title: RNA_Sequencing_tumor-024

city: Rochester

first: Christine

middle: T

last: Nguyen

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: RNA-024

data_processing:
For RNA-seq, transcript-level read counts were quantified by Kallisto, summarized into gene level by tximport, normalized by trimmed mean of M values method, and log2-transformed. Genes differentially expressed between groups were identified using the voom function in the Bioconductor package limma with precision weights, filtered by FDR-adjusted p<0.05 and fold-change ≥2.0 or ≤-2.0. Gene set enrichment analysis (GSEA) was performed using EGSEA. Differential gene expression analysis between groups was performed using empirical Bayes regression models in limma voom with precision weights. For multiple comparisons, p-value was adjusted using the Benjamini-Hochberg  false discovery rate (FDR) correction. Spearman’s correlation ρ was used for measuring statistical dependence between normalized and log2-transformed expression level of different genes, and between gene expression of the pathways of interest. P<0.05 was considered statistically significant. Statistical analysis was performed using R (v3.8.2) and Bioconductor (release 3.8).
Assembly: GRCh38
Supplementary files format and content: ATM_PAAD.rnaseq.kallisto.raw.txi.tpm.txt

source_name: Pancreatic cancer

extract_protocol:
DNA from pancreatic ductal adenocarcinoma (PDAC) tumor samples and adjacent normal tissue was extracted using a proprietary method (SeqPlus method for DNA Isolation from FFPE, Genuity Science).
RNA: Library preparation for RNA-seq was performed using 100 ng of total RNA and a TruSeq Stranded Total RNA (Degraded RNA) v2 RNA Exome Library and TS RNA Access capture protocol (Illumina)

value: Pancreatic cancer

value: Germline ATM PV carrier


title: iPSC, NDF-K, DRB_TT_seq_20min_Rep2

status: Public on Aug 05 2025

type: SRA

city: Piscataway

first: Jia

last: Fei

state: NJ

address: 604 Allison Rd

department: Department of Molecular Biology and Biochemistry

country: USA

institute: Rutgers University

description: Library name: Sample 14

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed and aligned to both the human reference genome (hg38) and S. pombe using STAR. PCR duplicates were removed using samtools. Mapped BAM files were used to analyze transcriptional wave peaks and RNA polymerase II elongation speed.
Assembly: hg38
Supplementary files format and content: bigWig and bam

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human iPSC cells were cultured in Essential 8 medium 1 (Gibco) following the vendor’s instruction. Rock inhibitor Y23672 (Selleck Chemicals) with a final concentration of 10 μM was used during cell passaging. Cells were kept in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
For TT-seq, RNA was purified by TRIzol Reagent (Invitrogen), 100 μg of RNA was mixed with 0.5 μg of S. pombe 4TU-labeled RNA as a spike-in control, and further the mixture was subjected to RNA fragmentation, biotinylation, and streptavidin pulldown.
RNA libraries were prepared using the Illumina Stranded Total RNA Prep with Ligation and Ribo-Zero Plus kit

tag: cell line

tag: cell type

value: hiPSC

tag: genotype

tag: treatment

value: Cells were treated with 0.1 mM DRB for 3 hours, followed by a 10-minute culture in meidum and then 10-minute labeling with 1 mM 4sU


title: 16 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 2

city: Austin

first: Vighnesh

middle: Vijay

last: Ghatpande

state: Austin

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Library name: 20221004_ITP_16cell_control_B
16cell_embryo_control_biol rep2

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 10 followed by deduplication using UMI-tools. As the last step, .ribo files are created. Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Assembly: Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/yeast_reference
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: Ribo-Seq

molecule: total RNA

organism: Mus musculus

source_name: preimplantation embryo

extract_protocol:
Flash-frozen single embryos were thawed on ice, 5µL of ITP lysis buffer (20 mM BisTris pH 7.2, 1.0% Triton-X100, 5mM MgCl2, 2.5 mM CaCl2, 100mM NaCl, 1 mM DTT, 0.1 mg/ml cycloheximide) was added to the droplet containing the embryo on the wall of the tube. Flash-frozen microdissected hippocampal tissue was thawed on ice and 10uL of lysis buffer (1% TritonX100, 50mM MgCl2, 0.1 mg/mL cycloheximide) was added to it. The tissue was homogenized with a pestle () until the solution was visibly clear. 4uL of the lysate was transferred to a 0.2mL PCR tube containing 1uL of 5X ITP lysis buffer (100 mM BisTris pH 7.2, 5.0% Triton-X100, 25mM MgCl2, 12.5 mM CaCl2, 500mM NaCl, 5 mM DTT, 0.5 mg/ml cycloheximide). For both the lysates, 1µL of RNaseI diluted 1:300 in the ITP lysis buffer was added and incubated at 37°C for 30 mins. 1µL of 0.7% SDS was added to stop RNaseI followed by running the lysate on an ITP chip. Ribosome footprints were eluted by collecting the RNA fragments between 19nt and 36nt markers on the ITP chip.
Ribosome profiling libraries were made using D-Plex Small RNA-Seq Kit (Diagenode) with the following modifications, a. 0.5µL PNK enzyme (NEB) was added along with the dephosphorylation reagent, b. The TSO was diluted 1:5, c. The cDNA was amplified for 16 cycles. The resulting libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent). Each library was mixed in equimolar proportion and cleaned up with AmpureXP beads (1.5X) and PAGE purified on a 10% PAGE. Resulting libraries were sequenced on NovaSeq 6000 SP PE.

treatment_protocol: For the mouse embryos, of the appropriate stages were treated with either 2ug/ml Harringtonine or DMSO for 30mins following which they were transferred to eppendorf tubes and flash frozen. For the mouse acute hippocampal sections, LTP was induced in areaCA1 region of the section by TBS stimulation and the induced regions were microdissected at mentioned time points. These microdissected tissues were transferred to 1.5ml eppendorf tubes and flash frozen.

tag: tissue

value: preimplantation embryo

value: DMSO

tag: time


title: iPSC, NDF-K, DRB_TT_seq_20min_Rep1

description: Library name: Sample 13


title: RNA_Sequencing_tumor-023

description: Library name: RNA-023


title: Slc17a5 OE M1-5

city: Beijing

first: Shaorong

last: Li

address: Tian Tan Xi Li No. 4

country: China

institute: Capital Mecidal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Monocyte

value: Slc17a5 overexpression plasmid transfection

value: LPS+IFNg


title: 16 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 1

description:
Library name: 20221004_ITP_16cell_control_A
16cell_embryo_control_biol rep1


title: F1_KO_Tau

city: St. Louis

first: Joanna

last: Jankowsky

state: MO

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
Read quality control, mapping, and abundance measurements  were performed by Novogene (Beijing, CN).
Gene counts were normalized and analyzed using the EdgeR pipeline (v3.38.4) in R.
Assembly: mm10
Supplementary files format and content: Comma separated variable file of matrix table with raw gene counts for every gene and every sample, not normalized for library size

