title: PBMC from pediatric SLE donor 4

description:
Library name: SLE_4
10x Genomics


title: PBMC from pediatric SLE donor 3

status: Public on Sep 05 2025

type: SRA

city: New York

first: Simone

last: Caielli

state: NY

address: 413 E 69th Street

department: Department of Pediatrics

country: USA

institute: Weill Cornell Medicine

description:
Library name: SLE_3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Single cell demultiplxing and gene counting were performed using 10X Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs were thawed and resuspended in RPMI containing 10% FBS for cell number and viability assessment.
Live PBMCs were enriched using the Dead Cell Removal Kit (Miltenyi) and resuspended in PBS with 1% BSA for scRNAseq processing using Chromium Single Cell 5’ V2 gene expression (10x Genomics). The samples were divided into four batches and loaded into different lanes of a 10x chip, aiming for a cell recovery of 10,000 per sample, following the manufacturer’s instructions. Paired-end sequencing was performed on the Illumina NovaSeq 6000.

tag: tissue

value: PBMC

tag: subject status

value: pediatric SLE donor


title: hippocampus, 10CBD, long-term,5

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

library_source: transcriptomic

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Tissues were collected and immediately submerged in stayRNA™ (A&A Biotechnology) reagent. After 24 of cooling (4C), tissues were frozen at -80C until the time of RNA isolation. For RNA isolation, tissue scrapes (10-20 mg) were homogenized and used for RNA isolation with AllPrep DNA/RNA (Qiagen) kit. Following isolation, RNA was controlled for quality with the TapeStation4150 system and quantified.
Libraries were prepared using CORALL mRNA-Seq V2 (Lexogen) following standard protocol.
RNA-Seq, stranded

treatment_protocol: The experiment was conducted on C57BL/6J laboratory mice strain (n=48), divided into subgroups receiving CBD at doses of 0.2, 10, or 20 mg/kg of body weight, and a control group receiving placebo, administered for 2 (short-term) or 28 (long-term) days. CBD was administered once a day via intraperitoneal injection. RNA-Seq analysis of the hippocampus was conducted to identify transcriptomic alternations induced by CBD treatment in this brain structure.

value: hippocampus

tag: treatment

value: 10CBD, long-term


title: LA52_07A_KTC_18049FL-58Q-07V1

city: Stanford

first: Yuning

last: Tang

state: CA

address: 279 Campus Drive, Beckman Center

institute: Stanford University

description: Library name: LA52_07A

library_source: genomic

data_processing:
Tuba-seq Ultra NGS processing scripts convert read counts for each barcode-sgRNA into absolute cell numbers based on spike-in reads. Tumor metrics for each sgRNA, with clonal resolution, are calculated for log-normal mean, tumor number, and total tumor burden. Confidence intervals and p-values are determined using bootstrap resampling. For detailed information on the analysis, please refer to the "Quantification and Statistical Analysis" section in the Methods of the manuscript titled "Functional Mapping of Epigenomic Regulators Uncovers Coordinated Tumor Suppression by the HBO1 and MLL1 Complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1.
Assembly: sgRNA library sequences included in the processed data file
Supplementary files format and content: The processed file is in .csv format. It contains the sequence of each sgRNA and the calculated metrics for tumors initiated with each Lenti-U6-sgRNA-Epigenomics/Cre vector in KT;H11-LSL-Cas9 mice. 'X_percentile_relative' indicates the size of the tumors at the Xth percentile of the tumor size distribution relative to the tumor size at the same percentile of the sgInert tumor size distribution. 'X_percentile_2.5P' and 'X_percentile_97.5P' represent the 95% confidence intervals for the Xth percentile.

molecule: genomic DNA

source_name: Lung

extract_protocol:
The tissues were homogenized in 20 ml lysis buffer (100mM NaCl, 20mM Tris, 10mM EDTA, 0.5% SDS) with 200 μl of 20 mg/ml Proteinase K (Life Technologies, AM2544). Homogenized tissues were incubated at 55°C overnight.  Genomic DNA was extracted with phenol-chloroform (ThermoFisher Scientific, 15593049) or the Qiagen Puregene Kit (Qiagen, 158063) and precipitated with ethanol. Plasmid DNA extraction was performed following QIAGEN Plasmid Plus Midi Kit instructions
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Tuba-seqUltra library preparation" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1

value: Lung

tag: cell type

value: Total lung

tag: genotype

value: KTC

tag: batch


title: LA52_11_KTC_18049FL-58Q-11V1

description: Library name: LA52_11


title: hippocampus, 10CBD, long-term,6


title: PBMC from pediatric SLE donor 2

description:
Library name: SLE_2
10x Genomics


title: hippocampus, 20CBD, long-term,5

value: 20CBD, long-term


title: LA52_06_KTC_18049FL-58Q-06V1

description: Library name: LA52_06


title: hippocampus, 10CBD, long-term,4


title: hippocampus, 20CBD, long-term,4


title: LA52_20_KTC_18049FL-58Q-20V1

description: Library name: LA52_20


title: LA52_05_KTC_18049FL-58Q-05V1

description: Library name: LA52_05


title: PBMC from pediatric SLE donor 6

description:
Library name: SLE_6
10x Genomics


title: PBMC from pediatric SLE donor 1

description:
Library name: SLE_1
10x Genomics


title: LA52_04_KTC_18049FL-58Q-04V1

description: Library name: LA52_04


title: LA52_03_KTC_18049FL-58Q-03V1

description: Library name: LA52_03


title: hippocampus, 10CBD, long-term,3


title: LA52_02_KTC_18049FL-58Q-02V1

description: Library name: LA52_02


title: PBMC from Healthy donor 5

description:
Library name: HD_5
10x Genomics

value: Healthy donor


title: hippocampus, 10CBD, long-term,2


title: hippocampus, 10CBD, long-term,1


title: sgKat7 mouse ID MT2178

description: Bulk-ATACseq

data_processing:
Demultiplexed FASTQ files were mapped to the GRCm38/mm10 assembly of the Mus musculus genome as 2×36mers using Bowtie (Langmead et al. 2009) with the following settings: -v 2 -k 2 -m 1 --best --strata. Mitochondrial reads were filtered, and duplicate reads were removed using picard-tools (version 1.99).
Browser tracks generation, fragment length estimation, TSS enrichment calculations, and other analyses were carried out using custom-written Python scripts https:// github.com/georgimarinov/GeorgiScripts. The refSeq annotation was used for evaluation of enrichment around TSSs. Peak calling was carried out using MACS2 (Feng et al. 2012), with the following settings: -g mm -f BAMPE --to-large --keep-dup all --nomodel. Peaks were compared against the ENCODE set of “blacklisted” regions to filter out likely artifacts.
The processed peaks were merged via iterative summits analysis to identify high-confidence peaks (https://github.com/corceslab/ATAC_IterativeOverlapPeakMerging, R version 4.2.2) (Corces et al. 2018; Granja et al. 2021). The GRCm38/mm10 ENCODE blacklist regions were obtained from (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz). The iterative summits were converted to .saf files using bedops (v2.4.41), and peak counts were generated by the featureCounts function in subread (v2.0.3).
Differential peak analysis was performed separately using DESeq2
Peak annotation was carried out using annotatepeaks.pl in HOMER
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: bed

source_name: FACS sorted lung neoplastic cells

growth_protocol: All mice were on a C57BL/6 background and kept in standard condition with 12hour light/dark cycle and ad libitum access to food and water.

extract_protocol: OMNI-ATAC protocol PMID: 33606259

treatment_protocol: Intratracheal transduction in mouse

value: FACS sorted lung neoplastic cells

tag: cell line

value: Ex vivo primary cells (not cell line)

value: Kras driven lung neoplastic cells

value: Lenti-sgRNA/Cre (see title for sgRNA used)


title: LA52_01_KTC_18049FL-58Q-01V1

description: Library name: LA52_01


title: sgSafe23 mouse ID MT2258 (inert sgRNA control)

description: Bulk-ATACseq


title: LA52_09A_KT_18049FL-58Q-09V1

description: Library name: LA52_09A

value: KT


title: hippocampus, 0.2CBD, long-term,6

value: 0.2CBD, long-term


title: PBMC from Healthy donor 4

description:
Library name: HD_4
10x Genomics


title: PBMC from Healthy donor 1

description:
Library name: HD_1
10x Genomics


title: sgSafe23 mouse ID HC2589 (inert sgRNA control)

description: Bulk-ATACseq


title: sgKat7 mouse ID MT2169

description: Bulk-ATACseq


title: sgKat7 mouse ID MT2164

description: Bulk-ATACseq


title: sgKat7 mouse ID LA930

description: Bulk-ATACseq


title: PBMC from Healthy donor 2

description:
Library name: HD_2
10x Genomics


title: sgSafe23 mouse ID MT2242 (inert sgRNA control)

description: Bulk-ATACseq


title: PBMC from Healthy donor 3

description:
Library name: HD_3
10x Genomics


title: hippocampus, 0.2CBD, long-term,3


title: hippocampus, 0.2CBD, long-term,4


title: sgSafe14 mouse_ID MT2114 (inert sgRNA control)

description: Bulk-ATACseq


title: sgSafe23 mouse_ID HC2589 (inert sgRNA control)

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE9

description:
Library name: SLE9
10x Genomics

data_processing:
Illumina basecall files (*.bcl) were converted to fastqs using cellranger v3.0.2 which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to hg38 genome and transcriptome using the cellranger v3.0.2 pipeline, which generates a gene - cell expression matrix.
Assembly: GRCh38
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format. Rows correspond to features in the order provided in features.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

extract_protocol:
10% DMSO + 90% FBS. PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells exhibiting a viability rate less than 70% were excluded. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII.
12,000 single cells were loaded into one lane of a 10X Genomics Chromium [Controller, X], targeting 6,000 barcoded single cells. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version [3, 3.1] chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000  targeting 100,000 raw read pairs per cell.


title: hippocampus, 0.2CBD, long-term,2


title: sgSafe23 mouse_ID MT2252 (inert sgRNA control)

description: Bulk-ATACseq


title: sgSafe23 mouse_ID MT2261 (inert sgRNA control)

