title: AD 16, DART-WT-treated

description: Library name: A16-WT


title: TMEM_Memory, RNA, Day30, rep4

status: Public on May 20 2025

type: SRA

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: PA

address: 3400 Civic Center Blvd

department: Penn Epigenetics Institute

country: USA

institute: University of Pennsylvania

description: Library name: Arm_P14_Day30_RNA_Rep4_S8

library_source: transcriptomic

data_processing:
FASTQ files were aligned using STAR 2.7.1a using mm10 Gencode reference genome.
Read counts of genes were quantified by featureCounts.
Normalized read counts were generated using DESeq2.
Genome tracks were created based on STAR processd bam files using bamCoverage.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count and normalized read count by DESeq2 values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Splenocytes

extract_protocol:
Total RNA (~30-120 ng) was extracted using RNA Clean & Concentrator-5 (ZYMO R1013) following manufacturer's instruction. mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760L) and following manufacturer's instructions.

tag: tissue

value: Splenocytes

tag: cell type

value: P14 CD8 T cells

tag: treatment

value: LCMV Armstrong infection


title: liver, IF1

city: Shanghai

first: Ziyun

last: Wu

state: Shanghai

address: 800 Dongchuan RD

department: Food Science and Engineering

country: China

institute: Shanghai Jiao Tong University

description:
Library name: FKRN230065050-1A
25

data_processing:
FASTQ output files were aligned to Mus musculus GRCh39 reference genomes using STAR with a 2-pass procedure. Genes (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM.
Assembly: Mus musculus GRCh39 reference genomes
Supplementary files format and content: tab-delimited text files include gene-id, expected_count, TPM, FPKM for each sample

source_name: liver

growth_protocol: Seven-week-old C57BL/6J male mice (n = 60) underwent a 20-hours fasting period (with free access to water) after a one-week acclimatization feeding. The animals were then divided into eight fiber diet groups, one AIN-93G regular diet (RD) group, and one calorie restriction (CR) group. After switching to the customized diet ad libitum, food and water intake were measured hourly over the next 4 hours (from 18:00 to 22:00).

extract_protocol:
Approximately 10 mg of liver tissue (left lobe) was immersed in 600 μl TRIzol, homogenized thoroughly, snap-frozen in liquid nitrogen, and stored at -80°C for RNA extraction the following day. All samples were ground using a high throughput tissue grinder at 300 g for 30 s (repeated three times). Following centrifugation at 14,000 g at 4°C for 10 min. RNA was extracted using M5 HiPer Universal Plus RNA Mini Kit (Mei5 Biotech, Beijing, China) according to manufacturer instructions. All RNA samples used had a RIN >8.
All RNA samples were sent to Novogene Co., Ltd (Beijing, China) for quality control (Sample QC). After RNA library preparation, cDNA libraries are sequenced on Illumina NovaSeq platforms using a paired-end 150 bp sequencing strategy. Approximately 6 G clean data and a >75% uniquely mapped reads rate for each sample were obtained for each sample. Six biological replicates were included.

treatment_protocol: Over the following 13 days, the CR group was fed the AIN-93G diet but was restricted to eating only during the most active 2-h period (18:00-20:00) of the circadian rhythm, while the other 9 groups were fed ad libitum. Water was provided ad libitum throughout the study. Food intake, water intake, and body weight were measured daily at 18:00. On Day 13 and 14, the same fasting and 4-h intake test protocol as on Day 0 and 1 was repeated. All mice were sacrificed, and hepatectomy was performed.

value: liver

tag: tissue region

value: left lobe

tag: genotype

value: Inulin Fiber Diet

tag: batch


title: TN_Naive, RNA, Day32, rep2

description: Library name: Naive_P14_Day32_RNA_Rep2_S10

value: Naive wild type


title: LU_RAS_KD_FlagGATAD2A_D0_WT_IP

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

description:
Library name: Sample34
antibody Flag

library_source: genomic

data_processing:
Raw data :The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and the corresponding sequencing quality information.
Evaluation of data (Data quality control) Sequence artifacts, including reads containing adapter contamination, low-quality and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used fastp to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read;   (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Clean sequencing datasets were aligned to the human reference genome (hg19) using Bowtie2 (v2.3.4.3) and processed with Samtools (v1.2). The resulting BAM files were converted into BigWig format using the bamCoverage tool from deepTools (v3.3.2.0.0)
Enriched binding peaks were identified by MACS2 (v2.1.1) after filtering against input controls
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: primary fibroblasts cells

growth_protocol: MEM, 10% fetal bovine serum, 1× penicillin/streptomycin. Cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
2 ug of total RNA was used for the construction of sequencing libraries.For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes.Then terminate crosslinking with glycine. Add Micrococcal Nuclease to each IP preparation, mix by turning the tube several times and incubate at 37°C for 20 minutes with frequent stirring to digest the DNA to approximately 150-900 bp in length.
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system（Agilent, USA）and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150, according to the effective library concentration and data amount required

treatment_protocol: The cells overexpressing Tet-on RASG12V were continuously induced with doxycycline for 0, 2, 4, 6, 8, and 10 days to induce senescence.  Crosslinked chromatin complexes were isolated from 1,6-Pr2GalNAz metabolically labeled cells and biotinylated. DNA was then purified using the MiniBEST DNA Fragment Purification Kit.

value: primary fibroblasts cells

value: Immortalized cells by hTERT

value: shGATAD2A, shJUN


title: AD 14, DART-WT-treated

city: Boston

first: Junming

last: Hu

state: MA

address: 75 E Concord St

institute: Boston University

description: Library name: A14-WT

data_processing:
Raw FASTQ files were assessed for quality using FastQC (v0.12.1) to evaluate read quality, GC content, and adapter contamination
Adaptor sequences and low-quality bases were trimmed using Trimmomatic with default parameters
Trimmed reads were aligned to the human reference genome GRCh38.111 using STAR aligner (v2.7.9a) in single-pass mode, generating coordinate-sorted BAM files
C>U editing events indicative of m6A were identified using the Bullseye pipeline, which compares APOBEC1-YTH–treated (i.e., DART-WT) samples to YTHmut controls (i.e., DART-Mut) to detect m6A-proximal C>U conversions. Events were filtered based on editing ratio, coverage, and DRACH motif presence
Assembly: GRCh38.111 (Ensembl release 111)
Supplementary files format and content: Bullseye output files are in BED format. Each file lists m6A sites with chromosome, position, strand, gene name, editing level, and transcript region (e.g., CDS or 3′UTR). These files show where m6A was detected in each sample.

source_name: Dorsolateral prefrontal cortex (Broadmann area 9)

extract_protocol:
RNA was harvested using the Rneasy Plus Kit (Qiagen). 50ng of total RNA was used for the DART reaction. RNA was repurified using the RNeasy Micro Kit (Qiagen). 3ng of total RNA was used as input for cDNA library construction.
cDNA libraries were generated using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio) following the manufacturer’s protocol.

tag: group

value: Alzheimer's disease

tag: dart treatment

value: Wildtype


title: liver, IFm5

description:
Library name: FKRN230065048-1A
23

value: Inulin Fiber Diet modified


title: TN_Naive, RNA, Day32, rep1

description: Library name: Naive_P14_Day32_RNA_Rep1_S9


title: AD 13, DART-WT-treated

description: Library name: A13-WT

value: Dorsolateral prefrontal cortex (Broadmann area 9)


title: TN_Naive, RNA, Day30, rep4

description: Library name: Naive_P14_Day30_RNA_Rep4_S4


title: LU_RAS_KD_FlagGATAD2A_D0_AA_IP

description:
Library name: Sample33
antibody Flag


title: liver, IFm4

description:
Library name: FKRN230065047-1A
22


title: LU_RAS_KD_FlagG2TAD2A_D10_WT_input

description:
Library name: Sample32
none

value: indece senescent D10,shGATAD2A, shJUN


title: liver, IFm3

description:
Library name: FKRN230065046-1A
21


title: TN_Naive, RNA, Day30, rep3

description: Library name: Naive_P14_Day30_RNA_Rep3_S3


title: AD 12, DART-WT-treated

description: Library name: A12-WT


title: LU_RAS_KD_FlagG2TAD2A_D10_AA_input

description:
Library name: Sample31
none


title: AD 10, DART-WT-treated

description: Library name: A10-WT


title: TN_Naive, RNA, Day30, rep2

description: Library name: Naive_P14_Day30_RNA_Rep2_S2


title: LU_RAS_KD_FlagG2TAD2A_D0_WT_input

description:
Library name: Sample30
none


title: AD 11, DART-WT-treated

description: Library name: A11-WT


title: liver, IFm2

description:
Library name: FKRN230065045-1A
20


title: LU_RAS_KD_FlagG2TAD2A_D0_AA_input

description:
Library name: Sample29
none


title: AD 9, DART-WT-treated

description: Library name: A9-WT


title: liver, IFm1

description:
Library name: FKRN230065044-1A
19


title: liver, CFm6

description:
Library name: FKRN230065043-1A
18

value: Cellulose Fiber Diet modified


title: TEX_Exhaustion, IgG, rep2

description: Library name: C13_IgG_Rep2_S17

data_processing:
Reads were aligned to mm10 Gencode reference genome using Bowtie2 v2.3.5 with options suggested by Henikoff (Skene et al., 2018).
Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools v1.1. Fragments between 40-700 bp were kept. Blacklist regions defined by ENCODE, random chromosomes and mitochondria were removed, and filtered bam files were used for downstream analysis.
Peaks were called using MACS v2.1 using the broadPeak setting with adjusted P-value cutoff of 0.01 in general, and customize parameters for broad histone mark. Consensus peaks per condition were merged to create final used union peak list.
Read counts were quantified across all samples based on union peak using featureCounts, and validated using bedtools coverage.
Genes proximal to peaks were annotated against mm10 genome using HOMER v4, ChIPseeker with 10k base pairs (bp) flank regions and GREAT.
For consistent visualization, DESeq2 normalization factors were used to adjust bam files to create normalized bigwig files using bamCoverage. Bigwig files of replicates were pooled together
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count and normalized read count by DESeq2 values for each Sample
Library strategy: CUT&Run

extract_protocol:
CUT&RUN experiments were performed as previously described (Skene et al., 2018) with slight modifications.
DNA library was prepared as previously descried (Liu et al., 2018) with slight modifications. Briefly, all DNA precipitated from pA-MN digestion was used for library preparation using NEBNext Ultra II DNA Library Prep Kit (NEB).

