title: MR-T24

description:
Library name: TR_M097_007
group2_FPKM


title: patient2_2 fibroblast cells

status: Public on Aug 30 2025

type: SRA

city: zhengzhou

first: xiaoli

last: zhang

address: 河南省郑州市二七区连云路15号院11号楼29号

country: China

institute: zhengzhou university

library_source: transcriptomic

data_processing:
Trimmomatic (version 0.36)
the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of human from GRCh38 using STRA software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KC Stranded mRNA Library Prep Kit for Illumina® following manufacturer's protocols

tag: tissue

value: skin

tag: cell line

value: fibroblast

tag: cell type

value: fibroblast cells


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep2, technology_rep1

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

department: Cell Biology

country: USA

institute: Duke University

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-RNA-1

data_processing:
library strategy: scHiCAR
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence).
RNA reads were aligned to the mouse genome (mm10) using STARsolo to generate filtered gene expression matrices. DNA R1 reads were aligned to mm10 using BWA via Snaptools, and the resulting BAM files were converted to fragment-level BED format. Paired-end DNA reads were aligned to mm10 using BWA-MEM with -SP mode, and mapped reads were parsed into deduplicated contact pairs using pairtools. For the RNA matrices, genes expressed in fewer than three cells and cells with fewer than 200 detected genes or lacking corresponding DNA barcodes were removed using Seurat. Filtered RNA barcodes were also used to retain matched cells in the ATAC and contact pair datasets.
Assembly: mm10
Supplementary files format and content: The processed data include RNA expression matrix files (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz), ATAC-seq fragment files (*.ATAC.tsv.gz), and deduplicated chromatin contact pair files (*.dedup.pairs.gz).

molecule: nuclear RNA

organism: Mus musculus

source_name: Tibialis Anterior

extract_protocol:
The Tibialis Anterior (TA) muscle were dissected by tweezer from adult mouse, then were treated by douncer to get the cells. Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For the nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.

value: Tibialis Anterior

tag: genotype

tag: treatment

value: BaCl2 acute muscle injury, day5


title: J82

city: Kagoshima

first: Gang

last: Li

address: 8-35-1 Sakuragaoka

department: Urology

country: Japan

institute: Graduate School of Medical and Dental Sciences, Kagoshima University

description:
Library name: TR_M097_008
group1_FPKM

data_processing:
Basecalls were performed using bcl2fastq2.
Adapter and low-quality sequences were removed by cutadapt (v1.2.1). After quality control, poly-A/T sequences were also removed by PRINSEQ (v0.19.2).
The trimmed reads were aligned to the reference human genome using TopHat (v2.0.13).
Mapped reads were assembled by Cufflinks (v2.2.1) , and the transcripts across all samples were merged by Cuffmerge. The “fragments per kilo base per million map reads” (FPKM) was calculated with Cuffquant, and differential expression analysis (calculating fold change and testing the statistical significance) between samples was performed with Cuffdiff (Cuffmerge, Cuffquant and Cuffdiff are programs involved in the Cufflinks package).
Assembly: GRCh37/hg19
Supplementary files format and content: xlsx files include FPKM values for each sample

growth_protocol: Cell lines were cultured in minimum essential medium (MEM) containing 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 μg/mL streptomycin in a humidified environment consisting of 95% air and 5% CO2 at 37 °C.

extract_protocol:
ISOGEN (Nippon Gene, Tokyo, Japan) was used to extract RNA of cultured cells according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: To establish MR-BCs, MMAE (CAS NO. 474645-27-7; MyBioSource) was added to the cells at increasing concentrations (4, 8, 16, 32, 64, 80, 100, and 128 nM) after cells had reached 30–50% confluence. After exposure to MMAE for 24 h, the MEM was replaced with fresh MMAE-free MEM until the surviving cells recovered favorably. When cells reached the same confluence, MMAE was added to the MEM again. Cells were exposed to each concentration 6–8 times. After approximately 10 months, cells that grew in the MEM with 128 nM MMAE were designated MR-T24 and MR-J82 cells.

value: epithelial carcinoma cells

value: WT


title: patient1_2 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: T24

description:
Library name: TR_M097_006
group1_FPKM


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-RNA-5


title: PC3, T_INPUT, rep2

city: Bellinzona

first: Jean-Philippe

last: Theurillat

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute of Oncology Research

library_source: genomic

data_processing:
Nextflow nf-core chipseq pipeline version 1.2.2 for ChIP-seq peak-calling, QC and differential analysis.
FASTQ files were first processed to BAM files using BWA software and aligned to reference to Genome assembly GRCh38
Peaks calling was performed using MACS2 software and created corresponding normalised bigWig files scaled to 1 million mapped reads using BEDTools.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Prostate

extract_protocol:
DNA extraction was performed using QIAquick PCR Purification Kit (Qiagen)
NebNext Ultra II DNA library prep with sample purification beads

value: Prostate

value: Epithelial

tag: chip antibody

value: Parental

value: Compound T


title: LuCaP-145.2, CTR_FOXA1, rep1

source_name: Fresh tumor

value: Fresh tumor

value: Overexpressing FOXA2

value: FOXA1 (ab23738 Abcam)


title: patient1_1 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-RNA-4


title: control_3 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-RNA-3


title: LuCaP-145.2, CTR_INPUT, rep1


title: PC3, T_FOXA1, rep1


title: PC3, T_FOXA2, rep1

value: FOXA2 (D56D6 CST)


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep2, technology_rep3

description: Library name: mouse_muscle_day5-scHiCAR-replicate2-RNA-3


title: Rib_GW_2

city: 连云港

first: J

last: W

address: 江苏省连云港市海州区苍梧路59号

institute: 江苏海洋大学

description: Library name: Rib_GW_2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without Rib_CA for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

value: Human Breast Cancer Cell


title: Rib_GW_1

address: 江苏省连云港市海州区苍梧路59号

description: Library name: Rib_GW_1


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-RNA-2


title: control_2 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号


title: PC3, T_INPUT, rep1


title: DMSO_2

address: 江苏省连云港市海州区苍梧路59号

description: Library name: DMSO_2

value: DMSO


title: mouse mucle, BaCl2  injure, day5, RNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day5-scHiCAR-replicate1-RNA-1


title: PC3, DMSO_FOXA2, rep2


title: control_1 fibroblast cells

address: 河南省郑州市二七区连云路15号院11号楼29号

value: skin


title: DMSO_1

address: 江苏省连云港市海州区苍梧路59号

description: Library name: DMSO_1


title: mouse mucle, BaCl2  injure, day0, RNA, biology_rep1, technology_rep5

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-RNA-5

value: BaCl2 acute muscle injury, day0


title: PC3, DMSO_FOXA1, rep2


title: ABCA3_WT+LV-ABCA3:GFP

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description:
Library name: Sample 10
WT_A549s_LV-ABCA3GFP

data_processing:
Reads were mapped to GRCh38 + GFP
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: CSV file having raw read count for each sample in singular file

source_name: lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum and 1% antibiotics in humidified air with 5% CO2 at 37C

extract_protocol:
Cells were lifted in TrypLE and RNA was harvested using a Zymo RNeasy Kit
RNA libraries for RNA-seq were prepared using a Total-RNA seq library prep kit.

treatment_protocol: Cells were transduced with VSVG LV-ABCA3:GFP (MOI=20) overnight

value: lung

value: alveolar basal epithelial cells

value: ABAC3 wild-type

value: transduced with LV-ABCA3


title: Akt/Nras/FoxoAAA_3

city: Honolulu

first: Xue

last: Wang

state: Hawaii

address: 701 Ilalo Street

institute: University of Hawaii Cancer Center

description:
Library name: Akt/Nras/FoxoAAA_3
Column name in Processed data_Tissue fpkm.txt: ARF3

data_processing:
Poor quality reads were trimmed using the fastq-mcf (1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Mm.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
After removing the duplicated genes, the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include FPKM values for each sample

source_name: liver tumor tissue

growth_protocol: Hydrodynamic tail vein injection was used to deliver DNA specifically into the hepatocytes to create mouse HCC. Mice were housed and monitored according to protocols approved by the committee for animal research at the University of California, San Francisco (Protocol number AN185770) and the University of Hawaii Cancer Center.

extract_protocol:
Total RNA was extracted from mouse Akt/Nras (n=3) HCCs, Akt/Nras/Foxo1AAA (n=3) HCCs, and FVB wild-type normal livers (n=4) using the Quick-RNA Miniprep Kit (Zymo Research, CA, USA)
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: liver tumor tissue

value: WT

value: Akt/Nras/FoxoAAA


title: mouse mucle, BaCl2  injure, day0, RNA, biology_rep1, technology_rep4

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-RNA-4

value: Tibialis Anterior


title: ABCA3_WT

description:
Library name: Sample 9
WT_A549s

value: untreated


title: PC3, DMSO_INPUT, rep2

value: Prostate

value: Epithelial

value: Parental


title: mouse mucle, BaCl2  injure, day0, RNA, biology_rep1, technology_rep3

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-RNA-3


title: Akt/Nras/FoxoAAA_1

description:
Library name: Akt/Nras/FoxoAAA_1
Column name in Processed data_Tissue fpkm.txt: ARF1


title: PC3, DMSO_FOXA2, rep1

value: FOXA2 (D56D6 CST)


title: Akt/Nras3

description:
Library name: Akt/Nras3
Column name in Processed data_Tissue fpkm.txt: AktRas3

value: Akt/Nras


title: ABCA3_E690K+LV-ABCA3:GFP

description:
Library name: Sample 8
ABCA3_E690K_A549s_LV-ABCA3GFP

value: ABCA3 E690K


title: PC3, DMSO_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)

value: DMSO


title: ABCA3_E690K

description:
Library name: Sample 7
ABCA3_E690K_A549s

value: lung


title: mouse mucle, BaCl2  injure, day0, RNA, biology_rep1, technology_rep2

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-RNA-2

value: BaCl2 acute muscle injury, day0


title: Akt/Nras2

description:
Library name: Akt/Nras2
Column name in Processed data_Tissue fpkm.txt: AktRas2