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using an RNeasy kit (Qiagen, cat # 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene (Beijing, CN)

value: Brain

tag: batch

tag: Sex

value: F

tag: strain

value: TMEM106b KO x MAPT P301L PS19

tag: age


title: F1_KO

value: KO

value: TMEM106B KO


title: iPSC, NDF-K, DRB_TT_seq_10min_Rep1

description: Library name: Sample 11

value: Cells were treated with 0.1 mM DRB for 3 hours, followed by a 10-minute labeling with 1 mM 4sU without DRB.


title: RNA_Sequencing_tumor-021

description: Library name: RNA-021


title: mESCs, pooled Crispr-Cas9 screen, day10, biological replicate 3

description: Library name: Crisprscreen_day10_biol rep3

library_source: other

data_processing:
NGS reads were trimmed to remove vector specific PCR handles using Cutadaptv1.18  with the following parameters: “-g ACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGGAAAGGACGAAACACCG -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAATTCCCACTCCTTTCAAGACC”. Trimmed reads were aligned to a custom fastq file for all the guides used in the screen using bowtie2 v2.3.4.3. Count table was made using a custom script
Assembly: Custom fasta file with guide sequences
Supplementary files format and content: gene_sgRNA_counts.txt
Library strategy: CRISPR Screen

molecule: other

extract_protocol:
The genomic locations of the identified uORF’s were used to design guide RNAs against the targets using CHOPCHOP v3 66 and IDT's CRISPR-Cas9 guide RNA design tool. The following criteria were used for choosing the best 2 guides per uORF: high on-target score, low mismatch score, position on the predicted uORF. In case of overlapping ORFs we chose guides which cut as far as possible from the annotated ORF. These guides were cloned into lentiCRISPR v2 (Addgene #52961) as a pool as described for the GeCKO Lentiviral CRISPR Toolbox 67. List of the guides and the oligos cloned for this screen is provided in Supplemental TableS7. Briefly, first the lentiCRISPRv2 vector plasmid (Addgene # 52961) was digested with BsmBI-v2 (NEB) for 1 hr at 37°C and heat inactivated at 80°C for 10 mins. The digested product was separated on a TBE-Agarose gel, 8kb band was cut and purified using gel extraction kit (Macherey-Nagel). The forward and reverse oligos for each guide sequence with flanking BsmB1 sites (IDT) were dephosphorylated with T4 PNK (NEB) at and hybridized as individual pairs by incubating at 37°C for 30 mins and inactivation at 95C for 10 mins followed by ramping down the temperature to 4°C at a speed of 5C/min. Equimolar quantities of all the hybridized guides were pooled together and ligated with 1ug pLentiCRISPRv2 linearised lentiCRISPR v2 plasmid at RT for 30 mins. Ligated product was transformed in 250µL of chemically competent NEB Stbl3 cells by heat shock at 40°C for 1 min followed by incubation in ice for 2 mins and recovery in 10 ml warmed SOC outgrowth medium (NEB) for 1hr. All cells were plated on a bioassay plate and incubated at 37°C O/N. Transformants were collected by scraping all the colonies off the plate in LB+Amp and plasmid was isolated using a plasmid maxiprep kit (Zymo) including endotoxin removal steps. This pooled guide library was then used for generating lentivirus. HEK293T cells were grown in T175 flasks and transfected with equimolar ratio of psPAX2, pMD2.G and the pLentiCRISPRv2_pooledlibrary plasmids using Lipofectamine 3000 reagent according to manufacturer's protocol. Viral titer was calculated by infecting mES cells with serial dilutions of virus followed by puromycin selection and colony counting. 1.3X105 mES cells were infected in a T25 flask with the pooled sgRNA lentivirus library at a multiplicity of infection of 0.3 such that there was at least 100X representation of each guide overnight. Next day the media was replaced with 2i ES growth media and cells were allowed to grow for 24hrs. From the next day infected cells were Puromycin selected using 2i ES growth media + 0.3µg/mL puromycin for 48 hrs. Post 2 day selection, the surviving cells were seeded in a T75 flask (considered as Day 1 for the screen) and kept on selection for 8 more days. A portion of these Day 1 cells was stored in -20℃ as input. After 20 cell division cycles or 10 days of growth, cells were harvested.
Genomic DNA was isolated using Zymo mini DNA isolation kit. Guide sequences were amplified from 5µg gDNA in a 100µL PCR reaction divided into four 25µL reactions for 22 cycles using custom made Illumina indexing primers to generate amplicon libraries. PCR products were cleaned with AmpureXP beads and quantified on a bioanalyzer. Guide amplicon libraries were sequenced using NovaSeq X with a PE150 chemistry.

treatment_protocol: mESCs were infected with a pool of lentivirus expressing guideRNAs specific to the target upstream translons identified from the associated ribosome profiling experiments.

value: Embryonic stem cells

value: pooled Crispr-Cas9 screen, day10


title: mESCs, pooled Crispr-Cas9 screen, day10, biological replicate 1

description: Library name: Crisprscreen_day10_biol rep1


title: F1_KI

value: KI

value: TMEM106b T186S KI


title: RNA_Sequencing_tumor-022

description: Library name: RNA-022

value: Pancreatic cancer

value: Germline ATM PV carrier


title: Slc17a5 OE M1-4


title: iPSC, NDF-K, DRB_TT_seq_0min_Rep2

description: Library name: Sample 10

value: hiPSC

value: Cells were treated with 0.1 mM DRB for 2 hours and 50 mins, followed by a 10-minute labeling with 1 mM 4sU in the continued presence of 0.1 mM DRB.