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE8

description:
Library name: SLE8
10x Genomics


title: sgPsip1 mouse_ID LA724

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE7

description:
Library name: SLE7
10x Genomics


title: sgPsip1 mouse_ID LA707

description: Bulk-ATACseq


title: sgPsip1 mouse_ID LA721

description: Bulk-ATACseq


title: sgKmt2a mouse_ID MT2256

description: Bulk-ATACseq


title: hippocampus, Control, long-term,6

value: Control, long-term


title: hippocampus, Control, long-term,5


title: hippocampus, 0.2CBD, long-term,5


title: sgKmt2a mouse_ID MT2329

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE6

description:
Library name: SLE6
10x Genomics


title: sgSafe23 mouse ID MT2252 (inert sgRNA control)

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE10

description:
Library name: SLE10
10x Genomics


title: sgKmt2a mouse_ID LA925

description: Bulk-ATACseq


title: hippocampus, Control, long-term,4


title: PBMC from pediatric SLE donor, SLE4

description:
Library name: SLE4
10x Genomics


title: sgMeaf6 mouse_ID MT2148

description: Bulk-ATACseq


title: PBMC from pediatric SLE donor, SLE5

description:
Library name: SLE5
10x Genomics


title: hippocampus, Control, long-term,3


title: Perturb-seq Amplicon library

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
Perturb-seq sgRNA Amplicon dataset from CRISPRa hepatocytes
RNA-757

data_processing:
*library strategy: Perturb-seq
The single-cell RNA-seq datasets were processed with 10x Genomics' Cell Ranger pipeline version 7.0.0 (Zheng et al., 2017) and mapped to a mouse genome mm39. For the perturb-seq library the Cell Ranger BAM file was subsequently then processed with CROP-seq analysis tools (Bock et al 2017) to map sgRNA reads from the unmapped reads in the BAM file and count sgRNA counts and UMIs.
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

source_name: G4 mESC line

extract_protocol:
A single cell suspension was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.
Amplicon sgRNA PCRs were performed for each of the 24 full length 10X cDNA samples of SAM ESCs transduced with the 475 sgRNA library, as previously described (Hill et al., 2018). Brieﬂy, 10 ng of full length 10X cDNA were used as starting material and each round of PCR ampliﬁcation with the primers described in Hill et al., 2018 (see also Table S6) was monitored by KAPA SYBR (KR0389) to avoid overcycling. After multiplexing, these enrichment sgRNA libraries were sequenced across two lanes of the Illumina Hiseq2500 Rapid Run, with 27 cycles for read 1, 267 cycles for read 2 and 8 cycles for i7 sample index.Indexed sequencing libraries were constructed using the reagents in the GemCode Single-Cell 30 Library Kit, following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) postligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantiﬁed by quantitative PCR (KAPA Biosystems Library Quantiﬁcation Kit for Illumina

treatment_protocol: Purified hepatocytes were transduced with either NTC sgRNA pools (containing NTC1 and NTC2 guides) or the pool of 122 target late-TR sgRNA lentiviral libraries by the spinfection method. In brief, the 20,000 cells were resuspended in 200μl of neutral embryonic hepatocyte medium; DMEM/F12 (Thermo, 11320074), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, 15140148), 0.5% HEPES (Merck, H0887-20ML), 55 μM b-mercaptoethanol (Thermo, 21985023), 0.1%BSA (SIGMA, A4503-10G), 0.01mg/ml Fibronectin (Corning, 356008), 5ng/ml mouse HGF (R&D, 2207-HG-025) and 3μM IWR-I (Merck, I0161), in the V-bottom 96-well low cell-binding plates (Sumitomo Bakelite, MS-9096V). The plates were centrifuged at 800G for 50 minutes at 22°C and placed in the cell culture incubator. 2 days later, the formed spheroids were transferred into the neutral embryonic hepatocyte medium supplemented with 1% Matrigel (Corning, 356230) and 10nM Insulin (Thermo, 41400045). 5 days later (7 days after transduction), the spheroids were dissociated by incubating with enzyme solution (KnockOut DMEM containing 2mg/ml Collagenase XI (MERCK), 2.55mg/ml DispaseII (Thermo), 0.05mg/ml DNaseI, 1mM CaCl2) at 37°C for 10 minutes, then stopped reaction by adding 4ml PBS (-). After centrifuge (180G, 1 minutes, at 4°C), the spheroids were resuspended into 1ml of 0.25% trypsin/EDTA solution and incubated at 37°C for 10 minutes. Obtained single cell suspension was centrifuged and resuspended in 0.6μM DAPI (Biolegend, 422801) containing FACS buffer. Viable and singlet mCherry-positive sgRNA integrated cells were FACS-sorted and applied for the single-cell RNA-seq analysis.

value: G4 mESC line


title: PBMC from pediatric SLE donor, SLE3

description:
Library name: SLE3
10x Genomics

value: PBMC


title: hippocampus, 0.2CBD, long-term,1


title: H3K36me3-AK58-spike_rep1

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

country: China

institute: Institute of Crop Sciences

description: Library name: H3K36me3-AK58-spike_rep1

data_processing:
For ChIP-seq data, quality control was conducted with fastp (v0.21.0), followed by read alignment to the wheat reference genome using Bowtie2 with default settings. Enriched regions were identified, and visualization files (BigWig) were generated using MACS2 and deepTools, respectively.
Assembly: ASM2589588v1
Supplementary files format and content: bigwig files of Chip-seq data

organism: Triticum aestivum

source_name: spike

extract_protocol:
Total RNA was extracted with TRIzolTM Reagent (Invitrogen; 15596-026), in ATAC-seq the nuclei were obtained using flow cytometry, in Chip-seq the wheat spike cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using an  focused-ultrasonicator (Covaris).
All library was constructed by Berry Genomics (Beijing, China), and sequenced with Illumina NovaSeq 6000. All sequencing data were 150bp paired-end reads.

value: spike


title: PBMC from pediatric SLE donor, SLE2

description:
Library name: SLE2
10x Genomics


title: H3K4me3-AK58-spike_rep1

description: Library name: H3K4me3-AK58-spike_rep1


title: H3K27me3-AK58-spike_rep2

description: Library name: H3K27me3-AK58-spike_rep2


title: PBMC from pediatric SLE donor, SLE1

description:
Library name: SLE1
10x Genomics


title: H3K27me3-AK58-spike_rep1

description: Library name: H3K27me3-AK58-spike_rep1


title: hippocampus, 20CBD, short-term,6

value: hippocampus

value: 20CBD, short-term


title: Atf3 KO Mes cells day 9 rep 3

city: 厦门

first: DC

last: JZY

address: 福建省厦门市厦门大学翔安校区

institute: 无

description:
Library name: Sample24
atf3-Day9-3

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9).
Adapter sequences and low-quality bases (Q < 20) were removed using Trimmomatic (v0.39).
Clean reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.2.1) with default parameters.
Gene-level read counts were obtained using featureCounts (v2.0.1).
Downstream analyses, including normalization and differential expression, were performed using DESeq2 (v1.30.1) in R (v4.1.0).
Assembly: mm10
Supplementary files format and content: All.fpkm.anno.txt

source_name: embryonic

growth_protocol: mESCs (AisenGene Bioscience) were cultured at 37 °C in 5% CO₂ in high-glucose Dulbecco's Modified Eagle Medium (DMEM; Hyclone) supplemented with 15% fetal bovine serum (FBS; BasalMedia), 100× penicillin-streptomycin (BasalMedia), 1 mM sodium pyruvate (GIBCO), 1 mM non-essential amino acids (GIBCO), 1 mM GlutaMAX (GIBCO), 0.1 mM β-mercaptoethanol (GIBCO), 1000 U/mL leukemia inhibitory factor (LIF; Millipore), 3 μM CHIR99021 (Sigma), and 1 μM PD0325901 (Sigma). Cells were maintained in an undifferentiated state by daily medium replacement and passaged every 3 days.

extract_protocol:
Total RNA was extracted from mESCs at days 0, 3, 6, and 9 of differentiation using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol. Poly(A)+ RNA was purified from total RNA using oligo(dT) beads, fragmented to ~200 bp, and reverse transcribed to synthesize first-strand cDNA. Second-strand cDNA was generated, followed by end repair, A-tailing, and ligation of Illumina sequencing adapters. Libraries were PCR-amplified (12 cycles) and sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Same as growth protocol.

value: embryonic

value: Stem cells

value: Mes cells

value: Atf KO

value: differentiation

value: Atf3 KO Mes cells day 9


title: H3K27AC-AK58-spike_rep1

description: Library name: H3K27AC-AK58-spike_rep1


title: sorted CD4+ T cells from pediatric SLE donor, SLE16

description:
Library name: SLE16
10x Genomics

extract_protocol:
Sorted live CD4+ T cells were resuspended in PBS supplemented with 0.2% non-acetylated BSA (Miltenyi) and viability was determined using trypan blue staining and measured on Countess FLII (Thermo-Fisher).
50,000 cells were loaded for capture on 10x Chromium system using the V3 single cell reagent kit for 3 prime RNA sequencing (10x Thechnologies). After capture and lysis, cDNAs from the cells were amplified as per 10x Chromium’s recommendations (10x Thechnologies. The amplified cDNAs were loaded on a single lane of NovaSeq 6000 for a depth of 50,000 reads per cell.

value: CD4+ T cells


title: ATAC-Zhongmei113-spike_rep1

description:
Library name: ATAC-Zhongmei113-spike_rep1
R105.pks.bedGraph

data_processing:
for ATAC-seq , quality control was conducted with fastp (v0.21.0), followed by read alignment to the wheat reference genome using Bowtie2 with default settings. Enriched regions were identified, and visualization files (bg) were generated using MACS2 and deepTools, respectively.
Assembly: ASM2589588v1
Supplementary files format and content: bedgraph files of  ATAC-seq.

extract_protocol:
ATAC-seq the nuclei were obtained using flow cytometry.
All library was constructed by Berry Genomics (Beijing, China), and sequenced with Illumina NovaSeq 6000. All sequencing data were 150bp paired-end reads.


