title: Whole genome DNA-seq of CD4T-1 with RE1 fragmentation

description:
Library name: DNA-CD4T-RE1
CD4T cells genomic DNA extracted was digested using RE1 combination in this study and sequenced using Illumina HiSeq X Ten Platform
DNA_rez_500K_counts.tsv


title: HEK293T, ASXL1 Transfection 1-1304, rep 3

status: Public on Jul 14 2026

type: SRA

city: Los Angeles

first: Isabella

last: Lin

address: 615 Charles E Young Dr S

country: USA

institute: University of California Los Angeles

description:
Library name: HEK293T_1304_Rep3
HEK293T_star_featureCounts_GeneTable_final.csv

library_source: transcriptomic

data_processing:
Samples were demultiplexed after sequencing, and fastq sequencing files were processed using established pipelines in the Arboleda lab. Raw read quality, adaptor content, and duplication rates were assessed with FastQC v0.11.8.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e (3) with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 (4) from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene.
Differential expression analysis was completed using DESeq2 v1.24.0 (5).
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts generated using featureCounts

molecule: total RNA

organism: Homo sapiens

source_name: Human embryonic kidney

growth_protocol: Human embryonic kidney (HEK293T) and colorectal adenocarcinoma (Caco-2) were maintained in DMEM with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA extraction via RNeasy Plus Mini Kit (Qiagen, 74136)
All samples were then prepared with QIAseq FastSelect −rRNA HMR (Qiagen, 334386) and TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599)

treatment_protocol: Using Lipofectamine™ 3000, cells were transfected with 2.5ug of plasmid or mock. Transfected cells were incubated for 48 hours transfection.

tag: tissue

value: Human embryonic kidney

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: Transfection

tag: batch


title: P301S mouse,shControl,48h,biological replicate4

city: Godinne

first: Nicolas

last: Debortoli

address: avenue Docteur G. Thérasse, 1

country: Belgium

institute: CHU UCL Namur

description:
Library name: PM203-3
column in raw_counts_run1.txt: PM203-3

data_processing:
Trimming and quality filtering with fastp
Mapping on reference genome with STAR using STARlong mode
Mapping quality evaluation with QUALIMAP
Count table generated with featureCounts
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing the output of featureCounts.
Supplementary files format and content: Columns are: GeneID, Chr, Start, End, Strand, Length and one column per sample containing raw counts.

molecule: polyA RNA

organism: Mus musculus

source_name: mild spinal cord

growth_protocol: At the age of two months, mice were exposed to spinal cord surgery. Preoperative analgesia was administered via subcutaneous injections of buprenorphine (0.05 mg/kg; Vetergesic) and carprofen (5 mg/kg; Rycarfa). Anesthesia was induced by intraperitoneal administration of ketamine (120 mg/kg; Nimatek) and xylazine (8 mg/kg; Sedaxylan). Mice of contusion group underwent C5 laminectomy followed by 30kDynes contusion while sham were only exposed to laminectomy. Postoperative analgesia included a second injection of buprenorphine at 6 and 24 hours post-surgery, as well as additional carprofen administrations at 24 and 48 hours. Mice were finally sacrificed two days post surgery by anesthetic overdose followed by cold saline intracardiac injection.

extract_protocol:
Spinal cord samples were homogenized in 500 µL of TRIzol reagent (Invitrogen, 15596018) using a grinder device and incubated at room temperature for 5 min. Homogenates were centrifuged at 15,800 × g for 10 min at 4 °C, and the supernatant was transferred to a new tube. Chloroform (200 µL) was added, and samples were vortexed and incubated for 3 min at room temperature. Following centrifugation at 15,800 × g for 15 min at 4 °C, 300 µL of the aqueous phase was collected and mixed with an equal volume of 70% ethanol. The mixture was then applied to an RNA extraction column (High Pure RNA Tissue Kit, Roche Diagnostics, 12033674001), and RNA was purified according to the manufacturer’s instructions.
Direct cDNA Library Prep Kit (SQK-NBD114.96; ONT)

treatment_protocol: Spinal cord tissues were immediately frozen in liquid nitrogen and stored at −80°C until further processing.

value: mild spinal cord

value: sham C5 laminectomy


title: testis, control lineage, PFOS 0.02 mg/L, biol rep3

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: TCR3C

data_processing:
The reads were first preprocessed with fastp (v0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to generate normalized count data for all samples.
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: testis_normExpr_DESeq2.tsv: Normalized expression values obtained from DESeq2 for all samples in tab-delimited text-file

organism: Oryzias latipes

source_name: testis

extract_protocol:
Total RNA was extracted from the testes of the control and BPA lineage using the Quick RNA/DNA Miniprep Plus Kit (#D-7003, Zymo Research, CA, USA), following the manufacturer's instructions.
Transcriptome libraries were prepared by Novogene Corporation (CA, USA) using the NEBNext Ultra II RNA Kit, following the manufacturer's protocol.

value: testis

tag: lineage

value: Control

value: PFOS 0.02 mg/L


title: Whole genome DNA-seq of CD4T-1 with dsF fragmentation

city: Atlanta

first: Francesca

last: Storici

state: GA

address: 950 State Street Nw, Krone Engineering Biosystems Building

department: Biological Sciences

institute: Georgia Institute of Technology

description:
Library name: DNA-CD4T-dsF
CD4T cells genomic DNA extracted was digested using dsFragmenstase and sequenced using Illumina HiSeq X Ten Platform
DNA_rez_500K_counts.tsv

library_source: genomic

data_processing:
Ribose-map for ribose-seq, bowtie2 and featurecounts for RNA-seq, bismark for WGBS, bowtie2 for DNA-seq
Assembly: GrCh38
Supplementary files format and content: bigWig, bedGraph,counts and TPM matrix

molecule: genomic DNA

source_name: blood

growth_protocol: standard human cell growth protocol

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit (CAT# 69504) for DNA isolation, RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment, MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher)
ribose-seq for rNMP capture, WGS with KAPA Hyper Prep library preparation,  WGBS with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA), RNA-seq with PolyA Selection & NEBNext Ultra II Directional kit

treatment_protocol: ribose-seq for rNMP capture, RNA-seq, bisulfite-seq and whole genome DNA-seq

value: blood

value: RNase H2A wild-type


title: HEK293T, ASXL1 Transfection 1-1304, rep 2

description:
Library name: HEK293T_1304_Rep2
HEK293T_star_featureCounts_GeneTable_final.csv


title: testis, control lineage, PFOS 0.02 mg/L, biol rep2

description: Library name: TCR2C


title: P301S mouse,shControl,48h,biological replicate3

description:
Library name: PM203-2
column in raw_counts_run1.txt: PM203-2


title: Treat group, rep3

city: Beijing

first: sitong

last: su

address: West District, Majiapu China Rehabilitation Research Center, Fengtai District, Beijing

country: China

institute: School of Rehabilitation Medicine, Capital Medical University, Beijing, China

description:
Library name: treat3
Female T10 SCI rat with  spinal cord electrical stimulation, spinal cord tissue

data_processing:
1.Quality control and preprocessing: Raw reads were preprocessed using fastp (version 0.23.2) to remove adapter sequences, reads with ambiguous bases (N > 5 bp), low-quality reads (Phred quality score ≤ 20 exceeding 40%), and trimmed via sliding window (window size = 4 bp, average quality threshold = 20).
2.Read alignment: Clean reads were aligned to the Rattus norvegicus reference genome using HISAT2 (version 2.2.1) with default parameters. The reference genome index was prepared from the appropriate reference sequence obtained from Ensembl or NCBI at the time of analysis. Alignment results were stored in SAM format, which was subsequently converted to BAM format for downstream analysis.
Assembly: mRatBN7.2
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes fpkm values for each Sample

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
Total RNA was extracted from the tissue; the extracted products were analyzed using an Agilent 4150 TapeStation (Agilent Technologies, Inc., Santa Clara, CA, USA) to assess their size distribution and integrity.
mRNA was enriched from total RNA using Oligo(dT) magnetic beads to remove rRNA and other non‑coding RNAs. The mRNA was fragmented, reverse‑transcribed into cDNA, and ligated with adapters. After PCR amplification, the library was purified with magnetic beads, quantified, normalized, pooled, and converted into DNA nanoballs (DNBs) before sequencing.

