs=25 --normalizeUsing BPM" for further visualization in the Integrated Genome Viewer. Peak calling was performed using the MACS2 software with the option "macs2 callpeak --broad -q 1e-5 -f BAMPE -g mm --keep-dup all". ChIPseeker was employed to identify the genomic distribution of the peaks, with the TSS region "tssRegion" set as (-3000, 3000) for annotation. The "narrowPeak" files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential modification were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig files and peak files(except for IgG samples)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: gastric organoid

extract_protocol:
We analyzed gastric organoids with two engineered genotypes: Trp53−/−; Pten−/− (TP) and Trp53−/−; Pten−/−; Arid1a−/− (TPA). sgRNAs targeting Pten and Arid1a were introduced into Trp53−/−; Cas9-EGFP gastric organoids to generate the corresponding genotypes. TP organoids served as the control group, and an IgG control was included to account for nonspecific background binding. Organoids from each group were collected for downstream CUT&Tag-seq library preparation and comparative differential binding analyses.
TP and TPA organoids were used for ARID1A CUT&Tag. The chromatin was combined with ChiTag™ 2.0 Transposome, then fragmented using Tagmentation Buffer for 1 h at 37 °C. ChIP DNA was purified using DNA Clean Beads and amplified using the PCR system from this kit. PCR conditions were as follows: 72 °C for 3 min, 98 °C for 30 s, followed by 10–25 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, then 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads. The purified ChIP DNA was used for library preparation.

value: gastric organoid

value: Trp53-/-; sgPten

tag: chip antibody


title: V3035

city: Evanston

first: Christina

last: Thapa

state: Illinois

address: 1001 University Place

department: Center for Psychiatric Genetics (CPG)

country: USA

institute: Endeavor Health

description: Library name: V3035

data_processing:
Trimmomatic was used to trim adapters and low quality reads and read ends. Then, both Spliced Transcripts Alignment to a Reference (STAR) and Burrows-Wheeler Aligner (BWA) was used for alignment resulting in gene expression counts tables and bam files, respectively. Final processed counts is provided.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values

organism: Homo sapiens

source_name: iPS Cells

extract_protocol:
Cells were lysed with 800ul of Buffer RLT Plus (QIAGEN #1053393). Cell lysates were processed using RNeasy Plus Mini Kit (QIAGEN #74134) to extract purified RNA.
Library was constructed by Novogene using Illumina NovaSeq X.

tag: Sex

value: Female

tag: lof target_gene

tag: ancestry

value: AA

tag: batch


title: pot1b, Zeocin, rep3

city: College Station

first: Dorothy

middle: E

last: Shippen

state: TX

address: 300 Olsen Blvd

department: Department of Biochemistry & Biophysics

institute: Texas A&M University

description: Library name: 23-pot1b-Zeocin

data_processing:
All data analysis was performed on the Galaxy Europe platform (https://usegalaxy.eu) (Batut et al., 2021).
Raw 2×50 bp paired-end reads were trimmed for adapters and low-quality bases using Trim Galore! tool.
Trimmed reads were aligned to the A. thaliana TAIR10_v90 genome with HISAT2, producing BAM files.
Gene-level read counts were obtained from BAMs using featureCounts.
Using the limma-voom tool, counts were normalized by TMM, voom-transformed, and differential expression assessed by empirical Bayes linear modeling.
Assembly: Arabidopsis thaliana TAIR10_v90
Supplementary files format and content: tab-delimited text files include read count values for each sample

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: 6-day-old WT and pot1b seedlings were grown on the MS media

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared in triplicate using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina).

treatment_protocol: Seedlings were treated with or without 20 μM of Zeocin (Thermo Fisher, USA) for 6 hr

value: Seedling

value: Zeocin


title: anti-ARID1A, Trp53-/-; sgPten; sgArid1a gastric organoid, rep2

description: Library name: CUTTag_ARID1A_TPA_2

value: Trp53-/-; sgPten; sgArid1a

value: ARID1A (Cell Signaling Technology, Cat# 12354)


title: CoCl2_M_Input

city: yangling

first: Jian

last: Sun

address: xinong road

institute: Northwest Agriculture & Forestry University

description: Library name: CoCl2_M_Input

data_processing:
Basecalls were performed using bcl2fastq v20.1 for Novaseg output.
ChlP-seq reads were trimmed from 3" end until the final base had a quality score > 30, usingTrimmomatic vO.33, dis carding reads left w ith < 20 bp.
ChlP-seq reads w ere aligned to the NCBI HZGC01 genome using Bowtie version 2.4.2. Only uniguely mapping reads w ith at most two mismatches were retained.
To create ChiP-seq coverage plots, the locations of the mapped ChiP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per milion.rpm) and reformatted in the bigwig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off g-value <=0.01. bigWig files were generated using the genomicRanges R package. Score represents thenormalized coverage of DNA fragments at a given genomic coordinate. Narrow Peak files were generated using MACs v2.2.7.1 with default settings.
Assembly: HZGC01
Supplementary files format and content: bigwig

organism: Ctenopharyngodon idella

source_name: Adipose tissue

extract_protocol:
1× 107 cells were fixed with 1% formaldehyde (Sigma-Aldrich, cat. no. F8775) for 10 min at room temperature, followed by quenching with 125 mM glycine for 5 min. After lysis, cell nuclei were pelleted by centrifugation at 1000 rpm for 5 min at 4°. The chromatin was fragmented through sonication to achieve an average DNA fragment size of 200–500 base pairs.
ChIP DNA libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB). End repair/A-tailing, adaptor ligation, and USER enzyme treatment were performed according to the manufacturer’s instructions. Libraries were amplified by 8–10 PCR cycles, size-selected, and purified using AMPure XP beads. Library quality was assessed by Qubit and high-sensitivity DNA chip analysis.

value: Adipose tissue

value: Primary Cells

value: preadipocyte


title: WT, Zeocin, rep3

description: Library name: 21-WT-Zeocin


title: Ube2fΔIEC mice-3, male, 8 weeks old, untreated with DSS

description: Library name: KO_3


title: Ube2fflox mice-3, male, 8 weeks old, untreated with DSS

description: Library name: WT_3


title: Trp53-/-; sgPten gastric organoid, rep1

description: Library name: ATAC_TP_rep1

data_processing:
To remove adapters from the 150 bp paired-end raw data, NGmerge was employed with the option "NGmerge -a -v -n 20". Bowtie2 software was used to construct an index for the mouse genome (mm10), followed by alignments using the option "--very-sensitive -X2000 -x mm10". Duplicates were removed using Picard's MarkDuplicates tool. Mitochondrial genome contamination was eliminated using SAMtools and awk commands, resulting in bam files. Normalized bw files were generated using deepTools with the option "bamCoverage -bs=1 --normalizeUsing BPM" for subsequent visualization in the Integrated Genome Viewer (IGV). The macs3 “macs3 hmmratac” standard workflow was utilized for peak calling in ATAC-seq. The genomic distribution of accessibility sites was determined using ChIPseeker with the option "annotatePeak", and the TSS region "tssRegion" was set as (-3000, 3000). The peak files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential accessibility were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig files and peak files

extract_protocol:
Gastric TP and TPA organoids (5×10^4 cells/each group) were harvested and resuspended in 1 mL ice-cold PBS, followed by centrifugation at 500 g for 5 min. The supernatant was removed, and the pellet was gently resuspended in 50 μL lysis buffer. Tubes were placed on ice for 5 min, then 950 μL wash buffer was added. The mixture was gently pipetted (blown) 5 times and centrifuged at 500 g for 5 min at 4 °C. The sediment was collected for downstream reactions.
ATAC-seq libraries were constructed using a Chromatin Profile Kit (Novoprotein, Cat. N248-01A). The sediment was resuspended in 40 μL fragmented mixture and transferred to PCR tubes for incubation at 37 °C for 30 min. The reaction was stopped by adding 10 μL stop buffer and incubating at 55 °C for 5 min. DNA extraction beads were used to purify the fragments. Transposed DNA fragments were amplified using the PCR system provided in the kit with the following conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 9–18 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, and a final extension at 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads.The Illumina X plus platform was utilized to sequence the library.


title: Ube2fflox mice-1, male, 8 weeks old, untreated with DSS

description: Library name: WT_1


title: pot1b, Zeocin, rep2

description: Library name: 15-pot1b-Zeocin


title: Control_M_IP

description: Library name: Control_M_IP


title: Sciatic nerve, Control_3

city: Columbus

first: Ana

middle: Isabel

last: Salazar Puerta

state: OH

address: 140 W 19th Ave Building 151

institute: The Ohio State University

description: Library name: S23

data_processing:
Clean reads were mapped to the mouse genome using Hisat2 (v2.0.5) -- this part was done by Novogene
Gene expression was quantified with featureCounts (v1.5.0-p3) and expressed as FPKM -- by Novogene
Assembly: r_4.3.1 -- Mus Musculus(GRCm39/mm39)
Supplementary files format and content: xls files include raw counts for each sample
Supplementary files format and content: xls files include fpkm values for each sample

source_name: Sciatic nerve

extract_protocol:
Total RNA from sciatic nerve tissue was collected afer 7 days in TRIzol Reagent (Invitrogen) and homogenized using poly-T oligo-attached magnetic beads. RNA was then isolated using the PureLink RNA Mini Kit (Invitrogen) followed by DNAse treatment (Thermo Fisher) to eliminate the presence of co-precipitated extracellular DNA.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. -- this part was done by Novogene

treatment_protocol: For the crush injury model, a 1 cm right unilateral incision was made on the skin on the medial-lateral portion of the limb just below the hip joint to expose the sciatic nerve, followed by its separation from the surrounding tissue and fascia. The crush injury was done by using 1 mm wide locking hemostatic forceps 2 times for 15 s with a 15s release in between. TNT was then performed on the sciatic nerves with either the EFF treatment or the empty vector pCMV6 (sham) as previously described[18, 20]. Briefly, the TNT reservoir was filled with 350 µl of the plasmid solution containing a concentration of 0.15-0.2μg/μL (depending on the formulation) for the plasmids. A positive electrode is connected to a 25-gauge needle positioned under the sciatic nerve, and a negative electrode connected to a gold electrode (Neon Electroporation System, Thermo Fisher) filled with a 0.9% sodium chloride saline solution is placed inside the plasmid reservoir. The TNT chip was then placed on top of the sciatic nerve and a total of 200 V, 100 ms, and 10 pulses, were used to deliver the respective plasmid treatment into the injured sciatic nerve.