title: Atf3 KO Mes cells day 9 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample23
atf3-Day9-2


title: sorted CD4+ T cells from pediatric SLE donor, SLE15

description:
Library name: SLE15
10x Genomics


title: ATAC-Tianxuan48hao-spike_rep1

description:
Library name: ATAC-Tianxuan48hao-spike_rep1
R104.pks.bedGraph


title: Atf3 KO Mes cells day 0 rep 3

address: 福建省厦门市厦门大学翔安校区

description: Library name: Sample1

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9).
Adapter sequences and low-quality bases (Q < 20) were removed using Trimmomatic (v0.39).
Clean reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.2.1) with default parameters.
Gene-level read counts were obtained using featureCounts (v2.0.1).
Downstream analyses, including normalization and differential expression, were performed using DESeq2 (v1.30.1) in R (v4.1.0).
Assembly: mm10
Supplementary files format and content: atf3-Day0-2_L1_1.fq.gz、atf3-Day0-2_L1_2.fq.gz


title: sorted CD4+ T cells from pediatric SLE donor, SLE14

description:
Library name: SLE14
10x Genomics


title: hippocampus, 20CBD, short-term,4


title: sgMeaf6 mouse_ID MT2180

description: Bulk-ATACseq

value: FACS sorted lung neoplastic cells

value: Ex vivo primary cells (not cell line)

value: Kras driven lung neoplastic cells


title: sgMeaf6 mouse_ID LA936

description: Bulk-ATACseq

value: Lenti-sgRNA/Cre (see title for sgRNA used)


title: ATAC-Shijiazhuang407-spike_rep2

description:
Library name: ATAC-Shijiazhuang407-spike_rep2
R103.pks.bedGraph


title: Atf3 KO Mes cells day 9 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample22
atf3-Day9-1


title: hippocampus, Control, long-term,2

value: Control, long-term


title: Atf3 KO Mes cells day 6 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample21
atf3-Day6-3

value: Atf3 KO Mes cells day 6


title: sorted CD4+ T cells from pediatric SLE donor, SLE13

description:
Library name: SLE13
10x Genomics

value: PBMC


title: hippocampus, 20CBD, short-term,2


title: ATAC-Shijiazhuang407-spike_rep1

description:
Library name: ATAC-Shijiazhuang407-spike_rep1
R103.pks.bedGraph

value: spike


title: hippocampus, Control, long-term,1

value: hippocampus


title: hippocampus, 20CBD, short-term,1

value: 20CBD, short-term


title: Atf3 KO Mes cells day 6 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample20
atf3-Day6-2

value: embryonic


title: sorted CD4+ T cells from pediatric SLE donor, SLE12

description:
Library name: SLE12
10x Genomics


title: ATAC-Jimei23-spike_rep2

description:
Library name: ATAC-Jimei23-spike_rep2
R102.pks.bedGraph


title: Atf3 KO Mes cells day 6 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample19
atf3-Day6-1

value: Stem cells


title: hippocampus, 10CBD, short-term,6

value: 10CBD, short-term


title: hippocampus, 20CBD, short-term,5


title: sorted CD4+ T cells from pediatric SLE donor, SLE10

description:
Library name: SLE10
10x Genomics


title: hippocampus, 10CBD, short-term,5


title: ATAC-Jimei23-spike_rep1

description:
Library name: ATAC-Jimei23-spike_rep1
R102.pks.bedGraph


title: ATAC-Beijing14hao-spike_rep1

description:
Library name: ATAC-Beijing14hao-spike_rep1
R106.pks.bedGraph


title: sorted CD4+ T cells from pediatric SLE donor, SLE9

description:
Library name: SLE9
10x Genomics


title: Atf3 KO Mes cells day 3 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample17
atf3-Day3-2

value: Mes cells

value: Atf KO

value: Atf3 KO Mes cells day 3


title: hippocampus, 20CBD, short-term,3


title: hippocampus, 10CBD, short-term,4


title: hippocampus, 10CBD, short-term,3


title: ATAC-AK58-spike_rep2

description:
Library name: ATAC-AK58-spike_rep2
AK58.pks.bedGraph


title: Atf3 KO Mes cells day 3 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample16
atf3-Day3-1

value: differentiation


title: ATAC-AK58-spike_rep1

description:
Library name: ATAC-AK58-spike_rep1
AK58.pks.bedGraph


title: sorted CD4+ T cells from pediatric SLE donor, SLE8

description:
Library name: SLE8
10x Genomics

value: CD4+ T cells


title: Atf3 KO Mes cells day 0 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample15
atf3-Day0-3

value: Atf3 KO Mes cells day 0


title: hippocampus, 10CBD, short-term,2


title: sorted CD4+ T cells from pediatric SLE donor, SLE7

description:
Library name: SLE7
10x Genomics


title: hippocampus, 10CBD, short-term,1


title: Atf3 KO Mes cells day 0 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample13
atf3-Day0-1


title: adult-wt1-repeat1

city: Hengyang City

first: Zhang

last: Ting

address: 28, West Changsheng Road Hengyang City,. Hunan Province, 421001, China.

institute: University of south China

description: Library name: sample7

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit: 0.5)
Trimmed sequence reads were mapped to GrC38/mm10 using CLC genomic benchwork(parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 lentg fraction: 0.8similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Drosophila melanogaster

source_name: adult whole fly

growth_protocol: Fly stocks and crosses were cultured at 25˚C on standard cornmeal food.

extract_protocol:
RNA was harvested using Rneasy mini pliu kit(Qiagen).1.3ug of total RNA wasused for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq LibraryPrepKit fllowing manufacturer's protocols.

value: adult whole fly

value: wildtype


title: sorted CD4+ T cells from pediatric SLE donor, SLE6

description:
Library name: SLE6
10x Genomics


title: sorted CD4+ T cells from pediatric SLE donor, SLE5

description:
Library name: SLE5
10x Genomics


title: adult-mut1-repeat2

description: Library name: sample6

value: mutant


title: Mes cells day 9 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample12
Wt-Day9-3

value: WT

value: Mes cells day 9


title: sorted CD4+ T cells from pediatric SLE donor, SLE11

description:
Library name: SLE11
10x Genomics

value: PBMC


title: hippocampus, 0.2CBD, short-term,6

value: hippocampus

value: 0.2CBD, short-term


title: sorted CD4+ T cells from pediatric SLE donor, SLE4

description:
Library name: SLE4
10x Genomics


title: Atf3 KO Mes cells day 3 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample18
atf3-Day3-3

value: embryonic


title: hippocampus, 0.2CBD, short-term,5


title: sorted CD4+ T cells from pediatric SLE donor, SLE3

description:
Library name: SLE3
10x Genomics


title: hippocampus, 0.2CBD, short-term,4


title: muscle-wt1-repeat2

description: Library name: sample4

source_name: adult muscle

value: adult muscle


title: sorted CD4+ T cells from pediatric SLE donor, SLE2

description:
Library name: SLE2
10x Genomics


title: Mes cells day 9 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample10
Wt-Day9-1

value: Stem cells


title: Mes cells day 6 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample9
Wt-Day6-3

value: Mes cells

value: Mes cells day 6


title: adult-wt1-repeat2

description: Library name: sample8


title: hippocampus, 0.2CBD, short-term,3


title: sorted CD4+ T cells from pediatric SLE donor, SLE1

description:
Library name: SLE1
10x Genomics


title: muscle-wt1-repeat1

description: Library name: sample3


title: Mes cells day 6 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample7
Wt-Day6-1


title: muscle-mut1-repeat2

description: Library name: sample2


title: sorted CD4+ T cells from healthy donor, HD10

description:
Library name: HD10
10x Genomics


title: hippocampus, 0.2CBD, short-term,2


title: Mes cells day 6 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample8
Wt-Day6-2


title: Mes cells day 3 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample6
Wt-Day3-3

value: Mes cells day 3


title: muscle-mut1-repeat1

description: Library name: sample1


title: hippocampus, 0.2CBD, short-term,1


title: Sample 60_9060

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Library name: Sample 60

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline, which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.38.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file compressed in .gz format includes information about all methylated positions on both strands, as well as columns for differential analysis and methylation annotations.
Library strategy: EM-seq

organism: Bos taurus

source_name: Blood

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
Enzymatic methyl-seq (EM-seq): DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines.

value: Blood

tag: condition

value: Diseased


title: hippocampus, Control, short-term,5

value: Control, short-term


title: Mes cells day 9 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample11
Wt-Day9-2

value: differentiation


title: sorted CD4+ T cells from healthy donor, HD8

description:
Library name: HD8
10x Genomics

value: CD4+ T cells


title: hippocampus, Control, short-term,6


title: sorted CD4+ T cells from healthy donor, HD9

description:
Library name: HD9
10x Genomics


title: Sample 59_8043

description: Library name: Sample 59


title: adult-mut1-repeat1

description: Library name: sample5

value: adult whole fly

value: mutant


title: sorted CD4+ T cells from healthy donor, HD7

description:
Library name: HD7
10x Genomics


title: Mes cells day 3 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample5
Wt-Day3-2

value: WT


title: hippocampus, Control, short-term,4


title: Mes cells day 3 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample4
Wt-Day3-1


title: sorted CD4+ T cells from healthy donor, HD6

description:
Library name: HD6
10x Genomics

value: PBMC


title: Mes cells day 0 rep 3

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample3
Wt-Day0-3

value: Mes cells day 0


title: hippocampus, Control, short-term,3

value: hippocampus


title: Sample 58_8031

description: Library name: Sample 58


title: sorted CD4+ T cells from healthy donor, HD5

description:
Library name: HD5
10x Genomics


title: Mes cells day 0 rep 2

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample2
Wt-Day0-2

value: embryonic


title: Sample 56_8010

description: Library name: Sample 56


title: Sample 57_8014

description: Library name: Sample 57


title: hippocampus, Control, short-term,1


title: Mes cells day 0 rep 1

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Sample1
Wt-Day0-1


title: hippocampus, Control, short-term,2


title: sorted CD4+ T cells from healthy donor, HD4

description:
Library name: HD4
10x Genomics


title: IFN-M1C1 IFN-M1C2

city: Jinan

first: zhang

last: shi

address: handong First Medical University

institute: handong First Medical University

description: MDMs-IFN

data_processing:
Crude nuclear pellets from macrophages were collected by centrifugation, resuspended in lysis buffer, and incubated on ice for 10 minutes. The chromatin was sheared by sonication at 4°C using a Bioruptor 300 at the highest setting for fifteen 1-minute cycles of 30 seconds on and 30 seconds off to generate chromatin fragments of approximately 200-400 bp in length. The soluble chromatin was diluted 1:10 with dilution buffer and precleared with protein A agarose beads. The precleared supernatant was incubated overnight at 4°C with antibodies against H3K27ac.
After washing, the immunoprecipitated material was eluted by adding 100 mM NaCl and incubating at 65°C for 12 hours. After removing protein and RNA, the enriched genomic DNA was extracted with phenol:chloroform:isoamyl alcohol followed by ethanol precipitation. The immunoprecipitated DNA was dissolved in water and analysed by ChIP-seq.
chip-seq reads were trimmed Trimmomatic V 0.33
chip-seq reads were aligned to hg38 or mm10 by Bowtie V1.1.2
Peaks were calling by MACS V 2.1.0
Assembly: hg38