title: frontal cortex, DNA, batch2, rep40

description:
brain_scHiCar_DNA_Astrocyte.pairsam.txt.gz
brain_scHiCar_DNA_CLA.pairsam.txt.gz
brain_scHiCar_DNA_Endothelial.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-1.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-2.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-3.pairsam.txt.gz
brain_scHiCar_DNA_L45IT.pairsam.txt.gz
brain_scHiCar_DNA_L56NP.pairsam.txt.gz
brain_scHiCar_DNA_L5ET.pairsam.txt.gz
brain_scHiCar_DNA_L5IT.pairsam.txt.gz
brain_scHiCar_DNA_L6b.pairsam.txt.gz
brain_scHiCar_DNA_L6CT.pairsam.txt.gz
brain_scHiCar_DNA_L6IT.pairsam.txt.gz
brain_scHiCar_DNA_Meis2.pairsam.txt.gz
brain_scHiCar_DNA_MGL.pairsam.txt.gz
brain_scHiCar_DNA_Oligo.pairsam.txt.gz
brain_scHiCar_DNA_OPC.pairsam.txt.gz
brain_scHiCar_DNA_PT.pairsam.txt.gz
brain_scHiCar_DNA_Pvalb.pairsam.txt.gz
brain_scHiCar_DNA_Sst.pairsam.txt.gz
brain_scHiCar_DNA_Subiculum.pairsam.txt.gz
brain_scHiCar_DNA_Vip.pairsam.txt.gz

data_processing:
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. The final DNA reads were mapped to genome by bwa mem with options -SP. Alignments were parsed, and paired end tags were generated using the pairtools with options --min-mapq 10.
For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence). The final fastq files were processed by STAR with parameter "--soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --soloUMIlen 12 -soloStrand Forward". The R package Seurat were used to the downstream analysis: (1) genes which expressed in less than three cells were removed. (2) Cells with unique feature counts under 100, greater than 5% mitochondrial RNA counts, and without DNA barcodes were removed.
Assembly: mm10
Supplementary files format and content: STARsolo output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz
Supplementary files format and content: .pairsam.txt.gz: list of all the contact pairs in each cell type (defined by RNA data in sciHiCAR)

source_name: frontal cortex

extract_protocol:
The frontal cortex were dissected by tweezer from adult mouse, then were treated by douncer to get the cells. Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For the nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.
sciHiCAR

value: frontal cortex


title: ABCA3_E292V+LV-ABCA3:GFP

description:
Library name: Sample 6
ABCA3_E292V_A549s_LV-ABCA3GFP

value: alveolar basal epithelial cells

value: ABCA3 E292V

value: transduced with LV-ABCA3


title: Akt/Nras1

description:
Library name: Akt/Nras1
Column name in Processed data_Tissue fpkm.txt: AktRas1

value: liver tumor tissue

value: WT


title: mouse mucle, BaCl2  injure, day0, RNA, biology_rep1, technology_rep1

description: Library name: mouse_muscle_day0-scHiCAR-replicate1-RNA-1

value: Tibialis Anterior


title: PC3, KD_FOXA2_H3K27AC, rep1

value: Prostate

value: H3K27AC (C15410196 Diagenode)

value: FOXA2 knockdown

value: Lentiviral infection, shFOXA2


title: PC3, DMSO_INPUT, rep1

value: Epithelial

value: Parental


title: Normal liver4

description:
Library name: Normal liver4
Column name in Processed data_Tissue fpkm.txt: NL4

source_name: normal liver

value: normal liver


title: PC3, KD_FOXA2_FOXA2, rep1

value: FOXA2 (D56D6 CST)


title: ABCA3_L101P+LV-ABCA3:GFP

description:
Library name: Sample 4
ABCA3_L101P_A549s_LV-ABCA3GFP

value: lung

value: ABCA3 L101P


title: Normal liver3

description:
Library name: Normal liver3
Column name in Processed data_Tissue fpkm.txt: NL3


title: Akt/Nras/FoxoAAA_2

description:
Library name: Akt/Nras/FoxoAAA_2
Column name in Processed data_Tissue fpkm.txt: ARF2

value: Akt/Nras/FoxoAAA


title: frontal cortex, DNA, batch2, rep38

value: frontal cortex


title: PC3, KD_FOXA2_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)


title: frontal cortex, DNA, batch2, rep37


title: ABCA3_L101P

description:
Library name: Sample 3
ABCA3_L101P_A549s

value: alveolar basal epithelial cells

value: untreated


title: Normal liver1

description:
Library name: Normal liver1
Column name in Processed data_Tissue fpkm.txt: NL1

value: WT


title: ABCA3_KO+LV-ABCA3:GFP

description:
Library name: Sample 2
ABCA3_KO_A549s_LV-ABCA3GFP

value: ABCA3 knockout

value: transduced with LV-ABCA3


title: Normal liver2

description:
Library name: Normal liver2
Column name in Processed data_Tissue fpkm.txt: NL2


title: PC3, KD_INPUT, rep2

value: Prostate

value: Lentiviral infection, DMSO


title: frontal cortex, DNA, batch2, rep36


title: frontal cortex, DNA, batch2, rep35


title: PC3, CTR_H3K27AC, rep1

value: H3K27AC (C15410196 Diagenode)


title: ABCA3_KO

description:
Library name: Sample 1
ABCA3_KO_A549s


title: frontal cortex, DNA, batch2, rep39


title: frontal cortex, DNA, batch2, rep34


title: Untreated CD19 CAR-T,Day4,sample3

city: shanghai

first: kaicheng

last: Zhou

state: shanghai

address: Jinke road 3728

department: Pharmacy school

institute: Fudan University

data_processing:
the Trim galore (version 0.4.5) was used to remove aptamers and low-quality bases
STAR (Spliced Transcripts Alignment to a Reference, version 2.7.10b), taking into account splice alignment.
featureCounts (version 2.0.6) count the mapped reads for each gene
Assembly: GRCh38
Supplementary files format and content: Raw counts
Supplementary files format and content: TPM

source_name: Blood

growth_protocol: mCAR-T and cmCAR-T cells were cultured in RPMI-1640 (MeilunBio, MA0215) supplemented with 10% FBS (Cytiva, SH30396.03).

extract_protocol:
Total RNA was extracted from cell samples using TRIzol Reagent (Thermo Fisher Scientific, 15596026CN)
RNA libraries for RNA-seq were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-0).

treatment_protocol: Control T cells (untransfected), Linear mRNA CAR-T or cmRNA CAR-T cells (n=3) were harvested at day 2 and day 4 post electroporation transfections.

value: Blood

value: PBMC

value: T cell

tag: time

value: Day 4


title: frontal cortex, DNA, batch2, rep33


title: ABCA3_E292V

description:
Library name: Sample 5
ABCA3_E292V_A549s

value: lung

value: ABCA3 E292V


title: Untreated CD19 CAR-T,Day4,sample2


title: PC3, CTR_FOXA1, rep1

value: Epithelial

value: Parental


title: OH3

city: Wuhan

first: Jinzhou

last: Xu

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital

description: Library name: OH3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.
The clean reads were mapped to the reference genome  using HISAT2 . FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: NCBI_GRCm39
Supplementary files format and content: txt file with FPKM values for each sample

source_name: subcutaneous transplanted tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: 5% PBS/OH2 intervention for 3 times

value: subcutaneous transplanted tumor

value: Protate cancer


title: PC3, CTR_INPUT, rep1


title: Untreated CD19 CAR-T,Day4,sample1


title: PC3, CTR_FOXA2, rep1

value: FOXA2 (D56D6 CST)


title: frontal cortex, DNA, batch2, rep32

value: frontal cortex


title: OH2

description: Library name: OH2

value: WT


title: Untreated CD19 CAR-T,Day2,sample3

value: Day 2


title: PC3, KD_FOXA1_H3K27AC, rep1

value: Prostate

value: FOXA1 knockdown

value: Lentiviral infection, shFOXA1


title: frontal cortex, DNA, batch1, rep31


title: PC3, KD_FOXA1_FOXA2, rep1


title: Untreated CD19 CAR-T,Day2,sample2

value: Blood


title: OH1

description: Library name: OH1


title: frontal cortex, DNA, batch1, rep30


title: PC3, KD_FOXA1_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)


title: Untreated CD19 CAR-T,Day2,sample1

value: PBMC

value: T cell


title: OH5

description: Library name: OH5


title: frontal cortex, DNA, batch2, rep28


title: frontal cortex, DNA, batch1, rep29


title: NC4

description: Library name: NC4


title: PC3, KD_INPUT, rep1

value: Lentiviral infection, DMSO


title: NC2

description: Library name: NC2


title: Untreated CD19 CAR-T,Day1,sample2

value: Day 1


title: frontal cortex, DNA, batch2, rep27


title: NC5

description: Library name: NC5


title: Untreated CD19 CAR-T,Day1,sample1


title: OH4

description: Library name: OH4


title: LNCaP, T_FOXA1, rep2

value: LNCaP

value: Epithelial

value: Compound T


title: NC1

description: Library name: NC1

value: subcutaneous transplanted tumor

value: Protate cancer


title: LNCaP, T_INPUT, rep2

value: Parental


title: LNCaP, T_FOXA1, rep1


title: Untreated CD19 CAR-T,Day1,sample3


title: Linear CD19 CAR-T,Day4,sample3

value: Day 4


title: frontal cortex, DNA, batch3, rep25

value: frontal cortex


title: NC3

description: Library name: NC3

value: WT


title: frontal cortex, DNA, batch4, rep26


title: Linear CD19 CAR-T,Day4,sample2


title: LNCaP, T_INPUT, rep1

value: Prostate


title: frontal cortex, DNA, batch3, rep24


title: LNCaP, DMSO_FOXA1, rep2

value: DMSO


title: frontal cortex, DNA, batch3, rep23


title: Linear CD19 CAR-T,Day4,sample1

value: Blood


title: frontal cortex, DNA, batch3, rep22


title: LNCaP, DMSO_INPUT, rep2


title: LNCaP, DMSO_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)


title: Linear CD19 CAR-T,Day2,sample1

value: PBMC

value: Day 2


title: Linear CD19 CAR-T,Day2,sample2

value: T cell


title: frontal cortex, DNA, batch3, rep21


title: thymic epithelial cell, Aebp2-ko, replicate 2, scATACseq

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

institute: Westlake Laboratory of Life Sciences and Biomedicine

description: Library name: KO2 TEC_scATAC

library_source: transcriptomic single cell

data_processing:
For bulkRNAseq, raw reads were mapped to the Mus musculus (mm10) reference genome using HISAT2. HISAT was run in a 2-pass approach with options “--score-min L,0.0,-0.2” and known splice sites for the first pass, and novel splice sites detected across all samples for the second pass. Gene-level count data was obtained using featureCounts program (http://bioinf.wehi.edu.au/featureCounts/). For scRNAseq and scATACseq, barcode processing and mapping to the mouse genome was performed with Cell Ranger v3.0. For Cut&tag, all peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: Mouse mm10
Supplementary files format and content: Excel file, matrix files and bigwig files

source_name: thymus

extract_protocol:
Thymi were isolated and cleaned to get rid of the residual fat and connective tissue, followed by a serial steps of enzymatic digestion with 0.15% mg/ml Liberase TM in RPMI 1640 at 37 °C. For adult thymi, CD45- cells were enriched with anti-CD45 beads and MACS LS columns (Miltenyi) followed by FACS sorting to harvest living CD45-Ter119-EpCAM+ thymic epithelial cells. The enriched total TECs or mTEChi (UEA1+MHCIIhi) were subjected to scRNA-seq, scATAC-seq, Cut&Tag, bulk RNA-seq.
Liraries for scRNAseq, scATACseq, Cut&tag, and bulkRNAseq were prepared following the manufactures' instructions described in the paper's method section.