value: Sciatic nerve

tag: strain


title: Trp53-/-; sgPten gastric organoid, rep2

description: Library name: ATAC_TP_rep2


title: pot1b, Mock, rep3

description: Library name: 19-pot1b-Mock

value: Mock


title: Sciatic nerve, EFF112_4

description: Library name: S29


title: Sciatic nerve, Control_2

description: Library name: S22


title: WT, Mock, rep3

description: Library name: 17-WT-Mock


title: pot1b, Zeocin, rep1

description: Library name: 07-pot1b-Zeocin


title: WT, Mock, rep2

description: Library name: 09-WT-Mock


title: Sciatic nerve, Control_1

description: Library name: S21


title: pot1b, Mock, rep2

description: Library name: 11-pot1b-Mock


title: WT, Zeocin, rep2

description: Library name: 13-WT-Zeocin


title: Sciatic nerve, EFF111_4

description: Library name: S8


title: WT, Zeocin, rep1

description: Library name: 05-WT-Zeocin


title: Sciatic nerve, EFF112_2

description: Library name: S27


title: WT, Mock, rep1

description: Library name: 01-WT-Mock


title: Sciatic nerve, Control_4

description: Library name: S24


title: Sciatic nerve, EFF111_3

description: Library name: S7


title: Sciatic nerve, EFF112_1

description: Library name: S26


title: Liver_tumor_84-week_biological rep 2

type: RNA

city: Washington

first: Rabindra

last: Roy

state: District Of Columbia

address: 3900 Reservoir Rd NW, Preclinical Science Building, Room# LF05

department: Oncology/Lombardi Comprehensive Cancer Center

institute: Georgetown University

description: Gene expression data from 84-week tumor

hyb_protocol: Following fragmentation, 12.5 ug of labeled cRNA were hybridized to GeneChip Rat Genome 230 2.0 Array for 16 hr at 45oC. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrx GeneChip Scanner 3000.

data_processing:
The array raw data was generated by Affymetrix GeneChip Operating Software (GCOS). The Rat Genome 230 2.0 Array includes a set of rat maintenance genes as a tool to normalize or scale the data prior to performing data comparisons.
Algorithm: ExpressionStat 5.0

label: biotin

organism: Rattus norvegicus

source_name: LEC rat_84-week old_liver_tumor

label_protocol: Biotinylated cRNA were prepared according to Affymetrix GeneChip 3’IVT Express Kit manual (P/N 702646 Rev. 7 Affymetrix): 100 ng of total RNA was used to synthesize labeled cRNA.

growth_protocol: Long Evan Cinnamon (LEC) Rats were maintained under standard conditions following the IACUC-approved protocol (#07-065).

extract_protocol: Total RNA was isolated from the 84-week adjacent normal and 84-week tumor LEC liver tissue using the RNAeasy (Qiagen, Valencia, CA) kit according to the manufacturer’s instructions.

treatment_protocol: Liver tissues were collected from three LEC rats at 84 weeks, paraffin-embedded, and stained with hematoxylin and eosin (H and E). Eighty-four-week adjacent normal (late chronic hepatitis, tumor-adjacent normal) and 84-week tumor tissue sections were identified after histopathological review by a pathologist who was board-certified for hematopathology, anatomic pathology, and clinical pathology.

value: Long Evans Cinnamon Rat

tag: age

value: 84 week

value: liver

tag: tissue type

value: tumor


title: Sciatic nerve, EFF111_2

description: Library name: S6

value: WT


title: Liver_tumor_84-week_biological rep 3

description: Gene expression data from 84-week tumor


title: Liver_tumor_84-week_biological rep 1

description: Gene expression data from 84-week tumor


title: pot1b, Mock, rep1

description: Library name: 03-pot1b-Mock


title: Liver_normal adjacent to tumor_84-week_biological rep 2

description: Gene expression data from 84-week normal adjacent to tumor

source_name: LEC rat_84-week old_liver_normal adjacent to tumor

value: normal adjacent to tumor


title: Sciatic nerve, EFF111_1

description: Library name: S5


title: Liver_normal adjacent to tumor_84-week_biological rep 3


title: Liver_normal adjacent to tumor_84-week_biological rep 1


title: Sciatic nerve, EFF112_3

description: Library name: S28


title: Sciatic nerve, Sham_2

description: Library name: S2


title: RNA-seq of CD4+ T cells co-cultured with CD8+ T cells

city: Guangzhou

first: ye

last: chen

state: Guangdong

address: Tianhe Center, Tianhe District

institute: sun yat-sen university

description: Library name: CD4_CD8

data_processing:
Raw reads were quality-checked with FastQC and trimmed to remove adapters and low-quality bases.
Trimmed reads were aligned to the mouse reference genome using STAR.
Gene-level counts were generated using featureCounts with GTF annotation.
Differential expression analysis was performed using DESeq2 in R.
Assembly: Mus musculus genome assembly (mm10).
Supplementary files format and content: Processed data include raw gene count matrices and normalized expression tables.

source_name: spleen

growth_protocol: Naïve CD4⁺ T cells were FACS-sorted from mouse spleen and lymph nodes and cultured in complete RPMI-1640 at 37 °C, 5% CO₂ under iTreg-inducing conditions; for CD4–8 iTreg, naïve CD4⁺ T cells were co-cultured with naïve CD8⁺ T cells.

extract_protocol:
CD4⁺ T cells were FACS-sorted after 3 days of iTreg induction, and total RNA was extracted using TRIzol followed by column purification with on-column DNase I treatment; RNA integrity was assessed by Bioanalyzer.
Stranded poly(A)+ RNA-seq libraries were prepared according to the manufacturer’s protocol and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Cells were stimulated with anti-CD3/anti-CD28 in the presence of TGF-β1 and IL-2 to induce iTreg differentiation, with or without CD8⁺ T-cell co-culture.

value: spleen

value: CD4+ iTreg(primary cell)


title: Sciatic nerve, Sham_4

description: Library name: S25


title: SN_Cut_3

description: Library name: SN_8

data_processing:
Clean reads were mapped to the mouse genome using Hisat2 (v2.0.5) -- this part was done by Novogene
Gene expression was quantified with featureCounts (v1.5.0-p3) and expressed as FPKM -- by Novogene
Assembly: r_4.3.1 -- Mus Musculus(GRCm39/mm39)
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: fpkm values for each sample

extract_protocol:
Total RNA from sciatic nerve tissue was collected afer 13 weeks in TRIzol Reagent (Invitrogen) and homogenized using poly-T oligo-attached magnetic beads. RNA was then isolated using the PureLink RNA Mini Kit (Invitrogen) followed by DNAse treatment (Thermo Fisher) to eliminate the presence of co-precipitated extracellular DNA.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. -- this part was done by Novogene

treatment_protocol: For the isograft model, 7-10 week-old C57BL/6 mice served as both donors and recipients. The sciatic nerve tissue from the donor mice was exposed and treated with TNT as previously described, and a 1.3cm segment of sciatic nerve was measured and dissected from the level of the exiting nerve root to just beyond the sciatic trifurcation. The right sciatic nerve of the recipient mice was exposed, treated with TNT, and then transected 3 mm proximal to the distal trifurcation. The harvested nerve graft was measured and cut to 1cm and then sutured into the nerve gap. The distal end of the donor graft was positioned facing the proximal nerve stump of the recipient, using 10-0 nylon microsutures, secured with loose knots to allow optimal regeneration. TNT was also applied to the proximal and distal stumps of the recipient’s sciatic nerve prior to grafting. The experimental groups included mice treated with grafting without TNT (graft only) as the graft control, mice subjected to a 1 cm graft dissection without repair (cut no-repair) as the negative control, and mice with no injury (control) as the positive control.


title: SN_Cut_2

description: Library name: SN_6


title: RNA-seq of CD4+ T cells co-cultured without CD8+ T cells

description: Library name: CD4 only


title: SN_Cut_1

description: Library name: SN_3


title: SN_EFF_3

description: Library name: SN_21


title: SN_EFF_2

description: Library name: SN_18


title: Sciatic nerve, Sham_3

description: Library name: S3


title: SN_Sham_4

description: Library name: SN_19


title: SN_EFF_1

description: Library name: SN_14


title: Donor86_Untreated

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: Untouched CD14+CD16− monocytes isolated from peripheral blood of a healthy adult donor and cultured for 2 hours without immune complex stimulation.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v2 8×60K microarrays (Design ID 039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the one‑color scan setting for 8×60K SurePrint G3 Human GE arrays (Scan Area 61 × 21.6 mm, Scan Resolution 3 µm, Dye channel set to Green, and Green PMT set to 100%)

data_processing: The scanned images were analyzed using Agilent Feature Extraction Software version 10.7.3.1 with the default one‑color extraction parameters (protocol GE1_107_Sep09 and design grid 039494_D_F_20120411) to obtain background‑subtracted and spatially detrended processed signal intensities. Features flagged by Feature Extraction as non‑uniform outliers were excluded from downstream analysis. The raw data was quantile normalized. Batch effects were normalized using ComBat.

source_name: Peripheral blood monocytes, Untreated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from sorted cells using the RNeasy Plus Micro kit (Qiagen, Valencia, CA)

treatment_protocol: Untouched CD14⁺CD16⁻ monocytes isolated from the peripheral blood of healthy adult donors (N = 6) were incubated for 2 hours either unstimulated or stimulated with lupus-associated immune complexes (ICs). ICs were generated by combining U1-snRNP (5 μg/mL) with pooled anti–U1-snRNP antibody–positive serum (5%), dsDNA (5 μg/mL) with pooled anti–dsDNA antibody–positive serum (5%), or Ro60 (5 μg/mL) with pooled anti–Ro60 antibody–positive serum (5%).

tag: agent

value: Untreated

tag: developmental stage

value: healthy adult


title: SN_Sham_3

description: Library name: SN_17


title: SN_Sham_5

description: Library name: SN_20


title: Donor51_Untreated


title: Sciatic nerve, Sham_1

description: Library name: S1


title: SN_Sham_2

description: Library name: SN_16


title: SN_Graft_1

description: Library name: SN_1


title: SN_Graft_5

description: Library name: SN_24


title: Donor86_snRNP_IC

description: Untouched CD14+CD16− monocytes isolated from peripheral blood of a healthy adult donor and stimulated for 2 hours with snRNP-containing lupus immune complexes.

source_name: Peripheral blood monocytes, snRNP_IC


title: Donor51_Ro_IC

description: Untouched CD14+CD16− monocytes isolated from peripheral blood of a healthy adult donor and stimulated for 2 hours with Ro60-containing lupus immune complexes.