value: LCMV clone 13 infection


title: TN_Naive, RNA, Day30, rep1

description: Library name: Naive_P14_Day30_RNA_Rep1_S1

value: Splenocytes


title: LU_RAS_D10_H3K4me3_IP

description:
Library name: Sample28
antibody H3K4me3

value: indece senescent D10


title: AD 8, DART-WT-treated

description: Library name: A8-WT


title: liver, CFm5

description:
Library name: FKRN230065042-1A
17


title: AD 7, DART-WT-treated

description: Library name: A7-WT


title: liver, CFm4

description:
Library name: FKRN230065041-1A
16


title: TEX_Exhaustion, IgG, rep1

description: Library name: C13_IgG_Rep1_S2

value: P14 CD8 T cells


title: TMEM_Memory,IgG, rep2

description: Library name: Arm_IgG_Rep2_S18

value: LCMV Armstrong infection


title: TMEM_Memory,IgG, rep1

description: Library name: Arm_IgG_Rep1_S3


title: LU_RAS_D10_H3K4me1_IP

description:
Library name: Sample27
antibody H3K4me1


title: LU_RAS_D10_H3K27me3_IP

description:
Library name: Sample26
antibody H3K27me3


title: liver, CFm3

description:
Library name: FKRN230065040-1A
15

value: liver

value: left lobe


title: LU_RAS_D10_H3K27AC_IP

description:
Library name: Sample25
antibody H3K27ac


title: AD 5, DART-WT-treated

description: Library name: A5-WT


title: AD 6, DART-WT-treated

description: Library name: A6-WT


title: liver, CFm2

description:
Library name: FKRN230065039-1A
14


title: LU_RAS_D4_H3K4me3_IP

description:
Library name: Sample24
antibody H3K4me3

value: indece senescent D4


title: TN_Naive, IgG,rep2

description: Library name: Naive_IgG_Rep2_S16

value: Naive wild type


title: AD 4, DART-WT-treated

description: Library name: A4-WT


title: liver, CFm1

description:
Library name: FKRN230065038-1A
13


title: TN_Naive, IgG,rep1

description: Library name: Naive_IgG_Rep1_S1


title: LU_RAS_D4_H3K4me1_IP

description:
Library name: Sample23
antibody H3K4me1

value: primary fibroblasts cells

value: Immortalized cells by hTERT


title: AD 3, DART-WT-treated

description: Library name: A3-WT

value: Alzheimer's disease


title: TEX_Exhaustion, CTCF, Day32, rep4

description: Library name: Cl13_P14_Day32_CTCF_Rep4_S16


title: liver, CF6

description:
Library name: FKRN230065037-1A
12

value: Cellulose Fiber Diet


title: AD 1, DART-WT-treated

description: Library name: A1-WT

value: Wildtype


title: liver, CF5

description:
Library name: FKRN230065036-1A
11


title: liver, CF4

description:
Library name: FKRN230065035-1A
10


title: TEX_Exhaustion, CTCF, Day32, rep3

description: Library name: Cl13_P14_Day32_CTCF_Rep3_S15


title: LU_RAS_D2_H3K4me3_IP

description:
Library name: Sample20
antibody H3K4me3

value: indece senescent D2


title: LU_RAS_D4_H3K27AC_IP

description:
Library name: Sample21
antibody H3K27ac


title: Control 19, DART-WT-treated

description: Library name: C19-WT

value: Dorsolateral prefrontal cortex (Broadmann area 9)

value: Control/non-AD


title: LU_RAS_D2_H3K4me1_IP

description:
Library name: Sample19
antibody H3K4me1


title: liver, CF3

description:
Library name: FKRN230065034-1A
9


title: liver, CF2

description:
Library name: FKRN230065033-1A
8


title: Control 17, DART-WT-treated

description: Library name: C17-WT


title: LU_RAS_D2_H3K27me3_IP

description:
Library name: Sample18
antibody H3K27me3


title: TEX_Exhaustion, CTCF, Day32, rep1

description: Library name: Cl13_P14_Day32_CTCF_Rep1_S13

value: LCMV clone 13 infection


title: TMEM_Memory, CTCF, Day30, rep4

description: Library name: Arm_P14_Day30_CTCF_Rep4_S16

value: Splenocytes


title: TMEM_Memory, CTCF, Day30, rep3

description: Library name: Arm_P14_Day30_CTCF_Rep3_S15


title: liver, CF1

description:
Library name: FKRN230065032-1A
7


title: LU_RAS_D2_H3K27AC_IP

description:
Library name: Sample17
antibody H3K27ac


title: TMEM_Memory, CTCF, Day30, rep2

description: Library name: Arm_P14_Day30_CTCF_Rep2_S14


title: Control 16, DART-WT-treated

description: Library name: C16-WT


title: liver, CR6

description:
Library name: FKRN230065031-1A
6

value: calorie restriction


title: TEX_Exhaustion, CTCF, Day32, rep2

description: Library name: Cl13_P14_Day32_CTCF_Rep2_S14

value: P14 CD8 T cells


title: Control 15, DART-WT-treated

description: Library name: C15-WT


title: liver, CR5

description:
Library name: FKRN230065030-1A
5


title: LU_RAS_D0_H3K4me3_IP

description:
Library name: Sample16
antibody H3K4me3

value: indece senescent D0


title: AD 2, DART-WT-treated

description: Library name: A2-WT


title: LU_RAS_D4_H3K27me3_IP

description:
Library name: Sample22
antibody H3K27me3


title: LU_RAS_D0_H3K4me1_IP

description:
Library name: Sample15
antibody H3K4me1


title: Control 14, DART-WT-treated

description: Library name: C14-WT


title: TN_Naive, CTCF, Day32, rep4

description: Library name: Naive_P14_Day32_CTCF_Rep4_S16


title: liver, CR3

description:
Library name: FKRN230065028-1A
3

value: liver


title: TN_Naive, CTCF, Day32, rep3

description: Library name: Naive_P14_Day32_CTCF_Rep3_S15


title: Control 13, DART-WT-treated

description: Library name: C13-WT


title: liver, CR4

description:
Library name: FKRN230065029-1A
4

value: left lobe


title: LU_RAS_D0_H3K27AC_IP

description:
Library name: Sample13
antibody H3K27ac


title: liver, CR2

description:
Library name: FKRN230065027-1A
2


title: LU_RAS_D10_input

description:
Library name: Sample12
none

value: indece senescent D10


title: TN_Naive, CTCF, Day32, rep1

description: Library name: Naive_P14_Day32_CTCF_Rep1_S13

value: Naive wild type


title: Control 10, DART-WT-treated

description: Library name: C10-WT


title: Control 18, DART-WT-treated

description: Library name: C18-WT


title: LU_RAS_D4_input

description:
Library name: Sample11
none

value: primary fibroblasts cells

value: indece senescent D4


title: TN_Naive, CTCF, Day32, rep2

description: Library name: Naive_P14_Day32_CTCF_Rep2_S14


title: Control 12, DART-WT-treated

description: Library name: C12-WT


title: liver, CR1

description:
Library name: FKRN230065026-1A
1


title: TN_Naive, CTCF, Day30, rep4

description: Library name: Naive_P14_Day30_CTCF_Rep4_S12


title: LU_RAS_D2_input

description:
Library name: Sample10
none

value: Immortalized cells by hTERT


title: Control 11, DART-WT-treated

description: Library name: C11-WT


title: TMEM_Memory, CTCF, Day30, rep1

description: Library name: Arm_P14_Day30_CTCF_Rep1_S13

value: LCMV Armstrong infection


title: TN_Naive, CTCF, Day30, rep3

description: Library name: Naive_P14_Day30_CTCF_Rep3_S11


title: Testis, Psma7 s8KO, PD13

city: Hang Zhou

first: Chao

last: Yu

address: 866 Yuhangtang Rd, Xi Hu Qu

institute: Zhejiang University

description:
Library name: Psma7_s8ko_PD13
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger) using default parameters.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: testis

extract_protocol:
Single-cell suspensions were prepared from PD13 mouse testis tissue following the Chromium Single Cell 3' Solution protocol (V3 chemistry). The testis samples were washed twice with cold 1× phosphate-buffered saline (PBS). Cell viability was assessed using a Haemocytometer (Thermo Fisher Scientific). Cell concentration was then measured using Countstar and adjusted to 1000 cells/μl. For samples with concentrations below the required threshold (less than 400 cells/μl), cells were pelleted and resuspended in a reduced volume, followed by recounting to confirm the new concentration.
The single-cell testis suspension was loaded into Chromium microfluidic chips with 3' V3 chemistry and barcoded using a 10× Chromium Controller (10X Genomics). RNA from the barcoded testis cells underwent reverse transcription, and sequencing libraries were constructed using reagents from a Chromium Single Cell 3' V3 reagent kit (10X Genomics) following the manufacturer's protocol. Sequencing was performed on Illumina NovaSeq according to the manufacturer's instructions.

value: testis

tag: age

value: 13 days old

tag: Sex

value: male

value: Psma7 F/-;Stra8-Cre KI/+


title: Testis, WT, PD13

description:
Library name: WT_PD13
10X Genomics

value: Psma7 F/+


title: Control 8, DART-WT-treated

description: Library name: C8-WT

value: Dorsolateral prefrontal cortex (Broadmann area 9)

value: Control/non-AD

value: Wildtype


title: LU_RAS_D0_input

description:
Library name: Sample9
none

value: indece senescent D0


title: TN_Naive, CTCF, Day30, rep2

description: Library name: Naive_P14_Day30_CTCF_Rep2_S10

value: Splenocytes

value: P14 CD8 T cells


title: LU_RAS_D0_H3K27me3_IP

description:
Library name: Sample14
antibody H3K27me3


title: LU_RAS_COGCseq_D10_IP

description:
Library name: Sample8
metabolic chemical reporter

value: indece senescent D10


title: Tumor, SH, rep 4

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: SH_M24
GEX (3' mRNA) library

data_processing:
Fastq files from each 10x Genomics library were processed via the Cellranger Count pipeline v. 3.1.0
Assembly: mm10
Supplementary files format and content: tab-demilited filtered feature, barcode, and matrix files

source_name: Tumor, lung

extract_protocol:
Mice were sacrificed via cervical dislocation and then tumors were dissected from the lung and placed in cold DMEM + Y27632 (ROCK Inhibitor, Selleckchem #S1049) (1:1000) and DNAse I (Worthington Biochemical Corporation #LS002058) (1:50) until ready for dissociation. Tumor tissue was cut into small pieces then dissociated in a solution of HBSS, Y27632 (1:1000), DNase I (1:50) and Protease from Bacillus licheniformis (Sigma #P5380) (1:20). The tumor suspension was triturated through a cut pipette tip then placed on a rocker in a cold room. This process was repeated every five minutes until the tumor was visibly broken down. Cells were filtered through a 70 μM filter and washed with fully supplemented DMEM. Cells were pelleted and cryopreserved with FBS + Y27632 (1:500), DNase I (1:50) and DMSO (1:10).
Dissociated tumor cell viability of each sample was checked by acridine orange and propidium iodide staining using the LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems) and concentrated to 800 live cells/μL in 0.04% BSA in PBS. The 10X Genomics Chromium Controller and the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (PN-100075) were used for processing cells according to the manufacturer’s recommendations (Document#CG000183 Rev C). Library preparation was done by loading approximately 16,000 cells per sample onto the Chromium Chip B, targeting a 10,000-cell recovery per sample. Gel beads in emulsion (GEMs) were created by encapsulating single cells, reverse transcription reagents and gel beads coated with barcoded oligos in an oil droplet. Reverse transcription was used to create cDNA libraries tagged with a cell barcode and unique molecular index (UMI). cDNA libraries were purified using Dynabeads MyOne SILANE (Invitrogen) before 11 amplification cycles after GEMs were broken. Amplified cDNA libraries were purified with SPRIselect magnetic beads (Beckman Coulter) and quantified using an Agilent Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). After these SPRIselect beads were used for fragmentation, end repair, A-tailing and double-sided size selection, Illumina-compatible adapters were ligated onto the size selected cDNA fragments. These were then purified and amplified with uniquely identifiable indexes. After purification, the finalized sequencing libraries were visualized using the Bioanalyzer High Sensitivity DNA chip, normalized to 20 nM, and pooled.