value: thymus

value: thymic epithelial cell

value: knockout


title: frontal cortex, DNA, batch3, rep20


title: LNCaP, DMSO_INPUT, rep1

value: LNCaP

value: Epithelial


title: thymic epithelial cell, Aebp2-ko, replicate 1, scATACseq

description: Library name: KO TEC_scATAC


title: LNCaP, OE_FOXA2_FOXA1, rep2

value: FOXA2 overexpression

value: Lentiviral infection, DMSO


title: Linear CD19 CAR-T,Day1,sample3

value: Day 1


title: LNCaP, OE_FOXA2_H3K27AC, rep2

value: H3K27AC (C15410196 Diagenode)


title: Linear CD19 CAR-T,Day1,sample2


title: frontal cortex, DNA, batch3, rep17

value: frontal cortex


title: frontal cortex, DNA, batch3, rep18


title: thymic epithelial cell, Aebp2-flox, replicate 1, scATACseq

description: Library name: WT TEC_scATAC

value: wild type


title: thymic epithelial cell, Aebp2-flox, replicate 2, scATACseq

description: Library name: WT2 TEC_scATAC


title: LNCaP, OE_FOXA2_H3K27AC, rep1

value: Prostate


title: LNCaP, OE_FOXA2_INPUT, rep2


title: mouse KC pancreas, DIO-CD, 3

city: Davis

first: Gerardo

last: Mackenzie

state: California

address: 1 Shields Ave

institute: University of California Davis

description:
Library name: Sample 9
Column name in AllSamples_norm_counts.txt: DIOCD_3

data_processing:
Paired sequence reads were aligned to mm10/GRCm38 mouse genome using HISAT2 tool  through Galaxy, ver 22.05
Aligned reads were counted using the feature Counts tool and normalized by DESeq2 tool accessed through Galaxy, ver 22.05
Assembly: mm10/GRCm38
Supplementary files format and content: txt file containing nomalized counts for all samples

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (QIAGEN), and residual amounts of DNA were removed using an on-column RNase-Free DNase Set (QIAGEN)
Library preparation and RNA-sequencing were performed by Novogene Co. mRNA was enriched using oligo(dT) beads, and rRNA was removed using the Ribo-Zero kit. The mRNA was fragmented, and cDNA was synthesized by using mRNA template and random hexamers primer, after which a second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added for the second-strand synthesis, followed by adaptor ligation and size selection.

value: Pancreas

value: KC

value: DIO-CD

tag: batch


title: Circular CD19 CAR-T,Day4,sample3

value: Blood

value: PBMC

value: Day 4


title: Linear CD19 CAR-T,Day1,sample1

value: T cell


title: mouse KC pancreas, DIO-CD, 2

description:
Library name: Sample 8
Column name in AllSamples_norm_counts.txt: DIOCD_2


title: Circular CD19 CAR-T,Day4,sample2


title: frontal cortex, DNA, batch3, rep16


title: LNCaP, OE_FOXA2_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)


title: Linear CD19 CAR-T,Day2,sample3

value: Day 2


title: frontal cortex, DNA, batch3, rep15


title: Circular CD19 CAR-T,Day4,sample1


title: frontal cortex, DNA, batch3, rep19


title: mouse KC pancreas, DIO-CD, 1

description:
Library name: Sample 7
Column name in AllSamples_norm_counts.txt: DIOCD_1


title: mouse KC pancreas, DIO, 3

description:
Library name: Sample 6
Column name in AllSamples_norm_counts.txt: DIO_3

value: DIO


title: LNCaP, OE_FOXA2_INPUT, rep1

value: LNCaP

value: Epithelial

value: FOXA2 overexpression


title: frontal cortex, DNA, batch3, rep14

description:
brain_scHiCar_DNA_Astrocyte.pairsam.txt.gz
brain_scHiCar_DNA_CLA.pairsam.txt.gz
brain_scHiCar_DNA_Endothelial.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-1.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-2.pairsam.txt.gz
brain_scHiCar_DNA_L23IT-3.pairsam.txt.gz
brain_scHiCar_DNA_L45IT.pairsam.txt.gz
brain_scHiCar_DNA_L56NP.pairsam.txt.gz
brain_scHiCar_DNA_L5ET.pairsam.txt.gz
brain_scHiCar_DNA_L5IT.pairsam.txt.gz
brain_scHiCar_DNA_L6b.pairsam.txt.gz
brain_scHiCar_DNA_L6CT.pairsam.txt.gz
brain_scHiCar_DNA_L6IT.pairsam.txt.gz
brain_scHiCar_DNA_Meis2.pairsam.txt.gz
brain_scHiCar_DNA_MGL.pairsam.txt.gz
brain_scHiCar_DNA_Oligo.pairsam.txt.gz
brain_scHiCar_DNA_OPC.pairsam.txt.gz
brain_scHiCar_DNA_PT.pairsam.txt.gz
brain_scHiCar_DNA_Pvalb.pairsam.txt.gz
brain_scHiCar_DNA_Sst.pairsam.txt.gz
brain_scHiCar_DNA_Subiculum.pairsam.txt.gz
brain_scHiCar_DNA_Vip.pairsam.txt.gz


title: Circular CD19 CAR-T,Day2,sample3


title: frontal cortex, DNA, batch3, rep13


title: mouse KC pancreas, DIO, 2

description:
Library name: Sample 5
Column name in AllSamples_norm_counts.txt: DIO_2


title: Circular CD19 CAR-T,Day2,sample2


title: mouse KC pancreas, CD, 3

description:
Library name: Sample 3
Column name in AllSamples_norm_counts.txt: CD_3

value: CD


title: Circular CD19 CAR-T,Day1,sample3

value: Day 1


title: frontal cortex, DNA, batch3, rep11

value: frontal cortex


title: mouse KC pancreas, CD, 2

description:
Library name: Sample 2
Column name in AllSamples_norm_counts.txt: CD_2


title: frontal cortex, DNA, batch3, rep12


title: LNCaP, CTR_INPUT, rep2

value: Prostate

value: Parental


title: frontal cortex, DNA, batch3, rep9


title: Circular CD19 CAR-T,Day1,sample2


title: mouse KC pancreas, CD, 1

description:
Library name: Sample 1
Column name in AllSamples_norm_counts.txt: CD_1

value: Pancreas

value: KC


title: LNCaP, CTR_FOXA1, rep1

value: Lentiviral infection, DMSO


title: LNCaP, CTR_FOXA2, rep1

value: FOXA2 (D56D6 CST)


title: Circular CD19 CAR-T,Day1,sample1

value: Blood

value: PBMC


title: frontal cortex, DNA, batch3, rep8


title: LNCaP, CTR_H3K27AC, rep2

value: H3K27AC (C15410196 Diagenode)


title: LNCaP, CTR_INPUT, rep1


title: H660, KD_H3K27AC, rep1

value: Epithelial neuroendocrine

value: H3K27AC knockdown

value: Lentiviral infection, shH3K27AC


title: LNCaP, CTR_FOXA1, rep2

value: LNCaP

value: Epithelial

value: FOXA1 (ab23738 Abcam)


title: frontal cortex, DNA, batch3, rep10


title: KDM5A, B16-OVA, CUTTag, LD_A3

city: Beijing

first: Tantan

address: Haidian  District

institute: Tsinghua University

data_processing:
After quality control by FastQC, Nestera adapters were trimmed by Cutadapt, and clean paired-end reads were mapped to the mm10 reference genome using Bowtie2. Only concordantly mapped pairs were kept for further analysis. Peak calling was performed using MACS3.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: B16-OVA melanoma cells

extract_protocol:
The fragment DNA were extracted by 150 µl tris saturated phenol and 150 µl chloroform.
CUT&Tag for the B16-OVA cells and cDC1s were carried out according to the instruction of CUT&Tag assay kit (Vazyme).  The PCR on the CUT&Tag was performed with the following protocol: 3 min at 72 °C and 3 min at 95 °C, followed by 15 cycles of 10 s at 98 °C, and 5 s at 60 °C, with a final extension at 72 °C for 1 min.

value: B16-OVA melanoma cells


title: TCR-peptide_stimulated_CD8,scTCRseq

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

institute: zhejiang university

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 1 OX Genomics Cell Ranger pipeline (https:/ /support. I Oxgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) .
Assembly: nm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+T cell

extract_protocol:
CD8+ T cells from mice immunized with the self-reactive peptides mix were labeled with CellTrace Violet (CTV) dye and restimulated with the self-peptides in vitro.The CD44+ CTVlow CD8+ T cells were sorted by flow cytometry for single-cell sequencing.
CD44+CTVlowCD8+ T cells were sorted from peptides stimulated lymphocytes and utilized to prepare 5' gene expression (GEX) and paired T cell receptor (TCR) libraries using the 5' Chromium Next GEM Single Cell v2 (Dual Index) reagents and protocol provided by 10X Genomics

value: CD8+T cell

value: WT

value: self-peptide stimulated


title: frontal cortex, DNA, batch3, rep7

value: frontal cortex


title: Circular CD19 CAR-T,Day2,sample1

value: T cell

value: Day 2


title: KDM5A, B16-OVA, CUTTag, LD_A2


title: peptide_stimulated_CD8,scRNAseq


title: KDM5A, cDC1, CUTTag, BD_A3

source_name: cDC1 cells

value: cDC1 cells


title: UC-P12 Tissue

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

description: Library name: Sample 2

data_processing:
After sequencing, read quality was assessed using FastQC, and high-quality reads were mapped to the canine reference genome CanFam3.1. Kallisto or CellRanger was used to conduct read alignment and gene expression counts for bulk and single-nuclei RNA sequencing, respectively (Bray et al., 2016; Zheng et al., 2017). Next, single-nuclei RNA sequencing data was normalized and log transformed using R package Seurat (Butler et al., 2018; Hao et al., 2021, 2024; Satija et al., 2015; Stuart et al., 2019) R and corresponding R scripts were then used for data preparation procedures, analysis procedures, and visualization (R Core Team, 2018). The data was stored on GitHub and figshare repositories, and Zenodo was used to create Digital Object Identifiers (DOIs) for publication citations. Gene Set Enrichment Analysis with the fgsea package was used for pathway analysis, and gene signatures were acquired from the Molecular Signatures Database (MSigDB) (Korotkevich et al.; Liberzon et al., 2011).
Assembly: canine reference genome CanFam3.1
Supplementary files format and content: snRNAseq_Tux_cellTypes_CLEAN.RData

organism: Canis lupus familiaris

source_name: bladder tissue

extract_protocol:
For single-nuclei samples, frozen tissues were received at Azenta, South Plainfield, NJ, USA in dry-ice and stored in liquid nitrogen until further processing. Nuclei extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec, Auburn, CA, USA) following manufacturer’s guidelines with gentle MACS Dissociation and C tubes. Upon isolation, the nuclei were counted using AO/PI dye on the Nexcelom Cellaca MX before loading onto the Chromium Controller.
Single-nuclei RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). Loading onto the Chromium Controller was performed to target capture of ~6,000 GEMs per sample for downstream analysis and processed through the Chromium Controller following the standard manufacturer’s specifications. The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to loading onto an Illumina NovaSeq XPlus instrument. The samples were sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics. Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command.