title: iPSC, NDF-K, DRB_TT_seq_0min_Rep1

description: Library name: Sample 9


title: Slc17a5 OE M1-2

value: Monocyte


title: iPSC, NDF-K, DRB_TT_seq_10min_Rep2

description: Library name: Sample 12


title: RNA_Sequencing_tumor-019

description: Library name: RNA-019


title: Slc17a5 OE M1-1

value: Slc17a5 overexpression plasmid transfection


title: iPSC, NDF-WT, DRB_TT_seq_20min_Rep2

description: Library name: Sample 8

value: NDF WT

value: Cells were treated with 0.1 mM DRB for 3 hours, followed by a 10-minute culture in meidum and then 10-minute labeling with 1 mM 4sU


title: mESCs, pooled Crispr-Cas9 screen, day0, biological replicate 2

description: Library name: Crisprscreen_day0_biol rep2

value: pooled Crispr-Cas9 screen, day0


title: RNA_Sequencing_tumor-018

description: Library name: RNA-018


title: Slc17a5 OE M1-3

value: LPS+IFNg


title: mESCs, pooled Crispr-Cas9 screen, day10, biological replicate 2

description: Library name: Crisprscreen_day10_biol rep2


title: RNA_Sequencing_tumor-017

description: Library name: RNA-017


title: mESCs, pooled Crispr-Cas9 screen, day0, biological replicate 1

description: Library name: Crisprscreen_day0_biol rep1


title: iPSC, NDF-WT, DRB_TT_seq_20min_Rep1

description: Library name: Sample 7


title: iPSC, NDF-WT, DRB_TT_seq_10min_Rep2

description: Library name: Sample 6


title: RNA_Sequencing_tumor-016

description: Library name: RNA-016


title: M2-4

value: Empty plasmid transfection


title: RNA_Sequencing_tumor-020

description: Library name: RNA-020


title: Mammary gland epithelial organoids, Estradiol 11 days, rep 2

city: Québec

first: Étienne

last: Audet-Walsh

state: Québec

address: 2705 boulevard Laurier

country: Canada

institute: CRCHU de Québec

description: Library name: GM_Org_E2_11d-2

data_processing:
Timming : trim_galore/cutadapt
QC : FastQC & MultiQC
Pseudoalignement : Kallisto
Normalization : tximport/DESeq2
Assembly: GRCm39 (vM25)
Supplementary files format and content: Comma separated values, with genes on rows and sample on columns. Values are normalized counts.

source_name: Mammary gland

growth_protocol: Mammary glands were extracted, and epithelial cells were purified following protocols described in Lacouture and al. (2021). Organoids were cultured in EpiCult-B mouse medium (StemCell) during 12 days before collect and RNA extraction. During the first 24h of culture, medium was supplemented with 5% FBS.

extract_protocol:
Total RNA was isolated and purified using NEB Monarch Total RNA Miniprep Kit.
Library was constructed using NEBNext Ultra II Directionnal RNA library prep kit for Illumina.

treatment_protocol: Organoids were treated with either Estradiol (10nM) or Ethanol (96%; 1:1,000) during 11 days.

value: Mammary gland

value: Epithelial cells

value: Wild Type

value: Estradiol (E2)

value: 11 days


title: Mammary gland epithelial organoids, Estradiol 11 days, rep 3

description: Library name: GM_Org_E2_11d-3


title: RNA_Sequencing_tumor-015

description: Library name: RNA-015


title: iPSC, NDF-WT, DRB_TT_seq_0min_Rep1

description: Library name: Sample 4


title: iPSC, NDF-WT, DRB_TT_seq_10min_Rep1

description: Library name: Sample 5

value: Cells were treated with 0.1 mM DRB for 3 hours, followed by a 10-minute labeling with 1 mM 4sU without DRB.


title: iPSC, NDF-K, TT_seq_Rep2

description: Library name: Sample 3

value: Cells were labeled with 1 mM 4-thiouridine (4sU) for 10 minutes.


title: M2-2


title: mESCs, pooled Crispr-Cas9 screen, day0, biological replicate 3

description: Library name: Crisprscreen_day0_biol rep3

value: Embryonic stem cells


title: Mammary gland epithelial organoids, Control 11 days, rep 3

description: Library name: GM_Org_Ctrl_11d-3

value: 96% Ethanol (Ctl)


title: Mammary gland epithelial organoids, Estradiol 11 days, rep 1

description: Library name: GM_Org_E2_11d-1


title: M2-3


title: M2-1


title: iPSC, NDF-K, TT_seq_Rep1

description: Library name: Sample 2

value: hiPSC


title: RNA_Sequencing_tumor-012

description: Library name: RNA-012

value: Pancreatic cancer

value: Germline ATM PV carrier


title: Mammary gland epithelial organoids, Control 11 days, rep 2

description: Library name: GM_Org_Ctrl_11d-2


title: M2-5

value: Monocyte


title: M2-6


title: RNA_Sequencing_tumor-014

description: Library name: RNA-014


title: Mammary gland epithelial organoids,Control 11 days, rep 1

description: Library name: GM_Org_Ctrl_11d-1


title: RNA_Sequencing_tumor-011

description: Library name: RNA-011


title: EpiC-FB, NDF-K, RNA_seq_Rep2

description: Library name: Sample 8

data_processing:
RNA-Seq sequencing data were trimmed and aligned to the hg19 reference genome and the ERCC Spike-in RNA annotation using Hisat2. Total reads from each gene were calculated using featureCounts. The standard curve for normalization was calculated as described in Schertzer et al. Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs. Bio Protoc 10, doi:10.21769/bioprotoc.3772 (2020). Statistics analysis was performed using JMP Pro (JMP Statistical Discovery).Differential gene expression analysis was performed using DESeq2, and the results were visualized using the EnhancedVolcano (https://github.com/kevinblighe/EnhancedVolcano) package.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: EpiC-FB

extract_protocol:
For RNA-seq, RNA was purified by TRIzol Reagent (Invitrogen), after DNase I treatment, 1 μg of RNA with ERCC RNA Spike-in Mix 1 was used for library construction.
The RNA-seq libraries were prepared with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB E7775S).

value: EpiC-FB


title: M1-5


title: RNA_Sequencing_tumor-013

description: Library name: RNA-013


title: RNA_Sequencing_tumor-010

description: Library name: RNA-010


title: M1-4


title: GB520_Normal

city: New York

first: Danielle

last: Keahi

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: Library name: GB520_Normal_RNAseq

data_processing:
Transcript abundance was determined using Salmon (v0.8.1)
Assembly: TxDb.Mmusculus.UCSC.mm10.knownGene (v3.4.0)
Supplementary files format and content: CSV file of Salmon TPM output

source_name: Cerebellum

growth_protocol: Mice were monitored for tumor formation or humane euthanasia endpoints and medulloblastoma tumors or normal cerebellum was dissected from freshly euthanized animals prior to flash freezing

extract_protocol:
Tumor samples were homogenized using the TissueLyser II and RNA was isolated with the Zymo RNA Extraction kit for RNAseq samples
Library preparation and sequencing was performed at Genewiz with the NEB Ultra II RNA Library Prep Kit for Illumina