value: Tumor, lung

tag: cell line

value: SNL

value: Sox2high; Nkx2-1-/-; Lkb1-/-; safe harbor sgRNA


title: Tumor, SH, rep 3

description:
Library name: SH_M21
GEX (3' mRNA) library


title: LU_RAS_COGCseq_D4_IP

description:
Library name: Sample7
metabolic chemical reporter

value: primary fibroblasts cells

value: Immortalized cells by hTERT

value: indece senescent D4


title: TN_Naive, CTCF, Day30, rep1

description: Library name: Naive_P14_Day30_CTCF_Rep1_S9

value: Naive wild type


title: Control 6, DART-WT-treated

description: Library name: C6-WT


title: Tumor, SH, rep 2

description:
Library name: SH_M20
GEX (3' mRNA) library


title: TEX_Exhaustion, H3K9me3, Day32, rep4

description: Library name: Cl13_P14_Day32_H3K9me3_Rep4_S8

value: LCMV clone 13 infection


title: LU_RAS_COGCseq_D2_IP

description:
Library name: Sample6
metabolic chemical reporter

value: indece senescent D2


title: Control 5, DART-WT-treated

description: Library name: C5-WT


title: TEX_Exhaustion, H3K9me3, Day32, rep3

description: Library name: Cl13_P14_Day32_H3K9me3_Rep3_S7


title: LU_RAS_COGCseq_D0_IP

description:
Library name: Sample5
metabolic chemical reporter


title: TEX_Exhaustion, H3K9me3, Day32, rep2

description: Library name: Cl13_P14_Day32_H3K9me3_Rep2_S6


title: Control 4, DART-WT-treated

description: Library name: C4-WT


title: Tumor, SH, rep 1

description:
Library name: SH_M16
GEX (3' mRNA) library


title: LU_RAS_COGCseq_D10_input

description:
Library name: Sample4
metabolic chemical reporter


title: Control 9, DART-WT-treated

description: Library name: C9-WT


title: Control 3, DART-WT-treated

description: Library name: C3-WT


title: LU_RAS_COGCseq_D4_input

description:
Library name: Sample3
metabolic chemical reporter


title: TEX_Exhaustion, H3K9me3, Day32, rep1

description: Library name: Cl13_P14_Day32_H3K9me3_Rep1_S5


title: Tumor, PTEN, rep 2

description:
Library name: PTEN_M74
GEX (3' mRNA) library

value: PTEN

value: Sox2high; Nkx2-1-/-; Lkb1-/-; Pten sgRNA


title: Control 2, DART-WT-treated

description: Library name: C2-WT

value: Dorsolateral prefrontal cortex (Broadmann area 9)

value: Control/non-AD


title: LU_RAS_COGCseq_D2_input

description:
Library name: Sample2
metabolic chemical reporter


title: TMEM_Memory, H3K9me3, Day30, rep4

description: Library name: Arm_P14_Day30_H3K9me3_Rep4_S2

value: LCMV Armstrong infection


title: TMEM_Memory, H3K9me3, Day30, rep3

description: Library name: Arm_P14_Day30_H3K9me3_Rep3_S1

value: Splenocytes


title: Tumor, PTEN, rep 1

description:
Library name: PTEN_M100
GEX (3' mRNA) library


title: Control 7, DART-WT-treated

description: Library name: C7-WT

value: Wildtype


title: LU_RAS_COGCseq_D0_input

description:
Library name: Sample1
metabolic chemical reporter

value: indece senescent D0


title: Tumor, p53, rep 4

description:
Library name: p53_M45
GEX (3' mRNA) library

value: Tumor, lung

value: Sox2high; Nkx2-1-/-; Lkb1-/-; Trp53 sgRNA


title: TMEM_Memory, H3K9me3, Day30, rep2

description: Library name: Arm_P14_Day30_H3K9me3_Rep2_S4

value: P14 CD8 T cells


title: HC8

city: Beijing

first: Zhuxiao

last: Xie

address: NO.1 Dongjiaomin Lane

institute: Beijing Tongren Hostipal

description: Library name: Sample 17

library_source: other

data_processing:
Assembly: GRCh38
Supplementary files format and content: count values
1. Adapter trimming: Cutadapt v1.18 was used to remove adapter sequences with default parameters.
2. Quality control: A R script was used to perform quality control, with the following criteria:
(1) For each sample, reads with low quality values are removed to ensure the proportion of bases reaching Q30 is higher than 85%.
(2) Reads with a content of unknown base N (N represents an unidentifiable base) greater than or equal to 10% are removed;
(3) Reads without a 3' adapter sequence are removed;
(4) Sequences shorter than 15 or longer than 35 nucleotides are removed.
3. ncRNA and repeat sequence annotation: Bowtie v1.0.0 was used to align the Clean Reads with the Silva database, GtRNAdb database, Rfam database, and Repbase database respectively to filter out ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and other non-coding RNAs (ncRNAs) as well as repetitive sequences, and obtain unannotated reads containing miRNAs.
4. Genome alignment: Bowtie v1.2.1.1 was used to align the unannotated reads to the reference genome (GRCh38) with the parameter ” -v 0 ”.
5.miRNA identification and quantification: Bowtie v1.2.1.1 was used to align the reads that have been mapped to the reference genome with the pre-miRNA sequences in the known miRNA database miRBase (v22). Reads that align to the regions of known mature miRNA sequences are considered to be identified known miRNAs. miRDeep2 v2.0.5 was used to identify novel miRNA with the parameter ” -g -1 -b 0”. miRDeep2 was used to count the number of reads mapped to each miRNA.

molecule: other

source_name: Peripheral blood

extract_protocol:
RNA was extracted by Exosome RNA Purification Kit (5202050-50T) and RNA integrity was verified using Agilent 2100 Bioanalyzer.
Small RNA libraries was constructed by using the QIAseq miRNA Library Kit (Qiagen, Frederick, MD).

value: Peripheral blood

tag: subject status

value: healthy control


title: TMEM_Memory, H3K9me3, Day30, rep1

description: Library name: Arm_P14_Day30_H3K9me3_Rep1_S3


title: Tumor, p53, rep 3

description:
Library name: p53_M44
GEX (3' mRNA) library


title: HC7

description: Library name: Sample 16


title: Tumor, PTEN, rep 4

description:
Library name: PTEN_M99
GEX (3' mRNA) library


title: 30.0 ug-AgPVP_5

city: Durham

first: Joshua

last: Harrill

address: 109 TW Alexander Dr

institute: US EPA

description:
Library name: GRC371B-7_S9
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-7_S9

data_processing:
Raw data were aligned, trimmed, and normalized using Partek™ Flow™ software(Partek Inc., St. Louis, MO), with pre- and post-alignment quality checks.
Assembly: hg38
Supplementary files format and content: comma-separated .csv file includes normalized counts for each sample

source_name: Retina

growth_protocol: ARPE-19 cells were stored in vapor phase liquid nitrogen upon receipt from ATCC. For each of the biological replicates in RNA-seq, one vial of passage 1 cells was thawed to produce all technical replicates. Cells were cultured in sterile DMEM/F12 medium supplemented with 1.5 g/L sodium bicarbonate, 10% FBS, and 100 U/mL penicillin/streptomycin. Sodium hydroxide was added to the media as necessary to attain a pH of 7.4, and all cultures were maintained at 37°C in incubators with 5% CO2

extract_protocol:
Total RNA was extracted from cells using a mirVana™ RNA extraction kit (Life Technologies, Grand361 Island, NY).  RNA purity was assessed by using an RNA 6000 Nano LabChip™ Kit with a 2100 Bioanalyzer (Agilent Technologies,364 Palo Alto, CA). RNA sample concentrations were checked with a Qubit™ RNA BR Assay Kit.
Poly (A) selection done using the Apollo 324™ System (IntegenX Inc., Pleasanton, CA). cDNA library prep was performed using the PrepX™ mRNA 48 366 Protocol on the Apollo 324™ System. PCR amplification took place across 14 cycles with 48 index primers, and the products were run through the Apollo 324™ PrepX™ PCR Cleanup 48 Protocol. The 2100 Bioanalyzer was used with a High Sensitivity DNA Chip to assess product quality and the resultant electropherogram was used to determine average size and concentration. A Qubit™ DNA HS Kit was then used to quantify the collected libraries. Equal amounts of each library were pooled into a total of 4 pools containing a maximum of 24 randomized libraries. The Qubit™ DNA HS Kit was again used to quantify the sequencing samples before they were denatured and diluted to a final concentration of 2.7 pM according to Illumina NextSeq 500 protocols. Samples were then sequenced using the Illumina NextSeq 500 (Illumina, San Diego, CA) with 75 single-read cycles

treatment_protocol: Dosing was performed manually by removing half of the cell culture media from each flask and replacing it with an equivalent volume of 2X concentrated test particle or fresh cell culture media as a negative control. Initial 1 mg/mL AgNP solutions were diluted in media such that the final concentrations applied to cells were 0.3, 1, 3, 10, and 30 μg/mL.

value: Retina

value: 30.0 ug-AgPVP


title: 30.0 ug-AgPVP_4

description:
Library name: GRC371B-4_S8
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-4_S8


title: Tumor, PTEN, rep 3

description:
Library name: PTEN_M80
GEX (3' mRNA) library


title: 30.0 ug-AgPVP_3

description:
Library name: GRC371-36_S21
column name in Partek_GRC371_Normalized_counts.csv:GRC371-36_S21


title: TN_Naive, H3K9me3, Day32, rep4

description: Library name: Naive_P14_Day32_H3K9me3_Rep4_S8

value: Naive wild type


title: HC6

description: Library name: Sample 15


title: TN_Naive, H3K9me3, Day32, rep3

description: Library name: Naive_P14_Day32_H3K9me3_Rep3_S7


title: HC5

description: Library name: Sample 14


title: 30.0 ug-AgPVP_1

description:
Library name: GRC371-29_S24
column name in Partek_GRC371_Normalized_counts.csv:GRC371-29_S24


title: 30.0 ug-AgPVP_2

description:
Library name: GRC371-34_S10
column name in Partek_GRC371_Normalized_counts.csv:GRC371-34_S10


title: Control 1, DART-WT-treated

description: Library name: C1-WT


title: Tumor, LN2A, rep 4

description:
Library name: LN2A_M7
GEX (3' mRNA) library


title: HC4

description: Library name: Sample 13


title: TN_Naive, H3K9me3, Day32, rep2

description: Library name: Naive_P14_Day32_H3K9me3_Rep2_S6


title: 30.0 ug-AgCitrate_3

description:
Library name: GRC371-44_S15
column name in Partek_GRC371_Normalized_counts.csv:GRC371-44_S15

value: 30.0 ug-AgCitrate


title: TN_Naive, H3K9me3, Day32, rep1

description: Library name: Naive_P14_Day32_H3K9me3_Rep1_S5


title: 30.0 ug-AgCitrate_2

description:
Library name: GRC371-47_S1
column name in Partek_GRC371_Normalized_counts.csv:GRC371-47_S1