source_name: Peripheral blood monocyte

extract_protocol:
RNA and DNA extraction and sequencing: Total RNA and DNA was extracted from the isolated CD14+ monocytes using TRIzol. After rRNA depletion, the remaining RNA and DNA was prepared for library preparation following Illumina's instructions. The resulting libraries were sequenced using Illumina Sequencing Technology on an Illumina Genome Analyzer II. ChIPseq for Flag, H3K4m1 and H3K4m3 DNA complexes.
Provide at least 1 ug (2 – 5 ug preferred) of total RNA at a concentration of at least 50 ng/ul (1 ug for Poly-A enrichment; 2 ug for ribo-depletion libraries; using less starting material is possible, but we can’t guarantee results). Please make sure that your RNA isolation protocol employs a DNAse digestion step or other means to remove DNA from the sample. On an agarose gel, DNA contamination will be visible as a smear of band of fragments considerably larger than the RNA (>10 kb).  To verify the purity of the RNA samples the 260/280 ratio should be between 1.8 and 2.1 and 260/230 ratio should be higher than 1.5.  Poly-A enrichment, ribo-depletion and strand specific library prep are among the commonly requested types of service (more technical details on this appear below). We suggest following the recommendations from Illumina – for human samples use total RNA with a bioanalyzer RIN score of 8 or better, for plant material RIN numbers can be lower and tissue-specific (this is mainly a function of the chloroplast content). Libraries for slightly degraded RNA samples should be prepared using ribo-depletion protocols. If possible please avoid RNA extraction protocols involving Trizol or related phenol containing reagents (silica column based kits are less likely to retain contaminants). If using Trizol, protocols that contain a column based cleanup (e.g. Direct-zol, TRIzolPlus) have to be used.  Please note that an additional column cleanup is mandatory for RNA samples isolated from PAXgene tubes or with PAXgene kits. RNA samples should be eluted in molecular biology grade water, always stored in a -80 degree freezer and shipped on dry ice.  All RNA samples require a Bioanalyzer sample QC (or equivalent).  Such QC traces can be submitted by the customers or we can run the QC  for a fee instead.
Provide at least 1 ug (2 – 5 ug preferred) of total RNA at a concentration of at least 50 ng/ul (1 ug for Poly-A enrichment; 2 ug for ribo-depletion libraries; using less starting material is possible, but we can’t guarantee results). Please make sure that your RNA isolation protocol employs a DNAse digestion step or other means to remove DNA from the sample. On an agarose gel, DNA contamination will be visible as a smear of band of fragments considerably larger than the RNA (>10 kb).  To verify the purity of the RNA samples the 260/280 ratio should be between 1.8 and 2.1 and 260/230 ratio should be higher than 1.5.  Poly-A enrichment, ribo-depletion and strand specific library prep are among the commonly requested types of service (more technical details on this appear below). We suggest following the recommendations from Illumina – for human samples use total RNA with a bioanalyzer RIN score of 8 or better, for plant material RIN numbers can be lower and tissue-specific (this is mainly a function of the chloroplast content). Libraries for slightly degraded RNA samples should be prepared using ribo-depletion protocols. If possible please avoid RNA extraction protocols involving Trizol or related phenol containing reagents (silica column based kits are less likely to retain contaminants). If using Trizol, protocols that contain a column based cleanup (e.g. Direct-zol, TRIzolPlus) have to be used.  Please note that an additional column cleanup is mandatory for RNA samples isolated from PAXgene tubes or with PAXgene kits. RNA samples should be eluted in molecular biology grade water, always stored in a -80 degree freezer and shipped on dry ice.  All RNA samples require a Bioanalyzer sample QC (or equivalent).  Such QC traces can be submitted by the customers or we can run the QC  for a fee instead.

value: Peripheral blood monocyte


title: Sample 54_8002

description: Library name: Sample 54


title: PVR,scRNAseq

city: Tianjin

first: ye

last: zhisheng

address: qixiangtai road no.22

institute: tianjin medical university general hospital

data_processing:
Raw FASTQ sequencing data was using CellRanger 3.0.1 for demutiplexing, barcoded processing and gene counting.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Eye

extract_protocol:
Total cells were extracted from lesions using trypsin (25200114, Thermo Fisher Scientific).
Construction of RNA-seq library was completed by Novogene company (Beijing,China).

value: Eye

value: PVR lesion

tag: strain


title: Sample 55_8009

description: Library name: Sample 55


title: sorted CD4+ T cells from healthy donor, HD3

description:
Library name: HD3
10x Genomics


title: MITO-1c-sIOs

city: Basel

first: Ilhan

middle: E

last: Acar

address: Klingelbergstrasse 48

department: BSSE

country: Switzerland

institute: ETH Zurich

data_processing:
Sequence reads were trimmed for adaptor sequences using cutadapt (v 4.0).
Reads were checked for overall quality and problems before and after trimming with FastQC (v0.11.9)
After FastQC, reads were aligned to the reference mouse genome using STAR (v 2.7.9a)
Aligned reads were counted with htseq-count (v 1.99.2) to create a count matrix for downstream analyses.
Assembly: mm10
Supplementary files format and content: raw_counts.xlsx

source_name: small intestine

extract_protocol:
RNA was extracted from cells using the RNeasy plus mini kit (QIAGEN) following the manufacture protocol, including adding β-mercaptoethanol to the lysis buffer.
RNA-seq libraries were prepared from extracted and enriched RNA using the Illumina Nextera XT DNA library preparation kit (Illumina, TG-131-2001).

value: small intestine

value: organoids

tag: group

value: MITO


title: sorted CD4+ T cells from healthy donor, HD1

description:
Library name: HD1
10x Genomics


title: IFN-M1B1 IFN-M1B2

description: MDMs-IFN


title: Sample 53_7146

description: Library name: Sample 53

value: Blood

value: Diseased


title: Sample 52_7139

description: Library name: Sample 52


title: IFN-M1A1 IFN-M1A2

description: MDMs-IFN


title: MITO-1-sIOs


title: ACTB-4-sIOs

value: ACTB


title: Sample 51_7095

description: Library name: Sample 51


title: Creatine-2

city: Zhengzhou

first: Xiaojun

last: Zhou

state: Henan

address: 100 Lianhua Street

department: College of Bioengineering

institute: Henan University of Technology

description: Library name: sample4

data_processing:
For analysis of RNA-seq results, RNA-seq reads quality was evaluated using FastQC (v0.11.9, https:// www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the human genome GRCh38 by Hisat2 (v2.2.1) with default parameters.
FeatureCounts were used to summary raw counts from bam files
Differential genes' expression were performed by DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Extract total RNA from cell samples and assess the concentration and purity using the Nanodrop2000. Evaluate the integrity of the RNA through agarose gel electrophoresis. The RNA Integrity Number (RIN) is determined using an Agilent2100. For constructing a single library, a minimum of 1 µg of RNA is required, with a concentration of at least 50 ng/µL and an OD260/280 ratio between 1.8 and 2.2. 1.5μg of total RNA was used for the construction of sequencing libraries.
The RNA library for sequencing was meticulously prepared in accordance with the manufacturer's guidelines using the TruSeq™ RNA Sample Preparation Kit.

value: CRC cells

value: Creatine


title: LPS-M1C1 LPS-M1C2

description: MDMs-LPS


title: Creatine-1

description: Library name: sample3


title: LPS-M1B1 LPS-M1B2

description: MDMs-LPS


title: ACTB-3-sIOs


title: Ctrl-2

description: Library name: sample2

value: Ctrl


title: Sample 50_7059

description: Library name: Sample 50


title: LPS-M1A1 LPS-M1A2

description: MDMs-LPS


title: ACTB-2-sIOs


title: sorted CD4+ T cells from healthy donor, HD2

description:
Library name: HD2
10x Genomics

value: CD4+ T cells


title: M0C1 M0C2

description: MDMs-PBS


title: ACTB-1-sIOs


title: Sample 48_7025

description: Library name: Sample 48


title: GFP-4-sIOs

value: GFP


title: M0A1 M0A2

description: MDMs-PBS


title: M0B1 M0B2

description: MDMs-PBS


title: BCap37 tumor, TM, 2

city: Wuxi

first: Junjie

last: Yan

address: No. 20 Qianrong Road

institute: Jiangsu Institute of Nuclear Medicine

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tumor

value: human breast cancer

value: WT

value: TM


title: BCap37 tumor, TM, 3


title: Sample 47_7022

description: Library name: Sample 47


title: Sample 46_7014

description: Library name: Sample 46


title: BCap37 tumor, TM, 1


title: GFP-3-sIOs


title: GFP-2-sIOs


title: GFP-1-sIOs


title: BCap37 tumor, LM, 3

value: LM


title: Sample 45_6121

description: Library name: Sample 45


title: Sample 44_6101

description: Library name: Sample 44


title: BCap37 tumor, LM, 2


title: DPP4-4-sIOs


title: Ctrl-1

description: Library name: sample1


title: Sample 43_6100

description: Library name: Sample 43


title: Sample 49_7040

description: Library name: Sample 49


title: DPP4-3-sIOs


title: Sample 42_6050

description: Library name: Sample 42


title: BCap37 tumor, G, 3

value: Ga


title: DPP4-2-sIOs

value: small intestine


title: Sample 41_6043

description: Library name: Sample 41


title: BCap37 tumor, G, 2


title: DPP4-1-sIOs

value: organoids


title: BCap37 tumor, G, 1


title: BCap37 tumor, saline, 3

value: Saline


title: Sample 39_5139

description: Library name: Sample 39

value: Blood


title: Sup_kidney of METTL3-cKO Models mice Replicate 2

type: RNA

city: Hefei

first: Bingbing

last: Hou

state: China

address: No. 218 Jixi Road, Hefei 230032, China

institute: Department of Urology, First Affiliated Hospital of Anhui Medical University

description:
raw data file:
cKO-METTL3-3.txt
Biological replicate 2 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-3(Sup,Normalized)

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

scan_protocol: the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

source_name: SUP kidney (METTL3 knockout)

label_protocol: The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol.

growth_protocol: Mice were housed in animal facility room that is always maintained at 18-24 ℃ and at 30-50% humidity. Ad libitum access to food and water was provided to mice at all times.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.The total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.