value: Cerebellum


title: RNA_Sequencing_tumor-009

description: Library name: RNA-009


title: EpiC-FB, NDF-K, RNA_seq_Rep1

description: Library name: Sample 7


title: M1-3

value: LPS+IFNg


title: RNA_Sequencing_tumor-008

description: Library name: RNA-008


title: M1-2

value: Empty plasmid transfection


title: GB519_Normal

description: Library name: GB519_Normal_RNAseq


title: EpiC-FB, NDF-WT, RNA_seq_Rep2

description: Library name: Sample 6


title: GB512_Normal

description: Library name: GB512_Normal_RNAseq


title: EpiC-FB, NDF-WT, RNA_seq_Rep1

description: Library name: Sample 5


title: M1-1


title: M1-6


title: RNA_Sequencing_tumor-007

description: Library name: RNA-007


title: iPSC, NDF-WT, TT_seq_Rep1

description: Library name: Sample 1


title: CPC, NDF-K, RNA_seq_Rep2

description: Library name: Sample 4

source_name: CPC

value: CPC


title: GB508_Normal

description: Library name: GB508_Normal_RNAseq


title: T-DM1 sensitive_sample-10

type: RNA

city: Riyadh

first: Syed

middle: S

last: Islam

address: Thakkassassi Street

department: Molecular Oncology

country: Saudi Arabia

institute: King Faisal Specialist Hospitalm Research Center

description: Long non-coding RNA expression from treatment resistant and sensitive samples

hyb_protocol: not provided

scan_protocol: Raw signal intensities were captured and normalized in quantile method by GeneSpring GX v12.1

data_processing: The raw data were extracted using the Agilent  Feature Extraction software (version 11.0.1.1)

source_name: Blood serum_020

label_protocol: 1 ug of RNA was labeled using Cy3

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Mini Lit (Qiagen, USA) following manufacturers protocol. RNA concentration was measured by NanoDrop ND-1000 and RNA quality was assessed by Agilent BioAnalyzer (Agilent Technologies, Santa Clara, USA)

value: Whole blood serum

tag: gender

value: Female


title: T-DM1 sensitive_sample-9

source_name: Blood serum_019


title: RNA_Sequencing_tumor-006

description: Library name: RNA-006


title: GB361_Normal

description: Library name: GB361_Normal_RNAseq


title: RNA_Sequencing_tumor-005

description: Library name: RNA-005


title: GB370_Normal

description: Library name: GB370_Normal_RNAseq

source_name: Normal adjacent cerebellum

value: Normal adjacent cerebellum


title: CPC, NDF-WT, RNA_seq_Rep2

description: Library name: Sample 2


title: T-DM1 sensitive_sample-8

source_name: Blood serum_018


title: CPC, NDF-WT, RNA_seq_Rep1

description: Library name: Sample 1


title: RNA_Sequencing_tumor-003

description: Library name: RNA-003


title: GB370_Tumor

description: Library name: GB370_Tumor_RNAseq

source_name: Medulloblastoma

value: Medulloblastoma


title: NDF_K161A_MNase

description: Library name: Sample2

library_source: genomic

data_processing:
MNase-seq sequencing data were trimmed with Fastp (version 0.23.4) and Trim Galore! (version 0.6.7) Programs and aligned to the hg19 reference genome using Bowtie2 (version 2.5.3). Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools (version 1.15.1). The bam files generated by Bowtie2 were further analysis by Danpos (version 2.2.2), the wig files generated by Danpos were converted to bigwig files with UCSC Tool wigToBigWig. The nucleosome coverage an metagene profiles were further generated by Deeptools and normalized base on the reads of 2,437 transcriptionally inactive genes in cluster 4 (Figure 4c).
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
1 million iPSC cells per biological replicate were applied for MNase-seq. The MNase digestion time was optimized beforehand to yield ~80% mononucleosomes and ~20% dinucleosomes. The 140 – 180 bp fragments correspond to mono-nucleosomes were selected with 6% native gel for library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to kit instructions
MNase-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.


title: T-DM1 sensitive_sample-6

source_name: Blood serum_016


title: RNA_Sequencing_tumor-002

description: Library name: RNA-002


title: GB344_Normal

description: Library name: GB344_Normal_RNAseq


title: CPC, NDF-K, RNA_seq_Rep1

description: Library name: Sample 3


title: T-DM1 sensitive_sample-7

source_name: Blood serum_017


title: OE-NOP14,RNAseq,231

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

data_processing:
Raw reads were trimmed by fastp(v0.23.4) to obtain clean reads. Then clean reads were mapped by STAR (v2.7.11a) to hg38, and gene counts were generated through featureCounts (v2.0.6) with parameters "-t exon  -p  --countReadPairs"
Assembly: hg38
Supplementary files format and content: txt

source_name: Breast

extract_protocol:
The total RNA samples were treated with VAHTS mRNA Capture Beads (Vazyme) to enrich polyA+ RNA before constructing the RNA-seq libraries.
RNA-seq libraries were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions. Briefly, polyA+ RNA samples were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer

value: Breast

value: The triple-negative breast cancer cell line


title: Dermal fibroblast microtissue, Q-peptide-treated

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

institute: University of Toronto

description: Library name: Q_noTGFb

data_processing:
Clean reads were identified and extracted using fastp software, then aligned to a reference genome using HISAT2 (2.2.1) to build the reference genome and align the reads.
Read counts were determined using featureCounts (2.0.6).
Assembly: hg38
Supplementary files format and content: text file listing raw gene counts for each sample

source_name: GFP-HDFCs-ad

growth_protocol: GFP-HDFCs-ad were suspended in a chitosan-collagen hydrogel and seeded in an organ-on-a-chip device (Biowire II), where the cell-hydrogel solution compacted to form a dermal microtissues. Microtissues ere maintained in DMEM supplemented with 1% Penicillin-Streptomycin, 1% GlutaMAX Supplement, 1% HEPES, and 10% fetal bovine serum for two days prior to extraction.

extract_protocol:
Total RNA was extracted with Qiazol. Tissues were lyzed with Qiazol, chloroform was added for phase separation, isopropanol was used to precipitate RNA from the aqueous phase, and samples were washed twice with 75% ethanol before being resuspended in 12 µL of Ultrapure RNase-free water.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. RNA strands were fragmented, then the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. This was followed by A-tailing, adapter ligation, size selection, amplification, and purification, to produce the library, which was checked using Qubit and real-time PCR for quantification, and bioanalyzer for size distribution detection. The libraries were then pooled and put through Illumina sequencing.