value: bladder tissue


title: frontal cortex, DNA, batch3, rep6


title: frontal cortex, DNA, batch3, rep4


title: H660, KD_FOXA2, rep1

value: Prostate

value: FOXA2 (D56D6 CST)

value: FOXA2 knockdown

value: Lentiviral infection, shFOXA2


title: UC-P12 Organoid

description: Library name: Sample 1

source_name: bladder organoid

value: bladder organoid


title: H3K4me3, B16-OVA, CUTTag, LD_H3K4me3


title: P14_Tis_Trigone_Bladder_R3

description: Library name: Sample 52

data_processing:
After sequencing, read quality was assessed using FastQC, and high-quality reads were mapped to the canine reference genome CanFam3.1. Kallisto or CellRanger was used to conduct read alignment and gene expression counts for bulk and single-nuclei RNA sequencing, respectively (Bray et al., 2016; Zheng et al., 2017). Next, single-nuclei RNA sequencing data was normalized and log transformed using R package Seurat (Butler et al., 2018; Hao et al., 2021, 2024; Satija et al., 2015; Stuart et al., 2019) R and corresponding R scripts were then used for data preparation procedures, analysis procedures, and visualization (R Core Team, 2018). The data was stored on GitHub and figshare repositories, and Zenodo was used to create Digital Object Identifiers (DOIs) for publication citations. Gene Set Enrichment Analysis with the fgsea package was used for pathway analysis, and gene signatures were acquired from the Molecular Signatures Database (MSigDB) (Korotkevich et al.; Liberzon et al., 2011).
Assembly: canine reference genome CanFam3.1
Supplementary files format and content: Rdata file

extract_protocol:
Organoids were preserved for bulk RNA-sequencing by removing them from Matrigel using Cell Recovery Solution, as previously described (Nicholson et al., 2025). The cell pellet was resuspended in 100 µL PBS, moved to a cryovial containing 900 µL RNAlater, and stored at -80°C. For RNA extractions, organoid samples were thawed and transferred to 15 mL tubes, washed with 2 mL of PBS, and centrifuged at 1,200 x g (4°C) for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in 1 mL of Trizol (Invitrogen; 15596026). Next, each sample was briefly vortexed. Tissues that were either flash frozen or stored in RNALater (if stored in RNALater a wash with PBS was done) were transferred from cryovials to microcentrifuge tubes, 800 µL of Trizol were added to each tube, and tissues were homogenized using a pestle. Both samples (tissue and organoids) were left at room temperature for five minutes prior to centrifuging at 12,000 x g (4°C) for 10 minutes. Supernatant was then transferred to a microcentrifuge tube, and 160 µL or 200 µL of chloroform (Alfa Aesar; J67241) were added for tissues and organoids, respectively. The samples were then vigorously mixed by shaking for 20 seconds and after sitting at room temperature for 2-3 minutes, the samples were spun at 10,000 x g for 18 minutes (4°C). The aqueous top layer was collected and moved to a sterile RNase-free tube before adding an equal amount of 100% RNA-free ethanol (Fisher; BP2818-500). Up to 700 µL were loaded in a Qiagen RNeasy column and collection tube (RNeasy Mini kit; Qiagen; 74104). Samples were then centrifuged at 8,000 x g for 30 seconds, the collection tube waste was discarded, and DNase treatment was performed according to Qiagen’s protocol (Qiagen; 79254). In a new collection tube, 500 µL buffer RPE was added to the column, and the samples were again spun. After discarding the flow-through, this step was repeated, with samples now spun for 2 minutes at 8,000 x g. The flow-through was discarded again, and the samples were centrifuged at the same settings for 1 minute. Then, 50 µL of RNase-free water (Sigma; W4502-50ML) was added to the column and incubated for 2 minutes. Samples were centrifuged twice at 8,000 x g for 1 minute. RNA concentration was determined with a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and samples were kept at -80°C until shipped.
RNA extraction, library preparation, and sequencing were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

tag: patient #


title: frontal cortex, DNA, batch3, rep3


title: H660, KD_FOXA1, rep1

value: Epithelial neuroendocrine

value: FOXA1 knockdown

value: Lentiviral infection, shFOXA1


title: P14_Tis_Trigone_Bladder_R2

description: Library name: Sample 51


title: H660, CTR_FOXA2, rep1

value: Parental

value: Lentiviral infection, DMSO


title: mouse KC pancreas, DIO, 1

description:
Library name: Sample 4
Column name in AllSamples_norm_counts.txt: DIO_1

value: Pancreas

value: KC

value: DIO


title: H660, CTR_H3K27AC, rep1

value: H3K27AC (C15410196 Diagenode)


title: frontal cortex, DNA, batch3, rep5

value: frontal cortex


title: H660, CTR_FOXA1, rep1

value: FOXA1 (ab23738 Abcam)


title: frontal cortex, DNA, batch3, rep2


title: P14_Tis_Trigone_Bladder_R1

description: Library name: Sample 50

value: bladder tissue


title: frontal cortex, DNA, batch3, rep1


title: LNCaP, CTR_H3K27AC, rep1

value: Prostate

value: LNCaP

value: Epithelial


title: Female-Exp 1

city: Guangzhou

first: Wenchang

address: No. 78, Zhongshan 2nd Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

description: Female-Exp 1_count

data_processing:
Library preparation for Transcriptome sequencing:A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected,adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing (Novogene Experimental Department):The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality Control: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.
Reads mapping to the reference genome:Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level:FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm38.100   Mus musculus
Supplementary files format and content: tab-delimited text files include counts for each Sample ...

source_name: LHb brain tissue

extract_protocol:
Mice were euthanized by rapid cervical dislocation. Their brains were sliced on a brain matrix (RWD Life Science, Shenzhen, China) in ice-cold dissection buffer (2.6 mM KCl, 1.23 mM NaH2PO4, 26.2 mM NaHCO3, 5 mM kynurenic acid, 212.7 mM sucrose, 10 mM dextrose, 0.5 mM CaCl2, 1 mM MgCl2). The LHb was rapidly dissected out on ice and snap-frozen on dry ice. Total RNA was extracted using the RNAeasy Micro Kit following the manufacturer’s protocol (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were immunized with an intraperitoneal (i.p.) injection with the arthritogenic monoclonal antibody 5-clones cocktail (Col II mAbs, dissolved in sterile saline, 50 mg/kg body weight; Chondrex, cat# 53010), followed by 3 days later an i.p. injection with lipopolysaccharide (LPS, dissolved in sterile saline, 1 mg/kg body weight; Chondrex, cat# 53010).7 The control group was injected with the same dose of vehicle.

value: LHb brain tissue

tag: strain

value: BALB/c

tag: Sex

value: female

tag: age

value: 3 month old

value: Collagen antibody induced arthritis


title: H660, KD_INPUT, rep1

value: Epithelial neuroendocrine

value: Parental


title: P14_Tis_Apex_Bladder_R3

description: Library name: Sample 49


title: KDM5A, cDC1, CUTTag, BD_A2

value: cDC1 cells


title: Female-Exp 2

description: Female-Exp 2_count


title: frontal cortex, RNA, batch2, rep40


title: Female-Exp 3

description: Female-Exp 3_count


title: frontal cortex, RNA, batch2, rep39


title: Female-Ctrl 3

description: Female-Ctrl 3_count

value: Control


title: LNCaP, FOXA2-RES, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_OE_3

data_processing:
Nextflow nf-core rnaseq pipeline version 3.6
Adapter and quality trimming to FastQ files using Trim Galore wrapper around tools Cutadapt and FastQC.
Trimmed and quality checked sequence reads were mapped to hg38 genome build using STAR and quantified using Salmon with default parameters.
Read count extraction and normalisation were performed using DESeq R package.
Assembly: hg38
Supplementary files format and content: Comma-separated values text file contains the count matrix  resulted from variance stabilizing transformation using DESeq2 package.

extract_protocol:
QIAGEN RNAeasy Mini Kit
NEBNext Ultraexpress RNA Library Prep Kit for Illumina (E3330S - New England BioLabs Inc.) was employed with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis (E7490 -  New England BioLabs Inc.) with the addition of barcode sequences

value: FOXA2 overexpression

value: Lentiviral infection, ARCC4


title: P14_Tis_Apex_Bladder_R1

description: Library name: Sample 47


title: H660, CTR_INPUT, rep1


title: Female-Ctrl 1

description: Female-Ctrl 1_count


title: frontal cortex, RNA, batch2, rep38

value: frontal cortex


title: P14_Tis_Apex_Bladder_R2

description: Library name: Sample 48


title: LNCaP, FOXA2-RES, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_OE_2


title: frontal cortex, RNA, batch2, rep37


title: LNCaP, FOXA2-RES, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_OE_1


title: P14_Org_Trigone_Bladder_R3

description: Library name: Sample 45

value: bladder organoid


title: Male-Exp 2

description: Male-Exp 2_count

value: male


title: frontal cortex, RNA, batch2, rep36


title: frontal cortex, RNA, batch2, rep35


title: Male-Exp 3

description: Male-Exp 3_count


title: LNCaP, CTR-RES, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_WT_2

value: Prostate


title: P14_Org_Trigone_Bladder_R1

description: Library name: Sample 43


title: Male-Ctrl 3

description: Male-Ctrl 3_count


title: frontal cortex, RNA, batch2, rep34


title: LNCaP, CTR-RES, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_WT_1

value: LNCaP


title: P14_Org_Apex_Bladder_R3

description: Library name: Sample 42


title: frontal cortex, RNA, batch2, rep33


title: LNCaP, FOXA2-E, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_OE_3

value: Epithelial

value: Lentiviral infection, Enzalutamide


title: Female-Ctrl 2

description: Female-Ctrl 2_count

value: LHb brain tissue

value: BALB/c


title: Male-Ctrl 1

description: Male-Ctrl 1_count

value: 3 month old


title: P14_Org_Apex_Bladder_R2

description: Library name: Sample 41


title: frontal cortex, RNA, batch2, rep32


title: P12_Tis_Bladder_R3

description: Library name: Sample 46

value: bladder tissue


title: P14_Org_Apex_Bladder_R1

description: Library name: Sample 40


title: frontal cortex, RNA, batch1, rep31


title: LNCaP, CTR-RES, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_RES_WT_3