treatment_protocol: For establishment of the CaOx nephrocalcinosis model, male mice were injected intraperitoneally either with glyoxalate (200 μl) at 100 mg/kg or saline daily for 7days

tag: Sex

value: male

tag: age

value: 6-8 weeks

value: kidney

value: METTL3 knockout

value: glyoxylate

tag: rip antibody

value: none (input)


title: Young Day 5 post resection, replicate 5

city: Bethesda

first: Olivier

last: Duverger

state: MD

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a custom GRCm38.vM11 mouse genome that was modified to include common mouse transgenes, ERCCs and SIRVs using STAR v2.5.2a in single-pass mode with the --quantMode GeneCounts parameter.
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a GRCm38.vM11 genome annotation GTF which included common mouse transgenes, ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38.vM11
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Bone callus from young skeletally immature mice 5 days post rib resection

extract_protocol:
Composite tissue (bone and intercostal muscle) was dissected from the rib cage at different stages of rib regeneration (baseline, D0, D2, D5, D14) and snap frozen. Frozen tissue was ground using a mortar and pestle kept in liquid nitrogen. Powdered frozen tissue was immediately transferred to a clear tube and total RNA was extracted using TriPure Isolation Reagent (Sigma-Aldrich) followed by PureLink™ RNA Mini Kit (Thermo Fisher Scientific).
Library preparation was performed according to the manufacturer’s instructions for the Illumina TruSeq stranded library kit. The libraries were then pooled and sequenced on separate runs on a NovaSeq 6000 sequencer (Illumina) on 150bp paired-end mode.

value: 7 weeks

value: not applicable

value: Wild Type


title: IP_kidney of METTL3-cKO Models mice Replicate 3

description:
raw data file:
cKO-METTL3-4.txt
Biological replicate 3 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-4(IP,Normalized)

source_name: IP kidney (METTL3 knockout)

value: Affinity purified anti-m6A rabbit polyclonal antibody (Synaptic Systems, 202003)


title: BCap37 tumor, saline, 2

value: tumor

value: human breast cancer

value: WT


title: Sup_kidney of METTL3-cKO Models mice Replicate 3

description:
raw data file:
cKO-METTL3-4.txt
Biological replicate 3 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-4(Sup,Normalized)


title: IP_kidney of METTL3-cKO Models mice Replicate 1

description:
raw data file:
cKO-METTL3-2.txt
Biological replicate 1 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-2(IP,Normalized)


title: IP_kidney of METTL3-cKO Models mice Replicate 2

description:
raw data file:
cKO-METTL3-3.txt
Biological replicate 2 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-3(IP,Normalized)


title: Young Day 5 post resection, replicate 4

value: Bone callus from young skeletally immature mice 5 days post rib resection


title: BCap37 tumor, LM, 1

value: LM


title: Sup_kidney of METTL3-cKO Models mice Replicate 1

description:
raw data file:
cKO-METTL3-2.txt
Biological replicate 1 of 3. kidney of METTL3-cKO Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
cKO-METTL3-2(Sup,Normalized)


title: Sample 38_5116

description: Library name: Sample 38

value: Diseased


title: Sup_kidney of WT Models mice Replicate 3

description:
raw data file:
WTM3.txt
Biological replicate 3 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM3(Sup,Normalized)

source_name: SUP kidney


title: Sample 37_5098

description: Library name: Sample 37

value: Blood


title: Young Day 5 post resection, replicate 2


title: BCap37 tumor, saline, 1

value: Saline


title: Sup_kidney of WT Models mice Replicate 1

description:
raw data file:
WTM1.txt
Biological replicate 1 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM1(Sup,Normalized)

value: male

value: 6-8 weeks


title: FRD1, ∆glpR, treatment, replicate 3

city: Birmingham

first: Jessica

last: Scoffield

state: Alabama

address: 1720 2nd Ave S

department: Microbiology

institute: The University of Alabama at Birmingham

data_processing:
Reads were mapped to the P. aeruginosa reference genome GCF_000006765.1 using RNA STAR
Determination of read counts and normalization were performed using featureCounts
Assembly: GCF_000006765.1
Supplementary files format and content: tabular file with counts for each sample

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: P. aeruginosa cultures were grown in 2mL of SCFM2 +/- tobramycin at 37oC shaking and 250 rpm.

extract_protocol:
Pellets were resuspended in Trizol and cells were lysed using a BeadBlaster24, pelleting debris after bead beating. RNA was extracted from the lysate using the Zymo Research Direct-zol RNA MiniPrep kit using spin columns and DNAse digestion.
Performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices.

treatment_protocol: Culture tubes receiving treatment were prepared with 5 μg/mL tobramycin prior to inoculation with P. aeruginosa.

value: bacterial cells

value: glpR knockout

value: 5 μg/mL tobramycin


title: Young Day 2 post resection, replicate 4

source_name: Bone callus from young skeletally immature mice 2 days post rib resection

value: 7 weeks


title: Sample 40_6030

description: Library name: Sample 40


title: FRD1, ∆glpR, treatment, replicate 2


title: Sample 35_5057

description: Library name: Sample 35


title: Young Day 2 post resection, replicate 3

value: Bone callus from young skeletally immature mice 2 days post rib resection

value: not applicable


title: Young Day 5 post resection, replicate 3

value: Wild Type


title: Sample 34_5055

description: Library name: Sample 34


title: INS-1E cells, IL-1βlow + CYT, biol rep 3

city: Pilar

first: Marcelo

middle: Javier

last: Perone

state: Buenos Aires

address: Av. Juan Domingo Perón 1500

country: Argentina

institute: Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral

description: Library name: Sample12

data_processing:
Analyses were conducted in RStudio (R version 4.3.3) using Bioconductor packages. Raw sequencing reads underwent quality control using FastQC (version v0.11.9) to assess read quality. Preprocessing, including adapter trimming and filtering of low-quality reads was performed using the rfastp package (version 1.12.0)
The rat reference genome (mRatBN7.2, assembly GCF_015227675.2) was downloaded from NCBI and used to build a reference index with the Rsubread package (version 2.16.1). This index was subsequently used for read alignment.
Read quantification was carried out with the featureCounts function from the Rsubread package, using the Rattus norvegicus gene annotation file (mRatBN7.2 GTF). The resulting count matrix was exported for further statistical analysis.
Assembly: mRatBN7.2, assembly GCF_015227675.2
Supplementary files format and content: Raw counts are provided in a comma-separated values (CSV) file, with genes in rows and samples in columns.

organism: Rattus norvegicus

growth_protocol: The rat β-cell line INS-1E was cultured at 37 °C in a humidified atmosphere containing 5% (vol./vol.) CO2 in complete RPMI 1640 culture medium [11 mM glucose, 10% (vol./vol.) heat-inactivated fetal bovine serum (FBS), penicillin (50 IU/ml), streptomycin (50 μg/ml), L-glutamine (2 mmol/l), 2-mercaptoethanol (50 μmol/l), HEPES (10 mmol/l) and sodium pyruvate (1 mmol/l)].

extract_protocol:
Total RNA was extracted from INS-1E cells using TRIzol reagent (Thermo Fisher Scientific, Carlsbad, CA, USA) following the manufacturer's instructions.
RNA sequencing libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina), following manufacturer's protocols.

treatment_protocol: INS-1E cells were conditioned with IL-1β 10 pg/ml for 72h (IL-1βlow), with fresh cytokine added every 24h without replacing the culture media. Then, the culture media was renewed, and cells were challenged with a proinflammatory cytokine mixture (CYT: IL-1β 100 pg/ml + IFN-g 5 ng/ml) for 16h.

value: insulinoma beta cell

value: IL-1β 10 pg/ml for 72h; IL-1β 100 pg/ml + IFN-γ 5 ng/ml for 16h


title: Young Day 2 post resection, replicate 2


title: FRD1, ∆glpR, treatment, replicate 1


title: Sample 33_5034

description: Library name: Sample 33


title: FRD1, ∆glpR, no treatment, replicate 3


title: INS-1E cells, CYT, biol rep 3

description: Library name: Sample11

value: WT

value: IL-1β 100 pg/ml + IFN-γ 5 ng/ml for 16h


title: IP_kidney of WT Models mice Replicate 2

description:
raw data file:
WTM2.txt
Biological replicate 2 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM2(IP,Normalized)

source_name: IP kidney

value: kidney

value: glyoxylate

value: Affinity purified anti-m6A rabbit polyclonal antibody (Synaptic Systems, 202003)


title: Young Day 2 post resection, replicate 1


title: IP_kidney of WT Models mice Replicate 1

description:
raw data file:
WTM1.txt
Biological replicate 1 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM1(IP,Normalized)


title: Young Day 14 post resection, replicate 4

source_name: Bone callus from young skeletally immature mice 14 days post rib resection


title: INS-1E cells, IL-1βlow, biol rep 3

description: Library name: Sample10

value: IL-1β 10 pg/ml for 72h


title: Sample 31_1098

description: Library name: Sample 31

value: Blood

value: Diseased


title: FRD1, ∆glpR, no treatment, replicate 2

value: bacterial cells


title: FRD1, ∆glpR, no treatment, replicate 1

value: glpR knockout


title: Sample 32_3020

description: Library name: Sample 32


title: INS-1E cells, untreated, biol rep 3

description: Library name: Sample9

value: untreated


title: FRD1, wildtype, treatment, replicate 3

value: wildtype

value: 5 μg/mL tobramycin


title: Sample 30_5067

description: Library name: Sample 30

value: Controls


title: Young Day 14 post resection, replicate 3

value: Bone callus from young skeletally immature mice 14 days post rib resection

value: 7 weeks

value: not applicable

value: Wild Type


title: Young Day 14 post resection, replicate 2


title: IP_kidney of WT Models mice Replicate 3

description:
raw data file:
WTM3.txt
Biological replicate 3 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM3(IP,Normalized)