source_name: Peripheral blood monocytes, Ro_IC


title: Donor51_dsDNA_IC

description: Untouched CD14+CD16− monocytes isolated from peripheral blood of a healthy adult donor and stimulated for 2 hours with dsDNA-containing lupus immune complexes.

source_name: Peripheral blood monocytes, dsDNA_IC


title: Donor50_Ro_IC


title: Donor86_Ro_IC


title: Donor50_dsDNA_IC


title: Donor86_dsDNA_IC


title: SN_Graft_2

description: Library name: SN_12


title: Donor50_snRNP_IC


title: SN_Graft_4

description: Library name: SN_22


title: SN_Control_4

description: Library name: SN_10


title: SN_Control_5

description: Library name: SN_11


title: SN_Control_2

description: Library name: SN_5


title: Donor51_snRNP_IC


title: Naïve_4

description: Library name: IV_16

source_name: PMEFs

growth_protocol: Fibroblasts were purchased from EMD Millipore-Sigma (PMEF-HL) and cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher) supplemented with 10% fetal bovine serum (FBS, VWR) and 1% penicillin/streptomycin (GIBCO) at 37 °C in a humidified air chamber containing 5% CO2.

extract_protocol:
Total RNA was isolated from the cells with TRIzol Reagent (Invitrogen) and using the PureLink RNA Mini Kit (Invitrogen) following the protocol recommended by the manufacturer. Isolated RNA was treated with DNase (Thermo Fisher) to eliminate the presence of co-precipitated extracellular DNA
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. -- this part was done by Novogene

treatment_protocol: Once the cells reached a confluency level greater than 80%, they were detached, and 1.0 x 106 cells were resuspended in 100 µl of electrolytic buffer for subsequent non-viral cell transfection using a Neon transfection system (Thermo Fisher). Cells were co-transfected with three plasmid vectors encoding for Etv2, Fli1, and Foxc2 at 0.05-0.1 µg/µl, pCMV6 (sham/empty vector) was used as a control with the same final gene concentration (0.15-0.2 µg/µl). Following the procedure assigned by the manufacturer (Invitrogen: Neon Transfection System), the cells were transfected for 30ms with 1 pulse at 1425 V.

value: PMEFs

value: Fibroblasts


title: SN_Control_3

description: Library name: SN_7


title: Donor35_Untreated


title: Naïve_1

description: Library name: IV_13


title: Donor35_dsDNA_IC


title: EFF112_3

description: Library name: IV_11


title: Naïve_3

description: Library name: IV_15


title: Naïve_2

description: Library name: IV_14


title: EFF112_1

description: Library name: IV_9


title: RNA-Control-rep2

city: Chengdu

first: Hao

last: Jiang

address: 37 Guoxue Alley, Wuhou District

department: National Clinical Research Center for Geriatrics

institute: West China Hospital, Sichuan University

description: Library name: S3

data_processing:
RNA-seq:data were aligned to the rn6 reference genome using Hisat2, and feature counting was performed using FeatureCounts. Differential expression analysis between groups was conducted using DESeq2.
Assembly: rn6
Supplementary files format and content: txt,raw counts of genes for all samples in RNA-seq

source_name: BMSCs

growth_protocol: Isolated BMSCs were cultured in α-MEM supplemented with 10% FBS. The medium was changed every 2 days. When cells reached 70–80% confluence, they were passaged and seeded for experiments.

extract_protocol:
RNA-seq:Total RNA was extracted from muscle samples using TRIzol.
RNA-seq: The mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit. Library quantity and quality were assessed using a Qubit 2.0 Fluorometer and an Agilent 2100 Bioanalyzer.

treatment_protocol: For hypoxic culture, BMSCs were maintained in a tri-gas incubator at 1% O2 for 7 days.

value: BMSCs

value: normal


title: RNA-Control-rep1

description: Library name: S2


title: Donor33_snRNP_IC


title: Donor33_dsDNA_IC


title: EFF111_4

description: Library name: IV_8


title: EFF112_2

description: Library name: IV_10


title: Donor50_Untreated


title: EFF111_2

description: Library name: IV_6


title: EFF111_1

description: Library name: IV_5


title: Donor10_snRNP_IC


title: Donor35_snRNP_IC


title: Donor35_Ro_IC


title: Donor10_Ro_IC


title: Sham_4

description: Library name: IV_4


title: RNA-Hypoxia-rep3

description: Library name: S8

value: 1% O₂


title: EFF112_4

description: Library name: IV_12


title: RNA-Control-rep3

description: Library name: S4


title: RNA-Hypoxia-rep1

description: Library name: S6


title: EFF111_3

description: Library name: IV_7


title: Sham_1

description: Library name: IV_1


title: Donor33_Ro_IC


title: ATAC-Control-rep2

description: Library name: AS3

data_processing:
ATAC-seq:The raw data were processed with the ENCODE ATAC-seq pipeline. Then we aligned reads to the reference genome (rn6) build with Bowtie2. Duplicates were removed using. The model-based analysis of ChIP-seq (MACS2) was used to identify the peak regions with options -f BAM -B -g rat -p 0.05 --SPMR --keep-dup all --call-summits --nomodel --shift -100 --extsize 200. Mitochondrial reads were also removed before the analysis.The bigWig files and the TSS coordinates obtained from the UCSC Genome Browser KnownGene table were used as input for the computeMatrix function of deepTools. This matrix was used for plotHeatmap function to generate the heatmap. The number of raw reads mapped to peaks were counted using ATAC_IterativeOverlapPeakMerging. UMAP analysis was performed to evaluate the similarity between the samples. Difference analysis software DESeq2 was used to analyze the differences between groups.
Assembly: rn6
Supplementary files format and content: txt,counts of peaks for all samples in ATAC-seq

extract_protocol:
ATAC-seq:Briefly, Approximate 50,000 BMSCs cells were transferred into a fresh tube and diluted in 1 ml ATAC lysis buffer containing 10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, and 0.01% Digitonin for 5 min on ice. After centrifuging, the supernatant was carefully aspirated. Nuclei were mixed in 50 ul transposition reaction mixture for 30 mins at 37 °C.
ATAC-seq: the DNA was purified with MinElute Purification Kit. The eluted DNA was PCR amplified for 11 cycles. The libraries were then size selected with AmpureXP Beads. Finally, the samples were sequenced on Hiseq-SE50.RNA-seq: The mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit. Library quantity and quality were assessed using a Qubit 2.0 Fluorometer and an Agilent 2100 Bioanalyzer.


title: ATAC-Control-rep3

description: Library name: AS4


title: ATAC-Hypoxia-rep1

description: Library name: AS7


title: lnc13-KO-CD8-RAP-lnc13RAP rep 1

city: New York

first: Ruxiao

last: Yang-Fischer

state: NY

institute: Columbia University

description: Library name: lnc13-KO-CD8-RAP-lnc13RAP rep 1

data_processing:
For RAP-seq, reads were aligned using BWA and the relative signal was calculated, in 150bp windows with 75bp step size, using DeepTools bamCoverage and normalized to both bin sizes and number of reads to generate the .bigwig files.
Assembly: mm39
Supplementary files format and content: .bigwig

source_name: spleen+lymph nodes

extract_protocol:
For RAP-seq experiments, 25 million primary CD8 T cells, followed by 2mM DSG and 3% formaldehyde was used for crosslinking. Lysed whole cells were fractionated to obtain intact nuclei. Nuclei were lysed and chromatin was fractionated with a combination of sonication and TURBO DNase diestion. Lysate was incubated with antisense single stranded 5’ biotinylated DNA probes tiling the entire lnc13 transcript but does not bind to Il18rap. Streptavidin-magnetic beads were used to enrich for lnc13 and bound chromatin was eluted by RNaseH digestion.
NEBNext Ultra II DNA Library Prep Kit was used for RAP-seq samples.

value: spleen+lymph nodes

value: CD8 T cell


title: RNA-Hypoxia-rep2

description: Library name: S7


title: Sham_3

description: Library name: IV_3


title: ESI017 AMLC treated 2 day rep2

city: Cincinnati

first: Aryeh

last: Warmflash

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Library name: X2d_1

data_processing:
Salmon v1.9.01
Assembly: GRCh38 (GCA_000001405.15 no_alt_analysis_set, hg38 alias)
Supplementary files format and content: Tab-delimited text files and CSV tables.

source_name: emrbyonic stem cells

extract_protocol:
RNA was harvested using the RNaqueous Kit from Invitrogen. The samples went through gel and Agilent 2100 as quality control for RNA integrity and DNA contamination.
The library construction is done by Novogene, the samples went through a polyA enrichment before sequencing.

value: emrbyonic stem cells

value: amnion differentiation


title: ATAC-Control-rep1

description: Library name: AS2


title: lnc13-WT-CD8-RAP-input rep 1

description: Library name: lnc13-WT-CD8-RAP-input rep 1


title: lnc13-WT-CD8-RAP-lnc13RAP rep 1

description: Library name: lnc13-WT-CD8-RAP-lnc13RAP rep 1


title: Sham_2

description: Library name: IV_2


title: ATAC-Hypoxia-rep2

description: Library name: AS8


title: RNA-Seq of Human sorted BM terminal erythroblasts-M4

city: Zhengzhou

first: Shihui

last: Wang

state: Henan

address: No. 7 Weiwu Road, Zhengzhou, Henan, China

department: Institute of Hematology

institute: Henan Provincial People’s Hospital

description:
Library name: NDMM-4-P7-terminal
MM_ery_4th

data_processing:
Low-quality reads were removed and filtered by fastp[13]. Filtered reads were quantified by Kallisto[14] using the mm10 transcriptome index. Pairwise comparison of two groups was performed by DESeq2 [15].
Assembly: mm10
Supplementary files format and content: tab-delimited test files includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted BM primary erythroid progenitor cells or terminal erythroblasts. RNA isolation, cDNA library construction, and sequencing were performed at the Annoroad Gene Technology Institute using the Illumina platform with a PE150 strategy.
RNA was extracted from sorted bone marrow-derived erythroid progenitor cells and terminal erythroblasts, followed by library preparation and Illumina PE150 sequencing. After quality control with fastp, reads were aligned to the hg38 reference genome using kallisto for expression quantification. Differential expression analysis was performed with DESeq2 (|FC|≥1, p<0.05, adjusted p<0.25). Principal component analysis (PCA) was conducted on normalized counts, and Gene Ontology (GO) enrichment analysis was performed using Metascape (p<0.001) to functionally characterize differentially expressed genes.