title: Male-Exp 1

description: Male-Exp 1_count

value: Collagen antibody induced arthritis


title: P13_Org_Urethra_R3

description: Library name: Sample 39

source_name: urethra organoid

value: urethra organoid


title: P14_Org_Trigone_Bladder_R2

description: Library name: Sample 44


title: P13_Org_Urethra_R2

description: Library name: Sample 38


title: frontal cortex, RNA, batch1, rep29


title: LNCaP, CTR-E, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_WT_1

source_name: Prostate

value: Parental


title: P13_Org_Urethra_R1

description: Library name: Sample 37


title: frontal cortex, RNA, batch2, rep28


title: P12_Org_Bladder_R3

description: Library name: Sample 36


title: frontal cortex, RNA, batch2, rep27


title: LNCaP, FOXA2, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_OE_3

value: Lentiviral infection, DMSO


title: P12_Org_Bladder_R2

description: Library name: Sample 35


title: LNCaP, FOXA2, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_OE_2

value: FOXA2 overexpression


title: LNCaP, FOXA2-E, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_OE_2


title: P12_Org_Bladder_R1

description: Library name: Sample 34


title: frontal cortex, RNA, batch1, rep30


title: LNCaP, FOXA2-E, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_OE_1


title: LNCaP, CTR-E, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_WT_3


title: frontal cortex, RNA, batch3, rep25


title: LNCaP, CTR-E, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_E_WT_2


title: LNCaP, FOXA2, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_OE_1


title: P06_Org_V8_Urine_R3

description: Library name: Sample 33

source_name: urine organoid

value: urine organoid


title: LNCaP, CTR, rep3

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_WT_3


title: frontal cortex, RNA, batch3, rep24

value: frontal cortex


title: P06_Org_V8_Urine_R2

description: Library name: Sample 32


title: frontal cortex, RNA, batch3, rep23


title: LNCaP, CTR, rep2

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_WT_2


title: frontal cortex, RNA, batch3, rep22


title: P06_Org_V8_Urine_R1

description: Library name: Sample 31


title: LNCaP, CTR, rep1

description:
Processed data file: ncounts_LNCaP_F2_Enza_ARCC4.csv
Sample name in processed data file: LnCaP_WT_1


title: frontal cortex, RNA, batch4, rep26


title: P06_Org_V5_Urine_R3

description: Library name: Sample 30


title: frontal cortex, RNA, batch3, rep21


title: P06_Org_V5_Urine_R2

description: Library name: Sample 29


title: PC3, PLKO, rep3

data_processing:
Nextflow nf-core rnaseq pipeline version 3.6
Adapter and quality trimming to FastQ files using Trim Galore wrapper around tools Cutadapt and FastQC.
Trimmed and quality checked sequence reads were mapped to hg38 genome build using STAR and quantified using Salmon with default parameters.
Read count extraction and normalisation were performed using DESeq R package.
Assembly: hg38
Supplementary files format and content: Comma-separated values text file contains the count matrix  resulted from variance stabilizing transformation using DESeq2 package and the results from differential expression analysis comparing FOXA2 overexpression in LNCaP cells against parental controls with DMSO, Enzalutamide and androgen receptor degrader treatment respectively.

value: Lentiviral infection


title: frontal cortex, RNA, batch3, rep20


title: P06_Org_V5_Urine_R1

description: Library name: Sample 28


title: PC3, PLKO, rep1


title: PC3, PLKO, rep2


title: frontal cortex, RNA, batch3, rep19


title: frontal cortex, RNA, batch3, rep18


title: PC3, T, rep3

value: Compound T


title: frontal cortex, RNA, batch3, rep17


title: P06_Org_V4_Urine_R3

description: Library name: Sample 27


title: genomic DNA from  liver tissue E-NO8

type: genomic

city: Shinjuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35 shinanomachi

department: Pathology

institute: Keio University School of Medicine

description: Metabolic dysfunction-associated steatohepatitis

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina iScan Protocol

data_processing: GenomeStudio methylation software

label: Cy5 and Cy3

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: Phenol-chloroform extraction followed by dialysis

value: Liver

tag: gender

value: M


title: P06_Org_V4_Urine_R1

description: Library name: Sample 25


title: frontal cortex, RNA, batch3, rep16


title: PC3, T, rep1

value: Prostate

value: Epithelial


title: PC3, T, rep2


title: P06_Org_V4_Bladder_R3

description: Library name: Sample 24

value: bladder organoid


title: genomic DNA from  liver tissue E-NO4


title: genomic DNA from  liver tissue E-NO6


title: PC3, DMSO, rep3

value: DMSO


title: frontal cortex, RNA, batch3, rep15


title: P06_Org_V4_Bladder_R2

description: Library name: Sample 23


title: genomic DNA from  liver tissue E-NO9

value: F


title: frontal cortex, RNA, batch3, rep14


title: P06_Org_V4_Bladder_R1

description: Library name: Sample 22


title: genomic DNA from  liver tissue E-NW10


title: PC3, DMSO, rep2


title: genomic DNA from  liver tissue E-NO5


title: PC3, DMSO, rep1


title: P06_Org_V2_Urine_R3

description: Library name: Sample 21


title: genomic DNA from  liver tissue E-NO7


title: genomic DNA from  liver tissue E-NO1


title: P06_Org_V4_Urine_R2

description: Library name: Sample 26


title: frontal cortex, RNA, batch3, rep12


title: genomic DNA from  liver tissue E-NW8


title: P06_Org_V2_Urine_R2

description: Library name: Sample 20


title: genomic DNA from  liver tissue E-NO3


title: genomic DNA from  liver tissue E-NO2


title: frontal cortex, RNA, batch3, rep11


title: PC3, DKD, rep3

value: FOXA1 and FOXA2 kockdown


title: frontal cortex, RNA, batch3, rep13


title: frontal cortex, RNA, batch3, rep10


title: PC3, DKD, rep2


title: P09_Org_Urine_R1

description: Library name: Sample 18


title: P09_Org_Urine_R2

description: Library name: Sample 19


title: genomic DNA from  liver tissue E-NT9

description: Hepatocellular carcinoma


title: UBQ_19A_HOM_Rep03

city: Indianapolis

first: Shreedharan

last: Sriram

state: IN

address: 9330 Zionsville Rd

institute: Corteva Agriscience

description: Library name: AS2630020

data_processing:
Please refer to associated manuscript
Assembly: Glycine max Williams82 reference genome and annotations (version W82.a4.v1) downloaded from JGI Phytozome
Supplementary files format and content: AS263_W82a4v1_gene_counts_table.SOY.txt: tab-delimited text file which includes raw gene count values for each Sample

organism: Glycine max

source_name: developing seed

growth_protocol: Please refer to associated manuscript

extract_protocol:
Total RNA was isolated from ground frozen tissue with RNeasy (Qiagen Inc.), according to the manufacturer's protocol. Total RNA was then analyzed for quality and quantity with either the Bioanalyzer RNA Nano kit (Agilent Technologies) or the Fragment Analyzer with RNA  kit (Agilent Technologies) and normalized to 1 μg input per sample.
Sequencing libraries were prepared using the Illumina Stranded mRNA library kit, according to vendor protocol (Illumina Inc. San Diego, CA). Briefly, mRNAs were isolated via attachment to oligo(dT) beads, fragmented, and reverse transcribed into cDNA by random hexamer primers with Superscript II reverse transcriptase (Life Technologies). The resulting cDNAs were end repaired, 3′-A-tailed, and ligated with Illumina indexed TruSeq adapters. Ligated cDNA fragments were PCR-amplified with Illumina RNA/DNA UDI indexed-primers, purified with AmpureXP Beads (Beckman Coulter Genomics), and checked for quality and quantity with the Agilent TapeStation 4200 system with D1000 ScreenTape. Libraries were combined into one sequencing pool based on equal-nm pooling, and pool then diluted to 2 nM. The pool was denatured according to Illumina sequencing protocols, hybridized, and clustered on an appropriate Illumina flowcell targeting 20M reads per sample.   Samples were sequenced using Single-Read 100bp reads.

treatment_protocol: Please refer to associated manuscript

value: developing seed

value: 35 days after flowering


title: P10_Org_Urine_R3

description: Library name: Sample 17


title: genomic DNA from  liver tissue E-NT8

description: Hepatocellular carcinoma


title: genomic DNA from  liver tissue E-NW9


title: genomic DNA from  liver tissue E-NW7


title: frontal cortex, RNA, batch3, rep8

source_name: frontal cortex


title: genomic DNA from  liver tissue E-NT5

description: Hepatocellular carcinoma


title: P10_Org_Urine_R1

description: Library name: Sample 15


title: frontal cortex, RNA, batch3, rep6


title: UBQ_19A_HOM_Rep01

description: Library name: AS2630018


title: P10_Org_Urine_R2

description: Library name: Sample 16


title: UBQ_19A_HOM_Rep02

description: Library name: AS2630019


title: frontal cortex, RNA, batch3, rep5


title: genomic DNA from  liver tissue E-NW4


title: genomic DNA from  liver tissue E-NT6

description: Hepatocellular carcinoma


title: frontal cortex, RNA, batch3, rep7


title: genomic DNA from  liver tissue E-NW5


title: genomic DNA from  liver tissue E-NT10

description: Hepatocellular carcinoma


title: UBQ_15A_HOM_Rep02

description: Library name: AS2630016


title: UBQ_15A_HOM_Rep03

description: Library name: AS2630017


title: P11_Org_Urine_R3

description: Library name: Sample 14


title: P11_Org_Urine_R1

description: Library name: Sample 12


title: P11_Org_Urine_R2

description: Library name: Sample 13


title: UBQ_33A_NULL_Rep06

description: Library name: AS2630006


title: genomic DNA from  liver tissue E-NT3

description: Hepatocellular carcinoma


title: frontal cortex, RNA, batch3, rep4


title: genomic DNA from  liver tissue E-NW3


title: genomic DNA from  liver tissue E-NW2


title: P06_Org_V1_Urine

description: Library name: Sample 11


title: frontal cortex, RNA, batch3, rep3


title: P05_Org_Urine

description: Library name: Sample 10


title: P08_Org_Urine

description: Library name: Sample 9


title: UBQ_33A_NULL_Rep05

description: Library name: AS2630005


title: UBQ_33A_NULL_Rep04

description: Library name: AS2630004


title: UBQ_15A_HOM_Rep01

description: Library name: AS2630015


title: mouse astrocytes, rep2-2

data_processing:
Trim the adaptor sequence in read1.
Then fastq file were processed by nf-core/hicar.
Assembly: mm10
Supplementary files format and content: .pairsam.txt.gz: list of all contact pairs in HiCAR