value: male

value: 6-8 weeks

value: WT


title: Sample 29_5043

description: Library name: Sample 29


title: INS-1E cells, IL-1βlow + CYT, biol rep 2

description: Library name: Sample8

value: insulinoma beta cell

value: IL-1β 10 pg/ml for 72h; IL-1β 100 pg/ml + IFN-γ 5 ng/ml for 16h


title: FRD1, wildtype, treatment, replicate 2


title: Young Day 14 post resection, replicate 1


title: INS-1E cells, CYT, biol rep 2

description: Library name: Sample7

value: IL-1β 100 pg/ml + IFN-γ 5 ng/ml for 16h


title: Sample 28_5031

description: Library name: Sample 28

value: Blood


title: INS-1E cells, IL-1βlow, biol rep 2

description: Library name: Sample6

value: IL-1β 10 pg/ml for 72h


title: FRD1, wildtype, treatment, replicate 1

value: bacterial cells


title: Young Day 0 post resection, replicate 4

source_name: Bone callus from young skeletally immature mice at the same day of rib resection (Day 0)


title: FRD1, wildtype, no treatment, replicate 3


title: Young Day 0 post resection, replicate 3

value: Bone callus from young skeletally immature mice at the same day of rib resection (Day 0)


title: FRD1, wildtype, no treatment, replicate 2

value: wildtype


title: Sample 26_4098

description: Library name: Sample 26


title: Sample 25_4080

description: Library name: Sample 25


title: Young Day 0 post resection, replicate 2


title: INS-1E cells, IL-1βlow + CYT, biol rep 1

description: Library name: Sample4


title: INS-1E cells, CYT, biol rep 1

description: Library name: Sample3


title: Young Day 0 post resection, replicate 1


title: Sample 36_5058

description: Library name: Sample 36

value: Diseased


title: FRD1, wildtype, no treatment, replicate 1


title: Young baseline, replicate 6

source_name: Composite tissue (bone, bone marrow, and intercoastal muscle) from young skeletally immature mice collected after rib resection


title: Sup_kidney of WT Models mice Replicate 2

description:
raw data file:
WTM2.txt
Biological replicate 2 of 3. kidney of WT Models mice, mice treated with intraperitoneal injection of glyoxylate for 7d
WTM2(Sup,Normalized)

value: kidney

value: glyoxylate

value: none (input)


title: Sample 23_4050

description: Library name: Sample 23

value: Controls


title: PA01, ∆glpR, treatment, replicate 2

value: glpR knockout

value: 5 μg/mL tobramycin


title: INS-1E cells, IL-1βlow, biol rep 1

description: Library name: Sample2


title: INS-1E cells, untreated, biol rep 1

description: Library name: Sample1

value: untreated


title: Young baseline, replicate 4

value: Composite tissue (bone, bone marrow, and intercoastal muscle) from young skeletally immature mice collected after rib resection

value: 7 weeks

value: not applicable

value: Wild Type


title: PA01, ∆glpR, treatment, replicate 3


title: Sample 22_4047

description: Library name: Sample 22

value: Blood


title: Sample 27_5008

description: Library name: Sample 27


title: Young baseline, replicate 3


title: INS-1E cells, untreated, biol rep 2

description: Library name: Sample5

value: insulinoma beta cell

value: WT


title: Sample 21_4046

description: Library name: Sample 21


title: PA01, ∆glpR, no treatment, replicate 3

value: bacterial cells


title: PA01, ∆glpR, no treatment, replicate 2


title: Lung RNA-seq from SCID mouse treated with Tsc1-null EVs, sample 1353

city: Abilene

first: Magdalena

last: Karbowniczek

state: TX

address: 1718 Pine Street

department: Immunotherapeutics and Biotechnology

institute: Texas Tech University Health Sciences Center

description: Library name: 1353-MT

data_processing:
First, the sequencing reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
Gene expression levels were then estimated with RSEM v1.2.15. The gene expression data was normalized using the TMM (trimmed mean of M-values) method.
Differentially expressed genes were identified using the edgeR program, with genes showing a p-value of less than 0.05 and a fold change greater than 1.5 being considered significant
GO enrichment analysis was performed using Goseq, and pathway analysis was carried out using Kobas.
Assembly: mm10
Supplementary files format and content: TMM_allSamples.csv

source_name: lung

growth_protocol: E15.5 mouse embryo neural tube (NT) derived cells were grown in 2D culture on plates using 15% EV-free FBS DMEM/F12 media. The media was supplemented with 20 ng/ml EGF, 20 ng/ml bFGF, 20 ng/ml IGF, 1% B-27, 1% N2 supplement, and 1% penicillin/streptomycin. The cells were incubated at 37°C with 5% CO2 until they reached approximately 80% confluence. For specific 2D culture experiments, cells were plated at equal numbers in DMEM medium containing 10% FBS depleted of EV by standard ultracentrifugation. The cell lines were routinely tested for mycoplasma.

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen)
The sequencing was performed on an Illumina platform, producing Paired-End reads. The raw reads were trimmed and have a sequence length ranging from 50-151 bp. The quality scores were encoded using the Sanger / Illumina 1.9 standard.

treatment_protocol: Labeled CD9+CD63+CD81+ EVs, derived from either Tsc1-null or wild type E15.5 mouse embryo neuronal progenitors, were injected into the tail vein of female SCID mice. Forty-eight hours after the EV injection, the mice received an intravenous (i.v.) injection of 0.5x10^6 rat ELT3 cells. The metastatic burden was then assessed 72 hours later by measuring the amount of rat DNA in the lungs of the mice.

value: lung

value: MT


title: Lung RNA-seq from SCID mouse treated with Tsc1-null EVs, sample 1352

description: Library name: 1352-MT


title: Lung RNA-seq from SCID mouse treated with Tsc1-null EVs, sample 1351

description: Library name: 1351-MT


title: Sample 24_4072

description: Library name: Sample 24


title: Old Day 5 post resection, replicate 4

source_name: Bone callus from old skeletally mature mice 5 days post rib resection

value: > 10 months


title: Sample 19_4035

description: Library name: Sample 19

source_name: Blood


title: PA01, ∆glpR, no treatment, replicate 1


title: Old Day 5 post resection, replicate 3

value: Bone callus from old skeletally mature mice 5 days post rib resection


title: Lung RNA-seq from SCID mouse treated with WT EVs, sample 1350

description: Library name: 1350-WT


title: PA01, wildtype, treatment, replicate 3

value: wildtype


title: Sample 17_4001

description: Library name: Sample 17

value: Controls


title: Sample 18_4033

description: Library name: Sample 18


title: Lung RNA-seq from SCID mouse treated with WT EVs, sample 1348

description: Library name: 1348-WT


title: PA01, wildtype, treatment, replicate 2


title: Old Day 5 post resection, replicate 2


title: Old Day 5 post resection, replicate 1


title: PA01, ∆glpR, treatment, replicate 1

value: glpR knockout


title: PA01, wildtype, treatment, replicate 1

value: 5 μg/mL tobramycin


title: 06_KO3_RNAseq

first: Anjali

last: Dhall

address: 37 Convent Drive

department: DTB

institute: NCI

description:
Library name: Sample6
Read Length 2x150 bp

data_processing:
STAR aligner used for qualtification of read counts for RNA-seq data
Assembly: mm39
Supplementary files format and content: Read count expression matrix.

source_name: spleen

growth_protocol: Fresh murine primary splenocytes

extract_protocol:
Total RNA was extracted by TRIzol (Invitrogen), and then purification using PureLink RNA Mini Kit (Cat No. 12183018A; Invitrogen) with DNase treatment (QIAGEN). 2100 Expert (Agilent) was used for RNA quality and quantity assessment. RIN (the RNA Integrity Number) of all samples were above 9.0.
Library was prepared for splenocytes using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB #E7400) and NEBNext Ultra II Directional RNA Library Prep Kit from Illumina (NEB #E7760). For PCR amplification (13 cycles) NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB, E6440) were used. Dual index (101x8x8x101) pair-end sequencing of the final 750 pM library was performed using the Illumina NextSeq2000 P2 Reagents (200cycles) on the Illumina NextSeq2000 instrument. The total number of reads was 550M. Biotinylated, target-specific oligos combined with Ribo-Zero ribosomal RNA (rRNA) removal beads were used for the removal of rRNA library construction for splenocytes. Illumina TruSeq Stranded Total RNA Library Preparation kit and paired-end sequencing of 6 pooled RNA-seq samples was performed on HiSeq. Following RNA fragmentation and cleavage, small pieces are converted to complementary DNA (cDNA) with reverse transcriptase and random primers and, consequently 2nd strand cDNA synthesis with DNA Polymerase I and RNase H. A standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a sequencing ready library from the double-strand cDNA as input. After that, purified product was quantified using qPCR followed by cluster generation and pair-end sequencing on HiSeq.

value: spleen

value: Total splenocytes

value: Murine total splenocyes


title: Sample 16_3135

description: Library name: Sample 16


title: Old Day 2 post resection, replicate 4

source_name: Bone callus from old skeletally mature mice 2 days post rib resection

value: not applicable


title: Sample 15_3131

description: Library name: Sample 15


title: Old Day 2 post resection, replicate 3

value: Bone callus from old skeletally mature mice 2 days post rib resection

value: Wild Type


title: Young baseline, replicate 2

value: Composite tissue (bone, bone marrow, and intercoastal muscle) from young skeletally immature mice collected after rib resection

value: 7 weeks


title: Sample 20_4044

description: Library name: Sample 20

value: Blood


title: 05_KO2_RNAseq

description:
Library name: Sample5
Read Length 2x150 bp


title: Sample 13_3081

description: Library name: Sample 13


title: PA01, wildtype, no treatment, replicate 3

value: bacterial cells


title: PA01, wildtype, no treatment, replicate 1


title: 03_WT3_RNAseq

description:
Library name: Sample3
Read Length 2x150 bp

value: Wild-type


title: Sample 12_3078

description: Library name: Sample 12


title: Old Day 2 post resection, replicate 1

value: > 10 months


title: 02_WT2_RNAseq

description:
Library name: Sample2
Read Length 2x150 bp


title: CC125, Chlamydomonas reinhardtii, repeat 3

city: Shanghai

first: Fanchen

last: Wang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

description: Library name: CC125-3

data_processing:
The sequencing data derived RNA-seq were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Hisat2 (v2.2.1). Transcript assembling and expression quantification were performed by used of StringTie (v2.2.3).
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: gtf files: tab-delimited text files include gene imformation and FPKM values for each Sample.

organism: Chlamydomonas reinhardtii

growth_protocol: The C. reinhardtii strains (CC125 and CC5325) were cultured mixotrophically in TAP medium on a rotary shaker at 25 °C, with a light intensity of 20 μmol photons m-2∙s-1.