value: Spinal cord

value: Whole tissue

value: Wild-type

value: T10 SCI+spinal cord electrical stimulation


title: HEK293T, ASXL1 Transfection 1-1304, rep 1

description:
Library name: HEK293T_1304_Rep1
HEK293T_star_featureCounts_GeneTable_final.csv


title: P301S mouse,shControl,48h,biological replicate2

description:
Library name: PM200b-4
column in raw_counts_run1.txt: PM200b-4


title: testis, control lineage, PFOS 0.02 mg/L, biol rep1

description: Library name: TCR1C


title: Treat group, rep2

description:
Library name: treat2
Female T10 SCI rat with spinal cord electrical stimulation, spinal cord tissue


title: P301S mouse,shControl,48h,biological replicate1

description:
Library name: PM200b-2
column in raw_counts_run1.txt: PM200b-2


title: Treat group, rep1

description:
Library name: treat1
Female T10 SCI rat with spinal cord electrical stimulation, spinal cord tissue


title: testis, BPA lineage, PFOS 0.002 mg/L, biol rep3

description: Library name: TBR3B

value: BPA

value: PFOS 0.002 mg/L


title: nonIBD_Appx-NIBD-002

city: Edmonton

first: John Maringa

last: Githaka

state: AB

address: 5-73 Medical Sciences Building, University of Alberta

department: Biochemistry

country: Canada

institute: University of Alberta

data_processing:
RNAseq analysis was performed using the GenPipes's ‘StringTie’ pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for raw count matrix
Supplementary files format and content: Excel file for DESeq2 analysis

source_name: Appendix

extract_protocol:
Total RNA was extracted from the appendix tissues collected from the cohort, 10 IBD (CD=8, UC=2) and 5 non-IBD (3 with FAP and 2 with AA), using a modified protocol based on the acid guanidinium-phenol-chloroform method for RNA sequencing (Table S1). 27,28 RNA quality and quantity were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) and NanoDrop 1000 Spectrophotometers (Thermo Fisher Scientific). Samples with an RNA integrity number (RIN) greater than 7.0 were selected for RNA library preparation and sequencing.
The Illumina Stranded mRNA Prep Kit (Illumina) was used for RNA library preparation from the total RNA (350 ng/μl) of each sample, employing the poly-A enrichment method. The quality and concentration of cDNA fragments (~350 bp) were evaluated prior to sequencing. RNA libraries were then paired-end sequenced using the Illumina NovaSeq PE100 platform at the Génome Québec Innovation Centre (QC, Canada).

value: Appendix

value: Appendix cells

tag: subject status

value: non-IBD


title: nonIBD_Appx-NIBD-001


title: P301S mouse,contusions,48h,biological replicate7

description:
Library name: PM205-2
column in raw_counts_run2.txt: PM205-2

value: mild spinal cord contusion


title: testis, BPA lineage, PFOS 0.002 mg/L, biol rep2

description: Library name: TBR2B


title: Model group, rep3

description:
Library name: model3
Female T10 spinal cord injury (SCI) rat, spinal cord tissue

value: T10 SCI model induction


title: nonIBD_Appx-AA-003


title: P301S mouse,contusions,48h,biological replicate6

description:
Library name: PM200-2
column in raw_counts_run2.txt: PM200-2

value: mild spinal cord


title: testis, BPA lineage, PFOS 0.002 mg/L, biol rep1

description: Library name: TBR1B

value: testis


title: Model group, rep2

description:
Library name: model2
Female T10 spinal cord injury (SCI) rat, spinal cord tissue


title: P301S mouse,contusions,48h,biological replicate5

description:
Library name: PM202-2
column in raw_counts_run1.txt: PM202-2


title: nonIBD_Appx-AA-002


title: testis, control lineage, PFOS 0.002 mg/L, biol rep3

description: Library name: TCR3B

value: Control


title: nonIBD_Appendix-IBD-FAB


title: P301S mouse,contusions,48h,biological replicate4

description:
Library name: PM203b-3
column in raw_counts_run1.txt: PM203b-3


title: Model group, rep1

description:
Library name: model1
Female T10 spinal cord injury (SCI) rat, spinal cord tissue


title: IBD_Appendix-IBD-008

value: IBD


title: testis, control lineage, PFOS 0.002 mg/L, biol rep2

description: Library name: TCR2B


title: testis, control lineage, PFOS 0.002 mg/L, biol rep1

description: Library name: TCR1B


title: P301S mouse,contusions,48h,biological replicate3

description:
Library name: PM203b-2
column in raw_counts_run1.txt: PM203b-2


title: IBD_Appendix-IBD-007


title: Control group, rep3

description:
Library name: control3
Female normal  Sprague‑Dawley rat, spinal cord tissue

value: No treatment


title: P301S mouse,contusions,48h,biological replicate2

description:
Library name: PM203b-1
column in raw_counts_run1.txt: PM203b-1


title: testis, BPA lineage, PFOS 0.0 mg/L, biol rep3

description: Library name: TBR3A

value: PFOS 0.0 mg/L


title: Control group, rep2

description:
Library name: control2
Female normal  Sprague‑Dawley rat, spinal cord tissue

value: Spinal cord


title: Control group,rep1

description:
Library name: control1
Female normal  Sprague‑Dawley rat, spinal cord tissue

value: Whole tissue


title: IBD_Appendix-IBD-006


title: H5/PBS-24-d14

status: Public on Jul 15 2026

type: protein

city: Irvine

first: Li

last: Liang

state: CA

address: 847 Health Sciences

institute: University of California Irvine

hyb_protocol: The microarray slides were probed with mouse sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. Mouse IgG  secondary antibody conjugated to AF647, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.

molecule: protein

source_name: Plasma

tag: days post prime immunization


title: P301S mouse,contusions,48h,biological replicate1

description:
Library name: PM200b-1
column in raw_counts_run1.txt: PM200b-1


title: testis, BPA lineage, PFOS 0.0 mg/L, biol rep2

description: Library name: TBR2A


title: RNA-seq of HEK293-WT replicate 2

description:
Library name: RNA-HEK293T-WT-2
RNA samples were extracted from HEK293T WT using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv

source_name: human embryonic kidney

value: human embryonic kidney

value: RNase H2A wild-type


title: IBD_Appendix-IBD-005


title: HUVEC + miR-1 + VEGF_3

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street, TAC S440, PO Box 208057

department: Internal Medicine, PCCSM section

institute: Yale University School of Medicine

description: Library name: LCSUSA-10854_V_miR_1_V20_3

data_processing:
For differential miRNA analysis: Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80). For isomiR analysis: MicroRNA sequencing data were pre-processed using the TrimGalore tool to remove adapter sequences and low-quality bases. Only reads between 16 and 30 nucleotides in length were retained for downstream analyses. miRNA isoforms (isomiRs) were mapped, quantified, and annotated using our previously published workflow based on the miRge 2.0 pipeline, which enables the identification of canonical miRNAs and multiple classes of isomiRs, including 5′- and 3′-shifted isoforms and single-nucleotide variants. Quality control and filtering steps were applied to retain high-confidence miR-1 isomiRs only prior to downstream analyses. A detailed description of the computational pipeline, filtering criteria, and isomiR annotation strategy is available in Distefano et al, Cancer Research, 2022.
Assembly: GRCh38/hg38
Supplementary files format and content: .xlsx file with genes in the rows and samples in the column
Supplementary files format and content: Excel file with TPM values or read counts

source_name: HUVEC

growth_protocol: HUVECs were purchased from Vascular Biology and Therapeutics tissue culture core facility at Yale Univeristy, cultured in M199 (Gibco) medium containing 20% FBS (heat inactivated, Gibco), 1% ECGS and 1% penicillin and streptomycin

extract_protocol:
Total RNA were isolated from cells harvested in Trizol using phenol-chlroform extraction protocol.
1ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA sample Prep Kits (Illumina, San Diego, USA)

treatment_protocol: HUVECs were transduced by miR-1 lentivitus for 36 hours, followed by serum-starved for 6 hours and traetment with VEGF (10ng/ml) or PBS for 24 hours

value: HUVEC

value: Primary endothelial cells

value: 24 hour


title: RNA-seq of HEK293-WT replicate 1

description:
Library name: RNA-HEK293T-WT-1
RNA samples were extracted from HEK293T WT using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv


title: testis, BPA lineage, PFOS 0.0 mg/L, biol rep1

description: Library name: TBR1A

value: BPA


title: HUVEC + miR-1 + VEGF_2

description: Library name: LCSUSA-10854_V_miR_1_V20_2


title: testis, control lineage, PFOS 0.0 mg/L, biol rep3

description: Library name: TCR3A


title: IBD_Appendix-IBD-004

value: Appendix

value: Appendix cells


title: RNA-seq of HEK293T-RNH2AKO-T3-8 replicate 2

description:
Library name: RNA-HEK293T-RNH2AKO-T3-8-2
RNA samples were extracted from RNASEH2A-KO (T3-8) cells using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv

value: RNase H2A KO (T3-8)


title: IBD_Appendix-IBD-003


title: HUVEC + miR-1 + VEGF_1

description: Library name: LCSUSA-10854_V_miR_1_V20_1


title: RNA-seq of HEK293T-RNH2AKO-T3-8 replicate 1

description:
Library name: RNA-HEK293T-RNH2AKO-T3-8-1
RNA samples were extracted from RNASEH2A-KO (T3-8) cells using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv


title: testis, control lineage, PFOS 0.0 mg/L, biol rep2

description: Library name: TCR2A


title: IBD_Appendix-IBD-002


title: HUVEC + miR-1 + no VEGF_3

description: Library name: LCSUSA-10854_V_miR_1_3


title: IBD_Appendix-IBD-0011


title: testis, control lineage, PFOS 0.0 mg/L, biol rep1

description: Library name: TCR1A


title: HUVEC + miR-1 + no VEGF_2

description: Library name: LCSUSA-10854_V_miR_1_2


title: RNA-seq of HEK293T-RNH2AKO-T3-17 replicate 1

description:
Library name: RNA-HEK293T-RNH2AKO-T3-17-1
RNA samples were extracted from RNASEH2A-KO (T3-17) cells using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv

value: RNase H2A KO (T3-17)