treatment_protocol: Transforming growth factor beta was added at a concentration of 5 ng/mL at the time of seeding. QHREDGS peptide was conjugated to the chitosan that formed the hydrogel in which the cells tissues were grown.

value: GFP-HDFCs-ad

value: Human dermal fibroblast


title: GB517_Normal

description: Library name: GB517_Normal_RNAseq


title: Si-ADAR,RNAseq,AGS,rep2

source_name: stomach

value: stomach

value: AGS

value: Human gastric cancer cell line


title: T-DM1 sensitive_sample-2

source_name: Blood serum_012


title: RNA_Sequencing_tumor-004

description: Library name: RNA-004

source_name: Pancreatic cancer

value: Pancreatic cancer

value: Germline ATM PV carrier


title: Dermal fibroblast microtissue, control

description: Library name: noQ_noTGFb


title: Alveolar Bone hTNF-tg 3

city: Dresden

first: Darja

last: Andreev

address: Fetscherstraße 105

department: Center for Regenerative Therapies Dresden (CRTD)

country: Germany

institute: Technische Universität Dresden

description: Library name: AlvBone_TNF_3

data_processing:
Sequences were aligned to the Mus musculus transcriptome (GRCm39) using Kallisto (v0.46.0) and abundance data was extracted from the Kallisto output.
Read count extraction was performed using the R package tximport (Version 1.22.0).
Data normalization was performed using the R package edgeR (Version 3.36.0).
Differential gene expression analysis was performed using the R package limma (Version 3.50.3).
Assembly: GRCm39
Supplementary files format and content: TSV Files contain abundance data for each sample.
Supplementary files format and content: Microsoft Excel Worksheet contains TPM data for each sample.

source_name: Alveolar Bone

extract_protocol:
RNA was extracted from alveolar bone, TMJ, and ankle joint tissues using RNA-Solv® Reagent (VWR; Cat# R6830-02) following the manufacturer’s protocol. Tissues were homogenized using the Precellys® Steel Kit (VWR; Cat# P000910-LYSK0-A) on the Precellys® 24 homogenizer (VWR).
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Cat# E7770) following the manufacturer’s instructions.

value: Alveolar Bone

value: C57BL/6 strain Tg197

value: 11 weeks


title: Dermal fibroblast microtissue, TGFb- and Q-peptide-treated

description: Library name: Q_TGFb


title: D20 LY29 rep 1

city: Los Angeles

first: Nils

last: Lindstrom

state: California

address: 1425 San Pablo St, BCC 413

institute: University of Southern California

description:
Library name: D20 LY29 R1
M13

data_processing:
For processed data, STAR alignment of fastq files to the genome was performed following fastqc check. The feature counts tables were generated from the resulting .bam files using featurecounts and are provided here as .txt files file.
Assembly: Homo sapiens, hg38, Ensembl 105 annotation
Supplementary files format and content: Tab-delimited .txt file includes raw feature counts for each sample

source_name: Kidney organoid

growth_protocol: Takasato et al., 2016 Nature Protocols

extract_protocol:
whole organoids were collected into a cell lysis buffer and total RNA was extracted using Qiagen Rneasy kit
bulk mRNA sequencing

treatment_protocol: organoids were treated with DMSO, CHIR, LY29, and LDN in different combinations described between day 10 and 13 of differentiation

value: Kidney organoid

value: iPSCs (male)

value: WT


title: Alveolar Bone hTNF-tg 1

description: Library name: AlvBone_TNF_1

value: Female


title: Si-ADAR,RNAseq1395rep2

source_name: Lung

value: Lung

value: Human lung adenocarcinoma cells


title: T-DM1 resistant_sample-9

source_name: Blood serum_009

value: Whole blood serum


title: Si-ADAR,RNAseq,1395,rep1


title: D20 LL2 rep 1

description:
Library name: D20 LL2 R1
M18


title: T-DM1 resistant_sample-7

source_name: Blood serum_007


title: D20 LDN rep 2

description:
Library name: D20 LDN R2
M35


title: Alveolar Bone Control 2

description: Library name: AlvBone_Ctrl_2


title: Si-ADAR,RNAseq,549,rep2

value: Breast

value: The triple-negative breast cancer cell line


title: GB359_Normal

description: Library name: GB359_Normal_RNAseq

value: Normal adjacent cerebellum


title: D20 LCL2 rep 2

description:
Library name: D20 LCL2 R2
M39


title: RNA_Sequencing_tumor-001

description: Library name: RNA-001


title: NDF_WT_MNase

description: Library name: Sample1

value: hiPSC


title: GB359_Tumor

description: Library name: GB359_Tumor_RNAseq

value: Medulloblastoma


title: T-DM1 sensitive_sample-5

source_name: Blood serum_015


title: PCDH-NOP14,RNAseq,231


title: T-DM1 sensitive_sample-4

source_name: Blood serum_014


title: GB344_Tumor

description: Library name: GB344_Tumor_RNAseq


title: T-DM1 sensitive_sample-3

source_name: Blood serum_013


title: Alveolar Bone hTNF-tg 4

description: Library name: AlvBone_TNF_4


title: T-DM1 resistant_sample-3

source_name: Blood serum_003


title: T-DM1 sensitive_sample-1

source_name: Blood serum_011


title: Si-ADAR,RNAseq,AGS,rep1

value: stomach

value: AGS

value: Human gastric cancer cell line


title: D20 LCL2 rep 1

description:
Library name: D20 LCL2 R1
M20


title: Temporomandibular joint hTNF-tg 3

description: Library name: TMJ_TNF_3

source_name: Temporomandibular joint

value: Temporomandibular joint

value: C57BL/6 strain Tg197


title: D20 LY29 rep 2

description:
Library name: D20 LY29 R2
M32

value: Kidney organoid


title: Alveolar Bone hTNF-tg 2

description: Library name: AlvBone_TNF_2

value: Alveolar Bone

value: 11 weeks


title: NC-ADAR,RNAseq,AGS

description: AGS-SiNC


title: T-DM1 resistant_sample-10

source_name: Blood serum_010

value: Female


title: Dermal fibroblast microtissue, TGFb-treated

description: Library name: noQ_TGFb

value: GFP-HDFCs-ad

value: Human dermal fibroblast


title: D20 LCL1 rep 2

description:
Library name: D20 LCL1 R2
M38

value: iPSCs (male)