extract_protocol:
Total RNA was extracted using Trizol (Sangon) according to the manufacturer's instructions. rRNA was depleted from total RNA using the Ribo-off rRNA Depletion Kit (Vazyme).
RNA library construction was then performed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme), following the manufacturer's instructions. The libraries were assessed using the Agilent 2100 Bioanalyzer and sequenced on the Illumina platform using 150 bp paired-end sequencing.

value: WT


title: Old Day 2 post resection, replicate 2


title: 04_KO1_RNAseq

description:
Library name: Sample4
Read Length 2x150 bp


title: Old Day 14 post resection, replicate 3

source_name: Bone callus from old skeletally mature mice 14 days post rib resection


title: Lung RNA-seq from SCID mouse treated with WT EVs, sample 1349

description: Library name: 1349-WT

value: lung


title: Sample 11_3067

description: Library name: Sample 11

value: Controls


title: Sample 10_3059

description: Library name: Sample 10


title: CC125, Chlamydomonas reinhardtii, repeat 2

description: Library name: CC125-2


title: lens epithelium,cx50ko,biorep3

city: Berkeley

first: Xiaohua

last: Gong

address: 695 Minor Hall

department: School of Optometry

institute: University of California, Berkeley

description:
10X Genomics
combinedko-barcodes.tsv
combinedko-features.tsv
combinedko-matrix.mtx

data_processing:
Sequencing data was processed through the 10x Genomics Cell Ranger (Cell Ranger Version 2.2.0) Analysis Pipelines. Reads were aligned to the mouse reference genome GRCm38.3 (mm10) and were quantified using the mouse reference index provided by 10x genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lens Epithelium

extract_protocol:
The lens epithelial cells were isolated based on a previously published procedure. 36 Mice at 1- month-old were used for lens primary epithelial cell culture. Briefly, lenses were dissected from enucleated eyeballs of CO2-euthanized mice in Advanced DMEM/F-12 media (Gibco Invitrogen, Cat# 12634-010, Waltham, MA). The lenses were cleaned by removing the surrounding tissues and were incubated in 0.05% Trypsin-EDTA (Gibco, Cat# 25300-054) at 37°C for 10 minutes. Lens capsules were peeled off and transferred into 2 U/mL dispase (Sigma, Cat# D4693) for 5 minutes at 37°C. Then equal volumes of 10TrypLE (Gibco, Cat# A12177- 02) were added for 10 minutes. The suspended epithelial cells from lens capsules were spun down at 1000 rpm for 5 minutes, and the cell pellet was resuspended in PBS.
Collected lens epithelial cells pooled from three WT littermates and four Cx50KO littermates were used for single-cell RNA sequencing in the Functional Genomics Laboratory (FGL) at UC Berkeley. Single-cell cDNA libraries were prepared from the isolated cells using the Chromium Single Cell 3′ System according to the manufacturer’s instructions. The protocol from 10x employed v3.1 chemistry with the following modification was used: the cell suspension was directly added to the reverse transcription master mix, along with the appropriate volume of water to achieve the  7 approximate cell capture target. Completed libraries were sequenced on Illumina 100PE Collected lens epithelial cells pooled from three WT littermates and four Cx50KO littermates were used for single-cell RNA sequencing in the Functional Genomics Laboratory (FGL) at UC Berkeley. Single-cell cDNA libraries were prepared from the isolated cells using the Chromium Single Cell 3′ System according to the manufacturer’s instructions. The protocol from 10x employed v3.1 chemistry with the following modification was used: the cell suspension was directly added to the reverse transcription master mix, along with the appropriate volume of water to achieve the  7 approximate cell capture target. Completed libraries were sequenced on Illumina 100PE HiSeq4000 to produce 10x recommended reads.

value: Lens Epithelium

value: lens epithelial cells

value: connexin50 knockout


title: 01_WT1_RNAseq

description:
Library name: Sample1
Read Length 2x150 bp

value: spleen

value: Total splenocytes


title: Old Day 14 post resection, replicate 2

value: Bone callus from old skeletally mature mice 14 days post rib resection

value: not applicable


title: Old Day 14 post resection, replicate 4

value: Wild Type


title: Old Day 14 post resection, replicate 1


title: Sample 14_3119

description: Library name: Sample 14


title: CC125, Chlamydomonas reinhardtii, repeat 1

description: Library name: CC125-1


title: lens epithelium,cx50ko,biorep2


title: lens epithelium,cx50ko,biorep1


title: Old Day 0 post resection, replicate 4

source_name: Bone callus from old skeletally mature mice at the same day of rib resection (Day 0)


title: Sample 8_2092

description: Library name: Sample 8


title: CC5325KO, Chlamydomonas reinhardtii, repeat 2

description: Library name: CC5325KO-2

value: Dnmt1 KO


title: Sample 7_2074

description: Library name: Sample 7


title: lens epithelium,wildtype,biorep4

description:
10X Genomics
combinedwt-barcodes.tsv
combinedwt-features.tsv
combinedwt-matrix.mtx


title: Old Day 0 post resection, replicate 3

value: Bone callus from old skeletally mature mice at the same day of rib resection (Day 0)


title: Sample 6_2063

description: Library name: Sample 6

value: Blood


title: CC5325, Chlamydomonas reinhardtii, repeat 3

description: Library name: CC5325-3


title: Old Day 0 post resection, replicate 2


title: Sample 9_2105

description: Library name: Sample 9


title: CC5325, Chlamydomonas reinhardtii, repeat 2

description: Library name: CC5325-2


title: lens epithelium,wildtype,biorep2


title: lens epithelium,wildtype,biorep1


title: Sample 4_2043

description: Library name: Sample 4


title: CC5325KO, Chlamydomonas reinhardtii, repeat 3

description: Library name: CC5325KO-3


title: Sample 5_2051

description: Library name: Sample 5


title: Old Day 0 post resection, replicate 1


title: CC125, Chlamydomonas reinhardtii, DEA treatment, repeat 2

description: Library name: CC125_DEA2

data_processing:
The sequencing data derived from WGBS were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Bismark (v0.24.2). Deduplication and methylation extraction were performed by used of deduplicate_bismark and bismark_methylation_extractor (both sub-tools in Bismark).
By taking the average of the values for each site, we merged the data from 2 experimental replicates to obtain the processed data.
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: bed files: tab-delimited text files include 5mC or 5gmC sites information and modification level for each Sample.

extract_protocol:
Total DNA was isolated using the CTAB method.
The treated DNA was then for sequencing library preparation, following the manufacturer’s protocol (Vazyme). Briefly, DNA libraries were generated by 3' adapter ligation, extension, 5' adapter ligation and library amplification.


title: CC5325, Chlamydomonas reinhardtii, repeat 1

description: Library name: CC5325-1


title: Old baseline, replicate 4

source_name: Composite tissue (bone, bone marrow, and intercoastal muscle) from old skeletally mature mice collected after rib resection


title: Old baseline, replicate 3

value: Composite tissue (bone, bone marrow, and intercoastal muscle) from old skeletally mature mice collected after rib resection


title: CC125, Chlamydomonas reinhardtii, DEA treatment, repeat 1

description: Library name: CC125_DEA1


title: Perturb-seq scRNA library

city: Berlin

first: Alexandre

last: Magalhaes

address: Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

description:
Perturb-seq dataset from CRISPRa hepatocytes
RNA-756

data_processing:
*library strategy: Perturb-seq
The single-cell RNA-seq datasets were processed with 10x Genomics' Cell Ranger pipeline version 7.0.0 (Zheng et al., 2017) and mapped to a mouse genome mm39. For the perturb-seq library the Cell Ranger BAM file was subsequently then processed with CROP-seq analysis tools (Bock et al 2017) to map sgRNA reads from the unmapped reads in the BAM file and count sgRNA counts and UMIs.
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

source_name: G4 mESC line

extract_protocol:
A single cell suspension was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.
Amplicon sgRNA PCRs were performed for each of the 24 full length 10X cDNA samples of SAM ESCs transduced with the 475 sgRNA library, as previously described (Hill et al., 2018). Brieﬂy, 10 ng of full length 10X cDNA were used as starting material and each round of PCR ampliﬁcation with the primers described in Hill et al., 2018 (see also Table S6) was monitored by KAPA SYBR (KR0389) to avoid overcycling. After multiplexing, these enrichment sgRNA libraries were sequenced across two lanes of the Illumina Hiseq2500 Rapid Run, with 27 cycles for read 1, 267 cycles for read 2 and 8 cycles for i7 sample index.Indexed sequencing libraries were constructed using the reagents in the GemCode Single-Cell 30 Library Kit, following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) postligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantiﬁed by quantitative PCR (KAPA Biosystems Library Quantiﬁcation Kit for Illumina

value: G4 mESC line


title: Old baseline, replicate 2

value: > 10 months


title: Sample 2_1126

description: Library name: Sample 2


title: CC5325KO, Chlamydomonas reinhardtii, DEA treatment, repeat 2

description: Library name: CC5325KO_DEA2


title: lens epithelium,wildtype,biorep3


title: Sample 1_1100

description: Library name: Sample 1


title: Adult liver 10x Genomics

data_processing:
The single-cell RNA-seq datasets were processed with 10x Genomics' Cell Ranger pipeline version 7.0.0 (Zheng et al., 2017) and mapped to a mouse genome mm39
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