title: RNA-seq of HEK293T-RNH2AKO-T3-17 replicate 2

description:
Library name: RNA-HEK293T-RNH2AKO-T3-17-2
RNA samples were extracted from RNASEH2A-KO (T3-17) cells using RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment. Samples were sent to Admera Health for RNA library prep using PolyA Selection & NEBNext Ultra II Directional kit followed by sequencing with NovaSeq X Plus with 10B flow cell (PE150)
HEK_tpm.csv


title: IBD_Appendix-IBD-0010


title: HUVEC + miR-1 + no VEGF_1

description: Library name: LCSUSA-10854_V_miR_1_1


title: ribose-seq of hESC-H9 genomic DNA with dsF+RE1 fragmentation

description:
Library name: FS201
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

library_source: other

molecule: other

source_name: embryo

value: embryo


title: pCEC.3

city: Wenzhou

first: zhengbiao

last: zhu

state: Zhejiang

address: Ouhai District

department: The Affiliated Eye Hospital of Wenzhou Medical University

institute: Wenzhou Medical University

description: Library name: pCEC.3

data_processing:
RNA-seq data processing was performed in R using the edgeR package. Raw count data were imported to construct a DGEList object and normalized using the trimmed mean of M-values (TMM) method to account for library size differences. Normalized expression values were calculated as counts per million (CPM) and used for downstream analyses.
Assembly: mm10
Supplementary files format and content: csv file

source_name: Primary Corneal Endothelial Cells

growth_protocol: Primary CECs and primary NCCs were resuspended in DMEM supplemented with 10% FBS, 1% NEAA, and 1% L-glutamine, and maintained at 37°C in a 5% CO₂ atmosphere.

extract_protocol:
Total RNA was extracted using the E.Z.N.A Total RNA kit (Omega Bio-tek)
Sequencing libraries were prepared with the NEBNext Ultra RNA Library Prep Kit (NEB), clustered using the HiSeq PE Cluster Kit v4-cBot-HS (Illumina), and sequenced on an Illumina platform to generate 150-bp paired-end reads.

treatment_protocol: NCCs were plated at 1 × 10⁴ cells/well on gelatin-coated 24-well plates. At 80% confluence, medium was switched to differentiation medium: DMEM/F12 supplemented with 5% KSR, 1% NEAA, 0.1 mM 2-mercaptoethanol, and 5 μM SB431542 (Sigma-Aldrich). Medium was refreshed every 2 days. CEC-like clusters emerged by day 4; colonies were characterized on day 12.

value: Primary Corneal Endothelial Cells


title: pCEC.2

description: Library name: pCEC.2


title: Whole genome bisulfite-seq of CD4T-4

description:
Library name: BS-CD4T-4
The extracted DNA was fragmented by S-series Focused-ultrasonicator (Covaris, Woburn, MA) using the 200-bp target peak size protocol. Fragmented DNA was then size selected (200600 bp) with an Agencourt AMPure XP bead-based (#A63880, Beckman Coulter, Brea, CA) size selection protocol. The DNA end repair step was performed with End-It DNA End-Repair Kit (#ER81050, Epicentre, Madison, WI). After the end-repair step, A-tailing (#M0202, New England Biolabs, Ipswich, MA) and ligation steps were performed to ligate the methylated adaptors. Bisulfite treatment of gDNA was performed using the MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher). Purified gDNA was treated with CT conversion reagent in a thermocycler for 10 min at 98 C, followed by 2.5 h at 640 C. Bisulfite-treated DNA fragments remain single-stranded as they are no longer complementary. Low-cycle (48) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA) which can tolerate uracil residues. The final library fragments contain thymines and cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.

value: blood


title: IBD_Appendix-IBD-001

value: IBD


title: GWI model, GW chemicals-exposed mice

first: Kwang-Mook

last: Jung

address: 3105 Gillespie NRF

department: Anatomy&Neurobiology

institute: University of California, Irvine

description:
Library name: GWI_Veh
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads (FASTQ) were aligned to the mouse reference genome GRCm38/mm10 using Cell Ranger, and gene‑by‑cell count matrices (10x HDF5 format) were generated and imported into R for downstream analysis.
Assembly: mouse reference genome GRCm38/mm10
Supplementary files format and content: Gene values for each cell types (excel) and matrix file

molecule: nuclear RNA

source_name: Brain (hippocampus)

extract_protocol:
Single nuclei were isolated using a Miltenyi gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany), and suspensions were loaded onto a 10x Genomics Chromium Controller (Next GEM Single Cell 3' v3.1).
Libraries were sequenced on an Illumina platform with paired‑end 150‑bp reads (PE150) to a depth of at least 25,000 reads per nucleus; library preparation and sequencing were performed by Novogene (Beijing, People’s Republic of China).

value: Brain (hippocampus)

value: GW chemicals

tag: Sex

value: male


title: ribose-seq of hESC-H9 genomic DNA with RE1 fragmentation

description:
Library name: FS199
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: Whole genome bisulfite-seq of CD4T-3

description:
Library name: BS-CD4T-3
The extracted DNA was fragmented by S-series Focused-ultrasonicator (Covaris, Woburn, MA) using the 200-bp target peak size protocol. Fragmented DNA was then size selected (200600 bp) with an Agencourt AMPure XP bead-based (#A63880, Beckman Coulter, Brea, CA) size selection protocol. The DNA end repair step was performed with End-It DNA End-Repair Kit (#ER81050, Epicentre, Madison, WI). After the end-repair step, A-tailing (#M0202, New England Biolabs, Ipswich, MA) and ligation steps were performed to ligate the methylated adaptors. Bisulfite treatment of gDNA was performed using the MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher). Purified gDNA was treated with CT conversion reagent in a thermocycler for 10 min at 98 C, followed by 2.5 h at 640 C. Bisulfite-treated DNA fragments remain single-stranded as they are no longer complementary. Low-cycle (48) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA) which can tolerate uracil residues. The final library fragments contain thymines and cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.


title: APPdp APOE3-3

city: Tempe

first: David

last: Brafman

state: Arizona

address: ECG RM346/ISTB4

department: SBHSE

institute: Arizona State University

description: Library name: A_WT_3_x000D_

data_processing:
RNA sequencing was performed by BGI Americas using the DNBseq platform with paired-end 150 bp reads. The samples had an average yield of 6.64G data per sample.
Assembly: NCIB Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201 was used as the reference genome
Supplementary files format and content: xlsx format of transcripts per million (TPM) for Non-Demented Control lines and UCSD241i-APP2-3 lines.

growth_protocol: HiPSC derrived hNPCs were differentiated into neurons following previously published protocols (Knittel et al. 2022), with modifications to enhance cell attachment and differentiation efficiency. Corning® Enhanced Attachment Microcarriers (MCs) were coated with 15 μg/mL poly-L-ornithine (PLO) and incubated overnight at 4°C. Following PLO coating, MCs were washed twice with PBS and once with DMEM/F12 (Life Technologies) before being coated with 20 μg/mL Laminin diluted in DMEM/F12. Laminin coating was incubated overnight at 4°C. The Laminin solution was then removed, and MCs were suspended in neural expansion media before seeding hNPCs. With these modifications, hNPCs were differentiated into neurons according to Knittel et al. for 30–35 days. Upon completion of differentiation, cells were dissociated and plated onto 24-well Cultrex-coated plates.

extract_protocol:
RNA was isolated from neural cultures between days 7–10 post-dissociation. Cells were lysed in cold TRIzol™ Reagent (ThermoFisher) and incubated at 65 °C for 5 minutes. Chloroform (200 µL per 1 mL TRIzol) was added, samples were vortexed, incubated on ice for 5 minutes, and centrifuged at 10,000 × g for 5 minutes at 4 °C. The aqueous phase was collected, mixed 1:1 with 70% ethanol, and RNA was purified using the NucleoSpin RNA Kit (Macherey-Nagel).
Following QC of RNA samples, BGI's polyA_selected RNA library kit was selected for library construction.

value: neurons and astrocytes

value: APPdp, APOE3 (+/+)

value: hiPSC neural differentation

value: rep 3


title: Control, Vehicle-exposed mice

description:
Library name: Ctrl_Veh
10x Genomics

value: Vehicle


title: ribose-seq of hESC-H9 genomic DNA with dsF fragmentation, replicate 2

description:
Library name: FS198
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A wild-type


title: APPdp APOE3-2

description: Library name: A_WT_2

value: rep 2


title: Whole genome bisulfite-seq of CD4T-2

description:
Library name: BS-CD4T-2
The extracted DNA was fragmented by S-series Focused-ultrasonicator (Covaris, Woburn, MA) using the 200-bp target peak size protocol. Fragmented DNA was then size selected (200600 bp) with an Agencourt AMPure XP bead-based (#A63880, Beckman Coulter, Brea, CA) size selection protocol. The DNA end repair step was performed with End-It DNA End-Repair Kit (#ER81050, Epicentre, Madison, WI). After the end-repair step, A-tailing (#M0202, New England Biolabs, Ipswich, MA) and ligation steps were performed to ligate the methylated adaptors. Bisulfite treatment of gDNA was performed using the MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher). Purified gDNA was treated with CT conversion reagent in a thermocycler for 10 min at 98 C, followed by 2.5 h at 640 C. Bisulfite-treated DNA fragments remain single-stranded as they are no longer complementary. Low-cycle (48) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA) which can tolerate uracil residues. The final library fragments contain thymines and cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.