value: WT


title: T-DM1 resistant_sample-2

source_name: Blood serum_002

value: Whole blood serum


title: D20 LL2 rep 2

description:
Library name: D20 LL2 R2
M37


title: Alveolar Bone Control 4

description: Library name: AlvBone_Ctrl_4


title: T-DM1 resistant_sample-8

source_name: Blood serum_008


title: T-DM1 resistant_sample-1

source_name: Blood serum_001


title: D20 CTRL rep 2

description:
Library name: D20 CTRL R2
M30

value: DMSO control


title: NC-ADAR,RNAseq,231

source_name: Breast

value: Breast

value: The triple-negative breast cancer cell line


title: NC-ADAR,RNAseq,1395

value: Lung

value: Human lung adenocarcinoma cells


title: Alveolar Bone Control 3

description: Library name: AlvBone_Ctrl_3


title: Temporomandibular joint Control 4

description: Library name: TMJ_Ctrl_4


title: Temporomandibular joint Control 3

description: Library name: TMJ_Ctrl_3


title: PCDH,cmc-na,RNAseq,rep2

data_processing:
Raw reads were trimmed by fastp(v0.23.4) to obtain clean reads. Then clean reads were mapped by STAR (v2.7.11a) to hg38, and gene counts were generated through featureCounts (v2.0.6) with parameters "-t exon  -p  --countReadPairs"
Assembly: hg38
Supplementary files format and content: csv

value: cmc-na


title: Si-ADAR,RNAseq,231,rep1


title: siPOU2F1-3

city: Wuhan

first: Bin

address: Donghu Road 115

institute: Department of Epidemiology and Biostatistics, School of Public Health; Wuhan University

description: Library name: siPOU2F1-3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by StringTie (v2.1.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
HCT116 cells were cultured in 10 cm cell plates and subsequently treated with siControl and siPOU2F1. After 48 hours of transfection, total RNA from HCT116 cells was harvested using TRIzol reagent (Invitrogen, USA)
2 μg total RNA was used for RNA sequencing library preparation using the NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (E7420L).

value: Colorectal cancer cells

value: POU2F1 knockdown


title: T-DM1 resistant_sample-6

source_name: Blood serum_006


title: D20 LDN rep 1

description:
Library name: D20 LDN R1
M16

value: Kidney organoid


title: Alveolar Bone Control 1

description: Library name: AlvBone_Ctrl_1

source_name: Alveolar Bone

value: Alveolar Bone


title: Si-ADAR,RNAseq,,549,rep1


title: T-DM1 resistant_sample-5

source_name: Blood serum_005


title: D20 CL3 rep 1

description:
Library name: D20 CL3 R1
M15

source_name: Kidney organoid


title: Temporomandibular joint Control 1

description: Library name: TMJ_Ctrl_1

value: Temporomandibular joint

value: 11 weeks


title: PCDH,CX5461,RNAseq,rep3


title: PCDH,CX5461,RNAseq,rep2


title: D20 CL2 rep 2

description:
Library name: D20 CL2 R2
M33


title: Temporomandibular joint hTNF-tg 4

description: Library name: TMJ_TNF_4

value: C57BL/6 strain Tg197

value: Female


title: NC-ADAR,RNAseq,549


title: T-DM1 resistant_sample-4

source_name: Blood serum_004


title: D20 CL2 rep 1

description:
Library name: D20 CL2 R1
M14

value: iPSCs (male)


title: Ankle hTNF-tg 3

description: Library name: Ankle_TNF_3

source_name: Ankle joint

value: Ankle joint


title: sicontrol-1

description: Library name: sicontrol-1

value: WT


title: Si-ADAR,RNAseq,231,rep2


title: ADAR-OE,cmc-na,RNAseq,rep3


title: Temporomandibular joint hTNF-tg 2

description: Library name: TMJ_TNF_2


title: D20 LCL1 rep 1

description:
Library name: D20 LCL1 R1
M19


title: D20 CL3 rep 2

description:
Library name: D20 CL3 R2
M34


title: D20 CTRL rep 1

description:
Library name: D20 CTRL R1
M11

value: DMSO control


title: PCDH,cmc-na,RNAseq,rep3

value: Breast


title: siPOU2F1-2

description: Library name: siPOU2F1-2


title: Ankle hTNF-tg 1

description: Library name: Ankle_TNF_1


title: Temporomandibular joint Control 2

description: Library name: TMJ_Ctrl_2


title: Temporomandibular joint hTNF-tg 1

description: Library name: TMJ_TNF_1


title: Ankle Control 4

description: Library name: Ankle_Ctrl_4


title: PCDH,CX5461,RNAseq,rep1

value: The triple-negative breast cancer cell line


title: hiPSC-NMP_Day6

first: Miao

last: Xu

address: No. 31 Huatuo St., Daxing District, Beijing, P.R.China

institute: National Institutes for Food and Drug Control

description: Library name: Sample3

library_source: transcriptomic single cell

data_processing:
①A CeleScope v2.2.0dev1 (Singleron Biotechnologies, Nanjing, China) pipeline (https://github.com/singleron-RD/CeleScope/blob/master/doc/user_guide.md) was applied to transform raw data, delete low quality reads and align to the GRCh38 reference genome. ②The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v7.1.0 (10x Genomics, USA) (https:/support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cell barcodes, unique molecular identifiers (UMIs) and expression matrix files were obtained for subsequent bioinformatics analysis using R package Seurat (v4.4.0).
Assembly: Human; GRCh38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: iPSC-derived Neuromesodermal progenitor cells_day6

extract_protocol:
①Cells in different time points (day-1, 3, 6, 12, 18) during differentation were digested by 0.75X TripLE and harvested, then washed and resuspended in DPBS prior to scRNA-seq using Singleron GEXSCOPE® protocol. ②After iPSC-spNPG transplantation into SCI mice, chimeric spinal tissue containing injury lesions and grafted iPSC-spNPG cells were collected and immediately snap frozen in liquid nitrogen. Following nuclei isolation, Hochest+ nuclei were sorted into wash buffer and transferred immediately for loading onto the 10X Chromium instrument to perform snRNA-seq.
①Cells were sampled at distinct time points (day-1, 3, 6, 12 and 18) and processed for scRNA-seq libraries construction using Singleron GEXSCOPE® protocol (Singleron). Single-cell suspensions were loaded onto a SCOPE-chip microfluidic device. Through gravity-based sedimentation under Poisson distribution principles, individual cells were isolated into customized microwells. PolyT-conjugated molecularly barcoded beads (containing unique Cell Barcode and UMI sequences) were subsequently added to each well, ensuring one bead per cell 168. Cells were lysed in situ, and mRNA was captured by hybridization of the poly(A) tail to the bead’s polyT oligonucleotides. Reverse transcription was performed to generate barcoded cDNA, incorporating Illumina R1 primer sequences, UMI, and Singleron Barcode.The pooled barcoded cDNA was purified using magnetic beads, amplified by PCR, and size-selected with SPRIselect reagent. During library construction, Illumina R2 primer sequences, P5/P7 adapters, and sample indexes were added to generate paired-end sequencing libraries compatible with Illumina platforms. ②Library was performed according to the manufacter's instructions (single cell 3’v2protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primersequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooledbarcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCRand the apropiated sized fragments were selected with SPRlselect reagent forsubsequent library construction. During the library construction llumina R2 primersequence, paired-end constructs with P5 and P7 sequences and a sample indexwere added.