value: Bone marrow

value: Erythroid-terminal erythroblasts

value: terminal erythroblasts


title: Donor33_Untreated


title: ESI017 AMLC treated 4 day rep2

description: Library name: X4d_1

value: WT


title: ESI017 Control rep1

description: Library name: ctrl

value: Pluripotency maintenance


title: lnc13-WT-CD8-RAP-input rep 2

description: Library name: lnc13-WT-CD8-RAP-input rep 2


title: Donor10_dsDNA_IC


title: lnc13-WT CD8 unstim-biol rep 2

description:
Library name: lnc13-WT CD8 unstim-biol rep 2
unstim KOvWT DEseq2.txt

data_processing:
Reads were aligned using Tophat (tissue samples, mm10) or RNA-STAR (CD8 IEL samples, mm39). Gene counts were counted using FeatureCounts and differential expression were done using DESeq accounting for variation between cages. For RAP-seq, reads were aligned using BWA and the relative signal was calculated, in 150bp windows with 75bp step size, using DeepTools bamCoverage and normalized to both bin sizes and number of reads to generate the .bigwig files.
Assembly: mm39
Supplementary files format and content: DEseq2.txt

molecule: polyA RNA

source_name: small intestine

extract_protocol:
RNA was extracted using Zymo RNA quickFor whole tissue RNA, samples were extracted and flash frozen in liquid nitrogen. Then, samples are homogenized with mortar and pestle containing small amounts of liquid nitrogen to keep samples frozen. Homogenized samples were then transferred to TRIzol®. TRIzol® RNA extraction was then performed as directed by the product protocol. For extraction of RNA from cells, we utilized Quick-RNA Miniprep Kit (Zymo).
NEBNext Ultra II RNA library prep kit for Illumina for tissue, LPL and IEL samples. NEBNext Single Cell/Low input RNA library Prep kit for CD8 samples. NEBNext Ultra II DNA Library Prep Kit for illumina for RAP samples.

value: small intestine

value: CD8 T IEL


title: lnc13-WT-CD8-RAP-lnc13RAP rep 2

description: Library name: lnc13-WT-CD8-RAP-lnc13RAP rep 2


title: ATAC-Hypoxia-rep3

description: Library name: AS9


title: lnc13-KO CD8 IL15-biol rep 3

description:
Library name: lnc13-KO CD8 IL15-biol rep 3
IL15 KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM terminal erythroblasts-M5

description:
Library name: NDMM-5-P7-terminal
MM_ery_5th


title: lnc13-KO-CD8-RAP-lnc13RAP rep 2

description: Library name: lnc13-KO-CD8-RAP-lnc13RAP rep 2


title: Donor10_Untreated

value: Untreated

value: healthy adult


title: RNA-Seq of Human sorted BM terminal erythroblasts-H5

description:
Library name: Healthy-5-P7_terminal
healthy_ery_5th


title: lnc13-WT CD8 unstim-biol rep 1

description:
Library name: lnc13-WT CD8 unstim-biol rep 1
unstim KOvWT DEseq2.txt


title: ESI017 AMLC treated 2 day rep1

description: Library name: X2d


title: ESI017 AMLC treated 4 day rep1

description: Library name: X4d


title: lnc13-WT CD8 unstim-biol rep 3

description:
Library name: lnc13-WT CD8 unstim-biol rep 3
unstim KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM terminal erythroblasts-H4

description:
Library name: Healthy-4-P7_terminal
healthy_ery_4th


title: RNA-Seq of Human sorted BM terminal erythroblasts-H6

description:
Library name: Healthy-6-P7_terminal
healthy_ery_6th


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M6

description:
Library name: NDMM-6-P8-Progenitor
MM_prog_6th

value: Erythroid-progenitor cells

value: primary erythroid progenitor cells


title: lnc13-KO CD8 unstim-biol rep 1

description:
Library name: lnc13-KO CD8 unstim-biol rep 1
unstim KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M5

description:
Library name: NDMM-5-P8-Progenitor
MM_prog_5th


title: lnc13-KO CD8 IL15-biol rep 2

description:
Library name: lnc13-KO CD8 IL15-biol rep 2
IL15 KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M4

description:
Library name: NDMM-4-P8-Progenitor
MM_prog_4th


title: lnc13-KO CD8 IL15-biol rep 1

description:
Library name: lnc13-KO CD8 IL15-biol rep 1
IL15 KOvWT DEseq2.txt


title: lnc13-KO CD8 unstim-biol rep 2

description:
Library name: lnc13-KO CD8 unstim-biol rep 2
unstim KOvWT DEseq2.txt


title: lnc13-WT CD8 IL15-biol rep 3

description:
Library name: lnc13-WT CD8 IL15-biol rep 3
IL15 KOvWT DEseq2.txt


title: lnc13-KO CD8 unstim-biol rep 3

description:
Library name: lnc13-KO CD8 unstim-biol rep 3
unstim KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H6

description:
Library name: Healthy-6-P8_Progenitor
healthy_prog_6th


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H7

description:
Library name: Healthy-7-P8_Progenitor
healthy_prog_7th


title: PT19

first: Andrew

last: Gunderson

address: 460 W. 10th Avenue

department: Department of Surgery

description:
Library name: PT19
11x11mm FFPE Visium Cytassist

data_processing:
Raw sequencing fastq files were processed using SpaceRanger v2.1.1, to raw gene counts.
Output processed files were opened and analyzed in Seurat v5. Raw counts were normalized and transformed using SCTransform.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain raw counts, SCTransformed gene expression, and an aligned H&E image as a Seurat v5 object, saved as a .RDS R data object.
Library strategy: Spatial Transcriptomics

source_name: Pancreas-PDAC tumor

extract_protocol:
FFPE tumor sections were cut into 10um sections with a microtome
Spatial gene expression libraries were generated using 10x Genomics Visium CytAssist for FFPE Spatial Gene Expression 11mm Kit.

value: Pancreas-PDAC tumor

value: Female

tag: diagnosis

value: PDAC


title: PT27

description:
Library name: PT27
11x11mm FFPE Visium Cytassist

value: Male


title: lnc13-WT CD8 IL15-biol rep 1

description:
Library name: lnc13-WT CD8 IL15-biol rep 1
IL15 KOvWT DEseq2.txt


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H5

description:
Library name: Healthy-5-P8_Progenitor
healthy_prog_5th


title: non-lymphoid cluster region, GEX

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA74118

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on NovaSeq X Plus platform in 151+151 base paired-end mode.
Illumina Real Time Analysis v4 (RTA4) software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0, 10x Genomics) for UMI counting for each gene-cell (barcode) combination.
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene and cell (barcode) combination

source_name: salivary glands

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. The cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: salivary glands

value: cells in non-lymphoid cluster region

tag: library type

value: mRNA


title: lnc13-KO-DQ8 CD8ab IEL biol rep 3

description: Library name: lnc13-KO-DQ8 CD8ab IEL biol rep 3

data_processing:
Reads were aligned using TopHat. Gene counts were counted using FeatureCounts6 and differential expression were done using DESeq accounting for variation between cages
Assembly: mm10
Supplementary files format and content: featureCount.txt

tag: tissue


title: lnc13-WT CD8 IL15-biol rep 2

description:
Library name: lnc13-WT CD8 IL15-biol rep 2
IL15 KOvWT DEseq2.txt


title: lnc13-KO-DQ8 CD8ab IEL biol rep 1

description: Library name: lnc13-KO-DQ8 CD8ab IEL biol rep 1


title: lymphoid cluster region, GEX

description: Library name: GA73510

value: cells in lymphoid cluster region


title: PT8

description:
Library name: PT8
11x11mm FFPE Visium Cytassist


title: 1-fold_S28

city: Xiamen

first: Weida

last: Huang

state: Fujian

address: Xiangshan Street

department: School of Public Health

institute: Xiamen University

description:
Library name: Sample 28
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)

data_processing:
Reads were processed with a custom pipeline. Adapter trimming was performed using cutadapt (v5.0), retaining reads of 16–30 nt in length. The sequences were aligned to miRNA mature sequences (miRBase v22) using Bowtie2 (v2.5.2).
Supplementary files format and content: csv file include RPM values for each sample

source_name: plasma

growth_protocol: MRC5 cells infected with HCMV were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Nucleic acid extraction was performed from 600 μL of each simulated specimen using the miRNeasy Serum/Plasma Kit (Qiagen).
Small RNA libraries were constructed using the VAHTS Small RNA Library Prep Kit for Illumina V2 (Vazyme).

treatment_protocol: Simulated specimens were prepared in three groups (n=10 per group) at volume ratios of plasma to HCMV supernatant to PBS of 90:10:0, 90:5:5, and 90:2.5:7.5, respectively.

value: plasma

value: HCMV spiked-in

tag: ratio

tag: group


title: lnc13-WT-DQ8 CD8ab IEL biol rep 2

description: Library name: lnc13-WT-DQ8 CD8ab IEL biol rep 2

tag: cell type


title: lnc13-KO-DQ8 IEL-biol rep 1

description: Library name: lnc13-KO-DQ8 IEL-biol rep 1

value: IEL


title: 1-fold_S26

description:
Library name: Sample 26
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)

tag: treatment


title: lnc13-KO-DQ8 IEL-biol rep 2

description: Library name: lnc13-KO-DQ8 IEL-biol rep 2

value: small intestine


title: 1-fold_S25

description:
Library name: Sample 25
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: PT6

description:
Library name: PT6
11x11mm FFPE Visium Cytassist


title: lnc13-WT-DQ8 IEL-biol rep 1

description: Library name: lnc13-WT-DQ8 IEL-biol rep 1


title: 1-fold_S24

description:
Library name: Sample 24
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: 1-fold_S22

description:
Library name: Sample 22
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: 1-fold_S30

description:
Library name: Sample 30
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: 1-fold_S23

description:
Library name: Sample 23
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: 2-fold_S20

description:
Library name: Sample 20
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)

value: 90:5:5 (Plasma:HCMV:PBS)


title: 1-fold_S27

description:
Library name: Sample 27
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: 1-fold_S29

description:
Library name: Sample 29
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: lnc13-KO-DQ8 LPL-biol rep 1