title: HC3

description: Library name: Sample 12


title: Tumor, LN2A, rep 2

description:
Library name: LN2A_M4
GEX (3' mRNA) library


title: TN_Naive, H3K9me3, Day30, rep4

description: Library name: Naive_P14_Day30_H3K9me3_Rep4_S2


title: HC2

description: Library name: Sample 11


title: 30.0 ug-AgCitrate_1

description:
Library name: GRC371-38_S23
column name in Partek_GRC371_Normalized_counts.csv:GRC371-38_S23


title: Tumor, LN2A, rep 1

description:
Library name: LN2A_M3
GEX (3' mRNA) library


title: TN_Naive, H3K9me3, Day30, rep3

description: Library name: Naive_P14_Day30_H3K9me3_Rep3_S1


title: HC1

description: Library name: Sample 10


title: Tumor, p53, rep 2

description:
Library name: p53_M43
GEX (3' mRNA) library


title: 30.0 ug-AgBPEI_4

description:
Library name: GRC371B-3_S10
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-3_S10

value: 30.0 ug-AgBPEI


title: Tumor, p53, rep 1

description:
Library name: p53_M38
GEX (3' mRNA) library


title: TN_Naive, H3K9me3, Day30, rep2

description: Library name: Naive_P14_Day30_H3K9me3_Rep2_S2


title: AE9

description: Library name: Sample 9

value: patient with anti-NMDAR encephalitis


title: AE8

description: Library name: Sample 8


title: 30.0 ug-AgBPEI_2

description:
Library name: GRC371B_23
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_23


title: TN_Naive, H3K9me3, Day30, rep1

description: Library name: Naive_P14_Day30_H3K9me3_Rep1_S1


title: 30.0 ug-AgBPEI_3

description:
Library name: GRC371-45_S14
column name in Partek_GRC371_Normalized_counts.csv:GRC371-45_S14


title: TEX_Exhaustion, H3K27me3, Day32, rep4

description: Library name: Cl13_P14_Day32_H3K27me3_Rep4_S12

value: LCMV clone 13 infection


title: AE7

description: Library name: Sample 7


title: chondrocytes (Nf2f/f;Prx1-CRE)-3

city: hangzhou

first: shali

last: wu

address: YUHANGTANG  road 866

institute: zhejiang university

description: Library name: Sample6

data_processing:
OmicStudio
Assembly: mm10

source_name: chondrocytes

extract_protocol:
RNA was harvested using Trizol. 1.5 ug of total RNA was used for theconstruction of sequencing libraries
NEBNextR Magnesium RNA Fragmentation Module; Invitrogen SuperScriptTM II Reverse Transcriptase; E. coli DNA polymerase I and RNase H treatment; dUTP Solution insertion.

value: chondrocytes


title: chondrocytes (Nf2f/f;Prx1-CRE)-1

description: Library name: Sample4


title: Tumor, LN2A, rep 3

description:
Library name: LN2A_M5
GEX (3' mRNA) library


title: 30.0 ug-AgBPEI_1

description:
Library name: GRC371-10_S3
column name in Partek_GRC371_Normalized_counts.csv:GRC371-10_S3


title: AE6

description: Library name: Sample 6


title: TEX_Exhaustion, H3K27me3, Day32, rep3

description: Library name: Cl13_P14_Day32_H3K27me3_Rep3_S11


title: chondrocytes (Nf2f/f)-3

description: Library name: Sample3


title: chondrocytes (Nf2f/f)-2

description: Library name: Sample2


title: AE5

description: Library name: Sample 5


title: 3.0 ug-AgPVP_4

description:
Library name: GRC371B-5_S7
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-5_S7

value: 3.0 ug-AgPVP


title: TEX_Exhaustion, H3K27me3, Day32, rep2

description: Library name: Cl13_P14_Day32_H3K27me3_Rep2_S10

value: Splenocytes


title: TEX_Exhaustion, H3K27me3, Day32, rep1

description: Library name: Cl13_P14_Day32_H3K27me3_Rep1_S9


title: AE4

description: Library name: Sample 4


title: TMEM_Memory, H3K27me3, Day30, rep4

description: Library name: Arm_P14_Day30_H3K27me3_Rep4_S4

value: LCMV Armstrong infection


title: WTA_423_Beyer_Shakiba_6_S6

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
Library name: WTA_423_Beyer_Shakiba_6_S6
BD Rhapsody, targeted panel of genes

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
the BD Rhapsody Sequence Analysis Pipeline 2.2.1 was used to align reads against the gencode mouse reference genome (M23) and generate molecular counts per bioproduct per identified nucleus and metrics related to the different steps
Downstream analysis was performed using the R packages Seurat (V4.3.0.1) and Signac (V1.10.0)
For chromatin accessibility data, peak calling with MACS3 was performed on nuclei passing the RNA quality control
After QC, a total of 48,110 nuclei were subjected to downstream analysis.
The transcriptomic data was log-normalized, scaled and centered, followed by dimensionality reduction (PCA) on the top 5,000 variable genes as identified by the vst method.
The ATAC data was normalized by computing the term-frequency inverse-document-frequency (TF-IDF), followed by determining top features and running dimensionality reduction through singular value decomposition (SVD).
Assembly: mm10 + sequences corresponding to the sample tag barcodes
Supplementary files format and content: gene-expression and ATAC matrix

source_name: Spleen and LNs

extract_protocol:
After sacrificing of the mice, splenocytes and lymph node cells were pooled and CD4+ T cells were enriched by negative selection using the MagniSort Mouse CD4 T cell enrichment Kit according to the manuscript. Subsequently CD4+ T cells were surface stained with anti-CD3, anti-CD4, anti-CD25, anti-CD62L and anti-CD44 and naive CD3+CD4+CD25-CD44low/-CD62L+ T cells were sorted. Naive CD4⁺ T cells were differentiated under TH1 and TH17 conditions.
Whole transcriptome, ATAC and sample tag libraries were obtained according to the manufacturer’s protocol (BD Biosciences) followed by index PCR to ligate sequencing indices.

value: Spleen and LNs

value: CD45+ CD3+ CD4+ T cells

value: Satb1fl/fl x CD4-CreERT2+/+

value: Tamoxifen/oil


title: AE3

description: Library name: Sample 3

value: Peripheral blood


title: chondrocytes (Nf2f/f;Prx1-CRE)-2

description: Library name: Sample5


title: 3.0 ug-AgPVP_2

description:
Library name: GRC371-12_S10
column name in Partek_GRC371_Normalized_counts.csv:GRC371-12_S10


title: AE2

description: Library name: Sample 2


title: TMEM_Memory, H3K27me3, Day30, rep3

description: Library name: Arm_P14_Day30_H3K27me3_Rep3_S3

value: P14 CD8 T cells


title: WTA_423_Beyer_Shakiba_5_S5

description:
Library name: WTA_423_Beyer_Shakiba_5_S5
BD Rhapsody, targeted panel of genes

value: Satb1fl/fl x CD4-CreERT2wt/+


title: TMEM_Memory, H3K27me3, Day30, rep2

description: Library name: Arm_P14_Day30_H3K27me3_Rep2_S8


title: WTA_423_Beyer_Shakiba_4_S4

description:
Library name: WTA_423_Beyer_Shakiba_4_S4
BD Rhapsody, targeted panel of genes


title: AE1

description: Library name: Sample 1


title: TMEM_Memory, H3K27me3, Day30, rep1

description: Library name: Arm_P14_Day30_H3K27me3_Rep1_S7


title: 3.0 ug-AgCitrate_4

description:
Library name: GRC371B-1_S17
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-1_S17

value: Retina

value: 3.0 ug-AgCitrate


title: 3.0 ug-AgPVP_5

description:
Library name: GRC371-9_S6
column name in Partek_GRC371_Normalized_counts.csv:GRC371-9_S6


title: WTA_423_Beyer_Shakiba_2_S2

description:
Library name: WTA_423_Beyer_Shakiba_2_S2
BD Rhapsody, targeted panel of genes


title: TN_Naive, H3K27me3, Day32, rep4

description: Library name: Naive_P14_Day32_H3K27me3_Rep4_S12

value: Naive wild type


title: 3.0 ug-AgCitrate_3

description:
Library name: GRC371B_39
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_39


title: WTA_423_Beyer_Shakiba_1_S1

description:
Library name: WTA_423_Beyer_Shakiba_1_S1
BD Rhapsody, targeted panel of genes


title: chondrocytes (Nf2f/f)-1

description: Library name: Sample1


title: WTA_423_Beyer_Shakiba_3_S3

description:
Library name: WTA_423_Beyer_Shakiba_3_S3
BD Rhapsody, targeted panel of genes


title: White-2 (Blood CD45RA+ Tconv, Blood donor 5)

city: Mainz

first: Niklas

last: Beumer

address: Langenbeckstrase 1

institute: University Medical Center Mainz

description: Library name: White_2__Blood_CD45RA_Tconv__Blood_donor_5

data_processing:
All analyses that used the programming language R were performed using R v4.0.0. Alignment and methylation calling was performed based on a described workflow (https://doi.org/10.1038/nprot.2013.118) that employs a customized version of methylCtools. The workflow was modified as follows: Trimmomatic (v0.30) PE was used to trim adaptor sequences with the options “-threads 12 -phred33 ILLUMINACLIP:xxx:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:36”. Here, “xxx” refers to a Fasta file containing the adaptor sequences. Alignment to the hs37d5 reference genome (based on GRCh37) was performed using BWA-MEM (v0.7.8) with the “-T” parameter set to 0. Duplicates were marked using sambamba (v0.6.5) with the parameters “-t 1 -l 0 --hash-table-size=2000000 --overflow-list-size=1000000 --io-buffer-size=64” and not removed from the data. For the analysis of CpGs, we combined data on the two opposite cytosines of the same CpG by summing up their read counts. To compute position-wise coverage, we added the counts of methylated and unmethylated reads at each profiled position. Since all donors were female, we excluded positions on chromosome Y.
Assembly: hs37d5 (coordinates are equivalent to GRCh37)
Supplementary files format and content: methylated_read_counts_hs37d5_intervals_are_1_based_and_closed.tsv: Counts of methylated reads per CpG site. Genomic intervals are 1-based and closed.
Supplementary files format and content: all_read_counts_aka_coverage_hs37d5_intervals_are_1_based_and_closed.tsv: Counts of all reads (i.e. coverage) per CpG site. Genomic intervals are 1-based and closed.