title: Lung primary fibroblasts, WT, female 3, IgG

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

description: Library name: WTF3_IgG

data_processing:
Trimming: TrimGalore!
Alignment: Bowtie2 --very-sensitive -X 1000 –dovetail
Filtering: removal of improper pairs, multimapping, mitochondrial reads using samtools
Counting: bedtools coverage over 10kb genomic bins generated with bedtools makewindows
Assembly: GRCm39
Supplementary files format and content: bedgraphs of coverage in 10kb genomic bins
Library strategy: CUT&Tag

source_name: lung primary fibroblasts

growth_protocol: All cell lines were grown in humidified incubators at 5% CO2 and 5% O2 at 37 degrees Celsius. Primary lung cells were cultured in Eagle’s Minimum Essential Medium with 15% FBS and 1X Pen/Strep. Cell lines are regularly tested for mycoplasma contamination.

extract_protocol:
Cut&Tag was performed using the CUTANA CUT&Tag Kit from EpiCypher according to the manufacturer’s protocol, using H3K27me3 (EpiCypher, 13-0055t) and H3K9me3 (Cell Signaling, 13969S).
CUT&Tag

value: lung primary fibroblasts

value: WT


title: ribose-seq of hESC-H9 genomic DNA with dsF fragmentation, replicate 1

description:
Library name: FS197
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: Lung primary fibroblasts, WT, female 3, h3k9me3

description: Library name: WTF3_H3K9me3


title: ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 3

description:
Library name: FS189
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: Whole genome bisulfite-seq of CD4T-1

description:
Library name: BS-CD4T-1
The extracted DNA was fragmented by S-series Focused-ultrasonicator (Covaris, Woburn, MA) using the 200-bp target peak size protocol. Fragmented DNA was then size selected (200600 bp) with an Agencourt AMPure XP bead-based (#A63880, Beckman Coulter, Brea, CA) size selection protocol. The DNA end repair step was performed with End-It DNA End-Repair Kit (#ER81050, Epicentre, Madison, WI). After the end-repair step, A-tailing (#M0202, New England Biolabs, Ipswich, MA) and ligation steps were performed to ligate the methylated adaptors. Bisulfite treatment of gDNA was performed using the MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher). Purified gDNA was treated with CT conversion reagent in a thermocycler for 10 min at 98 C, followed by 2.5 h at 640 C. Bisulfite-treated DNA fragments remain single-stranded as they are no longer complementary. Low-cycle (48) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA) which can tolerate uracil residues. The final library fragments contain thymines and cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.


title: APPdp APOE3-1

description: Library name: A_WT_1

value: rep 1


title: PS1 E280A APOE3-3

description: Library name: T_PS1_3

source_name: Non-Demented Control

value: Non-Demented Control


title: Lung primary fibroblasts, WT, female 3, h3k27me3

description: Library name: WTF3_H3K27me3


title: ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 2

description:
Library name: FS188
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: HT29_SMAD4_biol rep 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Library name: HT29AP34

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20
STAR version 2.7.8a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.6.3-p1 was used to quantify reads for genes in GRCh38 version 105
Assembly: GRCh38 version 105
Supplementary files format and content: Tab-delimited gene counts

source_name: Colorectal cancer

extract_protocol:
RNA was isolated from cells using TRIzol™ reagent (Invitrogen, Carlsbad, USA) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without 0.5 µM BMPRi (K02288) for 3 hours

value: Colorectal cancer

value: with stable integration of pcDNA3-FLAG-SMAD4

value: Untreated


title: CTRL-E_1

city: 合肥

first: 曹硕

last: 曹

state: 安徽

address: 九龙路

institute: 安徽大学

description:
Library name: SAMPLE5
Ezh2_KO_CTRL_FRAS200000128-1a

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: tsv file of raw counts

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

value: stem cell


title: PS1 E280A APOE3-2

description: Library name: T_PS1_2


title: HT29_vector-control_biol rep 3

description: Library name: HT29AP33

value: with stable integration of pcDNA3.1-empty vector


title: CRIC-seq PARN IP rep2

first: NAIJING

last: HU

address: No.11 Xizhimen South Street, Xicheng District

institute: Peking University People's Hospital

description:
Library name: Sample 4
Replicates were merged for processing

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
The raw data from CRIC-seq libraries were processed with the RICpipe program (v1.0) for trimming and alignment to the mouse reference genome (mm10 version). The resulting alignments from STAR and bwa were then performed to RICpipe analysis for chimeric read extraction.
Assembly: mm10
Supplementary files format and content: Genome-wide CRIC-seq signal in bigwig format

source_name: Spleen

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
The procedure was adopted as previously described (Ye et al., 2023)

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days.

value: Spleen

tag: strain

value: B cells

value: Wild type

value: LPS treatement

tag: antibody

value: anti-PARN


title: Lung primary fibroblasts, WT, female 2, h3k9me3

description: Library name: WTF2_H3K9me3


title: ribose-seq of CD4T genomic DNA with dsF+RE1 fragmentation, replicate 1

description:
Library name: FS187
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: blood


title: PS1 E280A APOE3-1

description: Library name: T_PS1_1

value: neurons and astrocytes

value: hiPSC neural differentation


title: HT29_SMAD4_biol rep 2

description: Library name: HT29AP30


title: Lung primary fibroblasts, WT, female 2, h3k27me3

description: Library name: WTF2_H3K27me3

value: lung primary fibroblasts


title: APPdp APOE3, clone 1-3

description: Library name: A_Ch_c1_3

value: APPdp, APOE3ch (+/+)

value: rep 3


title: ribose-seq of CD4T genomic DNA with RE1 fragmentation

description:
Library name: FS186
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A wild-type


title: HT29_vector-control_biol rep 2

description: Library name: HT29AP29

value: Colorectal cancer


title: APPdp APOE3ch, clone 1-2

description: Library name: A_Ch_c1_2

value: rep 2


title: Lung primary fibroblasts, WT, female 1, h3k9me3

description: Library name: WTF1_H3K9me3

value: WT


title: Lung primary fibroblasts, WT, female 1, h3k27me3

description: Library name: WTF1_H3K27me3


title: Docetaxel-resistant MCF-7 cells_biol rep3

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

description: Library name: 58C

data_processing:
All sequencing data were mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa.gz file.
Then, estimated transcript abundances from Salmon were imported into R using the tximeta package and analysed with EdgeR
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Excel file with the matrix of reads counts

source_name: MCF-7 (HR+/HER2- breast cancer)

growth_protocol: All cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM), low glucose, supplemented with GlutaMAX™ and sodium pyruvate (#10567014, Gibco), 10% heat-inactivated fetal bovine serum (FBS; Merck Life Science), and 1% penicillin-streptomycin (Gibco). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from cancer cells using the Monarch Total RNA Miniprep Kit (New England Biolabs). Ribosomal RNA (rRNA) was depleted using the RiboCop rRNA Depletion Kit (Lexogen).
The rRNA-depleted RNA was then used for library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's instructions. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1μg total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing was performed on an AVITI platform (Element Biosciences), using 76-bp paired-end reads. Libraries were multiplexed to achieve a sequencing depth of approximately 20 million reads per sample.

treatment_protocol: Chemoresistant MCF-7 cells were continuously cultured with 20 ng/mL docetaxel.

value: MCF-7 (HR+/HER2- breast cancer)

value: Docetaxel 20 ng/mL


title: HT29_SMAD4_biol rep 1

description: Library name: HT29AP26

value: with stable integration of pcDNA3-FLAG-SMAD4

value: Untreated


title: Docetaxel-resistant MCF-7 cells_biol rep2

description: Library name: 58B


title: ribose-seq of CD4T genomic DNA with dsF fragmentation

description:
Library name: FS185
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: APPdp APOE3ch, clone 1-1

description: Library name: A_Ch_c1_1

value: rep 1


title: Lung primary fibroblasts, cGAS KO, female 3, IgG

description: Library name: dcGasF3_IgG

value: cGAS KO


title: HT29_vector-control_biol rep 1

description: Library name: HT29AP25

value: with stable integration of pcDNA3.1-empty vector


title: HCT116-SMAD4-/-_ biol rep 3

description: Library name: HCT116AP24

value: homozygous knockout of SMAD4 using CRSIPR-Cas9 gene editing


title: Lung primary fibroblasts, cGAS KO, female 3, h3k9me3

description: Library name: dcGasF3_H3K9me3


title: PS1 E280A APOE3ch, clone 3-2

description: Library name: T_PS1_Ch_c3_2

value: Non-Demented Control

value: neurons and astrocytes


title: Docetaxel-resistant MCF-7 cells_biol rep1

description: Library name: 58A


title: PS1 E280A APOE3ch, clone 3-1

description: Library name: T_PS1_Ch_c3_1

value: hiPSC neural differentation


title: HCT116-WT_ BMPRi_biol rep 3

description: Library name: HCT116AP22

value: BMPRi for 3 hours


title: Lung primary fibroblasts, cGAS KO, female 3, h3k27me3

description: Library name: dcGasF3_H3K27me3

value: lung primary fibroblasts


title: PS1 E280A APOE3ch, clone 2-2

description: Library name: T_PS1_Ch_c2_2


title: Parental MCF-7 cells_biol rep3

description: Library name: 57C

value: Vehicle


title: HCT116-WT_ biol rep 3

description: Library name: HCT116AP21

value: Colorectal cancer


title: Lung primary fibroblasts, cGAS KO, female 2, h3k9me3

description: Library name: dcGasF2_H3K9me3


title: Parental MCF-7 cells_biol rep2

description: Library name: 57B


title: PS1 E280A APOE3ch, clone 2-1

description: Library name: T_PS1_Ch_c2_1


title: PS1 E280A APOE3ch, clone 1-3

description: Library name: T_PS1_Ch_c1_3

value: rep 3


title: HCT116-SMAD4-/-_ biol rep 2

description: Library name: HCT116AP20


title: HCT116-WT_ BMPRi_biol rep 2

description: Library name: HCT116AP18

value: WT


title: Parental MCF-7 cells_biol rep1

description: Library name: 57A

value: MCF-7 (HR+/HER2- breast cancer)