source_name: Liver

growth_protocol: "8-week-old : C57BL/6 mice were euthanized by the cervical dislocation and 24-gauge intravenous catheter (BD) was inserted into the portal vein. The inferior vena cava was cut for the drainage of the circulation solutions. EGTA solution (Calcium-free Earle's balanced salt solution (EBSS; Thermo) supplemented with 0.5mM ethylene glycol-bis (β-aminoethyl ether) N, N, N',N'-tetra-acetic acid (EGTA) (Sigma)) was circulated by the peristaltic pump at 37 °C at a rate of 3.3ml/min for 8 minutes. Followingly, the Liberase solution (40μg/ml Liberase (MERCK) in the Ca/Mg-plus EBSS buffer (Thermo)) was circulated at 37 °C at a rate of 3.3ml/min for 9 minutes.The liver cells were released from the liver capsule in the cold PBS (-)() and harvested into the 50ml conical tube. The supernatant was discarded after the centrifuge (180G, 2 min, 22 °C) then the cell pellets were resuspended in 2ml of 0.25% Trypsin/EDTA (Thermo) and incubated in the water bath at 37 °C for 5 minutes. The reaction was stopped by giving the 3ml of wash buffer KnockOut DMEM containing 10%FCS and 0.05mg/ml DNaseI (Merck)), then cells were dissociated by gently pipetting with 5ml pipet. Cell suspension was filtrated through the 70μm strainer (MERCK). Cell suspension was transferred into the 15ml conical tube and centrifuged at 50G for 2 minutes at 4 °C, then the supernatant was discarded to remove the debris. The pellet was resuspended into the 5ml of wash buffer and centrifuged at 50G for 2 minutes at 4 °C and this step was repeated again, resulting in a total 3 times of washing. The cell pellet after 3rd time centrifuge was resuspended in 5ml of wash buffer and 10μl of the cell suspension was used for the cell counting. 10 million of cells were separated in the new tube and used for the following step. Cells were centrifuged at 180G 2 minutes at 4 °C and performed blocking by the normal mouse serum (Thermo) 5 minutes on ice. Then the cells were resupended in the 500ul of antibody solution (Ceacam1-APC:1/500, F4/80-Alexa488: 1/500) diluted in the FACS buffer and incubated on ice for 10 minutes. The cells were washed twice with FACS buffer and resuspended in the 0.5μlg/ml PI (Propidium Iodide, Biolegend) containing FACS buffer.  P10 neonatal liver: Mice were anesthetized and a 23-G butterfly needle was inserted into the left ventricle of the heart for the perfusion of the enzyme solution77. For the drainage, an incision was made on the right atrial appendage with scissors. Perfusion of the enzyme solution was done using the same solutions as an adult with a modified flow rate (EGTA solution: 3.3ml/min, 7 minutes, Liberase solution: 3.3ml/min 7 minutes).  P1 liver: Pups were euthanized by decapitation and the isolated liver tissue was gently minced into small pieces by forceps. The minced liver tissue was harvested and resuspended in 1ml of enzyme solution (KnockOut DMEM containing 2mg/ml Collagenase XI (MERCK), 2.55mg/ml DispaseII (Thermo), 0.05mg/ml DNaseI, 1mM CaCl2) in the 15ml conical tube. The tissue was incubated at 37°C for 10 minutes, then stopped reaction by adding 4ml PBS (-). After centrifuge (180G, 1 minutes, at 4°C), the cell pellet was resuspended into 2ml PBS (-) and centrifuged again (180G, 1 minutes, at 4°C). The cell pellet was resuspended into 1ml of 0.25% trypsin/EDTA solution and incubated at 37°C for 5 minutes. The reaction was stopped by adding 1ml of cold wash buffer and cell clumps are dissociated by pipetting with P1000 pipet. The cell suspension was centrifuged (50G, 2 min, 4°C) and resuspended in 1ml of cold wash buffer and pipetted to obtain single cell suspension. Cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 min, 4°C) to remove the debris. The resultant cell pellet was further resuspended into the red blood cell lysis buffer (Thermo) and incubated at room temperature for 5 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Ceacam1-APC:1/500.   E15.5 liver dissociation: Embryonic liver was isolated and minced into pieces by forceps. 2 liver tissues were harvested into the 15ml conical tube and resuspended into the 500μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 9 minutes. The reaction was stopped by adding a 1ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (50G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 minutes, 4°C). The resultant cell pellet was further resuspended into the red blood cell lysis buffer and incubated at room temperature for 3 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.

extract_protocol:
A single cell suspension was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.
A single cell suspension of individual cell lines was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.

value: Liver

tag: strain background

tag: time


title: CC5325KO, Chlamydomonas reinhardtii, DEA treatment, repeat 1

description: Library name: CC5325KO_DEA1


title: resected tumor samples from 15 mg dose cohort_5-Rep6

city: Cincinnati

first: Pankaj

middle: B.

last: Desai

state: OH

address: 231 Albert Sabin Way, Medical Science Building Suite 3303 (Desai Lab)

department: Pharmaceutical Sceinces

institute: University Of Cincinnati

description: Library name: PD18-8343A

data_processing:
The quality control of raw and aligned reads was performed using FastQC software
Differentially expressed genes were identified by fitting generalized linear model based on negative-binomial distribution of read counts as implemented in the edgeR Bioconductor package and FDR-adjusting p values.
Assembly: Sequence reads were aligned to the human reference genome (hg38) using the STAR aligner and the reads aligned to each known gene were counted based on the latest GENCODE definitions of gene features.
Supplementary files format and content: .xls files contain differential expression results comparing treated and control samples. Columns include name, gene ID, log2 fold change, adjusted p-value etc.
Supplementary files format and content: fastq.gz contain raw counts for each sample (R1 and R2)

source_name: resected tumor sample from 15 mg cohort - Replicate 6

extract_protocol:
The tumor tissue samples were stored in RNAlater™-ICE before being extracted with the mirVana miRNA Isolation Kit with total RNA extraction protocol to extract the total RNA.
The mRNA libraries were prepared, indexed, and pooled to obtain 50 to 100 million reads per sample. Library sequencing for 50 bp reads was performed using the Illumina HiSeq system.

value: Letrozole (15 mg)


title: P10 liver 10x Genomics


title: AM_RNA_329 rep3

data_processing:
RNA-seq data from liver samples of E11.5, E15.5, P1, P10, P30, and Adult stage mapped to a mouse genome mm39 using STAR aligner (Dobin et al., 2013). Count read tables were generated by the same program. Differential expression analysis was performed by the DEseq2 package (Love et al., 2014) in R version 4.2. (R-Core-Team, 2021). Differentially expressed genes were defined as having a fold-change bigger or equal to 1.5, an adjusted P-value smaller or equal to 0.01, and a minimum mean read count across the experiment samples of 50 reads.
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

growth_protocol: 8-week-old and P30 liver: C57BL/6 mice were euthanized by the cervical dislocation and 24-gauge intravenous catheter (BD) was inserted into the portal vein. The inferior vena cava was cut for the drainage of the circulation solutions. EGTA solution (Calcium-free Earle's balanced salt solution (EBSS; Thermo) supplemented with 0.5mM ethylene glycol-bis (β-aminoethyl ether) N, N, N',N'-tetra-acetic acid (EGTA) (Sigma)) was circulated by the peristaltic pump at 37 °C at a rate of 3.3ml/min for 8 minutes. Followingly, the Liberase solution (40μg/ml Liberase (MERCK) in the Ca/Mg-plus EBSS buffer (Thermo)) was circulated at 37 °C at a rate of 3.3ml/min for 9 minutes. The liver cells were released from the liver capsule in the cold PBS (-)() and harvested into the 50ml conical tube. The supernatant was discarded after the centrifuge (180G, 2 min, 22 °C) then the cell pellets were resuspended in 2ml of 0.25% Trypsin/EDTA (Thermo) and incubated in the water bath at 37 °C for 5 minutes. The reaction was stopped by giving the 3ml of wash buffer KnockOut DMEM containing 10%FCS and 0.05mg/ml DNaseI (Merck)), then cells were dissociated by gently pipetting with 5ml pipet. Cell suspension was filtrated through the 70μm strainer (MERCK). Cell suspension was transferred into the 15ml conical tube and centrifuged at 50G for 2 minutes at 4 °C, then the supernatant was discarded to remove the debris. The pellet was resuspended into the 5ml of wash buffer and centrifuged at 50G for 2 minutes at 4 °C and this step was repeated again, resulting in a total 3 times of washing. The cell pellet after 3rd time centrifuge was resuspended in 5ml of wash buffer and 10μl of the cell suspension was used for the cell counting. 10 million of cells were separated in the new tube and used for the following step. Cells were centrifuged at 180G 2 minutes at 4 °C and performed blocking by the normal mouse serum (Thermo) 5 minutes on ice. Then the cells were resupended in the 500ul of antibody solution (Ceacam1-APC:1/500, F4/80-Alexa488: 1/500) diluted in the FACS buffer and incubated on ice for 10 minutes. The cells were washed twice with FACS buffer and resuspended in the 0.5μlg/ml PI (Propidium Iodide, Biolegend) containing FACS buffer.  P10 neonatal liver: Mice were anesthetized and a 23-G butterfly needle was inserted into the left ventricle of the heart for the perfusion of the enzyme solution77. For the drainage, an incision was made on the right atrial appendage with scissors. Perfusion of the enzyme solution was done using the same solutions as an adult with a modified flow rate (EGTA solution: 3.3ml/min, 7 minutes, Liberase solution: 3.3ml/min 7 minutes).  P1 liver: Pups were euthanized by decapitation and the isolated liver tissue was gently minced into small pieces by forceps. The minced liver tissue was harvested and resuspended in 1ml of enzyme solution (KnockOut DMEM containing 2mg/ml Collagenase XI (MERCK), 2.55mg/ml DispaseII (Thermo), 0.05mg/ml DNaseI, 1mM CaCl2) in the 15ml conical tube. The tissue was incubated at 37°C for 10 minutes, then stopped reaction by adding 4ml PBS (-). After centrifuge (180G, 1 minutes, at 4°C), the cell pellet was resuspended into 2ml PBS (-) and centrifuged again (180G, 1 minutes, at 4°C). The cell pellet was resuspended into 1ml of 0.25% trypsin/EDTA solution and incubated at 37°C for 5 minutes. The reaction was stopped by adding 1ml of cold wash buffer and cell clumps are dissociated by pipetting with P1000 pipet. The cell suspension was centrifuged (50G, 2 min, 4°C) and resuspended in 1ml of cold wash buffer and pipetted to obtain single cell suspension. Cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 min, 4°C) to remove the debris. The resultant cell pellet was further resuspended into the red blood cell lysis buffer (Thermo) and incubated at room temperature for 5 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Ceacam1-APC:1/500.   E15.5 liver dissociation: Embryonic liver was isolated and minced into pieces by forceps. 2 liver tissues were harvested into the 15ml conical tube and resuspended into the 500μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 9 minutes. The reaction was stopped by adding a 1ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (50G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 minutes, 4°C). The resultant cell pellet was further resuspended into the red blood cell lysis buffer and incubated at room temperature for 3 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.   E11.5 liver dissociation: Embryonic liver was isolated and 3 to 4 liver tissues were harvested into the 15ml conical tube and resuspended into the 400μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 7 minutes. The reaction was stopped by adding a 0.8ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (180G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (180G, 2 minutes, 4°C). The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.

extract_protocol:
Harvested cells were homogenized, and total RNA was isolated using a RNeasy Plus Micro Kit (Qiagen).
The RNA-sequencing library was prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA BIOSYSTEMS) and sequenced on an Illumina HiSeq 4000 sequencer as 75-bp paired-end reads

value: Hepatocyte