source_name: Blood

extract_protocol:
To isolate T cells from human skin tissue, skin and underlying fat were first mechanically separated. Then, skin was cut into small pieces and digested (base medium DMEM (Gibco #41965), 4 mg/ml collagenase type IV (Sigma-Aldrich #C5138), 10 µg/ml DNAse I (Roche #11284932001), 2% fetal bovine serum, 10 mM HEPES). Digestion was performed directly in a GentleMACS C tube and the program “37_C_Multi_H” for 90 minutes, followed by centrifugation and filtration steps. Dead cell removal was performed with a dead cell removal kit (Miltenyi Cat# 130-090-101). To isolate T cells from human blood, leukocyte reduction chambers or buffy coats were used. Leukocytes were first diluted 1:3 with DPBS (Gibco #14190-094), and the resulting blood and PBS mixture was split in two fractions and underlaid with an equal amount of Pancoll (PAN biotech #P04-601000). Samples were centrifuged at 1,000xg for 20 minutes at RT, with acceleration set to 4 and brake to 0. The PBMC layer was isolated and washed twice by centrifugation steps. Cells were pre-enriched with either biotinylated anti-human CD4 (clone OKT4, Biolegend), biotinylated anti-human CD8 (clone HIT8a, Biolegend) or PE-labeled or biotinylated anti-human CD25 (Clone BC96, Biolegend), followed by column-based magnetic separation with anti-biotin or anti-PE ultrapure microbeads (Miltenyi Biotec #130-105-637 or #130-105-639) following manufacturer’s protocol. Cells were stained in 1.5 mL Eppendorf tubes or 96-well plates in FACS buffer (2% FCS in PBS). Surface staining was performed at 4 °C for 20 minutes in 50-100 µl staining volume. Antibodies were used, if not indicated otherwise, as recommended by the manufacturer. The following anti-human antibodies were used for surface staining: CD4 (OKT4/L200, Biolegend or BD Biosciences), CD3 (OKT3, Biolegend or BD Biosciences), TCR-β chain (IP26, Biolegend), CD8 (RPA-T8/HIT8a, Biolegend or BD Biosciences), CD19 (HIB19, Biolegend or BD Biosciences), CD25 (BC96/2A3, Biolegend or BD Biosciences), CD45RA (HI100, Biolegend or BD Biosciences), CD45RO (UCHL1, Biolegend), CD127 (A019D5, Biolegend), CD45 (HI30, BD Biosciences), CD14 (MφP9, BD Biosciences), CCR8 (433H, BD Biosciences). Flow cytometry data were analyzed using BD FlowJo™ (Version 10.6.2). Sorting was performed with a BD FACSAriaII™ or BD FACSFusion™ cell sorter with 85 µm nozzle and 45 psi of pressure. Post-sort quality controls were performed as applicable. Cells were sorted directly into 500 µL RLT+ lysis buffer (Qiagen AllPrep DNA/RNA Mini Kit Cat#80204). All procedures were performed in DNA low-bind tubes (Eppendorf #0030108051). From human skin samples, we sorted 3,500 to 10,000 Treg cells (CD45+CD3+TCRb+CD4+CD8-CD127-CD25+) and 5,500 to 10,000 Tconv cells (CD45+CD3+TCRb+CD4+CD8-CD127+CD25-). From human peripheral blood samples, we sorted 10,000 CD45RA+ Treg cells (CD45+CD3+TCRb+CD4+CD8-CD127-CD25+CD45RA+CD45RO-), 10,000 CCR8+ Treg cells (CD45+CD3+TCRb+CD4+CD8-CD127-CD25+CD45RA-CD45RO+CCR8+) and 10,000 CD45RA+ Tconv cells (CD45+CD3+TCRb+CD4+CD8-CD127+CD25-CD45RA+CD45RO-).
DNA was isolated using a DNA/RNA micro kit (Quiagen Cat#80284) and DNA quality and concentration was assessed using QubitTM (dsDNA HS Kit Cat#Q32851) and Tapestation 4200 with Genomic DNA Screentape (Agilent Cat#5067-5365). Tagmentation-based whole genome bisulfite sequencing (TWGBS) was essentially performed as described (https://doi.org/10.1007/978-1-4939-7481-8_6). Two differently barcoded libraries were generated each per sample. Corresponding libraries were pooled in equimolar amounts

value: Blood

value: CD45RA+ Tconv

value: Female


title: Yellow-2 (Blood CD45RA+ Tconv, Blood donor 3)

description: Library name: Yellow_2__Blood_CD45RA_Tconv__Blood_donor_3


title: TN_Naive, H3K27me3, Day32, rep3

description: Library name: Naive_P14_Day32_H3K27me3_Rep3_S11


title: 3.0 ug-AgCitrate_2

description:
Library name: GRC371-17_S19
column name in Partek_GRC371_Normalized_counts.csv:GRC371-17_S19


title: 3.0 ug-AgPVP_3

description:
Library name: GRC371B-13_S2
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-13_S2


title: TN_Naive, H3K27me3, Day32, rep2

description: Library name: Naive_P14_Day32_H3K27me3_Rep2_S10


title: ATAC_423_Beyer_Shakiba_6_S3

description:
Library name: ATAC_423_Beyer_Shakiba_6_S3
BD Rhapsody, targeted panel of genes

library_source: genomic single cell


title: White-1 (Blood CD45RA+ Treg, Blood donor 5)

description: Library name: White_1__Blood_CD45RA_Treg__Blood_donor_5

value: CD45RA+ Treg


title: TN_Naive, H3K27me3, Day32, rep1

description: Library name: Naive_P14_Day32_H3K27me3_Rep1_S9


title: ATAC_423_Beyer_Shakiba_5_S2

description:
Library name: ATAC_423_Beyer_Shakiba_5_S2
BD Rhapsody, targeted panel of genes


title: Purple-1 (Blood CD45RA+ Treg, Blood donor 4)

description: Library name: Purple_1__Blood_CD45RA_Treg__Blood_donor_4


title: 3.0 ug-AgPVP_1

description:
Library name: GRC371-11_S8
column name in Partek_GRC371_Normalized_counts.csv:GRC371-11_S8

value: 3.0 ug-AgPVP


title: 3.0 ug-AgCitrate_5

description:
Library name: GRC371B-14_S13
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-14_S13


title: ATAC_423_Beyer_Shakiba_4_S1

description:
Library name: ATAC_423_Beyer_Shakiba_4_S1
BD Rhapsody, targeted panel of genes


title: Yellow-1 (Blood CD45RA+ Treg, Blood donor 3)

description: Library name: Yellow_1__Blood_CD45RA_Treg__Blood_donor_3


title: 3.0 ug-AgBPEI_4

description:
Library name: GRC371-48_S5
column name in Partek_GRC371_Normalized_counts.csv:GRC371-48_S5

value: 3.0 ug-AgBPEI


title: White-5 (Blood CCR8+ Treg, Blood donor 8)

description: Library name: White_5__Blood_CCR8_Treg__Blood_donor_8

value: CCR8+ Treg


title: Purple-2 (Blood CD45RA+ Tconv, Blood donor 4)

description: Library name: Purple_2__Blood_CD45RA_Tconv__Blood_donor_4


title: TN_Naive, H3K27me3, Day30, rep4

description: Library name: Naive_P14_Day30_H3K27me3_Rep1_S5

value: Splenocytes


title: TN_Naive, H3K27me3, Day30, rep3

description: Library name: Naive_P14_Day30_H3K27me3_Rep4_S4


title: ATAC_423_Beyer_Shakiba_3_S3

description:
Library name: ATAC_423_Beyer_Shakiba_3_S3
BD Rhapsody, targeted panel of genes

value: Spleen and LNs

value: CD45+ CD3+ CD4+ T cells


title: 3.0 ug-AgBPEI_3

description:
Library name: GRC371B_36
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_36


title: TN_Naive, H3K27me3, Day30, rep1

description: Library name: Naive_P14_Day30_H3K27me3_Rep2_S6


title: Purple-5 (Blood CCR8+ Treg, Blood donor 7)

description: Library name: Purple_5__Blood_CCR8_Treg__Blood_donor_7


title: 3.0 ug-AgBPEI_1

description:
Library name: GRC371-23_S18
column name in Partek_GRC371_Normalized_counts.csv:GRC371-23_S18


title: Yellow-5 (Blood CCR8+ Treg, Blood donor 6)

description: Library name: Yellow_5__Blood_CCR8_Treg__Blood_donor_6


title: 3.0 ug-AgBPEI_2

description:
Library name: GRC371-24_S16
column name in Partek_GRC371_Normalized_counts.csv:GRC371-24_S16


title: ATAC_423_Beyer_Shakiba_1_S1

description:
Library name: ATAC_423_Beyer_Shakiba_1_S1
BD Rhapsody, targeted panel of genes

value: Tamoxifen/oil


title: ATAC_423_Beyer_Shakiba_2_S2

description:
Library name: ATAC_423_Beyer_Shakiba_2_S2
BD Rhapsody, targeted panel of genes

value: Satb1fl/fl x CD4-CreERT2+/+


title: Purple-6 (Fat Treg, Donor 8)

description: Library name: Purple_6__Fat_Treg__Donor_8

source_name: Subcutaneous fat

value: Subcutaneous fat

value: Treg


title: Spleen PMN-MDSCs, FXR_KO2

city: Guangzhou

first: Juan

last: He

state: Guangdong

address: No. 9, Jinshui Road

institute: Guangzhou Women and Children's Medical Center

description:
Library name: Sample 4
Column name in raw_genes_fpkm_expression.txt: FXR_KO2

data_processing:
Adapter and quality trimming: Raw reads were processed with Cutadapt (v1.9) to remove adapters
Read alignment and Transcript assembly: Clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Mapped reads were assembled into transcripts with StringTie (v1.3.4d) using default parameters.
Transcriptome merging: All sample transcriptomes were merged using gffcompare (v0.9.8) to generate a comprehensive transcriptome.
Expression quantification: Expression levels (FPKM) were calculated using StringTie and ballgown
Differential expression analysis: Differentially expressed mRNAs (fold change >2 or <0.5, p<0.05) were identified using edgeR or DESeq2, followed by GO and KEGG enrichment analyses.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: txt file includes FPKM and count values for each sample.

source_name: Spleen

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Spleen

value: PMN-MDSC

value: Myeloid cells

value: FXR knockout

value: Day 7


title: 3.0 ug-AgCitrate_1

description:
Library name: GRC371-14_S5
column name in Partek_GRC371_Normalized_counts.csv:GRC371-14_S5

value: Retina

value: 3.0 ug-AgCitrate


title: TEX_Exhaustion, H3K4me3, Day32, rep4

description: Library name: Cl13_P14_Day32_H3K4me3_Rep4_S16

value: P14 CD8 T cells

value: LCMV clone 13 infection


title: TEX_Exhaustion, H3K4me3, Day32, rep3

description: Library name: Cl13_P14_Day32_H3K4me3_Rep3_S15


title: 3.0 ug-AgBPEI_5

description:
Library name: GRC371B-10_S6
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-10_S6

value: 3.0 ug-AgBPEI


title: Spleen PMN-MDSCs, WT2

description:
Library name: Sample 2
Column name in raw_genes_fpkm_expression.txt: WT2

value: WT


title: Yellow-6 (Fat Treg, Donor 7)

description: Library name: Yellow_6__Fat_Treg__Donor_7

value: Female


title: 10.0 ug-AgPVP_4

description:
Library name: GRC371B-18_S4
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-18_S4

value: 10.0 ug-AgPVP


title: TEX_Exhaustion, H3K4me3, Day32, rep2

description: Library name: Cl13_P14_Day32_H3K4me3_Rep2_S14

value: Splenocytes


title: 10.0 ug-AgPVP_3

description:
Library name: GRC371-35_S22
column name in Partek_GRC371_Normalized_counts.csv:GRC371-35_S22


title: Red-6 (Fat Treg, Donor 6)

description: Library name: Red_6__Fat_Treg__Donor_6


title: Purple-9 (Skin Tconv, Donor 11)

description: Library name: Purple_9__Skin_Tconv__Donor_11

source_name: Skin

value: Skin

value: Tconv


title: Adult 7dpi4

city: Xi'an

first: Beibei

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

description: Library name: A_7dpi4

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: mm10
Supplementary files format and content: FPKM

source_name: Spinal cord

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

value: Spinal cord

value: Injury


title: Spleen PMN-MDSCs, WT1

description:
Library name: Sample 1
Column name in raw_genes_fpkm_expression.txt: WT1