treatment_protocol: In vitro differentiation of spinal neuron from iPSC; Spinal neural progenitor cell transplantation into SCI mice model

value: Pluripotent stem cell

value: Differentiation


title: ADAR-OE,cmc-na,RNAseq,rep1

value: cmc-na


title: hiPSC_Day-1

description: Library name: Sample1

value: iPSC


title: PCDH,cmc-na,RNAseq,rep1


title: D20 CHIR rep 1

description:
Library name: D20 CHIR R1
M12

value: CHIR (day 11-12)


title: D20 CHIR rep 2

description:
Library name: D20 CHIR R2
M31

value: Kidney organoid


title: sicontrol-2

description: Library name: sicontrol-2

value: Colorectal cancer cells


title: Ankle hTNF-tg 4

description: Library name: Ankle_TNF_4


title: siPOU2F1-1

description: Library name: siPOU2F1-1

value: POU2F1 knockdown


title: sicontrol-3

description: Library name: sicontrol-3


title: D14 LY29 rep 2

description:
Library name: D14 LY29 R2
M23


title: D20 CHIR-LDN rep 2

description:
Library name: D20 CHIR-LDN R2
M36

value: CHIR + LDN (day 11-12)


title: Ankle hTNF-tg 2

description: Library name: Ankle_TNF_2

value: C57BL/6 strain Tg197

value: 11 weeks


title: ADAR-OE,cmc-na,RNAseq,rep2


title: ADAR-OE,CX5461,RNAseq,rep1


title: D20 CHIR-LDN rep 1

description:
Library name: D20 CHIR-LDN R1
M17

value: iPSCs (male)


title: Transplantation of human iPSC-spNPG in mouse spinal cord, 1 week-post injection

description: Library name: Sample6

source_name: iPSC-spNPG transplantation at 1 week post-injection

value: Spinal cord

value: iPSC-derived spinal neural progenitor cells

value: Neural cells

value: Transplantation


title: Ankle Control 3

description: Library name: Ankle_Ctrl_3

value: Ankle joint

value: Female


title: ADAR-OE,CX5461,RNAseq,rep3

value: Breast

value: The triple-negative breast cancer cell line


title: iPSC, LEDGF, ChIP_Hex_Rep2

data_processing:
ChIP-Seq sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. Spike-in normalizations were performed as suggested by the manufacturer.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, after quenching and lysis, chromatin was sonicated with a Covaris S220 focused-ultrasonicator.
ChIP-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.

treatment_protocol: For auxin-inducible degron experiments, 0.5 mM 3-indoleacetic acid (IAA) (Sigma) or 0.1% (v/v) DMSO were added to the culture media of degron cells, for the specified duration. For 1,6-Hexanediol treatment, for ChIP-seq experiments, cells were treated with 1.5% 1,6-Hexanediol for 10 minutes.

tag: chip antibody

value: PSIP1 (Proteintech, 25504-1-AP)

value: hiPSC

value: WT


title: RNA-seq mouse Treg -WT replicate 2

city: Bethesda

first: Jyothi

last: Padiadpu

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
Crlf2fl/fl Foxp3YFP-Cre
WT2

data_processing:
The FASTQ files were generated using the bcl2fastq software for further analysis.
The sequence reads were mapped to the mouse genome (mm10) using Bowtie 2.2.6 and Tophat 2.2.1. Raw counts that fell on exons of each gene were calculated and normalized by RPKM (Reads Per Kilobase per Million mapped reads).
Assembly: mm10
Supplementary files format and content: tab limited file contains read counts in .txt file

source_name: spleen; lymph node

growth_protocol: Naive CD4+ T cells from pooled lymph nodes and spleen of CD45.1 mice were sorted as the live CD4+CD45RBhiCD25- population.

extract_protocol:
Treg cells from pooled lymph nodes and spleen of CD45.2 Foxp3YFP-Cre/Y mice or Foxp3YFP-Cre/YCrlf2fl/fl mice were sorted as live CD4+YFP+ population and used for RNA extraction
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina NovaSeq system.

treatment_protocol: Treg cells from pooled lymph nodes and spleen of CD45.2 Foxp3YFP-Cre/Y mice or Foxp3YFP-Cre/YCrlf2fl/fl mice were sorted as live CD4+YFP+ population.

value: spleen; lymph node

value: Treg


title: Ankle Control 2

description: Library name: Ankle_Ctrl_2


title: iPSC, LEDGF, ChIP_Hex_Rep1


title: PBL from P4

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

description:
Library name: P4-PBL
10X Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-multi software (v7.1.0 ) for CITEseq (5' RNA, FB and TCR) or Cell-Ranger ATAC software (v2.1.0)
Assembly: scRNAseq (GRCh38-2020-A) scTCRseq(GRCh38-alts-ensembl-7.1.0) scATACseq (GRCh38-r107)
Supplementary files format and content: CellRanger output files: D1-GEX_barcodes.tsv.gz, D1-GEX_features.tsv.gz, D1-GEX_matrix.mtx.gz, D1-TCR_filtered_contig_annotations.csv.gz
Supplementary files format and content: CellRanger-ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz

source_name: PBL

extract_protocol:
Dissociated tumor cells were labeled with EpCAM antibody (BD Bioscience). EpCAM+ live cells were sorted by FACS and subjected to single-cell ATAC sample preparation. Live PBL samples were also sorted for single-cell ATAC sample preparation.
Libraries were prepared according to manufactures' instruction (single-cell 5' immune profiling and single-cell ATAC) (10X Genomics)

treatment_protocol: 1 x 105 T cells were co-cultured with neoantigen MT-ND2 (A103T)-loaded DCs for 3 hours. After stimulation, the non-adherent T cells were harvested and stained with an anti-human Hashtag antibody  (TotalSeq-C) for 30 min (Biolegend). Unstimulated (Hashtag #4) and stimulated (Hashtag #5) T cells  were pooled for one single-cell sample preparation.