source_name: astrocyte

extract_protocol:
For Pvalb neuron, adult PvalbCre/+;Sun1-GFPlx/+ mice (five pooled per replicate) were deeply anaesthetized with isoflurane. The brains were harvested in chilled oxygenated artificial Cerebrospinal fluid followed by sectioning 500 μm slices spanning the cortex using adult mouse brain matrix on ice. Further, the cortical area was micro-dissected and collected in 1.5 ml microcentrifuge tubes in dry ice and stored at -80oC for later use. The cortical dissociation for single nuclei preparation and FACS sorting was performed following the published protocol with modification (Zemke, N.R., Armand, E.J., Wang, W. et al. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 624, 390–402 (2023). https://doi.org/10.1038/s41586-023-06819-6). Briefly, the cortical tissue was transferred into dounce homogenizer on ice in 1 ml chilled DB-DP buffer spiked with 0.1% Triton X-100 (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl pH 7.5, 25 mM DTT and 5 mM EDTA free protease inhibitor cocktail. Tissue was dounce homogenized with loose pestle for 10-15 strokes followed by tight pestle 15–20 strokes or until the solution was uniform. Nuclei were filtered using a 30 μm CellTrics filter into a LoBind tube and centrifuged at 1,000 rcf, for 10 min at 4 °C. The pellet was resuspended in 1 ml DB-DP buffer and centrifuged at 1000 rcf, 10 min at 4 °). The nuclei pellet were resuspended in 500 μl sort buffer (1 mM EDTA, 0.5% BSA in PBS) containing 0.5 µg/ml DAPI. A total of 100,000 GFP+ nuclei was sorted using Sony SH800S sorter into a LoBind tube containing collection buffer (1 mM EDTA, 5% fatty acid-free BSA in PBS). For astrocytes, mice were first perfused with PBS before the cortices were dissected and chopped into 1mm3 pieces. The cortex was then digested in papain (~7.5U/ml) at 33C for 45mins. Cells were centrifuged at 500 RCF for 10mins, resuspended in MACS buffer (0.002M EDTA, 0.2% milk peptone, 0.015M HEPES, 0.5% glucose, HBSS), and filtered through Celltrics filter to achieve single cell suspension. Myelin and microglia depletion from the cell suspension was achieved using Miltenyi myelin removal beads and Miltenyi anti-CD11b beads per the manufacturer’s instructions. Astrocytes were subsequently positively isolated using Miltenyi MACS Anti-ACSA-2 Microbead kit per manufacturer’s instructions.
Nuclei or cells were crosslinked by formaldehyde, quenched by Tris glycine. Then crosslinked cells or nuclei were treated by NPB, followed by tagmentation by Tn5. Then performed in situ digestion by MseI and in situ ligation by T4 DNA ligase. Samples were reverse crosslinked in the RCB buffer followed by DNA purification. The DNA was digested by NlaIII and circularized by T4 DNA ligase. At last, used primers that anchored on Tn5 adaptor to amply the final bulk HiCAR library.
bulk HiCAR

value: astrocyte


title: UBQ_33A_NULL_Rep03

description: Library name: AS2630003


title: frontal cortex, RNA, batch3, rep1


title: P06_Tis_V4_Bladder

description: Library name: Sample 8

value: bladder tissue


title: mouse astrocytes, rep1-2


title: UBQ_33A_NULL_Rep01

description: Library name: AS2630001


title: mouse astrocytes, rep2-1


title: P07_Org_Urethra

description: Library name: Sample 6

value: urethra organoid


title: genomic DNA from  liver tissue E-NT11

description: Hepatocellular carcinoma


title: mouse astrocytes, rep1-1


title: UBQ_33A_NULL_Rep02

description: Library name: AS2630002


title: P07_Org_Bladder

description: Library name: Sample 5


title: AML-A27 patient's bone marrow cells, post treatment

city: Tokyo

first: Kohei

last: Yamada

address: 2-1-1, Hongo, Bunkyo-ku

institute: Juntendo university

description:
Library name: AML-A27-post
10x Genomics

data_processing:
Raw reads (fastq files) were re-aligned using Cell Ranger (v7.0.0) (10x Genomics).
Assembly: GRCh38.p14
Supplementary files format and content: Processed data files include a gene-cell count matrix in Matrix Market format (matrix.mtx), with associated cell barcodes (barcodes.tsv) and gene annotations (features.tsv). Each entry in the matrix represents the UMI counts for a given gene in a given cell.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen). ScRNA-seq was performed using the 10x Chromium system (10x Genomics, Pleasanton, CA). In brief, approximately 2.0 x 10^6 cells, viability >85%, were suspended in 50μl of chilled phosphate-buffered saline + 0.04% bovine serum albumin (Thermo Fisher Scientific) .
Library was processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1 (Dual Index) (10x Genomics).

value: bone marrow

value: bone marrow mononuclear cells

value: TP53 mutation

value: Venetoclax,Azacitidine


title: genomic DNA from  liver tissue E-NT1

description: Hepatocellular carcinoma

value: Liver


title: P07_Org_Urine

description: Library name: Sample 7

value: urine organoid


title: P06_Org_V3_Bladder

description: Library name: Sample 4


title: genomic DNA from  liver tissue E-NT2

description: Hepatocellular carcinoma

value: M


title: genomic DNA from  liver tissue E-NT4

description: Hepatocellular carcinoma


title: AML-A27 patient's bone marrow cells, pre treatment

description:
Library name: AML-A27-pre
10x Genomics


title: mouse Pvalb neuron, rep4

city: Durham

first: Yarui

institute: Duke University

source_name: Pvalb neuron

value: Pvalb neuron


title: mouse Pvalb neuron, rep5


title: genomic DNA from  liver tissue E-NO18


title: P07_Tis_Bladder

description: Library name: Sample 3


title: PC3, DKD, rep1

value: Prostate

value: Epithelial

value: Lentiviral infection


title: AML-A16 patient's bone marrow cells, post treatment

description:
Library name: AML-A16-post
10x Genomics


title: genomic DNA from  liver tissue E-NO16


title: P07_Tis_Urethra

description: Library name: Sample 2

source_name: urethra tissue

value: urethra tissue


title: genomic DNA from  liver tissue E-NW11


title: AML-A16 patient's bone marrow cells, pre treatment

description:
Library name: AML-A16-pre
10x Genomics


title: P06_Tis_V3_Bladder

description: Library name: Sample 1


title: mouse Pvalb neuron, rep1


title: mouse Pvalb neuron, rep2


title: mouse Pvalb neuron, rep3


title: AML-A15 patient's bone marrow cells, post treatment

description:
Library name: AML-A15-post
10x Genomics


title: frontal cortex, RNA, batch3, rep2

value: frontal cortex


title: TD43_2 [HPVpos] [Tumor] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_Nonrespoder]

status: Public on Aug 29 2025

city: Philadelphia

first: Alban

last: Linnenbach

state: PA

address: 233 S. 10th Street, Building BLSB 412

department: Kimmel Cancer Center

institute: Thomas Jefferson University

description:
Library name: TD43_2
Column F

data_processing:
RNAseq reads were aligned to the reference genome using Hisat2 v2.0.5 software.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimeted text file incluses TPMs for each sample.

source_name: Head and Neck Squamous Cell Carcinoma

extract_protocol:
Nucleic acids were isolated by using Qiagen AllPrep DNA/RNA/microRNA Univerasl kits.
RNA libraries for RNA-seq were prepared using NEB Ultra II RNA Kit following manufacturer's protocols.

value: Head and Neck Squamous Cell Carcinoma

value: Durvalumab + Metformin


title: ATAC-Seq - HSC - young control 4

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: Regenerative Medicine

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

data_processing:
The ENCODE ATAC-seq pipeline v2.1.3 was used to process the FASTQ files, including adapter trimming, alignment to the reference genome, filtering and peak calling, and using the parameters "atac.pipeline_type" : "atac", "atac.align_only" : false, "atac.true_rep_only" : false, "atac.paired_end" : true, "atac.auto_detect_adapter" : true, "atac.multimapping" : 20, "atac.mapq_thresh" : 20.
Samtools v1.14 was used to index BAM files.
ATACseqQC v1.20.2, BSgenome v1.64.0, Bsgenome.Mmusculus.UCSC.mm10 v1.4.3 and TxDb.Mmusculus.UCSC.mm10.knownGene v3.10.0 in R v4.2.0 and Bioconductor v3.15.2 were used for quality control and Tn5 shifting.
A consensus set of peaks was defined by taking those peaks detected in at least 6 samples. This threshold was determined using Monte Carlo simulation. Briefly, a binary matrix was generated including all detected peaks as rows and all samples as columns, with 1 for presence of the peaks and 0 for absence. The binary matrix was randomized 1,000 times and the number of peaks detected in all possible minimum number of samples was calculated for each randomized matrix. The chosen minimum number of samples was the one where the mean number of consensus peaks in the simulated data was ≈10% of the number of consensus peaks in the empirical data (false positive rate, FPR). The final 57,289 consensus peaks were resized to have a width of 700 bp.
In R v4.2.0 and Bioconductor v3.15.2, the featureCounts function from Rsubread v2.10.5 was used to count the number of reads in consensus peaks with parameters largestOverlap = TRUE, countMultiMappingReads = TRUE, fraction = TRUE, isPairedEnd = TRUE, countReadPairs = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, minFragLength = 0, maxFragLength = 2000.
Assembly: mm10
Supplementary files format and content: Read count matrix (consensus peaks as rows, samples as columns)
Supplementary files format and content: BED file for the coordinates of the consensus peaks

source_name: Bone marrow

growth_protocol: LT-HSC were incubated for 16h in HBSS 10%FBS 1%P/S at 37ºC 3%O2 and 5%CO2.

extract_protocol:
Lysis buffer contains 0.15% NP40,TD buffer and Transposase (fromllumina Tagment DNA Enzyme and Buffer Small Kit, ref20034197).
Nextera XT kit (Illumina) was used to generate the libraries following manufacturer instructions.

treatment_protocol: Ri (RhoA inhibitor, Rhosin) was added to one of the aged cell samples to a concentration of 100µM for the 16h incubation commented above.