value: Spleen

value: PMN-MDSC


title: TN_Naive, H3K27me3, Day30, rep2

description: Library name: Naive_P14_Day30_H3K27me3_Rep3_S3

value: Naive wild type


title: TMEM_Memory, H3K4me3, Day30, rep4

description: Library name: Arm_P14_Day30_H3K4me3_Rep4_S8

value: LCMV Armstrong infection


title: 10.0 ug-AgPVP_2

description:
Library name: GRC371-27_S19
column name in Partek_GRC371_Normalized_counts.csv:GRC371-27_S19

value: Retina


title: TEX_Exhaustion, H3K4me3, Day32, rep1

description: Library name: Cl13_P14_Day32_H3K4me3_Rep1_S13


title: Yellow-9 (Skin Tconv, Donor 10)

description: Library name: Yellow_9__Skin_Tconv__Donor_10


title: 10.0 ug-AgCitrate_5

description:
Library name: GRC371B_38
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_38

value: 10.0 ug-AgCitrate


title: Adult 7dpi2

description: Library name: A_7dpi2


title: Purple-8 (Skin Treg, Donor 11)

description: Library name: Purple_8__Skin_Treg__Donor_11

value: Treg


title: Green-9 (Skin Tconv, Donor 7)

description: Library name: Green_9__Skin_Tconv__Donor_7


title: TMEM_Memory, H3K4me3, Day30, rep3

description: Library name: Arm_P14_Day30_H3K4me3_Rep3_S7

value: P14 CD8 T cells


title: TMEM_Memory, H3K4me3, Day30, rep2

description: Library name: Arm_P14_Day30_H3K4me3_Rep2_S6


title: 10.0 ug-AgPVP_1

description:
Library name: GRC371-13_S12
column name in Partek_GRC371_Normalized_counts.csv:GRC371-13_S12


title: 10.0 ug-AgPVP_5

description:
Library name: GRC371B-19_S14
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-19_S14


title: Adult 7dpi1

description: Library name: A_7dpi1


title: 10.0 ug-AgCitrate_4

description:
Library name: GRC371B-12_S1
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-12_S1


title: Yellow-8 (Skin Treg, Donor 10)

description: Library name: Yellow_8__Skin_Treg__Donor_10


title: TMEM_Memory, H3K4me3, Day30, rep1

description: Library name: Arm_P14_Day30_H3K4me3_Rep1_S5


title: Spleen PMN-MDSCs, FXR_KO1

description:
Library name: Sample 3
Column name in raw_genes_fpkm_expression.txt: FXR_KO1

value: Myeloid cells

value: FXR knockout

value: Day 7


title: Adult 3dpi4

description: Library name: A_3dpi4

value: WT


title: Green-8 (Skin Treg, Donor 7)

description: Library name: Green_8__Skin_Treg__Donor_7

value: Female


title: 10.0 ug-AgCitrate_2

description:
Library name: GRC371-2_S17
column name in Partek_GRC371_Normalized_counts.csv:GRC371-2_S17


title: Adult 3dpi3

description: Library name: A_3dpi3


title: TN_Naive, H3K4me3, Day32, rep3

description: Library name: Naive_P14_Day32_H3K4me3_Rep3_S11

value: Splenocytes


title: 10.0 ug-AgCitrate_1

description:
Library name: GRC371-1_S4
column name in Partek_GRC371_Normalized_counts.csv:GRC371-1_S4


title: HeLa cells treated with PDS, biol rep 3

city: Naples

first: Nunzia

last: Iaccarino

address: Via Domenico Montesano, 49

department: Pharmacy

country: Italy

institute: University of Naples Federico II

description: Library name: Sample 12

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted to fastq files using bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including raw counts

source_name: HeLa

extract_protocol:
Total RNA was extracted with a paramagnetic bead technology, using the Negedia RNA extraction service (NEGEDIA srl), and quantified with the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)1 which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).

value: HeLa

value: Cervical cancer cells


title: HeLa cells treated with PDS, biol rep 2

description: Library name: Sample 11


title: TN_Naive, H3K4me3, Day32, rep2

description: Library name: Naive_P14_Day32_H3K4me3_Rep2_S10


title: 10.0 ug-AgBPEI_5

description:
Library name: GRC371B_24
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_24

value: 10.0 ug-AgBPEI


title: TN_Naive, H3K4me3, Day32, rep1

description: Library name: Naive_P14_Day32_H3K4me3_Rep1_S9


title: Adult 7dpi3

description: Library name: A_7dpi3

value: Spinal cord

value: Injury


title: Adult 3dpi2

description: Library name: A_3dpi2


title: HeLa cells treated with PDS, biol rep 1

description: Library name: Sample 10


title: Adult 3dpi1

description: Library name: A_3dpi1


title: 10.0 ug-AgBPEI_4

description:
Library name: GRC371-39_S12
column name in Partek_GRC371_Normalized_counts.csv:GRC371-39_S12


title: Adult 1dpi3

description: Library name: A_1dpi3


title: 10.0 ug-AgBPEI_3

description:
Library name: GRC371B_35
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_35


title: TN_Naive, H3K4me3, Day30, rep4

description: Library name: Naive_P14_Day30_H3K4me3_Rep4_S4

value: Naive wild type


title: TN_Naive, H3K4me3, Day30, rep3

description: Library name: Naive_P14_Day30_H3K4me3_Rep3_S3


title: HeLa cells treated with Berberine, biol rep 3

description: Library name: Sample 9


title: HeLa cells treated with Berberine, biol rep 2

description: Library name: Sample 8


title: Adult 1dpi2

description: Library name: A_1dpi2


title: 10.0 ug-AgCitrate_3

description:
Library name: GRC371-40_S21
column name in Partek_GRC371_Normalized_counts.csv:GRC371-40_S21


title: HeLa cells treated with Berberine, biol rep 1

description: Library name: Sample 7


title: 10.0 ug-AgBPEI_2

description:
Library name: GRC371B_33
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_33


title: TN_Naive, H3K4me3, Day32, rep4

description: Library name: Naive_P14_Day32_H3K4me3_Rep4_S12


title: Adult 1dpi1

description: Library name: A_1dpi1


title: TN_Naive, H3K4me3, Day30, rep2

description: Library name: Naive_P14_Day30_H3K4me3_Rep2_S2


title: Adult Sham3

description: Library name: A_Con3

value: Sham operation


title: 10.0 ug-AgBPEI_1

description:
Library name: GRC371-7_S15
column name in Partek_GRC371_Normalized_counts.csv:GRC371-7_S15

value: Retina


title: TN_Naive, H3K4me3, Day30, rep1

description: Library name: Naive_P14_Day30_H3K4me3_Rep1_S1


title: HeLa cells treated with RHPS4, biol rep 3

description: Library name: Sample 6


title: 1.0 ug-AgPVP_5

description:
Library name: GRC371B_42
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_42

value: 1.0 ug-AgPVP


title: Adult Sham2

description: Library name: A_Con2


title: HeLa cells treated with RHPS4, biol rep 2

description: Library name: Sample 5


title: 1.0 ug-AgPVP_4

description:
Library name: GRC371B_26
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_26


title: Adult Sham1

description: Library name: A_Con1


title: TEX_Exhaustion, H3K27ac, Day32, rep4

description: Library name: Cl13_P14_Day32_H3K27ac_Rep4_S16

value: LCMV clone 13 infection


title: TEX_Exhaustion, H3K27ac, Day32, rep3

description: Library name: Cl13_P14_Day32_H3K27ac_Rep3_S15

value: P14 CD8 T cells


title: Neonatal 7dpi3

description: Library name: N_7dpi3


title: TEX_Exhaustion, H3K27ac, Day32, rep2

description: Library name: Cl13_P14_Day32_H3K27ac_Rep2_S14


title: 1.0 ug-AgPVP_2

description:
Library name: GRC371-28_S7
column name in Partek_GRC371_Normalized_counts.csv:GRC371-28_S7


title: HeLa cells, untreated, biol rep 3

description: Library name: Sample 3


title: TEX_Exhaustion, H3K27ac, Day32, rep1

description: Library name: Cl13_P14_Day32_H3K27ac_Rep1_S13


title: HeLa cells, untreated, biol rep 2

description: Library name: Sample 2


title: 1.0 ug-AgPVP_3

description:
Library name: GRC371B_31
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_31


title: 1.0 ug-AgPVP_1

description:
Library name: GRC371-20_S14
column name in Partek_GRC371_Normalized_counts.csv:GRC371-20_S14


title: Neonatal 7dpi1

description: Library name: N_7dpi1


title: TMEM_Memory, H3K27ac, Day30, rep4

description: Library name: Arm_P14_Day30_H3K27ac_Rep4_S8

value: LCMV Armstrong infection


title: 1.0 ug-AgNO3_4

description:
Library name: GRC371B_32
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_32

value: 1.0 ug-AgNO3


title: HeLa cells, untreated, biol rep 1

description: Library name: Sample 1


title: Neonatal 3dpi4

description: Library name: N_3dpi4


title: TMEM_Memory, H3K27ac, Day30, rep3

description: Library name: Arm_P14_Day30_H3K27ac_Rep3_S7


title: Neonatal 3dpi3

description: Library name: N_3dpi3


title: 1.0 ug-AgNO3_3

description:
Library name: GRC371B_45
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_45


title: DYP3, BD scRNA-seq

city: Zhengzhou

first: Yanfang

last: Lu

address: Weiwu road 7th

institute: Zhengzhou University

description: BD Rhapsody

data_processing:
For BD Rhapsody platform, after demultiplexing of bcl files by using Bcl2fastq2 v.2.20 from Illumina and assessment of reads quality, paired-end scRNA-seq reads were then filtered for valid cell barcodes using the barcode whitelist provided by BD. Then, the hg38 human transcriptome was used for read alignment. The expression matrix was imported into Seurat v3.1.0 for further preprocessing. The number of detected genes, the number of unique molecular identifiers (UMIs), as well as the fraction of UMIs corresponding to mitochondrial features, which altogether reflect the transcriptome quality of each cell, were calculated. Only genes that were expressed in at least 10 cells were included, and cells with >20% mitochondrial transcripts, or which transcribed fewer than 200 or more than 8,000 genes were removed. Sample tags were extracted from BD Rhapsody analysis pipeline (https://www.sevenbridges.com/bdgenomics/), and cells that had been identified as multiplets, negatives or that were labeled as ‘undetermined’ were eliminated.  For 10x Genomics platform, the raw sequencing data were demultiplexed and further converted into a single cell level gene counts matrix with Cell Ranger 3.1.0 with default parameters (https://github.com/10xGenomics/cellranger). Only the number of expected cells was adapted in accordance with the number of targeted (captured) cells in each experiment. The mRNA reads were mapped to the reference hg38 with the reads allowed to map to both exonic and intronic regions. For every type of hashing strategy, a specifc Feature Reference File was generated and used as input for Cell Ranger. Filtered count matrices were used for downstream analysis. CellPlex and TotalSeq-B samples from dual index libraries were mapped with cellranger version 6.1.1. To assign hashing tags for each cell, two strategies implemented in Seurat 3.1.4 package in R version 3.6.0 were evaluated on the fltered feature-barcode matrix generated by CellRanger: (i) HTODemux function with default parameters and (ii) incorporated into Seurat MULTIseqDemux function with argument autoTresh = TRUE. Subsequent clustering and visualization of the data sets was performed in R using Seurat version 3.1.4 functions as described in the “Demultiplexing with hashtag oligos (HTOs)” vignette available at (https://satijalab.org/seurat/v3.1/hashing_vignette.html). The hashing accuracy was calculated as the overlap between cells annotated using MULTISeqDemux, HTODemux functions, or GMM-Demux (https://github.com/CHPGenetics/GMM-Demux) and freemuxlet as a ground truth.
Assembly: hg38
Supplementary files format and content: Tab-separated text files inlcude raw counts for each sample