title: Lung primary fibroblasts, cGAS KO, female 1, h3k9me3

description: Library name: dcGasF1_H3K9me3


title: HCT116-WT_ biol rep 2

description: Library name: HCT116AP17


title: Lung primary fibroblasts, cGAS KO, female 2, h3k27me3

description: Library name: dcGasF2_H3K27me3


title: Lung primary fibroblasts, cGAS KO, female 1, h3k27me3

description: Library name: dcGasF1_H3K27me3


title: female Amlexanox_n3

city: Frankfurt

first: Ellen

last: Niederberger

address: Theodor-Stern-Kai 7

department: Institute for Clinical Pharmacology

institute: Goethe-University Frankfurt

description:
Library name: 1524_female_DMSO
Column name in raw_counts.txt: 1527_female_Amlexanox

data_processing:
The data was analyzed using Lexogens own data analysis pipeline now called Kangaroo, which was previously performed via the BlueBee genomics platform at that time the RNA-sequencing was performed.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
RNA was extracted from liver tissue using TRI Reagent.  The RNA concentration as well as the quality and integrity of RNA were controlled using RNA ScreenTape assays on a TapeStation 4150 (Agilent Technologies, Waldbronn, Germany) and Qubit RNA HS Assay Kits on a Qubit 3.0 Fluorometer
Sequencing libraries were prepared according to the workflow of the Quant Seq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen, Vienna, Austria)

treatment_protocol: Adeno-associated viral vectors encoding the gain-of-function variant D377Y of the murine PCSK9 (rAAV8-PCSK9D377Y) under the control of a liver-specific promoter  were administered via injection into the tail vein of mice (1.0 x10^11 viral genomes per mouse).  Afterwards, the mice were fed with a high-cholesterol/high-fat Paigen diet (PD, containing 16% fat, 1.25% cholesterol, and 0.5% sodium cholate ) to induce chronic hypercholesterolemia. After 8 weeks of diet feeding,  treatment with amlexanox (25 mg/kg BW, p.o.) or vehicle (DMSO) was started. Animals were treated daily for 5 days/week and the PD was proceeded for additional 8 weeks.

value: liver

value: female

value: wild type

value: Amlexanox


title: PS1 E280A APOE3ch, clone 1-2

description: Library name: T_PS1_Ch_c1_2

value: rep 2


title: female Amlexanox_n2

description:
Library name: 1523_female_Amlexanox
Column name in raw_counts.txt: 1523_female_Amlexanox


title: PS1 E280A APOE3ch, clone 1-1

description: Library name: T_PS1_Ch_c1_1

value: rep 1


title: Healthy, plasma, replicate 1

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: Library name: Sample_101

data_processing:
The AmpliSeq panel targets around 20,800 human RefSeq genes with >18,300 protein-coding genes.
The read quality was assessed using the FastQC software.
The reads were mapped to the human genome (GRCh38) using the STAR software, version 2.7.11b.
Transcript abundance was measured for the genes in the panel (the list of 20,800 genes in the panel was provided by the vendor) using the featureCounts software.
Expression normalization and differential gene expression calculations were performed using the DESeq2 software.
Assembly: GRCh38
Supplementary files format and content: Excel file of raw read count values for each Sample

source_name: Plasma extracellular vesicles

extract_protocol:
Extracellular vesicles were extracted using ExoQuick reagent and gentle centrifugation. Cell free RNA was isolated using a bead based method.
Illumina Ampliseq

value: Plasma extracellular vesicles

tag: disease

value: healthy


title: female Amlexanox_n1

description:
Library name: 1522_female_Amlexanox
Column name in raw_counts.txt: 1522_female_Amlexanox


title: BJ cells, 48hpi, replicate 3

city: Lyon

first: olivier

last: reynard

state: Auvergne-Rhône-Alpes

address: 21 avenue Tony Garnier

department: CIRI

country: France

institute: INSERM

data_processing:
Sequence quality control was checked using FastQC v0.11.8
Trimming was performed with Fastp 0.23.2 with options "-q 30-min_len 30"
Quantification was performed using Salmon 1.10.1 with the parameters “--gcBias --seqBias”. Index-building was performed by concatenating Nipah Bangladesh transcriptome with the Homo Sapiens transcriptome or the Pteropus Medius transcriptome
Assembly: Genbank GCF_000001405.40 for homo sapiens
Assembly: Genbank GCF_902729225.1 for pteropus giganteus
Assembly: Genbank GCA_003147825.1 for Nipah virus
Supplementary files format and content: tar file of salmon outputs including plaint text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: skin fibroblastic cell

growth_protocol: A549 cells were grown in DMEM medium supplemented with 10% of FCS and antibiotics. Bat and primary cells were grown in DMEM-F12 supplemented with 10% of FCS and antibiotic

extract_protocol:
RNA was isolated following manufacturer's instruction with Mini kit for RNA purification and treated with Dnase I (Macherey-Nagel, Cat#740955.50)
Librairies were assessed by poly-A enrichment using NEXTFLEX Poly(A) Beads 2.0 (Perkin-Elmer) and MGIEasy RNA Directional Library Prep Set User Manual (MGI-Tech) kits

value: skin fibroblastic cell

value: primary cell


title: HCT116-WT_ BMPRi_biol rep 1

description: Library name: HCT116AP14

value: BMPRi for 3 hours


title: Flecki cells, 48hpi, replicate 2

organism: Pteropus vampyrus


title: Flecki cells, 48hpi, replicate 1


title: BJ cells, 48hpi, replicate 1


title: Flecki cells, 0hpi, replicate 3


title: H9DIV390_A

city: Cambridge

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description: Batch 4

data_processing:
Low quality ends were disregarded during the mapping process. Only reads that were uniquely mapped to the transcriptome were used for UMI counting in CellRanger.
The data deriving from organoids were merged within each age group for analysis using the CellRanger function "cellranger aggr", except the two different 390-day-old organoid samples that were processed at different times.
Data was processed using Seurat and filtered for a minimum (200) and maximum number (5,000) of genes expressed per cell and for a maximum of 15% mitochondrial genes per cell. Log data normalisation was performed using the ‘NormalizeData’ function (scale factor of 10,000) in Seurat.
After running the ‘FindVariableGenes’ function, data were scaled using the ‘ScaleData’ function. For the merged object, samples were subset to approximately 15,000 cells per timepoint and batch correction was carried out using CAA in Seurat. Cell identities were assigned to the resulting clusters within the merged object. Cells of unknown identity or low-quality reads were removed from the downstream analysis.
Assembly: GRCh38
Supplementary files format and content: An RDS file containing the merged subsetted data and the metadata

source_name: H9 human embryonic stem cell (hESC)-derived cortical organoid

growth_protocol: H9 human embryonic stem cell-derived cortical organoids were generated and grown as slice cultures as described in Giandomenico et al., 2019. Organoids were grown in serum-free slice culture media (SFSCM): Neurobasal (Invitrogen, cat. #21103049), 1:50 (v/v) B27+A (Invitrogen, cat. #17504044), 0.5% (w/v) glucose, 1X (v/v) Glutamax supplemented with an antibiotic-antimycotic mix (ThermoFisher, cat. #15240062). The cultures were maintained in SFSCM at 37 °C and 5% CO2 with daily media changes.

extract_protocol:
Dissociation of cortical organoids slices (ALI-COs) was achieved by Accumax (Sigma, A7089) using the gentleMACS Octo Dissociator. The cell suspension was run through a 70μm strainer prior to processing in the 10X Genomics platform. scRNA-seq libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics, 120237) workflow.
The cell suspension (10,000 cells in 34 μl) was loaded onto a 10X Genomics Chromium Single Cell 3’ chip with the recommended amount of Mastermix. RNA extraction was performed according to the standard 10X Genomics Chromium workflow. The reverse transcriptase reaction and subsequent amplification (12 cycles) was carried out in a C1000 Touch Thermal Cycler (Bio-Rad). Before sequencing, libraries were quality tested using the 2100 Bioanalyzer Instrument (Agilent) and by qPCR.
Samples were pooled together and sequenced using the Illumina HiSeq4000 RTA platform. Sequencing data was converted to the standard fastq format by bcl2fastq. The "Cellranger count" code was run in CellRanger 2.1.1 using the GRCh38 human reference genome. STAR was utilized to align the reads.