description: Library name: lnc13-KO-DQ8 LPL-biol rep 1

value: LPL


title: lnc13-KO-DQ8 CD8ab IEL biol rep 2

description: Library name: lnc13-KO-DQ8 CD8ab IEL biol rep 2

value: CD8 T IEL


title: lnc13-WT-DQ8 IEL-biol rep 2

description: Library name: lnc13-WT-DQ8 IEL-biol rep 2


title: 2-fold_S19

description:
Library name: Sample 19
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 2-fold_S18

description:
Library name: Sample 18
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 1-fold_S21

description:
Library name: Sample 21
Simulated specimen; Ratio 90:2.5:7.5 (Plasma:HCMV:PBS)


title: lnc13-WT-DQ8 CD8ab IEL biol rep 3

description: Library name: lnc13-WT-DQ8 CD8ab IEL biol rep 3


title: lnc13-KO-DQ8 LPL-biol rep 2

description: Library name: lnc13-KO-DQ8 LPL-biol rep 2


title: lnc13-WT-DQ8 tissue-biol rep 1

description: Library name: lnc13-WT-DQ8 tissue-biol rep 1


title: 2-fold_S15

description:
Library name: Sample 15
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: lnc13-WT-DQ8 LPL-biol rep 1

description: Library name: lnc13-WT-DQ8 LPL-biol rep 1


title: lnc13-WT-DQ8 CD8ab IEL biol rep 1

description: Library name: lnc13-WT-DQ8 CD8ab IEL biol rep 1


title: 2-fold_S13

description:
Library name: Sample 13
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: MyoD-WT iMPC clone, Myf6-induced, F/R/C, rep 2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: WT_D14_2

data_processing:
Kallisto used for reference alignment + gene expression quantification
R package edgeR used for differential gene expression analysis
R package Mfuzz used for fuzzy clustering
Assembly: GRCm38.p6
Supplementary files format and content: Raw gene counts in txt format

source_name: iMPCs

growth_protocol: Before reprogramming, MEFs were cultured in 1:1 iMPC:MEF medium. iMPC medium: KnockOut DMEM, 10% FBS, 10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids Solution (100X), 1% GlutaMAX Supplement (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol, 10ng/mL bFGF. MEF medium: DMEM (High Glucose, L-glutamine, Phenol Red, Sodium Pyruvate), 10% FBS, 1% MEM Non-Essential Amino Acids Solution (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol. iMPCs clones were picked from reprogrammed cultures and cultured in iMPC medium with F/R/C (F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

extract_protocol:
To extract total RNA from cells in culture, cells were trypsinized for 5 minutes at 37°C, washed 1x with PBS and the RNA isolated using the RNeasy Mini Kit, including DNAse digestion. Samples were stored at -80°C until library preparation.
Library preparation from RNA was performed either at the Functional Genomics Center Zurich (FGCZ) of University of Zurich and ETH Zürich (Myf6-induced lentiviral reprogramming) or at Novogene UK (TetO-Myf6 and MyoD-KO reprogramming). At the FGCZ, the RNA quality was determined with a Fragment Analyzer (Agilent Technologies) and only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina) was used for library preparation. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent Technologies): the product was a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20 before sequencing. At Novogene, RNA quality was measured with the 5400 Fragment Analyser (Agilent Technologies) and only samples with RNA Integrity Number (RIN)≥ 9.1 were used for library preparation. Library preparation was carried out with a modified kit based on the TruSeq RNA Library Prep Kit (Illumina). Briefly, mRNA was purified from the total RNA samples by polyA enrichment using polyT oligo-attached magnetic beads. RNA was then fragmented and the first cDNA strand synthesized using random hexamer primers. The second strand of cDNA was then synthesized using dTTP (non-directional library), end-repaired, A-tailed, ligated with adapters, size selected, digested with USER enzyme, amplified and purified. The library concentration was checked with Qubit Fluorometer and RT-qPCR, while library fragment size was checked on a bioanalyzer.

treatment_protocol: On day 0 of the reprogramming process, medium was changed with iMPC medium only or with dox and/or F/R/C (dox: 2µg/mL doxycycline hyclate; F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

value: iMPCs

value: iMPC medium +F/R/C, generated from MEFs with Myf6 overexpression and F/R/C treatment

tag: time

value: established clone


title: lnc13-KO-DQ8 tissue-biol rep 2

description: Library name: lnc13-KO-DQ8 tissue-biol rep 2


title: 2-fold_S12

description:
Library name: Sample 12
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 2-fold_S16

description:
Library name: Sample 16
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 4-fold_S9

description:
Library name: Sample 9
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)

value: 90:10:0 (Plasma:HCMV:PBS)


title: 4-fold_S10

description:
Library name: Sample 10
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: MyoD-WT MEFs +Myf6+F/R/C, Day 12, rep3

department: Functional Genomics Center Zurich (FGCZ)

description: Library name: WT_D12_3

source_name: MEFs

value: MEFs

value: iMPC medium +Myf6+F/R/C

value: Day 12


title: 2-fold_S14

description:
Library name: Sample 14
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 2-fold_S17

description:
Library name: Sample 17
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: 2-fold_S11

description:
Library name: Sample 11
Simulated specimen; Ratio 90:5:5 (Plasma:HCMV:PBS)


title: lnc13-KO-DQ8 tissue-biol rep 1

description: Library name: lnc13-KO-DQ8 tissue-biol rep 1


title: lnc13-WT-DQ8 LPL-biol rep 2

description: Library name: lnc13-WT-DQ8 LPL-biol rep 2


title: lnc13-WT-DQ8 tissue-biol rep 2

description: Library name: lnc13-WT-DQ8 tissue-biol rep 2


title: MyoD-WT MEFs +Myf6+F/R/C, Day 12, rep2

description: Library name: WT_D12_2


title: MyoD-WT MEFs +Myf6+F/R/C, Day 6, rep2

description: Library name: WT_D6_2

value: Day 6


title: MyoD-WT iMPC clone, Myf6-induced, F/R/C, rep 1

description: Library name: WT_D14_1a


title: 4-fold_S8

description:
Library name: Sample 8
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: 4-fold_S5

description:
Library name: Sample 5
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: MyoD-WT MEFs +Myf6+F/R/C, Day 6, rep1

description: Library name: WT_D6_1


title: MyoD-WT MEFs +Myf6+F/R/C, Day 12, rep1

description: Library name: WT_D12_1


title: 4-fold_S7

description:
Library name: Sample 7
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: 4-fold_S4

description:
Library name: Sample 4
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: 4-fold_S3

description:
Library name: Sample 3
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: MyoD-WT MEFs +Myf6+F/R/C, Day 2, rep2

description: Library name: WT_D2_2

value: Day 2


title: MyoD-WT MEFs +Myf6+F/R/C, Day 2, rep1

description: Library name: WT_D2_1


title: MyoD-WT MEFs, Day 0, rep2

description: Library name: WT_D0_2

value: 1:1 iMPC:MEF media

value: Day 0


title: MyoD-WT MEFs, Day 0, rep3

description: Library name: WT_D0_3


title: MyoD-WT MEFs, Day 0, rep1

description: Library name: WT_D0_1


title: MyoD-KO iMPC clone, Myf6-induced, F/R/C, rep 2

description: Library name: KO_D14_2


title: 4-fold_S6

description:
Library name: Sample 6
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)

value: plasma

value: HCMV spiked-in


title: MyoD-WT MEFs +Myf6+F/R/C, Day 2, rep3

description: Library name: WT_D2_3


title: MyoD-KO iMPC clone, Myf6-induced, F/R/C, rep 1

description: Library name: KO_D14_1a


title: MyoD-KO MEFs +Myf6+F/R/C, Day 12, rep1

description: Library name: KO_D12_1


title: MyoD-KO MEFs +Myf6+F/R/C, Day 6, rep1

description: Library name: KO_D6_1


title: organoid derived from malignant ascites of gastric cancer patient before resistant to paclitaxel

city: Shanghai

first: Guo

last: Leilei

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

description:
Library name: P1N
10× Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and sample aggregation were performed using Cell Ranger software v2.1.1 (10x Genomics).
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: derived from paclitaxel non-resistant patient

extract_protocol:
To clarify the cellular diversity and heterogeneity in PDOs with diverse PTX response, we performed the single-cell RNA sequencing (scRNA-seq) in two organoids derived from malignant ascites of the same GC patient before (Primary) and after (Resistance) resistant to PTX. The concentration of the single-cell suspension was determined using a Countstar instrument and adjusted to 1,000 cells/μL. The cell suspension was loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) using the Single Cell 3′ Library and Gel Bead Kit v3.1 together with the Chromium Next GEM Chip G Single Cell Kit, following the manufacturer’s instructions. Approximately 6,000 cells were loaded into each channel. Captured cells were lysed, and the released RNA was barcoded during reverse transcription within individual GEMs. Reverse transcription was performed using an S1000™ Touch Thermal Cycler (Bio-Rad). The resulting cDNA libraries were generated, amplified, and quality-assessed using the Agilent 4200 system (Agilent). Finally, the libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina) with a minimum sequencing depth of 100,000 reads per cell using a paired-end 150 bp (PE150) sequencing strategy.
Library preparation was performed according to the manufacturer’s instructions using the Single Cell 3′ v2 protocol (10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the microfluidic chip to generate gel beads in emulsion (GEMs). Poly(A)+ RNA released from cell lysates within individual GEMs was reverse-transcribed into cDNA, incorporating an Illumina Read 1 (R1) primer sequence, a unique molecular identifier (UMI), and a cell-specific 10× barcode. Barcoded cDNA was subsequently purified using Silane DynaBeads (Thermo Fisher Scientific), amplified by PCR, and size-selected using SPRIselect reagent (Beckman Coulter) for downstream library construction. During library construction, the Illumina Read 2 (R2) primer sequence, paired-end adaptors containing P5 and P7 sequences, and a sample index were added.