value: Bone marrow

value: Hematopoietic stem cells

value: 10-16 weeks old

value: control

tag: sequencing batch


title: ATAC-Seq - HSC - aged control 5

value: >80 weeks old


title: ATAC-Seq - HSC - aged + RhoA-inhibitor (Ri) 5

value: RhoA-inhibitor (Ri) treatment


title: genomic DNA from  liver tissue E-NO20

value: Liver

value: F


title: genomic DNA from  liver tissue E-NO17

value: M


title: TD23_2 [HPVpos] [Tumor] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_Nonrespoder]

description:
Library name: TD23_2
Column E


title: TD43_1 [HPVpos] [Tumor] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TD43_1
Column J

value: Pre-treatment


title: TJU11_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_Nonrespoder]

description:
Library name: TJU11_2
Column D


title: TJU11_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TJU11_1
Column H


title: TJU10_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_Nonrespoder]

description:
Library name: TJU10_2
Column C


title: TJU16_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_minor Respoder]

description:
Library name: TJU16_2
Column F


title: TD5_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TD5_1
Column L


title: TJU10_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TJU10_1
Column G


title: TD5_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_minor Respoder]

description:
Library name: TD5_2
Column G


title: TD36_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TD36_1
Column J


title: TJU16_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TJU16_1
Column K


title: TJU19_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_minor Respoder]

description:
Library name: TJU19_2
Column C


title: TJU02_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_minor Respoder]

description:
Library name: TJU02_2
Column D


title: TD23_1 [Tumor] [HPVpos] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TD23_1
Column I


title: TJU02_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TJU02_1
Column I


title: 6703_V2+1 (MAIT)

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: 6703_V2+1

data_processing:
BCL files were converted to FASTQ files using Illumina bcl2fastq. FASTQ files were processed to a gene count matrix using a custom CGAT-Core (v0.6.15) pipeline. Briefly, sequencing quality was assessed using FASTQC (Babraham Bioinformatics; v0.12.1), then FASTQ files trimmed to remove adapter sequences using FLEXBAR (v3.0). Reads were aligned to the GRCh38 human genome using STAR (v2.7.10b) and reads mapping to each gene quantified using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt (tab-delimited file containing raw counts for each sample)

source_name: Blood

extract_protocol:
RNA from sorted MAIT cell samples was extracted as previously described (Barnitz et al., Methods Mol Biol, 2013). RNA quantity and integrity was assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and Agilent TapeStation and submitted to the Oxford Genomics Centre (Centre for Human Genetics, University of Oxford) for library generation and sequencing (Illumina NovaSeq 6000, 150 base pair paired-end reads).
NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, #E6240).

value: Blood

value: Mucosal-associated invariant T (MAIT) cells

tag: donor

tag: timepoint

tag: vaccine

tag: prior infection

value: FALSE


title: 6703_V2 (MAIT)

description: Library name: 6703_V2

tag: tissue


title: TJU19_1 [Tumor] [HPVpos] [Baseline] [pre-treatment] [First of 2 time points]

description:
Library name: TJU19_1
Column H


title: TD36_2 [Tumor] [HPVpos] [Surgery] [post treatment] [Second of 2 time points] [Primary Path Response_minor Respoder]

description:
Library name: TD36_2
Column E


title: genomic DNA from  liver tissue E-NW1


title: 6703_V1 (MAIT)

description: Library name: 6703_V1

tag: cell type


title: 6703_V1+1 (MAIT)

description: Library name: 6703_V1+1


title: 6451_V1+1 (MAIT)

description: Library name: 6451_V1+1

tag: regimen

value: Short


title: 6402_V2+1 (MAIT)

description: Library name: 6402_V2+1


title: 6402_V1 (MAIT)

description: Library name: 6402_V1


title: 6451_V1 (MAIT)

description: Library name: 6451_V1


title: 6402_V2 (MAIT)

description: Library name: 6402_V2


title: 6400_V2+1 (MAIT)

description: Library name: 6400_V2+1

value: Long


title: 6451_V2+1 (MAIT)

description: Library name: 6451_V2+1


title: frontal cortex, RNA, batch3, rep9

last: Diao

address: 307 Research Drive

data_processing:
For DNA reads, extracted 18bp cell barcode (barcode1, barcode2 and barcode3) to the name of reads. Added TACAGGGTGA to the end of barcode as barcode4, because the real barcode4 were already used during library demultiplex. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Trimmed the adaptor sequence in reads. The final DNA reads were mapped to genome by bwa mem with options -SP. Alignments were parsed, and paired end tags were generated using the pairtools with options --min-mapq 10.
For RNA reads, discarded the reads whose read1 contained TSO or mosaic sequence but without adaptor sequence using cutadapt. Extracted 18bp cell barcode (barcode1, barcode2 and barcode3) and 22bp (UMI and RNA sequence) to the name of reads. Trimmed the TSO, polyA and truseq sequence in read2 by cutadapt. Discarded the reads whose barcode has more than one mismatch, corrected the barcode containing one mismatch. Replaced read1 by 18bp cell barcode and 22bp (UMI and RNA sequence). The final fastq files were processed by STAR with parameter "--soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --soloUMIlen 12 -soloStrand Forward". The R package Seurat were used to the downstream analysis: (1) genes which expressed in less than three cells were removed. (2) Cells with unique feature counts under 100, greater than 5% mitochondrial RNA counts, and without DNA barcodes were removed.
Assembly: mm10
Supplementary files format and content: STARsolo output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz
Supplementary files format and content: .pairsam.txt.gz: list of all the contact pairs in each cell type (defined by RNA data in sciHiCAR)

extract_protocol:
The frontal cortex were dissected by tweezer from adult mouse, then were treated by douncer to get the cells. Cells were crosslinked by formaldehyde and quenched by Tris glycine. Nuclei were extracted by NPB buffer from the cells.
Nuclei were tagmentated by barcoded Tn5, RNA in the nuclei were reverse transcribed by barcoded primers. By doing two rounds of pool split and ligation, ligated the barcoded adaptor2 and adaptor3 to Tn5 adaptors and reverse transcription primers. Then did another round of pool split, each well contained 5000-90000 nuclei. Treated nuclei by SDS to release hybrid cDNA to supernatant from the nuclei. For the cDNA part, we performed reverse crosslink, template switch, double strand cDNA amplification, Tagmentation, PCR adding the 4th barcode for RNA library construction similar with split-seq. For the nuclei, we did in-situ digestion, in situ ligation, reverse crosslink, NlaIII digestion, circularization, PCR adding 4th barcode for DNA library construction similar with bulk HiCAR.
sciHiCAR

value: frontal cortex


title: genomic DNA from  liver tissue E-NO10


title: genomic DNA from  liver tissue E-NO13


title: 6400_V2 (MAIT)

description: Library name: 6400_V2


title: genomic DNA from  liver tissue E-NO11


title: 6400_V1+1 (MAIT)

description: Library name: 6400_V1+1


title: 6400_V1 (MAIT)

description: Library name: 6400_V1


title: 6451_V2 (MAIT)

description: Library name: 6451_V2


title: 6402_V1+1 (MAIT)

description: Library name: 6402_V1+1


title: genomic DNA from  liver tissue E-NO14


title: genomic DNA from  liver tissue E-NO12


title: AML-A15 patient's bone marrow cells, pre treatment

description:
Library name: AML-A15-pre
10x Genomics

value: bone marrow

value: bone marrow mononuclear cells

tag: genotype

value: TP53 mutation

tag: treatment

value: Venetoclax,Azacitidine


title: 6398_V1 (MAIT)

description: Library name: 6398_V1


title: 6398_V2 (MAIT)

description: Library name: 6398_V2


title: 6398_V2+1 (MAIT)

description: Library name: 6398_V2+1


title: 6398_V1+1 (MAIT)

description: Library name: 6398_V1+1


title: 6396_V2+1 (MAIT)

description: Library name: 6396_V2+1


title: 6396_V1 (MAIT)

description: Library name: 6396_V1


title: 6394_V1 (MAIT)

description: Library name: 6394_V1

value: TRUE


title: 6394_V2 (MAIT)

description: Library name: 6394_V2


title: 6394_V1+1 (MAIT)

description: Library name: 6394_V1+1


title: 6396_V1+1 (MAIT)

description: Library name: 6396_V1+1


title: 6396_V2 (MAIT)

description: Library name: 6396_V2


title: 6394_V2+1 (MAIT)

description: Library name: 6394_V2+1


title: 6393_V2 (MAIT)

description: Library name: 6393_V2


title: 6393_V2+1 (MAIT)

description: Library name: 6393_V2+1


title: genomic DNA from  liver tissue E-NO15


title: 6393_V1+1 (MAIT)

description: Library name: 6393_V1+1


title: 6393_V1 (MAIT)

description: Library name: 6393_V1


title: 6392_V2+1 (MAIT)

description: Library name: 6392_V2+1


title: 6392_V2 (MAIT)

description: Library name: 6392_V2


title: 6392_V1+1 (MAIT)

description: Library name: 6392_V1+1


title: 6388_V2 (MAIT)

description: Library name: 6388_V2


title: 6388_V1+1 (MAIT)

description: Library name: 6388_V1+1


title: 6388_V1 (MAIT)

description: Library name: 6388_V1


title: 5995_V2+1 (MAIT)

description: Library name: 5995_V2+1


title: 6383_V2 (MAIT)

description: Library name: 6383_V2


title: 5995_V1+1 (MAIT)

description: Library name: 5995_V1+1


title: 6383_V2+1 (MAIT)

description: Library name: 6383_V2+1


title: 6383_V1+1 (MAIT)

description: Library name: 6383_V1+1


title: 6383_V1 (MAIT)

description: Library name: 6383_V1


title: 5995_V2 (MAIT)

description: Library name: 5995_V2


title: 5918_V2+1 (MAIT)

description: Library name: 5918_V2+1


title: 5995_V1 (MAIT)

description: Library name: 5995_V1


title: 5918_V2 (MAIT)

description: Library name: 5918_V2


title: 5939_V1+1 (MAIT)

description: Library name: 5939_V1+1


title: genomic DNA from  liver tissue E-NO19


title: genomic DNA from  liver tissue E-NW6


title: 5918_V1 (MAIT)

description: Library name: 5918_V1


title: 6392_V1 (MAIT)

description: Library name: 6392_V1


title: 5457_V1 (MAIT)

description: Library name: 5457_V1


title: 5939_V1 (MAIT)

description: Library name: 5939_V1


title: 5457_V1+1 (MAIT)

description: Library name: 5457_V1+1


title: 5449_V2 (MAIT)

description: Library name: 5449_V2


title: 5449_V2+1 (MAIT)

description: Library name: 5449_V2+1


title: 5195_V1 (MAIT)

description: Library name: 5195_V1


title: 5449_V1 (MAIT)

description: Library name: 5449_V1


title: 5083_V2+1 (MAIT)

description: Library name: 5083_V2+1


title: 5083_V2 (MAIT)

description: Library name: 5083_V2


title: 3871_V2+1 (MAIT)