value: organoid

value: Female ESC line with no genetic modification

value: 390 days


title: female DMSO_n1

description:
Library name: 1525_female_DMSO
Column name in raw_counts.txt: 1524_female_DMSO

value: DMSO


title: female DMSO_n2

description:
Library name: 1527_female_Amlexanox
Column name in raw_counts.txt: 1525_female_DMSO


title: BJ cells, 0hpi, replicate 3


title: H9DIV390_B

description: Batch 4

value: H9 human embryonic stem cell (hESC)-derived cortical organoid


title: BJ cells, 48hpi, replicate 2


title: Flecki cells, 0hpi, replicate 2


title: BJ cells, 0hpi, replicate 2


title: H9DIV360

description: Batch 3

value: 360 days


title: Flecki cells, 0hpi, replicate 1


title: male Amlexanox_n2

description:
Library name: 1442_male_Amlexanox
Column name in raw_counts.txt: 1442_male_Amlexanox

value: liver

value: male


title: BJ cells, 0hpi, replicate 1


title: H9DIV290_3

description: Batch 3

value: 290 days


title: male Amlexanox_n1

description:
Library name: 1441_male_Amlexanox
Column name in raw_counts.txt: 1441_male_Amlexanox

value: wild type

value: Amlexanox


title: A549 cells, 48hpi, replicate 5

source_name: lung epithalial cell

value: lung epithalial cell

value: immortalized cell


title: H9DIV290_2

description: Batch 3


title: male DMSO_n2

description:
Library name: 1451_male_DMSO
Column name in raw_counts.txt: 1451_male_DMSO


title: male DMSO_n1

description:
Library name: 1450_male_DMSO
Column name in raw_ counts.txt: 1450_male_DMSO


title: A549 cells, 48hpi, replicate 3


title: H9DIV150_3

description: Batch 2

value: 150 days


title: PATGV cells, 48hpi, replicate 2

value: skin fibroblastic cell


title: A549 cells, 48hpi, replicate 2


title: H9DIV150_2

description: Batch 2


title: Brequiner treated wounded skin tissue 2 (day 9)

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

country: Japan

institute: Gunma University

description: Library name: B1_2_S22genesresults

data_processing:
Reads were aligned to the mm10 assembly of the mouse genome (NCBI Build 38, obtained from the UCSC Genome Browser website) using STAR aligner. Gene-level raw count data were used for downstream analyses. RNA-seq data were analyzed using the iDEP Genomics Suite (https://bioinformatics.sdstate.edu/idep/). Relative log expression (RLE) plots were used to assess data normalization and quality.
Differential gene expression analysis was performed using the Wald test for pairwise comparisons. For human samples, publicly available RNA-seq datasets comparing PG lesional skin and normal skin were analyzed. In mouse samples, brequinar-treated skin was compared with vehicle-treated skin and with unwounded skin. Gene Ontology (GO) terms (p < 0.01, fold change > 4 for human and p < 0.05, fold change > 1.5 for mouse) were obtained using ToppGene (https://toppgene.cchmc.org/).
Assembly: mm 10
Supplementary files format and content: csv file including normalized count value for all samples

source_name: Skin

extract_protocol:
Total RNA from skin tissue and cells were isolated using a RNeasy Mini Kit (Qiagen, Valencia, California). Total 100 ng
Library preparation was carried out using the KAPA mRNA HyperPrep kit (KAPA BIOSYSTEMS, KK8580) according to the manufacturer’s protocols. Library quality was assessed using an Agilent 4200 TapeStation (Agilent, CA, US). Paired-end sequencing was performed on a NextSeq 2000 platform (Illumina).

value: Skin

value: WT

value: Brequiner and wound


title: A549 cells, 48hpi, replicate 1


title: PATGV cells, 48hpi, replicate 1


title: H9DIV150_1

description: Batch 2

value: organoid

value: Female ESC line with no genetic modification


title: PATGV cells, 24hpi, replicate 5


title: Brequiner treated wounded skin tissue 1 (day 9)

description: Library name: B2_S21genesresults


title: A549 cells, 24hpi, replicate 5


title: H9DIV100

description: Batch 1

value: 100 days


title: PATGV cells, 24hpi, replicate 4


title: DMSO treated wounded skin tissue 3 (day 9)

description: Library name: D5_2_S20genesresults

value: DMSO and wound


title: DMSO treated wounded skin tissue 2 (day 9)

description: Library name: D2_2_S18genesresults


title: PATGV cells, 24hpi, replicate 3


title: lung-derived CD45+ immune cells post Reg1 KO CAR T treatment #2 TCR

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: Library name: KO2_TCR

data_processing:
The Cell Ranger v6 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix and TCR filtered contig annotations for single cells in each sample

source_name: lung

growth_protocol: CD45+ immune cells isolated from lung were used directly for experiments.

extract_protocol:
CD45+ immune cells were sorted and loaded onto the Chromium Controller according to their respective cell counts to target 10,000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 5’ v2 Library and Gel Bead Kit (10x Genomics)

value: lung

value: CD45+ immune cells

value: Sort-purified CD45+ immune cells


title: A549 cells, 24hpi, replicate 3


title: A549 cells, 24hpi, replicate 4


title: lung-derived CD45+ immune cells post Reg1 KO CAR T treatment #1 TCR

description: Library name: KO1_TCR


title: PATGV cells, 24hpi, replicate 2


title: DMSO treated wounded skin tissue 1 (day 9)

description: Library name: D2_S17genesresults


title: A549 cells, 24hpi, replicate 2


title: E14 TKO RNA Day0 rep1

city: Seoul

first: Yingying

last: Li

state: Seoul

address: 103 Daehak-ro

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description: Library name: E14_TKO_Day0_RNA_rep1

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics, 1x MEM non-Essential Amino Acids, 10mM 2-Mercaptoethanol, Leukemia inhibitory Factor, 1mM MEK1/2 inhibitor (PD0325901), 3mM GSK3 inhibitor (CHIR99021). Cells were cultured at 37°C at 5% CO2.

extract_protocol:
CUTnTag: CUT&Tag was carried out following the Epicypher protocol.  ChIP-seq: 3 x 106 cells were harvested and fixed sequentially with 2mM disuccinimidyl glutarate (DSG; Thermo Fisher, 20593) for 35 minutes followed by 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, and nuclei were isolated in NE buffer and extracted nuclei were then resuspended 1% SDS lysis buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS) and sonicated by Covaris S220 sonicator (Power 175 W, Duty 10%, 200 cycles per burst) for 430 seconds to generate DNA fragments of approximately 200bp. Sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA) and clarified by centrifugation at 13,000 rpm for 15 minutes at 4 °C. Chromatin was incubated overnight at 4 °C with Dynabeads protein A pre-bound to 2.4mg target antibody. 1 µg of Drosophila chromatin (Active Motif, #53083) and 0.1 µg of anti-Drosophila H2A.X antibody (Active Motif, #61686) were added per reaction to perform spike-in normalization. The next day, Dynabeads were washed three times with buffer A (140mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8), twice with buffer B (300mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8) and once with buffer C (250 mM LiCl, 10mM Tris-HCl pH 8, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate). RNA was removed by treatment with RNAse A at 37 °C for 30 minutes and crosslinks were reversed overnight at 65 °C in the presence of Proteinase K and SDS treatment. Eluted DNAs were size selected using SPRIselect beads (Beckman B23319).  RNA-seq: cells were resuspended in 1 ml of Trizol (ThermoFisher, 15596026) and incubated for 5 minutes at room temperature. Then, 0.2 ml of Chloroform (Sigma, C2432) was added and the solution was vortexed vigorously. The mixture was centrifuged at 13,000 rpm for 15 minutes at 4°C, and the upper phase was transferred to a fresh tube. RNA was precipitated using isopropanol (Duksan, 857) and washed with ice-cold 70% ethanol (Sigma, E7023). The precipitated RNA was dissolved in DEPC-treated water (Invitrogen, AM9915G).
CUTnTag: The eluted DNA was amplified using 2x PCR master mix (Epicypher, 15-1018) with i5 and barcoded i7 primers. Subsequently, library DNA was purified with SPRIselect beads (Beckman B23319) ).  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Library preparation was performed using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina, RS-122-2301).