value: Primary

value: gastric cancer organoid

value: gastric cancer malignant ascites

tag: genotype

value: WT


title: MyoD-KO MEFs +Myf6+F/R/C, Day 6, rep2

description: Library name: KO_D6_2


title: A375_WT_3

city: Madison

first: Karla

middle: Beatriz

last: Anaya Aldrete

state: Wisconsin

address: 1111 highland ave. WIMR2 room 7418

department: Dermatology

institute: University of Wisconsin Madison

description:
Library name: A375_WT_3
A3WT2

data_processing:
Processing of the sequencing data was performed using Pluto Bioscience software (https://pluto.bio/). Paired end fastq files were processed using the nf-core/rnaseq pipeline (v3.12.0) using auto strandedness (1,2). 1. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol (2020). doi: 10.1038/s41587-020-0439-x. 2. nf-core/rnaseq (latest version). https://nf-co.re/rnaseq. doi: 10.5281/zenodo.1400710.
Adapter sequences were removed with Trim Galore (3). Reads were aligned with STAR (4) to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM (5). 3. FelixKrueger/TrimGalore (latest version). https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/. doi: 10.5281/zenodo.5127898. 4. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2013). doi: 10.1093/bioinformatics/bts635. 5. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011). doi: 10.1186/1471-2105-12-323.
Differential expression analysis was performed comparing the groups: S6KO vs WildType. Genes were filtered to include only genes with at least 3 reads counted in at least 20% of samples in any group. Differential expression analysis was then performed with the DESeq2 R package (6). 6. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 15, 550 (2014).
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: rsem.merged.gene_counts.tsv: Raw gene‑level counts generated by RSEM, including expected counts and basic gene metrics

growth_protocol: SIRT6 KD and wild-type (WT) A375 cells were grown per recommendation from ATCC in DMEM media (Corning) supplemented with 10% FBS (Sigma, #F2442)

extract_protocol:
Cells were collected during exponential growth phase, pelleted, and frozen at -80°C until use. Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit with QiaShredder for homogenization per manufacturer’s protocol. RNA was quantified using BioTek Synergy H1 multimode plate reader with Take3 plate. To assess the integrity and quality of the RNA, we used the Qubit RNA IQ Assay by ThermoFisher (#Q33222)
Samples were prepared and sequenced on the Illumina NovaSeq 6000 platform using standard Novogene protocols. Library construction was perfomed by Novogene using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® for all the samples.

tag: cell line

value: epithelial malignant melanoma


title: organoid derived from malignant ascites of gastric cancer patient after resistant to paclitaxel

description:
Library name: P1T
10× Genomics

source_name: derived from paclitaxel resistant patient

value: paclitaxel-resistant


title: A375_WT_2

description:
Library name: A375_WT_2
A3WT1


title: MyoD-KO MEFs +Myf6+F/R/C, Day 2, rep3

description: Library name: KO_D2_3


title: MyoD-KO MEFs +Myf6+F/R/C, Day 2, rep1

description: Library name: KO_D2_1


title: A375_WT_4

description:
Library name: A375_WT_4
A3WT3


title: A375_S6KO_2

description:
Library name: A375_S6KO_2
A3S6KO2


title: MyoD-KO MEFs +Myf6+F/R/C, Day 12, rep3

description: Library name: KO_D12_3


title: MyoD-KO MEFs, Day 0, rep3

description: Library name: KO_D0_3


title: KBD6

city: Xi'an

first: Xuzhao

last: Bian

state: Shaan'xi

address: No.28 Xianning West Road

institute: xi'an jiaotong university

description: Library name: sample6

data_processing:
The preprocessing of the single-cell RNA sequencing (scRNA-seq) data began with the generation of unique molecular identifier (UMI) counts, which were achieved by aligning the raw sequencing reads (contained in FASTQ files) to the human reference genome (GRCh38 version 3.0.0) using CellRanger software (version 4.0) from the 10x Genomics website.The raw gene expression matrix was then subjected to stringent quality control (QC) procedures to identify and remove low-quality cells that could confound downstream analysis.  For datasets where initial processing yielded more than 10,000 captured cells, an additional critical step was performed to identify and remove potential doublets using DoubletFinder (v2.0.3). Key parameters used were pK = 0.09, which influences the proportion of artificial doublets generated relative to the real data, and nEXP = 0.075, representing the expected doublet formation rate used to scale the final doublet score thresholds. Other parameters within DoubletFinder were utilized at their default settings.
Assembly: GRCh38
Supplementary files format and content: Gene-cell count matrix：mtx

source_name: cartilage

extract_protocol:
Cartilage samples were harvested within an hour post-operation. After washing with phosphate-buffered saline (PBS) containing penicillin and streptomycin, the samples were cut into 1 mm³ fragments and pretreated with 0.25% trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in a 5% CO2 incubator for 30 minutes. The fragments were then centrifuged at 350×g for 5 minutes, and the supernatant was discarded. Subsequent digestion was performed in Dulbecco's Modified Eagle Medium/F12 (Gibco, Grand Island, NY, USA) with 0.2% type II collagenase (Gibco) at 37°C for 10-12 hours. Cell count and viability were determined using a fluorescence cell analyzer (Countstar Rigel S2) with Acridine Orange/Propidium Iodide (AO/PI) staining after erythrocyte removal (Miltenyi 130-094-183). Debris and dead cells were removed following the manufacturer’s protocols (Miltenyi 130-109-398/130-090-101).
The prepared single-cell suspension was used for cDNA library construction specifically designed for single-cell RNA sequencing using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). The pooled cDNA undergoes purification to remove reaction components, followed by PCR amplification to generate sufficient material. Sequencing of this library was performed on the Illumina NovaSeq 6000 platform.

value: cartilage

tag: disease

value: Kashin-Beck


title: KBD5

description: Library name: sample5


title: A375_S6KO_3

description:
Library name: A375_S6KO_3
A3S6KO3

tag: batch


title: 4-fold_S1

description:
Library name: Sample 1
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)

value: 90:10:0 (Plasma:HCMV:PBS)


title: A375_S6KO_1

description:
Library name: A375_S6KO_1
A3S6KO1


title: MyoD-KO MEFs +Myf6+F/R/C, Day 12, rep2

description: Library name: KO_D12_2

value: MEFs

tag: strain

value: iMPC medium +Myf6+F/R/C


title: 4-fold_S2

description:
Library name: Sample 2
Simulated specimen; Ratio 90:10:0 (Plasma:HCMV:PBS)


title: KBD3

description: Library name: sample3


title: KBD1

description: Library name: sample1


title: MyoD-KO MEFs, Day 0, rep1

description: Library name: KO_D0_1


title: KBD2

description: Library name: sample2


title: MyoD-KO MEFs +Myf6+F/R/C, Day 2, rep2

description: Library name: KO_D2_2


title: G361_WT_3

description:
Library name: G3WT3
G3WT3

data_processing:
Raw data reads from fastq files were processed by the University of Wisconsin Biotechnology Center in-house perl scripts. Reads containing the adapter sequences, poly-N stretches, or low-quality reads were excluded during preprocessing, and clean data was used for all subsequent analyses.
Reads were mapped to the reference genome using Hisat2 v2.0.5. To count reads mapping to each gene, featurecounts v1.5.0-p3 was employed and FPKM for each gene was calculated based on the number of reads mapping to it and its gene length.
The DESeq2Rpackage (1.20.0) was used to analyze the differential expression between our WT and the SIRT6 KD clones. The resulting p-values were adjusted using Benjamini and Hochberg's approach to calculate the false discovery rate. Genes with an adjusted p-value of ≤ 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCh38.p13
Supplementary files format and content: rsem_gene.txt: Raw gene‑level counts generated by RSEM, including expected counts and basic gene metrics
Supplementary files format and content: rsem_gene_rld.txt: Regularized log‑transformed gene expression values produced for variance‑stabilized downstream analysis
Supplementary files format and content: rsem_gene_TPM.txt: TPM‑normalized gene expression matrix generated from RSEM output for cross‑sample comparison.
Supplementary files format and content: edgeRglm_GENE_.csv: Differential expression results generated using the edgeR GLM method, including gene‑level log fold changes and associated statistical metrics.

growth_protocol: G361 cells were grown in McCoy’s 5A medium supplemented with 10% FBS (Sigma, #F2442)

extract_protocol:
Cells were collected during exponential growth phase, pelleted, and frozen at -80°C until use. Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit with QiaShredder for homogenization per manufacturer’s protocol. RNA was quantified using BioTek Synergy H1 multimode plate reader with Take3 plate. To assess the integrity and quality of the RNA, we used the Qubit RNA IQ Assay by ThermoFisher (#Q33222)
Samples were prepared and sequenced on the Illumina NovaSeq PE150 platform using standard Novogene protocols. Library construction was perfomed by Novogene using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® for all the samples.


title: TetO-Myf6 iMPC clone, Myf6-induced, F/R/C, rep 2

description: Library name: iMPC_2

value: iMPCs

value: M2-rtTA x TetO-Myf6

value: iMPC medium +F/R/C, generated from MEFs with Myf6 overexpression and F/R/C treatment

value: established clone


title: KBD4

description: Library name: sample4


title: TetO-Myf6 iMPC clone, Myf6-induced, F/R/C, rep 1

description: Library name: iMPC_1


title: G361_WT_1

description:
Library name: G3WT1
G3WT1


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 12, rep1

description: Library name: dFRC_D12_1

source_name: Thy1+ MEFs

value: Thy1+ MEFs

value: Day 12


title: G361_WT_2

description:
Library name: G3WT2
G3WT2


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 12, rep2

description: Library name: dFRC_D12_2


title: TetO-Myf6 iMPC clone, Myf6-induced, F/R/C, rep 3

description: Library name: iMPC_3


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 12, rep3

description: Library name: dFRC_D12_3


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 12, rep3

description: Library name: dox_D12_3

value: iMPC medium +Myf6


title: TetO-Myf6 MEFs iMPC medium, Day 12, rep3

description: Library name: nodox_D12_3

value: iMPC medium


title: MyoD-KO MEFs, Day 0, rep2

description: Library name: KO_D0_2

value: 1:1 iMPC:MEF media

value: Day 0


title: Vector-3

city: shanghai

first: Ma

last: mingjun

address: Shanghai First Maternity and Infant Hospital一妇婴保健院

institute: Tongji University

description:
Library name: Sample 3
Vector-3

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trmed sequence reads were mippedto GrC3/mmt0 usng cic genoric benchk panmeters mismath cost 2 insertion cot 3 dlen cost 3ledh facian 03 smianty tadior 08
Read count extraction and normalization were performed using ClC genomic benchwork
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: HEY

growth_protocol: HEY cells were cultured in DMEM (Gibco, USA) with 10% Fetal Bovine Serum (FBS, Gibco, USA) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from cells or human tissue using Trizol reagent (Takara, Japan)
All steps for sample preparation and library construction adhered strictly to the manufacturer's protocol (Novogene Co., Ltd., Tianjin, China).