description: Library name: 3871_V2+1


title: 3871_V2 (MAIT)

description: Library name: 3871_V2


title: 5083_V1+1 (MAIT)

description: Library name: 5083_V1+1


title: 3871_V1+1 (MAIT)

description: Library name: 3871_V1+1


title: 2689_V2 (MAIT)

description: Library name: 2689_V2


title: 2532_V2 (MAIT)

description: Library name: 2532_V2


title: 5083_V1 (MAIT)

description: Library name: 5083_V1


title: 3871_V1 (MAIT)

description: Library name: 3871_V1


title: 2689_V2+1 (MAIT)

description: Library name: 2689_V2+1


title: 2532_V1+1 (MAIT)

description: Library name: 2532_V1+1


title: TubA

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: TubA

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Assembly: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389 transriptome assembled with https://github.com/ejrsimr/transcriptome2star
Supplementary files format and content: single cell  count matrix in hdf5 format

organism: Schmidtea mediterranea

source_name: Dissociated tail fragments

growth_protocol: 4 mm planarians were fed approximately once a week prior to initiating RNA interference

extract_protocol:
Ten planarian tail fragments were transferred to a clean 35 mm Petri dish in ~1 mL planaria water. The water was replaced with 500 uL Calcium/Magnesium Free Buffer (CMFB: 15mM Hepes, 400mg/L NaH 2 PO4 , 800mg/L NaCl, 1200mg/L KCl, 800mg/L NaHCO3 , 240mg/L glucose, 1% BSA, pH7.3). Tissue was minced by repeatedly cutting with a razor blade, washed to a conical tube, and mechanically disrupted by forceful pipetting. Dissociated cells were pelleted by centrifugation, resuspended, and filtered through a 70 micron cell strainer.
Single cell libraries were constructed from live, single cell suspensions according to the manufacturer's directions using the Chromium iX single cell instrument and Chromium GEM-X Single Cell 3' Reagent kit v4 (10x Genomics), capturing ~13-15K cells per sample and sequencing to a minimum depth of 20,000 reads/cell on a Singular Genomics G4 instrument.

treatment_protocol: Planarians were fed RNAi food three times containing E. coli expressing dsRNA against unc-22 or tubulin alpha. One week after the final feeding, tails were amputated. 48 hours after amputation, tails were collected and dissociated for scRNA-seq

value: Dissociated tail fragments

value: Mixed cells

value: wildtype

value: tub-a(RNAi)


title: 2532_V2+1 (MAIT)

description: Library name: 2532_V2+1


title: UNC22

description: Library name: UNC22


title: 2436_V1+1 (MAIT)

description: Library name: 2436_V1+1


title: 2436_V2 (MAIT)

description: Library name: 2436_V2


title: 5195_V1+1 (MAIT)

description: Library name: 5195_V1+1


title: WT_6hpa_Section2

data_processing:
Raw data was demultiplex using Illumina bcl2fastq v2.20 into fastq formats.
The expression count UMI table was generated based on the open source SLIDE-seq pipeline software (https://github.com/MacoskoLab/slideseq-tools), with barcode error correction model.
A metadata annotation table was generated based on planarian gene markers.
42bp Read 1 Puck Structure JJJJJJJJTCTTCAGCGTTCCCGAGAJJJJJJJNNNNNNNNTTT, use bead_structure="8C18X7C8M1X|*T" when running pipeline
where “J” is a base in the bead’s spatial barcode, “N” is a base in the UMI, and that “T” is the first T in the polyT tail on the bead. The constant sequence in-between the 2 sets of J’s is the site we use for priming when sequencing the bead barcodes on our microscope.
Assembly: smed31
Supplementary files format and content: single cell UMI expression count table
Supplementary files format and content: puck.txt: puck coordinates

source_name: embedded planarian tissue fragments

growth_protocol: 6-8 mm animals were fed 1X per week in recirculation culture system prior to amputation

extract_protocol:
Tissue sections were processed as described previously for slide-seqV2 (Stickels et al. Nature Bioetechnology 2021)
cDNA libraries were prepared as previously described for slide-seqV2 (Stickels et al. Nature Bioetechnology 2021)

value: WT Intact animal embedded with tail fragments 6 hours post amputation

value: Intact animal and tail fragments

tag: time

value: 6 hours post amputation


title: WT_48hpa_Section1

value: WT Intact animal embedded with tail fragments 48 hours post amputation

value: 48 hours post amputation


title: 6388_V2+1 (MAIT)

description: Library name: 6388_V2+1

value: Blood

value: Mucosal-associated invariant T (MAIT) cells


title: 6704_V2+1 (tempus)

description: Library name: 6704_V2+1

data_processing:
BCL files were converted to FASTQ files using Illumina bcl2fastq. FASTQ files were processed to a gene count matrix using a custom CGAT-Core (v0.6.15) pipeline. Briefly, sequencing quality was assessed using FASTQC (Babraham Bioinformatics; v0.12.1), then FASTQ files trimmed to remove low quality bases and adapter sequences using Trimmomatic (v0.39). Reads were aligned to the GRCh38 human genome using STAR (v2.7.10b) and reads mapping to each gene quantified using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt (tab-delimited file containing raw counts for each sample)

extract_protocol:
Whole blood RNA was extracted from Tempus tubes in batches of 12-24 samples, with a mixture of vaccination groups and timepoints, using the Tempus Spin RNA Isolation Kit (Thermo Fisher Scientific). Samples were thawed, diluted in a 50 ml conical with 1× PBS, vortexed for 30 s, then centrifuged (3000 × g, 30 min, 4°C) to pellet RNA. Supernatants were removed and RNA pellets resuspended in RNA Purification Resuspension Solution, then transferred to purification filters for microcentrifuge RNA elution. RNA quantity and integrity was assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and Agilent TapeStation and submitted to the Oxford Genomics Centre (Centre for Human Genetics, University of Oxford) for library generation and sequencing (Illumina NovaSeq 6000, 150 base pair paired-end reads).
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, #E7760) with Globin & rRNA Depletion (New England Biolabs, #E7750).

value: FALSE

tag: library preparation_batch


title: 2436_V1 (MAIT)

description: Library name: 2436_V1

value: Long


title: 6704_V2 (tempus)

description: Library name: 6704_V2


title: WT_6hpa_Section1


title: 2532_V1 (MAIT)

description: Library name: 2532_V1

value: Short


title: 2436_V2+1 (MAIT)

description: Library name: 2436_V2+1


title: 6704_V1+1 (tempus)

description: Library name: 6704_V1+1


title: 24-075_AsP

first: Harutaka

last: Katano

address: 1-23-1 Toyama, Shinjuku

department: Department of Pathology

institute: National Institute of Infectious Diseases

description: Case Granulo12_24-075_AsP

data_processing:
Libraries were subjected to pair-end sequencing (300 cycles) on a Nextseq 1000 platform (Illumina, San Diego, CA).
Quality filtering, adapter trimming, and RNAseq analyzing was performed using CLC genomics workbench (version 23, Qiagen, Hilden, Germany).
Homo sapience refseq GRCh38.p13 was used as a reference genome of RNA sequences.
Assembly: Minimap2, CLC genomics workbench
Supplementary files format and content: ExpressonRNAseq.csv file including raw counts for each sample

source_name: Lung

extract_protocol:
Quick-DNA/RNA FFPE Miniprep Kit (Zymo Research).
Barcoded RNA-seq library was established with NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA) according to the manufacturer’s instructions.

value: Lung

value: FFPE


title: 24-074_SA

description: Case Granulo11_24-074_SA


title: 6703_V2+1 (tempus)

description: Library name: 6703_V2+1


title: WT_48hpa_Section2


title: 5918_V1+1 (MAIT)

description: Library name: 5918_V1+1


title: 6703_V1+1 (tempus)

description: Library name: 6703_V1+1


title: 24-070_GPA

description: Case Granulo7_24-070_GPA


title: 6703_V2 (tempus)

description: Library name: 6703_V2


title: 24-071_GPA

description: Case Granulo8_24-071_GPA


title: 6701_V2 (tempus)

description: Library name: 6701_V2


title: 24-068_Aspg

description: Case Granulo5_24-068_Aspg


title: 6701_V1+1 (tempus)

description: Library name: 6701_V1+1


title: 5449_V1+1 (MAIT)

description: Library name: 5449_V1+1


title: 24-069_GPA

description: Case Granulo6_24-069_GPA


title: 6701_V2+1 (tempus)

description: Library name: 6701_V2+1


title: 24-067_Aspg

description: Case Granulo4_24-067_Aspg


title: 6528_V2+1 (tempus)

description: Library name: 6528_V2+1


title: 6528_V2 (tempus)

description: Library name: 6528_V2


title: 24-066_Aspg

description: Case Granulo3_24-066_Aspg


title: 24-064_RN

description: Case Granulo1_24-064_RN


title: 24-072_SA

description: Case Granulo9_24-072_SA


title: 6701_V1 (tempus)

description: Library name: 6701_V1


title: 24-065_RN

description: Case Granulo2_24-065_RN


title: 6703_V1 (tempus)

description: Library name: 6703_V1


title: 24-073_SA

description: Case Granulo10_24-073_SA


title: 6528_V1+1 (tempus)

description: Library name: 6528_V1+1


title: 6704_V1 (tempus)

description: Library name: 6704_V1


title: 6528_V1 (tempus)

description: Library name: 6528_V1


title: Lu2778-7

description: Case Ctl-Lung5_Lu2778-7


title: tonsil-21

description: Case Ctl-Tonsil4_tonsil-21

source_name: Tonsil

value: Tonsil


title: 6527_V2+28 (tempus)

description: Library name: 6527_V2+28

tag: note

value: Designated as V1 for analysis


title: tonsil-11

description: Case Ctl-Tonsil1_tonsil-11


title: tonsil-18

description: Case Ctl-Tonsil3_tonsil-18


title: 6523_V1+1 (tempus)

description: Library name: 6523_V1+1


title: tonsil-17

description: Case Ctl-Tonsil2_tonsil-17


title: 6523_V2+28 (tempus)

description: Library name: 6523_V2+28


title: 6506_V2+1 (tempus)

description: Library name: 6506_V2+1


title: Lu2774-7

description: Case Ctl-Lung4_Lu2774-7


title: Lu2757-14

description: Case Ctl-Lung2_Lu2757-14


title: Lu2748-9

description: Case Ctl-Lung1_Lu2748-9


title: 6506_V1 (tempus)

description: Library name: 6506_V1


title: 6506_V2 (tempus)

description: Library name: 6506_V2


title: 18-82

description: Case NTM10_18-82


title: Lu2760-7

description: Case Ctl-Lung3_Lu2760-7


title: 18-081

description: Case NTM3_18-081