source_name: bone marrow

extract_protocol:
Leukemia cell lines are suspension cells. Cultured cells were washed and resuspended in PBS with 0.04%.
Multiplexed single-cell RNA sequencing Antibody-based barcoding on BD Rhapsody platform Cell concentration and viability were assessed using a Countess II Automated Cell Counter (Life) and 0.4% Trypan Blue (Thermo Fisher, #T10282). A total of 50,000 viable cells (>90%) from each of the four samples, including KG-1a, Kasumi-1 and two K562 samples (K562 treated differently and for another study), were labeled with a unique Sample Tag using BD Single-Cell Multiplexing Kit (BD Biosciences, #633781), following the manufacturer’s protocol. Briefly, 50,000 cells of each sample were resuspended in 200 µL BD Pharmingen Stain Buffer (FBS) (BD Biosciences, #554656). Sample Tag tubes were slightly centrifuged to collect the contents at the bottom. 180 µL cell suspension from each sample was transferred to a individual Sample Tag tube, and then was incubated at room temperature (15℃ to 25℃) for 20 minutes. After labeling, each cell suspension was transferred to a 15 mL tube (Corning, #430790) and washed three times with 2 mL BD Pharmingen Stain Buffer, centrifuged at 300 × g for 5 minutes, and then the supernatants were removed carefully not to perturb the pellet at the bottom. Finally, the cell pellet was resuspended in 620 µL cold Sample Buffer (BD Biosciences, #650000062), and the cell concentration and viability were detected. The tubes containing resuspensions were kept on ice until further processing.  Samples from 4 labeled cell suspensions were pooled in equal amounts to achieve approximately total 40,000 cells in 620 µL (inadequate volumes were supplemented with cold Sample Buffer). The BD Rhapsody cartridge with >200,000 microwells was primed, and 575 µL of the pooled single-cell suspension was loaded onto the cartridge and incubated at room temperature for 15 min. Next, Cell Capture beads were washed & loaded onto the cartridge, and incubated at room temperature for 3 min. Thereafter, the cartridge was washed twice with BD Sample Buffer to make sure that one magnetic bead binds to only one cell in a single microwell. Cells were then lysed, and the released mRNAs and antibody-linked sample tag oligos were captured by Cell Capture Beads. Beads were then retrieved and washed. The reverse transcription was immediately proceeded and Cell Capture Beads with cDNA were treated with Exonuclease I to clear redundant primers on Beads, preventing the subsequent library construction from the adverse effects. cDNA and sample tag libraries were prepared by using the BD Rhapsody Whole Transcriptome Analysis Amplification kit and BD Single-Cell Multiplexing kit (BD Biosciences). Final libraries were quantified with a Qubit Fluorometer using the Qubit dsDNA HS Kit (Thermo Fisher, #Q32854). Fragment distribution of libraries was traced by Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA kit. Sequencing was performed on a Illumina NovaSeq 6000 PE150 System.  Lipid-tagged barcoding on 10x Genomics platform (CellPlex) The cell concentration and viability of 18 samples (3 cell lines × 6 experimental conditions) were determined by Countess II Automated Cell Counter and 0.4% Trypan Blue. 2,500 single cells from each cell line in control group, and 1,500 single cells from each cell line in each drug treatment group, were expected to be obtained after multiplexed single-cell RNA sequencing, respectively. For control group, 600,000 cells from each cell line were prepared to be labeled with a unique tag of Cell Multiplexing Oligo (CMO, provided by the 10x Genomics 3’ CellPlex Kit, #1000261), respectively; while for each drug treatment group, 200,000 cells from each cell line, total 600,000 cells were pooled firstly, and then each group as a unit was labeled with a unique CMO tag, respectively. The labeling of CMO was performed according to the 10x Genomics CG00391 Rev A protocol, with minor adjustments. Briefly, 600,000 initiative cells were transferred to a 15-mL tube (total 8-tube cells to be labeled), and PBS + 0.04% BSA at room temperature was added to each tube for a total 1 mL volume. The cell suspension was gently pipetted, mixed, and then centrifuged at 300 × g for 5 minutes by using swinging-bucket rotor. The supernatant was discarded without disturbance to the pellet at the bottom of the tube. Subsequently, 50 µL CMOs (equilibrated to room temperature and mixed in advance) were added into each tube, and the pellet was resuspended by 10-15× gentle pipetting. The suspension was incubated for 5 min at room temperature. Next, to wash 3 times, chilled Wash & Resuspension Buffer (PBS + 1% BSA) was added to the tube (1.95 mL for the first time, and 2 mL for the second and third time). The suspension containing labeled cells was gently pipetted and centrifuged at 300 × g for 5 minutes at 4℃, and then the supernatant was removed carefully to avoid touching the pellet. Finally, the pellet was resuspended in 200 µL cold chilled Wash & Resuspension Buffer to obtain a concentration of ~1,500 cells/µL (assuming ~50% loss of 600,000 initiative cells), and the cell concentration and viability were detected. The tubes containing resuspensions were placed on ice until later use.  5× loading volume of each cell suspension was pooled to reduce the quantity deviation.  The one-in-five volume of pooled single-cell suspension was loaded onto the 10x Genomics Chromium Next GEM Chip G immediately. The cDNA and CMO tag libraries were constructed according to the standard manufacturer’s protocol from 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing. Fragment distribution of libraries was traced by Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA kit. Sequencing was performed on a Illumina NovaSeq 6000 PE150 System.  Antibody-based barcoding on 10x Genomics platform Six samples, including KG-1a treated with 1 µM Ara-C for 6 h, 12 h, 24 h and 48 h, and naïve and Ara-C resistant KG-1a were labeled according to an adapted BioLegend cell hashing protocol (TotalSeq™-B Antibodies and Cell Hashing with 10x Single Cell 3’ Reagent Kit v3 3.1 Protocol). Briefly, Labeling buffer (PBS + 1% BSA) and resuspension buffer (PBS + 0.04% BSA) were prepared in advance and were placed on ice before further using. For each sample, antibody mix was constituted by adding the 0.1 µg corresponding Hashtag antibody (Biolegend, TotalSeq-B Reagents) to 50 µL labeling buffer. The antibody mix was centrifuged at 14000 g, 4 ℃ for 10 min before use to avoid adding of sediment. Each sample containing 500,000 initiative cells was resuspended in 50 µL labeling buffer and incubated with 5 µL Human TruStain FcX (BioLegend, PN 422301) for 10 min to block nonspecifc antibody binding. Subsequently, the suspension was then gently mixed with the corresponding antibody mix supernatant for 10 times and incubated at 4℃ for 30 min. After incubation, 1.4 ml labeling buffer was added before the suspension was centrifuged at 300 g, 4℃ for 5 min. Further, the supernatant was removed, and the cells were rinsed with 1.5 ml labeling buffer twice. Finally, ~50% loss of 500,000 initiative cells were assumed, and the samples were resuspended with resuspension buffer to an ultimate density of 1-2×106 cells/mL. The quality of single-cell suspension was evaluated by 0.4% trypan blue staining and Countess II Automated Cell Counter.  All samples were mixed together at 5 times of loading amount and left on ice before use. The one-in-five volume of pooled single-cell suspension was loaded onto the 10x Genomics single-cell-B chip. The cDNA library was prepared according to the standard manufacturer’s protocol from 10x Genomics Single Cell 3' v3 Reagent Kits with Feature Barcoding technology for Cell Surface Protein, and then sequenced on a Illumina NovaSeq 6000 PE150 System.

value: bone marrow

value: KG-1a, Kasumi-1

value: leukemia cells


title: TMEM_Memory, H3K27ac, Day30, rep2

description: Library name: Arm_P14_Day30_H3K27ac_Rep2_S6

source_name: Splenocytes

value: Splenocytes


title: 1.0 ug-AgNO3_2

description:
Library name: GRC371-41_S9
column name in Partek_GRC371_Normalized_counts.csv:GRC371-41_S9


title: Neonatal 3dpi2

description: Library name: N_3dpi2

value: WT


title: TMEM_Memory, H3K27ac, Day30, rep1

description: Library name: Arm_P14_Day30_H3K27ac_Rep1_S5


title: HeLa cells treated with RHPS4, biol rep 1

description: Library name: Sample 4

value: HeLa

value: Cervical cancer cells


title: DYP2, 10x scRNA-seq

description: 10x Genomics


title: DYP1, 10x scRNA-seq

description: 10x Genomics

value: KG-1a, Kasumi-1, HL-60


title: Neonatal 3dpi1

description: Library name: N_3dpi1

value: Spinal cord

value: Injury


title: 1.0 ug-AgNO3_1

description:
Library name: GRC371-22_S1
column name in Partek_GRC371_Normalized_counts.csv:GRC371-22_S1


title: Neonatal 7dpi2

description: Library name: N_7dpi2


title: 1.0 ug-AgCitrate_6

description:
Library name: GRC371B-8_S3
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-8_S3

value: 1.0 ug-AgCitrate


title: E-hASCs, replicate 3, scRNAseq

first: Yifu

last: Zhu

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学

data_processing:
The scRNA-seq raw reads were processed through an internal pipeline to generate gene expression matrices. Raw sequencing reads were quality checked using FastQC v0.11.7 and Fastp to remove low quality reads, and adapter sequences were removed with cutadapt. After extracting the cell barcode and UMI, sequencing reads were mapped to the reference genome GRCh38((ensembl version 92 annotation) using STAR v2.5.3a. We used featureCounts v1.6.2 software to calculate the UMI counts and gene counts of each cell and cells with gene counts less than 200, gene counts at top 5%, UMI counts at top 5% and over 50% mitochondrial content were excluded. The Seurat v3.1.2 was used to perform data normalization, dimension reduction, clustering, and differential expression analysis
Assembly: homo_sapiens_ensembl_92
Supplementary files format and content: matrix table with raw gene counts with every gene and cell

source_name: hASCs obtained from elderly

extract_protocol:
The hASCs were isolated with 0.1% collagenase I from the abdominal subcutaneous fat (SAT) of 3 healthy infants and 3 elderly. Single-cell suspensions of primary hASCs with PBS were loaded onto microwell chip using the Singleron Matrix®Single Cell Processing System. Barcoding Beads are collected from the microwell chip, and mRNA captured by the Barcoding Beads was reverse transcribed into cDNA, followed by PCR amplification for the library construction.
The scRNA-seq libraries were constructed based on the protocol of the GEXSCOPE® Single Cell RNA Library Kits. Individual libraries were diluted to and pooled at a concentration of 4nM, and subsequently sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Primary Adipose Stem Cells

tag: developmental stage

value: elderly


title: TN_Naive, H3K27ac, Day32, rep3

description: Library name: Naive_P14_Day32_H3K27ac_Rep3_S11

value: Naive wild type


title: Sox11_WT_KO_RNA_seq, 1308-TKA, Par, TGF-β1, biol. replicate 2

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

institute: Albert-Ludwigs-Universität Freiburg

description:
1308Par_TGF2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2

data_processing:
Adapter sequences and poor quality reads were removed via FastP (Version 0.23.4)
Reads were mapped to the mouse reference genome (mmc10) using STAR aligner (Version 2.7.10b)
Read counts were normalized to the sequencing depths yielding the log2 counts per millions (CPM) as measures for gene expression levels.
Assembly: mm10
Supplementary files format and content: processed data after merging biological replicates: tab-delimited text files listing log2 CPM values per gene across all samples; CPM values of the two biological replicates were averaged and then subjected to log2 transformation; entries with "0" values had no CPM values, i. e. no detectable expression
Supplementary files format and content: processed data for individual biological replicates: tab-delimited text files listing log2 CPM values per gene across all samples; CPM values of each biological replicate were subjected to log2 transformation; entries with "0" values had no CPM values, i. e. no detectable expression

source_name: Small intestine

extract_protocol:
Total RNA was isolated using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany)
Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit/TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 (Illumina) and subjected to 2x151 bp paired-end sequencing on a Illumina Novaseq 6000 sequencing device at approximately 50 million reads per library.