treatment_protocol: no

value: HEY

value: Ovarian Cancer Cell lines

value: wt


title: G361_S6KD_3

description:
Library name: G3S6KO3
G3S6KO3

value: epithelial malignant melanoma


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 12, rep2

description: Library name: dox_D12_2


title: G361_S6KD_1

description:
Library name: G3S6KO1
G3S6KO1


title: TetO-Myf6 MEFs iMPC medium, Day 12, rep1

description: Library name: nodox_D12_1


title: oeCRISP3-3

description:
Library name: Sample 6
oeCRISP3-3

value: CRISP5 overexpression


title: Vector-1

description:
Library name: Sample 1
Vector-1


title: TetO-Myf6 MEFs iMPC medium, Day 12, rep2

description: Library name: nodox_D12_2


title: oeCRISP3-1

description:
Library name: Sample 4
oeCRISP3-1

value: CRISP3 overexpression


title: Vector-2

description:
Library name: Sample 2
Vector-2


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 6, rep3

description: Library name: dFRC_D6_3

value: iMPC medium +Myf6+F/R/C

value: Day 6


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 6, rep1

description: Library name: dFRC_D6_1

value: M2-rtTA x TetO-Myf6


title: HLM_2 cells, passage 12, biological replicate 1

city: Birmingham

first: Morgan

middle: Louise

last: Brown

state: Alabama

address: 1670 University Blvd.

institute: University of Alabama at Birmingham

description: Library name: MP12

data_processing:
Basecalls were performed using bclconvert version 4.0.3
Raw sequence FASTQ files were trimmed using TrimGalore! version 0.6.10 using parameters --clip_R1 1 -a A[10] --length 15
Trimmed FASTQ files were aligned to reference genome using STAR version 2.7.11b using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using HTSeq-count version 2.0.3 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCh38 p14 Release 44
Supplementary files format and content: Excel file containing raw counts for each Ensembl ID# for each sample

growth_protocol: HuH6 and HLM_2 cells were maintained in culture at 37° C in a humidified atmosphere of 5% CO2 in Dulbecco's Modified Eagles Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1 µg/mL penicillin/streptomycin, and 2 mmol/L L-glutamine

extract_protocol:
RNA was harvested using miRNeasy kit (Qiagen).
The NEBNext UltraDirectional RNA Library Prep Kit for Illumina library generation kit (New England Biolabs) was used per the manufacturer's instructions.

value: Metastatic hepatoblastoma

value: WT


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 6, rep2

description: Library name: dFRC_D6_2

value: Thy1+ MEFs


title: HLM_2 cells, passage 17,  biological replicate 2

description: Library name: MP17


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 6, rep3

description: Library name: dox_D6_3


title: HuH6 cells, passage 14, biological replicate 1

description: Library name: HP14

value: Hepatoblastoma


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 6, rep2

description: Library name: dox_D6_2

value: iMPC medium +Myf6


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 6, rep1

description: Library name: dox_D6_1


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 12, rep1

description: Library name: dox_D12_1

value: Day 12


title: HuH6 cells, passage 7, biological replicate 2

description: Library name: HUHP67


title: HEK 293T, 2WTCT48,rep3

city: Suzhou

first: Tao

last: Zhang

state: Jiangsu

address: No.28 Kehua Road

institute: Suzhou Vocational Health College

description:
Library name: Sample39
CT48-3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: HEK 293T

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose, supplemented with 10% fetal bovine serum (FBS), 50 U/mL penicillin, and 50 mg/mL streptomycin, and maintained at 37 °C in 5% CO₂.

extract_protocol:
RNA was harvested using Magzol Reagent (Magen，R4801-02). 1.4ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02 following manufacturer's protocols.

treatment_protocol: For synchronization, cells were plated in 3.5 cm plates and treated with 200 nM dexamethasone (DEX, Sigma-Aldrich, MO, USA) in PBS for 0.5 hours and initiated sample collection 24 hours after synchronization. Cells were harvested every 4 hours over a 48-hour period

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: Wildtype

value: dexamethasone shock for 30 minutes


title: HEK 293T, 2WTCT48,rep2

description:
Library name: Sample38
CT48-2


title: oeCRISP3-2

description:
Library name: Sample 5
oeCRISP3-2

value: HEY

value: Ovarian Cancer Cell lines

value: CRISP4 overexpression


title: HEK 293T, 2WTCT48,rep1

description:
Library name: Sample37
CT48-1


title: TetO-Myf6 MEFs iMPC medium, Day 6, rep3

description: Library name: nodox_D6_3

value: iMPC medium


title: TetO-Myf6 MEFs iMPC medium, Day 6, rep2

description: Library name: nodox_D6_2


title: HEK 293T, 2WTCT44,rep3

description:
Library name: Sample36
CT44-3


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 2, rep3

description: Library name: dFRC_D2_3

value: iMPC medium +Myf6+F/R/C

value: Day 2


title: TetO-Myf6 MEFs iMPC medium, Day 6, rep1

description: Library name: nodox_D6_1

value: M2-rtTA x TetO-Myf6

value: Day 6


title: HEK 293T, 2WTCT44,rep2

description:
Library name: Sample35
CT44-2


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 2, rep1

description: Library name: dFRC_D2_1


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 2, rep3

description: Library name: dox_D2_3


title: HEK 293T, 2WTCT40,rep2

description:
Library name: Sample32
CT40-2


title: HEK 293T, 2WTCT40,rep3

description:
Library name: Sample33
CT40-3


title: HEK 293T, 2WTCT40,rep1

description:
Library name: Sample31
CT40-1


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 2, rep2

description: Library name: dox_D2_2


title: HEK 293T, 2WTCT44,rep1

description:
Library name: Sample34
CT44-1


title: TetO-Myf6 MEFs +Myf6 in iMPC medium, Day 2, rep1

description: Library name: dox_D2_1


title: HEK 293T, 2WTCT36,rep3

description:
Library name: Sample30
CT36-3


title: TetO-Myf6 MEFs iMPC medium, Day 2, rep3

description: Library name: nodox_D2_3


title: TetO-Myf6 MEFs iMPC medium, Day 2, rep2

description: Library name: nodox_D2_2


title: HEK 293T, 2WTCT32,rep3

description:
Library name: Sample27
CT32-3


title: HEK 293T, 2WTCT36,rep1

description:
Library name: Sample28
CT36-1


title: HEK 293T, 2WTCT32,rep2

description:
Library name: Sample26
CT32-2


title: HEK 293T, 2WTCT36,rep2

description:
Library name: Sample29
CT36-2


title: HEK 293T, 2WTCT32,rep1

description:
Library name: Sample25
CT32-1


title: TetO-Myf6 MEFs, Day 0, rep2

description: Library name: MEF_D0_2

value: 1:1 iMPC:MEF media

value: Day 0


title: TetO-Myf6 MEFs, Day 0, rep3

description: Library name: MEF_D0_3

value: Thy1+ MEFs


title: TetO-Myf6 MEFs, Day 0, rep1

description: Library name: MEF_D0_1


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, H3K27me3 antibody, rep1

description: Library name: H8_308_doxFRC_D1_H3K27m3

data_processing:
deepTools, bamTools and bedTolls suite used for reference alignment
MACS2 used for narrow peak calling
R package DiffBind used for differential peak analysis
Assembly: GRCm39
Supplementary files format and content: Called narrow peaks
Supplementary files format and content: Normalized signals with Drosophila spike-in scaling factor in BigWig format
Library strategy: CUT&RUN

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: iMPC medium (KnockOut DMEM supplemented with 10% FBS, 10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids Solution (100X), 1% GlutaMAX Supplement (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol and 10ng/mL bFGF). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
24 hours after reprogramming initiation, cells were washed 1x with PBS and incubated with Accutase cell detachment solution at 37°C in 5% CO2 for 15 minutes. After inactivation with iMPC medium, cells were centrifuged and resuspended in 2% FBS in PBS. Cells suspensions were manually counted with a hemocytometer and 500k cells per reaction (2-3 reactions per condition) were transferred in a 1.5mL Protein Lo-Bind tube for preparation using the ChIC/CUT&RUN Assay Kit (Active Motif, 53180) according to manufacturer’s protocol. Briefly, cells were centrifuged and nuclei isolated with Complete Nuclei Isolation Buffer. Before the washes in Complete Dig-Wash Buffer, 5k Drosophila Spike-In Nuclei per reaction were added to the nuclei solution. Nuclei were then added to activated Concanavalin A Beads (10µL beads per reaction). Before incubation with primary antibody solution, the samples were divided in 2 PCR tubes (3 for one +Myf6+F/R/C sample) and incubated in either anti-HA Tag primary Antibody Buffer (1:100, MA5-27915, Invitrogen) or negative control anti-rabbit IgG primary Antibody Buffer (1:100, Active Motif, 53180, Part# 106138): additionally, one +Myf6+F/R/C sample was incubated in H3K27me3 primary Antibody Buffer (1:100, Active Motif, 39916) as positive control. All antibody buffers were supplemented with 1:50 Spike-In Antibody (Active Motif, 53183, Part# 106426). The samples were then incubated overnight at 4°C on a shaker for cell permeabilization and antibody binding. After washing, pAG-MNase (Active Motif, 53180, Part# 106130) was bound to the antibodies and the chromatin specifically digested. The chromatin fragments were then separated from the beads, purified with DNA Purification Columns SF, eluted in DNA Purification Elution Buffer, and either directly used for library preparation or frozen at -80°C until further use.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) was used for library preparation following the manufacturer’s protocol and the modifications suggested in the ChIC/CUT&RUN Assay Kit (Active Motif, 53180) protocol. Concisely, 25µL of chromatin fragments were end-repaired, the 5’-end phosphorylated and dA-tailed by incubating the fragments with the NEB Next Ultra II End Prep Enzyme Mix and Reaction Buffer for 30 minutes at 20°C and 1 hour at 50°C to avoid DNA melting. The non-indexed adaptor was diluted 1:25 in 10mM Tris-HCl with 10mM NaCl before ligation and the solution was then incubated with USER Enzyme. After ligation, a double-sided cleanup (0.4x and 1.6x) was performed with AMPure XP Beads-Based Reagent and the eluted product PCR-amplified using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England Biolabs, E7335) and NEBNext Ultra II Q5 Master Mix for 12 cycles. Following PCR amplification, the DNA fragments were double-side selected (0.4x and 1.2x) with AMPure XP Beads-Based Reagent and eluted in DNA Purification Elution Buffer, analyzed on the 4200 TapeStation System (Agilent Technologies) using the D5000 High Sensitivity ScreenTapes and reagents and stored at -20°C until sequencing.

treatment_protocol: iMPC medium was used either alone or supplemented with doxycycline (2µg/mL doxycycline hyclate) to induce Myf6 overexpression and/or F/R/C (F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

value: Mouse embryonic fibroblasts (MEFs)