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: PATGV cells, 24hpi, replicate 1


title: Unwounded skin tissue 4

description: Library name: N2_2_S16genesresults


title: PATGV cells, 8hpi, replicate 5


title: lung-derived CD45+ immune cells post control CAR T treatment #1 TCR

description: Library name: Ctrl1_TCR

value: wild type


title: A549 cells, 8hpi, replicate 5

value: lung epithalial cell


title: A549 cells, 24hpi, replicate 1

value: immortalized cell


title: lung-derived CD45+ immune cells post Reg1 KO CAR T treatment #2 gene expression

description: Library name: KO2_GEX


title: PATGV cells, 8hpi, replicate 4


title: Unwounded skin tissue 2

description: Library name: N11_S14genesresults


title: A549 cells, 8hpi, replicate 4


title: lung-derived CD45+ immune cells post Reg1 KO CAR T treatment #1 gene expression

description: Library name: KO1_GEX


title: PATGV cells, 8hpi, replicate 3


title: Unwounded skin tissue 1

description: Library name: N1_S13genesresults


title: A549 cells, 8hpi, replicate 3


title: lung-derived CD45+ immune cells post control CAR T treatment #2 gene expression

description: Library name: Ctrl2_GEX


title: PATGV cells, 8hpi, replicate 2


title: A549 cells, 8hpi, replicate 2


title: Cerebral cortex, risperidone 2

city: Philadelphia

first: Hyowon

last: Choi

state: PA

institute: Thomas Jefferson University

description:
Library name: Cerebral cortex, risperidone 2
10X Genomics

data_processing:
Reads were aligned to the mouse reference genome using Ensembl 98 annotations (prebuilt Cell Ranger reference mm10-2020-A, 10X Genomics, https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps#mouse-ref-2020-a) using Cell Ranger v8.0.1 and default settings.
Filtered count matrix was produced by Cell Ranger's call-calling algorithm.
Assembly: GCRm38 GENCODE vM23 Ensembl98
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
At PND 90, mice were euthanized and their brains were harvested, flash frozen in liquid nitrogen, and cerebral cortices were dissected. Nuclei were prepared from minced cortices according to Martin et al (https://dx.doi.org/10.17504/protocols.io.bi62khge), stained with DAPI (0.1 µg/mL) and sorted on SONY SH800 cell sorter with a 100 µm chip to remove non-nuclear debris. Sorted nuclei were pelleted at 600 xg and excess supernatant was removed, and the remaining liquid (~50 µL) was used to resuspend the nuclei.
Libraries were prepared using GEM-X Universal Gene Expression v4 kit (1000691, 10X Genomics) and sequenced on a NextSeq2000 (Illumina) using the read format, 28x10x10x90bp, to an average depth of ~16,000 reads per cell.

treatment_protocol: C57BL/6J mice were treated with daily risperidone (4 mg/kg, i.p.) or saline at post-natal day (PND) 22 for 21 consecutive days, followed by a drug washout period of 43 days.

value: Cortex

tag: age

value: PND 90

value: Risperidone


title: PATGV cells, 8hpi, replicate 1

value: skin fibroblastic cell


title: A549 cells, 8hpi, replicate 1


title: spleen-derived control CAR T cells TCR

description: Library name: spleenCtrl_TCR

data_processing:
The Cell Ranger v6 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger gene count matrix and TCR filtered contig annotations for single cells in each sample

source_name: spleen

growth_protocol: Control and Reg-1 KO B7H3 CAR T cells isolated from lung and spleen were used directly for experiments.

extract_protocol:
Control and Reg-1 KO B7H3 CAR T cells were sorted and loaded onto the Chromium Controller according to their respective cell counts to target 10,000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 5’ v2 Library and Gel Bead Kit (10x Genomics)

value: spleen

value: CAR T cells

value: B7H3 CAR T cells

value: Control

value: Sort-purified CAR T cells


title: Cerebral cortex, saline 2

description:
Library name: Cerebral cortex, saline 2
10X Genomics

value: WT

value: Saline


title: lung-derived control CAR T cells TCR

description: Library name: lungCtrl_TCR

value: lung


title: A549 cells, 0hpi, replicate 5


title: PATGV cells, 0hpi, replicate 4


title: Cerebral cortex, saline 1

description:
Library name: Cerebral cortex, saline 1
10X Genomics


title: A35B65L2

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 42

data_processing:
Sequencing reads were quality filtered and adapter trimmed prior to alignment.
Trimmed reads were aligned to the human reference genome.
Aligned reads were filtered to remove duplicates and low-quality mappings.
Accessible chromatin regions were identified using peak calling and normalized signal tracks were generated.
Assembly: hg38
Supplementary files format and content: BigWig files represent normalized ATAC-seq signal tracks for each sample.
Supplementary files format and content: avg_BigWig files represent normalized ATAC-seq signal tracks for averaged samples

source_name: Breast

growth_protocol: Human tumor samples were obtained from surgical resections and processed according to institutional protocols. Samples were flash frozen and stored at −80 °C until chromatin accessibility profiling.

extract_protocol:
Nuclei were isolated from frozen tumor tissue and subjected to transposition using Tn5 transposase to tag accessible chromatin regions.
ATAC-seq libraries were prepared using a standard transposase-based protocol followed by PCR amplification and size selection according to the manufacturer’s instructions.

treatment_protocol: No in vitro treatment was applied. Samples represent primary and metastatic tumor tissues collected at the time of surgery.

value: Breast

value: breast tumor cells


title: A549 cells, 0hpi, replicate 4


title: spleen-derived Reg-1 KO CAR T cells TCR

description: Library name: spleenKO_TCR

value: Reg-1 KO


title: Lung primary fibroblasts, WT, male 2

data_processing:
Trimming: TrimGalore!
Alignment: Bowtie2 --very-sensitive -X 1000 –dovetail
Filtering: removal of improper pairs, multimapping, mitochondrial reads and PCR duplicates using samtools and picard
Peak calling: Cleaned bam files were converted to bed format and used to call peaks with MACS2 with arguments -f BED --keep-dup "all" -q 0.01 --nomodel --shift -100 --extsize 200 for each sample individually. A unified peak set was generated  by first merging the peaksets of all samples using bedtools merge. Next, we identified regions which were called as peak in at least 2 samples using bedtools multiinter. Finally, we only kept peaks within the union peakset if they contained at least one of the regions called in 2 samples or more using bedtools intersect.
Counting: featureCounts -F SAF -p -B --read2pos 5 -O --fraction
Assembly: GRCm39
Supplementary files format and content: Unnormalized counts over called peaks and repeatitive elements

growth_protocol: All cell lines were grown in humidified incubators at 5% CO2 and 5% O2 at 37 degrees Celsius. Primary lung cells were cultured in Dulbecco’s modified Eagle’s medium nutrient mixture F12 with 15% FBS and 1X antibiotic-antimycotic. Cell lines are regularly tested for mycoplasma contamination.

extract_protocol: Nuclei were isolated and the library was prepared following the ATAC-seq protocol from Buenrostro et al.

value: lung primary fibroblasts

value: male


title: PATGV cells, 0hpi, replicate 3

value: immortalized cell


title: A549 cells, 0hpi, replicate 3

value: lung epithalial cell


title: lung-derived Reg-1 KO CAR T cells TCR

description: Library name: lungKO_TCR


title: Lung primary fibroblasts, WT, male 1


title: A549 cells, 0hpi, replicate 2


title: PATGV cells, 0hpi, replicate 1


title: spleen-derived control CAR T cells gene expression

description: Library name: spleenCtrl_GEX


title: Lung primary fibroblasts, WT, female 2

value: female


title: A549 cells, 0hpi, replicate 1


title: lung-derived control CAR T cells gene expression

description: Library name: lungCtrl_GEX


title: 4X_NC13_2_121024

city: Denton

first: Fanju

last: Meng

state: TX

address: 1155 Union Circle #305220

institute: University of North Texas

description: Library name: 4X_NC13_2_121024

data_processing:
RNA-seq reads were trimmed for adaptors using TrimGalore (version 0.6.10), and then mapped to the D. melanogaster reference genome (dm6) or zebrafish genome (GRCz11) using STAR (version 2.7.11b)
The transcript-level abundance was quantified with Salmon and then aggregated using tximport to obtain gene-level quantification.
Subsequent differential expression analysis was done using DESeq2
Statistical tests and plots for data visualization were generated in R and GraphPad
Assembly: dm6 and GRCz11
Supplementary files format and content: txt files with TPM count table and DEseq2 results

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Drosophila embryos of roughly the correct stage were observed by confocal imaging until they reached the desired timepoint and then flash frozen.

extract_protocol:
Embryos were then macerated in TRIzol with a needle to extract RNA and purified using Direct-Zol™ RNA MiniPrep Kit (Zymo Research) according to manufacturer’s protocol.
RNA libraries for batch 1, 2 and 5 were prepared with Illumina total RNA with rRNA depletion, and RNA libraries for batch 3 and 4 were prepared with SMART-Seq Total RNA Pico Input with UMIs according to user manual.