value: Small intestine

value: Intestinal organoid

value: Sox11 wildtype; Apc-/-, KrasG12D/+, Trp53R172H/+


title: TN_Naive, H3K27ac, Day32, rep4

first: Shelley

description: Library name: Naive_P14_Day32_H3K27ac_Rep4_S12

value: P14 CD8 T cells


title: E-hASCs, replicate 2, scRNAseq

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学


title: 1.0 ug-AgCitrate_5

description:
Library name: GRC371B-21_S19
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-21_S19

value: Retina


title: TN_Naive, H3K27ac, Day32, rep2

description: Library name: Naive_P14_Day32_H3K27ac_Rep2_S10


title: E-hASCs, replicate 1, scRNAseq

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学


title: Sox11_WT_KO_RNA_seq, 1308-TKA, Par, solvent, biol. replicate 2

description:
1308Par_Solv2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2

value: Solvent


title: 1.0 ug-AgCitrate_4

description:
Library name: GRC371-6_S11
column name in Partek_GRC371_Normalized_counts.csv:GRC371-6_S11


title: Sox11_WT_KO_RNA_seq, 1308-TKA, Par, TGF-β1, biol. replicate 1

description:
1308Par_TGF1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: TN_Naive, H3K27ac, Day32, rep1

description: Library name: Naive_P14_Day32_H3K27ac_Rep1_S9

value: Splenocytes


title: 1.0 ug-AgCitrate_3

description:
Library name: GRC371-46_S16
column name in Partek_GRC371_Normalized_counts.csv:GRC371-46_S16


title: I-hASCs, replicate 3, scRNAseq

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学

source_name: hASCs obtained from infants

value: infant


title: TN_Naive, H3K27ac, Day30, rep4

description: Library name: Naive_P14_Day30_H3K27ac_Rep4_S4


title: Sox11_WT_KO_RNA_seq, 1308-TKA, NT2, TGF-β1, biol. replicate 2

description:
1308NT2_TGF2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2


title: I-hASCs, replicate 2, scRNAseq

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学


title: TN_Naive, H3K27ac, Day30, rep3

description: Library name: Naive_P14_Day30_H3K27ac_Rep3_S3


title: 1.0 ug-AgCitrate_2

description:
Library name: GRC371-21_S24
column name in Partek_GRC371_Normalized_counts.csv:GRC371-21_S24


title: I-hASCs, replicate 1, scRNAseq

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学


title: 1.0 ug-AgCitrate_1

description:
Library name: GRC371-19_S20
column name in Partek_GRC371_Normalized_counts.csv:GRC371-19_S20


title: Sox11_WT_KO_RNA_seq, 1308-TKA, NT2, TGF-β1, biol. replicate 1

description:
1308NT2_TGF1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: Sox11_WT_KO_RNA_seq, 1308-TKA, Par, solvent, biol. replicate 1

description:
1308Par_Solv1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: TN_Naive, H3K27ac, Day30, rep2

description: Library name: Naive_P14_Day30_H3K27ac_Rep2_S2


title: FLASHseq, CFAP20tagged, rep2

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: RNAseI digested RNA

data_processing:
Paired-end reads are merged with bbmerge.sh v. 38.72 with the following command: bbmerge.sh in1={R1.fastq.gz} in2={R2.fastq.gz} out={merged.fastq.gz} outu1={unmerged.R1.fastq.gz} outu2={unmerged.R2.fastq.gz} ihist={histogram.txt} adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACAATCTC adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGG --mininsert=1. Short inserts (<20nt, after removal of the UMI and internal index) were removed with bbduk.sh v. 38.72 bbduk.sh in={infile} out={out} minlen=34. The UMI was removed from the reads and written to the header with UMI_tools v. 1.0.0: umi_tools extract --bc-pattern=NNNXXXXXXNNNNN -I {IN.fastq.gz} --3prime --stdout={OUT.fastq.gz}, followed by separation of replicates with flexbar v. 3.5.0: flexbar -r INPUT.fastq.gz -b barcodes.fa --barcode-trim-end RTAIL --barcode-error-rate 0.2 --zip-output GZ. Reads were aligned first to abundant RNAs such as tRNAs, snRNA, snoRNA and rRNAs, then to the genome with bowtie2 v. 2.3.5: bowtie2 --no-unal --un-gz -L 16 --very-sensitive-local -x bt2_index -U fastq_in.fastq.gz -o bam_out.bam. Unaligned reads were remapped to the genome with bbmap.sh v. 38.72 to capture spliced reads: bbmap.sh -Xmx50G in={fastq_in} out={bam_out} outu={unmapped_out} ref={reference.fa} sam=1.3 mappedonly=t mdtag=t trimreaddescriptions=t nodisk. Finally, PCR duplicates were removed using UMI-tools: umi_tools dedup -I in_bam -S out_bam --spliced-is-unique --soft-clip-threshold 3 --output-stats={stats}. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (Benaglia T, 2009). A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise. Read-density profiles around TSS coordinates were defined using the AnnotatePeaks.pl tool of HOMER, using the default normalization to 10 million reads. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Assembly: hg38
Supplementary files format and content: FLASHseq_200KbWindow_Above3kb_MinGap2kb_CFAP20KO_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: FLASHseq_200KbWindow_Above3kb_MinGap2kb_CFAP20KO_rep2.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: FLASHseq_200KbWindow_Above3kb_MinGap2kb_CFAP20tagged_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: FLASHseq_200KbWindow_Above3kb_MinGap2kb_CFAP20tagged_rep2.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO expressing FLASH-BIO-CFAP20

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

extract_protocol:
Cells on 15 cm dishes were washed with 6mL ice-cold PBS and UV-crosslinked with 0.199 mJ/cm2 UV-C light, after which cells were pelleted, snap-frozen in liquid nitrogen and stored at -80˚C until use. Pellets are resuspended in 600µL 1xNLB with protease inhibitors, briefly sonicated with a Bioruptor water bath sonicator (30s ON, 30s OFF, 5 cycles at 4˚C). Lysates were then centrifuged at 20k rcf for 10 minutes at 4˚C to remove insoluble material. Supernatant is transferred to a fresh tube with 25µL MyONE C1 streptavidin beads (Thermo), and incubated in the cold-room with end-to-end rotation for 60 minutes. Beads are washed once with high salt buffer, once with non-denaturing buffer and treated with 0.02U/µL RNaseI (Thermo) in 100µL non-denaturing buffer for 3 minutes at 37˚C, and immediately placed on ice to stop the reaction. Beads are then washed once with high salt buffer, and once with non-denaturing buffer. RNA-ends were repaired with T4 PNK, after which barcoded s-oligos were ligated with T4 RNA Ligase 1 for 90 minutes at 25˚C. The 3’-phosphate at the 3’-end of s-oligos were removed with rSAP, beads are then washed once with lithium dodecyl sulfate-buffer, once with protein lysis buffer, once with high salt buffer, and finally with non-denaturing buffer. The RNA was released with proteinase K treatment, and purified using Oligo Clean and Concentrator columns (Zymo).
Reverse transcription was carried out with SuperScript III, samples were then treated with RNaseH (NEB) in order to phosphorylate the 5’-end of the cDNA molecule. After a final round of purification with Oligo Clean and Concentrator columns (Zymo), the cDNA was circularised with CircLigaseII (Lucigen) and amplified with Q5 polymerase (NEB). PCR products were purified with SPRI beads, QCed with Bioanalyzer and subjected to high-throughput sequencing.
FLASH-seq (Ilik et al., 2020)

tag: genome used_to_map_to


title: TN_Naive, H3K27ac, Day30, rep1

city: Philadelphia

last: Berger

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Naive_P14_Day30_H3K27ac_Rep1_S1


title: Sox11_WT_KO_RNA_seq, 1308-TKA, NT2, solvent, biol. replicate 2

description:
1308NT2_Solv2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2


title: 1.0 ug-AgBPEI_3

description:
Library name: GRC371B_28
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_28

value: 1.0 ug-AgBPEI


title: 1.0 ug-AgBPEI_4

description:
Library name: GRC371B_43
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_43


title: Sox11_WT_KO_RNA_seq, 1308-TKA, NT2, solvent, biol. replicate 1

description:
1308NT2_Solv1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: FLASHseq, CFAP20tagged, rep1

description: RNAseI digested RNA

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO expressing FLASH-BIO-CFAP20


title: FLASHseq, CFAP20KO, rep2

description: RNAseI digested RNA

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO


title: 1.0 ug-AgBPEI_2

description:
Library name: GRC371B-15_S16
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-15_S16


title: Bile duct cells, DDC diet, Tomato negative

first: Wei-Chien

last: Yuan

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to mm10 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Assembly: mm10
Supplementary files format and content: Fragment files contain the chromosome (column 1) and Tn5-corrected coordinates (columns 2-3) of insertion sites around transposed fragments as well as the cellular barcode they correspond to (column 4).
Supplementary files format and content: BigWig files contain smoothed signal information for each sample for visualization in a genome viewer.

source_name: Biliary epithelial cells

extract_protocol:
Nuclei isolation was performed using the Omni-ATAC protocol for isolation of nuclei from frozen tissues. Nuclei were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1X PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (parts of the SureCell ATAC-Seq Library Prep Kit - 17004620, Bio-Rad). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

value: Biliary epithelial cells

value: DDC diet


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO56, TGF-β1, biol. replicate 2

description:
1308KO56_TGF2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2

value: Sox11 Kockout; Apc-/-, KrasG12D/+, Trp53R172H/+


title: Reprogrammed bile duct cells, DDC diet, Tomato positive

source_name: Hepatocyte derived reprogramming cells

value: Hepatocyte derived reprogramming cells


title: 1.0 ug-AgBPEI_1

description:
Library name: GRC371B_47
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_47

source_name: Retina


title: Hepatocytes, DDC diet

source_name: Hepatocytes

value: Hepatocytes

value: Normal chow


title: FLASHseq, CFAP20KO, rep1

description: RNAseI digested RNA


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO56, TGF-β1, biol. replicate 1

description:
1308KO56_TGF1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1

value: Small intestine