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3

value: iMPC medium+Myf6+F/R/C

tag: cut&run antibody

value: H3K27me3 (positive control)


title: HEK 293T, 2WTCT28,rep3

description:
Library name: Sample24
CT28-3

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: Wildtype


title: HEK 293T, 2WTCT28,rep2

description:
Library name: Sample23
CT28-2

value: dexamethasone shock for 30 minutes


title: HEK 293T, 2WTCT28,rep1

description:
Library name: Sample22
CT28-1


title: TetO-Myf6 MEFs iMPC medium, Day 2, rep1

description: Library name: nodox_D2_1


title: HEK 293T, 2WTCT24,rep3

description:
Library name: Sample21
CT24-3


title: HEK 293T, 2WTCT24,rep2

description:
Library name: Sample20
CT24-2


title: HEK 293T, 2WTCT24,rep1

description:
Library name: Sample19
CT24-1


title: G361_S6KD_2

description:
Library name: G3S6KO2
G3S6KO2

value: epithelial malignant melanoma


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, IgG antibody, rep1

description: Library name: H5_308_doxFRC_D1_IgG

value: IgG (isotype control)


title: HEK 293T, 2WTCT20,rep3

description:
Library name: Sample18
CT20-3


title: MEFs, 24h +Myf6 in iMPC medium, IgG antibody, rep2

description: Library name: H8_308_dox_D1_IgG

value: iMPC medium+Myf6


title: MEFs, 24h +Myf6 in iMPC medium, HA (Myf6) antibody, rep2

description: Library name: H8_308_dox_D1_HA

value: HA


title: TetO-Myf6 MEFs +Myf6+F/R/C in iMPC medium, Day 2, rep2

description: Library name: dFRC_D2_2

value: M2-rtTA x TetO-Myf6

value: iMPC medium +Myf6+F/R/C

value: Day 2


title: HEK 293T, 2WTCT20,rep2

description:
Library name: Sample17
CT20-2


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, IgG antibody, rep2

description: Library name: H8_308_doxFRC_D1_IgG


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, HA (Myf6) antibody, rep1

description: Library name: H5_308_doxFRC_D1_HA


title: HEK 293T, 2WTCT20,rep1

description:
Library name: Sample16
CT20-1


title: MEFs, 24h +Myf6 in iMPC medium, IgG antibody, rep1

description: Library name: H5_308_dox_D1_IgG


title: HEK 293T, 2WTCT16,rep3

description:
Library name: Sample15
CT16-3


title: HEK 293T, 2WTCT16,rep2

description:
Library name: Sample14
CT16-2


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, HA (Myf6) antibody, rep2

description: Library name: H8_308_doxFRC_D1_HA


title: HEK 293T, 2WTCT12,rep3

description:
Library name: Sample12
CT12-3


title: MEFs, 24h iMPC medium, HA (Myf6) antibody, rep2

description: Library name: H8_308_nodox_D1_HA

value: iMPC medium


title: MEFs, 24h iMPC medium, IgG antibody, rep2

description: Library name: H8_308_nodox_D1_IgG


title: HEK 293T, 2WTCT12,rep1

description:
Library name: Sample10
CT12-1


title: MEFs, 24h +Myf6 in iMPC medium, HA (Myf6) antibody, rep1

description: Library name: H5_308_dox_D1_HA


title: MEFs, 24h iMPC medium, HA (Myf6) antibody, rep1

description: Library name: H7_308_nodox_D1_HA


title: MEFs, 24h +Myf6 in iMPC medium, rep2

description: Library name: 329951_5-TM19_D1_dox

data_processing:
BWA-MEM used for reference alignment
MACS2 used for narrow peak calling
R package DESeq2 used for differential accessibility analysis based on consensus peaks
R package IRanges used for promoter overlap analysis
MEME suite used for motif analysis
Assembly: GRCm38.p6
Supplementary files format and content: Called narrow peaks in BigWig format
Supplementary files format and content: Consensus peak file in txt format

extract_protocol:
For ATAC-Seq, the protocol modifications of the Kestner Lab of the Omni-ATAC protocol were used (Ackermann et al., 2016; Corces et al., 2017). Cells were washed 1x with PBS and collected by incubating them with Accutase cell detachment solution at 37°C in 5% CO2 for 7 minutes. After inactivation with iMPC medium, cells were centrifuged and resuspended in sterile-filtered 2% BSA (Albumin (BSA) Fraction V, (pH 7.0)) in PBS. 50k cells per condition were transferred into 1.5mL Protein Lo-Bind tube. Cells were then spun down at 500g for 5 minutes at 4°C, washed with ice-cold PBS, spun down again with the same settings and resuspended in nuclei isolation buffer containing 10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Igepal, 0.1% TWEEN 20 and 0.01% Digitonin. After incubation for 3 minutes on ice, wash buffer containing 10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.1% TWEEN 20 was added to the nuclei and the samples were centrifuged at 500g at 4°C for 10 minutes. Each nuclei preparation was then resuspended in transposition reaction mix containing 25µL 2x Tagment DNA buffer (Illumina, 20034197), 16.5µL PBS, 0.5µL 10% TWEEN 20, 0.5µL 1% Digitonin, 2.5uL TDE1 Tagment DNA Enzyme (Illumina, 20034197) and 5µL nuclease-free H2O. The samples were then incubated at 37°C for 30mins at 1,000rpm. Tagmented DNA was then isolated and purified using MinElute Reaction Cleanup Kit according to manufacturer’s protocol and eluted in 10µL.
The purified transposed DNA was then amplified for 12 cycles using NEBNext High-Fidelity 2X PCR Master Mix and the custom Nextera PCR primers Ad1_noMX and Ad2.1-6 indexing primers at 1.25µM from Buenrostro et al., 2013. The amplified libraries were then purified from primers with a single left-side 1.8x AMPure XP Beads-Based Reagent beads purification. Samples were then eluted in 22µL elution buffer and a 1:15 dilution was analyzed on the 4200 TapeStation System (Agilent Technologies) using the D5000 High Sensitivity ScreenTapes and reagents.

value: heterozygous for both alleles


title: HEK 293T, 2WTCT16,rep1

description:
Library name: Sample13
CT16-1


title: HEK 293T, 2WTCT8,rep3

description:
Library name: Sample9
CT8-3


title: HEK 293T, 2WTCT8,rep2

description:
Library name: Sample8
CT8-2


title: MEFs, 24h iMPC medium, rep2

description: Library name: 329951_4-TM19_D1_-dox

value: Mouse embryonic fibroblasts (MEFs)


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, rep1

description: Library name: 329951_3-TM9_D1_doxFRC


title: HEK 293T, 2WTCT8,rep1

description:
Library name: Sample7
CT8-1


title: MEFs, 24h +Myf6 in iMPC medium, rep1

description: Library name: 329951_2-TM9_D1_dox


title: HEK 293T, 2WTCT4,rep3

description:
Library name: Sample6
CT4-3


title: HEK 293T, 2WTCT4,rep2

description:
Library name: Sample5
CT4-2


title: MEFs, 24h iMPC medium,  IgG antibody, rep1

description: Library name: H7_308_nodox_D1_IgG

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3


title: Il5RFP-cre (R5/+) Rptor+/+-2

city: 黄浦区

first: Lin

last: Hu

state: 上海市

address: 重庆南路280号

institute: 基础医学院

description: Library name: KO2

data_processing:
CLC genomics workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: excel files include FPKM values for each sample

source_name: adipose tissue

extract_protocol:
Sorting of ILC2 in the adipose tissue,then total RNA extracted by Trizol for sequencing libraries
RNA libraries for RNA-seq were prepared using Smart mRNA-seq library prep kit following manufacturer's protocols

value: adipose tissue


title: MEFs, 24h iMPC medium, rep1

description: Library name: 329951_1-TM9_D1_-dox


title: Il5RFP-cre (R5/+) Rptorf/f-2

description: Library name: WT2


title: HEK 293T, 2WTCT0,rep3

description:
Library name: Sample3
CT0-3


title: HEK 293T, 2WTCT4,rep1

description:
Library name: Sample4
CT4-1


title: HEK 293T, 2WTCT0,rep2

description:
Library name: Sample2
CT0-2


title: 3 Keratinocytes - TNF + IL-17A

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description:
Library name: KC_17
2x150 Sequence mode to obtain at approx. 20 million read pairs

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: xlsx

source_name: Skin

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Skin

value: Primary human keratinocytes


title: MLE-12 cells,Hyperoxia+Exo3,24h

city: Wuxi

first: Yahui

last: Zhou

address: No. 299-1 Qingyang Road, Liangxi District, Wuxi, Jiangsu, China

department: Department of Neonatology

institute: Affiliated Children’s Hospital of Jiangnan University

description: Library name: Sample Exo-O2-3

data_processing:
Raw sequencing reads were filtered to remove adaptor sequences, rRNA reads, low-quality reads, and short fragments.
Clean reads were aligned to the reference genome using HISAT2 (version 2.0.4).
Transcript assembly and quantification were performed using StringTie (version 1.3.0), and gene expression levels were calculated as FPKM values.
Differential gene expression analysis was conducted using edgeR. Genes with FDR ≤ 0.05 and fold change ≥ 2 were considered significantly differentially expressed.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files contain raw read counts for each sample.
Supplementary files format and content: CSV files contain normalized gene expression values (FPKM) for each sample.

growth_protocol: The lung AT II cell line (MLE-12)was cultured in 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin. The cells were incubated in an in-cubator at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from samples using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. RNA quantity and quality were assessed prior to library construction.
RNA libraries were prepared using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following the manufacturer’s instructions. Briefly, poly(A)+ mRNA was enriched using oligo(dT) magnetic beads, followed by fragmentation and cDNA synthesis. Libraries were quantified using Qubit 2.0 Fluorometer and validated using Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina NovaSeq 6000 platform.

treatment_protocol: Two types of cell models were established to model bronchopulmonary dysplasia (BPD) in vitro. One was induced by hyperoxia, and the other was induced by lipopolysaccharide (LPS). The cells in the hyperoxia group were placed in a high-oxygen incubator and exposed to 85% oxygen. The cells in the LPS group were maintained under normal oxygen conditions (21% O2) and treated with 100 ng/mL LPS. In the intervention groups, M2 macrophage-derived exosomes (M2-Exo) were added after hyperoxia or LPS treatment. The final concentration of M2-Exo was 10 µg/mL.

value: lung epithelial cell