value: whole embryo

tag: developmental stage


title: Lung primary fibroblasts, WT, female 1


title: H2A.ZGFP_4hpf_3

description: Library name: H2A.ZGFP_4hpf_3

organism: Danio rerio

value: H2A.Z Overexpression


title: 4X_NC11_combine

description: Library name: 4X_NC11_combine


title: Lung primary fibroblasts, cGAS KO, male 2

value: cGAS KO


title: H2A.ZGFP_4hpf_2

description: Library name: H2A.ZGFP_4hpf_2


title: lung-derived Reg-1 KO CAR T cells gene expression

description: Library name: lungKO_GEX

value: CAR T cells

value: B7H3 CAR T cells


title: 4X_NC11_1_121024

description: Library name: 4X_NC11_1_121024


title: Lung primary fibroblasts, cGAS KO, male 1


title: PATGV cells, 0hpi, replicate 5

value: skin fibroblastic cell


title: H2A.ZGFP_4hpf_1

description: Library name: H2A.ZGFP_4hpf_1


title: Cerebral cortex, risperidone 1

description:
Library name: Cerebral cortex, risperidone 1
10X Genomics

value: Cortex

value: WT

value: PND 90

value: Risperidone


title: 2X-1-Egg

description: Library name: 2X-1-Egg

value: Egg


title: 4X_Egg_combine

description: Library name: 4X_Egg_combine


title: Lung primary fibroblasts, cGAS KO, female 2


title: H2A.ZGFP_2.5hpf_3

description: Library name: H2A.ZGFP_2.5hpf_3


title: 1X-3-NC14

description: Library name: 1X-3-NC14


title: 4X_Egg_1_121024

description: Library name: 4X_Egg_1_121024


title: Lung primary fibroblasts, cGAS KO, female 1


title: H2A.ZGFP_2.5hpf_2

description: Library name: H2A.ZGFP_2.5hpf_2


title: 1X-2-NC14

description: Library name: 1X-2-NC14


title: 2X_NC13_combine

description: Library name: 2X_NC13_combine


title: CD8_plus_Tcells_Nc1Nc2ko_2

city: Würzburg

first: Stefan

last: Klein-Hessling

address: Josef-Schneider-Str. 2

department: Institute of Pathology

institute: University of Würzburg

data_processing:
Base calling with Illumina NextSeq RTA v3.9.25
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome (GRCm39) using STAR (Dobin et al., 2013) v2.7.2b with default parameters based on RefSeq annotation version 109
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 109 for GRCm39) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Assembly: GRCm39
Supplementary files format and content: Character (TAB) separated value file containing raw mRNA abundance measurements

source_name: CD8+ T cells

growth_protocol: Purified splenic CD8+T cells from 8-16 weeks old mice were activated for 2 d on antiCD3 (3µg/ml) antibody coated plastic dishes in the presence of antiCD28 (1µg/ml) and hIL-2 (50U/ml). Afterwards the cells were persistently stimulated by plate bound aCD3 (3µg/ml) Abs in medium containing IL-7 (50ng/ml) and IL-15 (15ng/ml) for additional 4 days.

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was > 8.3. cDNA libraries were prepared from total RNA with TruSeq mRNA Stranded Library Prep Kit from Illumina according to manufacturer’s instructions (1/2 volume). Libraries were quantified by QubitTM Flex Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with DNA 1000 Kit (Agilent). The average size of the pool were approximately 300 bp. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 25 million reads/sample in single-end mode with 100 nt read length on the NextSeq 2000 platform (Illumina).

value: CD8+ T cells


title: H2A.ZGFP_2.5hpf_1

description: Library name: H2A.ZGFP_2.5hpf_1


title: 1X-2-NC13

description: Library name: 1X-2-NC13


title: 2X_NC13_1_121024

description: Library name: 2X_NC13_1_121024


title: CD8_plus_Tcells_Nc1Nc2ko_1


title: 1X-1-NC13

description: Library name: 1X-1-NC13


title: WT_4hpf_3

description: Library name: WT_4hpf_3


title: 2X_NC11_combine

description: Library name: 2X_NC11_combine


title: CD8_plus_Tcells_Nc2ko_3


title: WT_4hpf_2

description: Library name: WT_4hpf_2


title: HCT116-SMAD4-/-_ biol rep 1

description: Library name: HCT116AP16

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20
STAR version 2.7.8a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.6.3-p1 was used to quantify reads for genes in GRCh38 version 105
Assembly: GRCh38 version 105
Supplementary files format and content: Tab-delimited gene counts

extract_protocol:
RNA was isolated from cells using TRIzol™ reagent (Invitrogen, Carlsbad, USA) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer

value: homozygous knockout of SMAD4 using CRSIPR-Cas9 gene editing

value: Untreated


title: non-diseased control_10_ADT

city: Nashville

first: Ana

last: Serezani

address: 1161 21st Ave. S, MCN B1320B

department: Medicine

institute: Vanderbilt Medical Center

description:
Library name: Sample 27_ADT
Antibody-derived oligonucleotide

data_processing:
CellRanger 6.0.0-6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: h5
Supplementary files format and content: Raw Matrix files
Library strategy: CITE-seq

source_name: Lung

extract_protocol:
Tissue samples were obtained from fibrotic lungs [Idiopathic Pulmonary Fibrosis (IPF), Interstitial Pneumonia with Autoimmune Features (IPAF), and Connective Tissue Disease-associated Interstitial Lung Disease (CTD-ILD), Nonspecific Interstitial pneumonia (NSID)] removed at the time of lung transplant surgery or non-fibrotic control lungs (declined donors) obtained at the time of organ procurement at Vanderbilt University Medical Center. Lung tissue biopsies were washed in PBS, minced, and frozen in RPMI media containing 10% DMSO until analysis. Minced lungs were thawed at 37oC for 3 minutes and digested in an enzymatic cocktail [Collagenase XI and DNAse I, type IV (Sigma)] and using a gentleMACS Octo Dissociator (Miltenyi Inc.) at 37°C and filtered using 100-μm sterile filters (Fisher). Whole lung cell suspensions (up to 1 million cells) were incubated with an Fc receptor blocking reagent (TrueStain FcX, BioLegend, USA) for 15 minutes, followed by staining with a panel of flow cytometry antibodies [anti-CD45 (APC-Cy7), anti-CD3 (PE-Cy5), and fourteen oligo-conjugated TotalSeq-C human antibodies (BioLegend)] for 30 minutes. Cells were washed three times with PBS containing 1% BSA and stained with a viability dye (Zombie Aqua kit, BioLegend). Up to 25,000 viable CD45⁺CD3⁺ cells were sorted per sample using a BD FACS ARIA and submitted for sequencing on the 10x Genomics Chromium platform. Briefly, 10,000 cells were loaded onto a 10x Chromium single-cell encapsulation chip, and libraries were prepared according to the manufacturer’s instructions. Sequencing was performed on Illumina platforms at a depth of at least 80 million reads per library.
10x_Single Cell 5' PE

value: Lung

value: Not apply

value: CD3+ T cell

tag: library type

value: ADT

tag: adt

value: TotalSeq_CD3 TotalSeq_CD8 TotalSeq_CD56 TotalSeq_CD4 TotalSeq_CD25 TotalSeq_CD45RO TotalSeq_PD1 TotalSeq_CD103 TotalSeq_CCR7 TotalSeq_CTLA4 TotalSeq_LAG3 TotalSeq_HLADR TotalSeq_CD57 TotalSeq_CD28 TotalSeq_KLRG1


title: 1X-3-Egg

department: Biological Sciences

description: Library name: 1X-3-Egg

tag: tissue

value: whole embryo


title: CTD-ILD_3a_ADT

description:
Library name: Sample23 _ADT
Antibody-derived oligonucleotide

tag: cell line


title: Flecki cells, 48hpi, replicate 3

tag: cell type

value: primary cell


title: female DMSO_n3

description:
Library name: 1530_female_DMSO
Column name in raw_counts.txt: 1530_female_DMSO

value: liver

value: female

tag: genotype

value: wild type

value: DMSO


title: 2X_NC11_2_121024

description: Library name: 2X_NC11_2_121024


title: CD8_plus_Tcells_Nc2ko_2

value: male


title: WT_4hpf_1

description: Library name: WT_4hpf_1

value: WT


title: spleen-derived Reg-1 KO CAR T cells gene expression

description: Library name: spleenKO_GEX

value: spleen

value: CAR T cells

value: B7H3 CAR T cells

value: Reg-1 KO

tag: treatment

value: Sort-purified CAR T cells


title: HCT116-WT_ biol rep 1

description: Library name: HCT116AP13

value: Colorectal cancer

value: Untreated


title: 1X-2-Egg

description: Library name: 1X-2-Egg

value: Egg

tag: batch


title: 2X_Egg_combine

description: Library name: 2X_Egg_combine


title: CD8_plus_Tcells_Nc2ko_1

value: CD8+ T cells


title: 2X_Egg_1

description: Library name: 2X_Egg_1

value: whole embryo


title: WT_2.5hpf_3

description: Library name: WT_2.5hpf_3


title: 1X-1-Egg

description: Library name: 1X-1-Egg


title: CD8_plus_Tcells_Nc1ko_3


title: WT_2.5hpf_2

description: Library name: WT_2.5hpf_2


title: male Amlexanox_n3

description:
Library name: 1443_male_Amlexanox
Column name in raw_counts.txt: 1443_male_Amlexanox

value: Amlexanox


title: 4X-H2Av-NC14-3

description: Library name: 4X-H2Av-NC14-3


title: 1X_NC14_combine

description: Library name: 1X_NC14_combine


title: CD8_plus_Tcells_Nc1ko_2


title: WT_2.5hpf_1

description: Library name: WT_2.5hpf_1


title: PATGV cells, 48hpi, replicate 5

value: skin fibroblastic cell

value: immortalized cell


title: 4X-H2Av-NC14-2

description: Library name: 4X-H2Av-NC14-2


title: 1X_NC14_1

description: Library name: 1X_NC14_1


title: CD8_plus_Tcells_Nc1ko_1


title: PATGV cells, 48hpi, replicate 4


title: H9DIV290_1

description: Batch 3

value: H9 human embryonic stem cell (hESC)-derived cortical organoid

value: organoid

value: Female ESC line with no genetic modification

value: 290 days


title: PATGV cells, 48hpi, replicate 3


title: A549 cells, 48hpi, replicate 4

value: lung epithalial cell