value: PBL


title: ADAR-OE,CX5461,RNAseq,rep2


title: D14 LY29 rep 1

description:
Library name: D14 LY29 R1
M3

value: Kidney organoid


title: Ankle Control 1

description: Library name: Ankle_Ctrl_1

value: 11 weeks


title: D14 LL2 rep 2

description:
Library name: D14 LL2 R2
M27

value: iPSCs (male)


title: D14 LDN rep 2

description:
Library name: D14 LDN R2
M25


title: iPSC, LEDGF, ChIP_Con_Rep2

value: No


title: pHGG-3058 single nuclei, Short-read

first: Julien

last: Jarroux

address: 413 E 69th St

department: Brain and Mind Research Institute

institute: Weill Cornell Medicine

description: Library name: pHGG-3058 single nuclei, Short-read

data_processing:
Illumina data was processed using cellranger-6.1.2.
Nanopore data was base-called into fastq files using Guppy, keeping reads with a quality score >7. Fastqs were then processed through Scisorseqr package.
Assembly: Human hg38
Supplementary files format and content: Cloupe browser from cellranger-6.1.2 and isoform expression matrixes

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Nuclei from pHGG patient-derived organoids were isolated and processed using the Chromium Next Gem Single Cell Multiome ATAC + Gene Expression kit from 10X Genomics (kit PN-1000285, chip PN-1000230, dual index kit PN-1000215).
The Chromium Single Cell Multiome Gene Expression Library was performed by following the manufacturer’s instructions, starting from 8,000 single-nuclei. For short-read sequencing, library was loaded on an Illumina NovaSeq 6000 with PE 2 × 100 paired-end kit, using the following sequencing read lengths: 28 cycles Read1, 10 cycles i7 index, 10 cycles i5 index, and 90 cycles Read2. For long-read sequencing, cDNA obtained from the 10X Genomics Single Cell Multiome ATAC + Gene Expression kit was used for amplification and exome enrichment. The amplified/enriched cDNA was then sequenced on the Oxford Nanopore Technology platform starting from ~200 fmol cDNA and using the Ligation Sequencing Kit (SQK-LSK114), according to the manufacturer’s protocol (Nanopore Protocol, Amplicons by Ligation, version ACDE_9163_v114_revO_29Jun2022). The ONT library was loaded onto a PromethION sequencer by using PromethION Flow Cell (FLO-PRO114M) and sequenced for 72 h.

value: Brain

value: pediatric high-grade glioma cell line 7316-3058

value: Glioma cell


title: Tumor cells from P3

description:
Library name: P3-Tu
10X Genomics

source_name: Hepatocellular carcinoma stage 2

value: Hepatocellular carcinoma stage 2

value: Tumor cells


title: Tumor cells from P4

description:
Library name: P4-Tu
10X Genomics


title: RNA-seq mouse Treg -WT replicate 1

description:
Crlf2fl/fl Foxp3YFP-Cre
WT1


title: Tumor cells from P2

description:
Library name: P2-Tu
10X Genomics

source_name: Metastatic colorectal cancer

value: Metastatic colorectal cancer


title: D14 LL2 rep 1

description:
Library name: D14 LL2 R1
M8


title: PBL from P3

description:
Library name: P3-PBL
10X Genomics


title: RNA-seq mouse Treg -KO replicate 2

description:
Foxp3YFP-Cre
KO2

value: KO


title: D14 LDN rep 1

description:
Library name: D14 LDN R1
M6


title: RNA-seq mouse Treg -WT replicate 3

description:
Crlf2fl/fl Foxp3YFP-Cre
WT3


title: D14 LCL2 rep 2

description:
Library name: D14 LCL2 R2
M29


title: PBL from P2

description:
Library name: P2-PBL
10X Genomics


title: iPSC, Pol II, ChIP_Hex_Rep2

value: RPB2 (GeneTex, GTX102535)


title: D14 LCL2 rep 1

description:
Library name: D14 LCL2 R1
M10


title: PBL from P1

description:
Library name: P1-PBL
10X Genomics


title: iPSC, LEDGF, ChIP_Con_Rep1

value: PSIP1 (Proteintech, 25504-1-AP)

value: hiPSC


title: RNA-seq mouse Treg -KO replicate 3

description:
Foxp3YFP-Cre
KO3

value: spleen; lymph node


title: iPSC, Pol II, ChIP_Hex_Rep1

value: WT


title: RNA-seq mouse Treg -KO replicate 1

description:
Foxp3YFP-Cre
KO1

value: Treg


title: iPSC, Pol II, ChIP_Con_Rep2


title: Tumor, WT, rep 8

city: Athens

first: Ryan

middle: Joseph

last: Weiss

state: GA

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Barcode adapters were removed by UCSD IGM sequencing core. FASTQ files were checked for quality control with FastQC (v0.11.5) and MultiQC (v1.9)
Reads were aligned to the GENCODE Mus Musculus M27 genome using the STAR aligner and reads were counted through RSEM (v1.3.3)
Counts <1 CPM were filtered out with ComBat and differential expression analysis was carried out with DESeq2 through the DEBrowser (v1.28.0a)
Assembly: GENCODE Mus musculus M27 genome
Supplementary files format and content: tab-delimited text files with FPKM, and TPM for each gene

source_name: Tumor

extract_protocol:
Tumor samples were incubated with TRIzol (Thermo Fisher) and homogenized using the TissueLyser II system (Qiagen). Samples were spun at >10,000 rpm to remove cell debris. Samples were incubated with 200 µL chloroform per 1mL Trizol for 2-3 min at room temperature. To separate the aqueous phase, samples were spun at >10,000rpm for 18min at 4C. The aqueous phase was separated into a new tube and an equal part of 70% Ethanol was added. RNA was isolation using the RNEasy kit (Qiagen) as described by the manufacturer with 1 extra Buffer RPE wash. RNA integrity was verified on a Tapestation (Agilent).
RNA libraries were prepared by the UCSD IGM sequencing core using the Illumina Total RNA Prep with Ribodepletion kit

treatment_protocol: PDAC cells were transplanted orthotopically into the pancreas of syngeneic mice. Tumor cells were harvested for RNA-seq after two weeks of growth.

value: Tumor

value: Pancreatic ductal adenocarcinoma


title: T cells from donor D1, unstimulated and stimulated, TCR

description:
Library name: D1-TCR
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-multi software (v7.1.0 ) for CITEseq (5' RNA, FB and TCR) or Cell-Ranger ATAC software (v2.1.0)
Assembly: scRNAseq (GRCh38-2020-A) scTCRseq(GRCh38-alts-ensembl-7.1.0) scATACseq (GRCh38-r107)
Supplementary files format and content: CellRanger output files: D1-GEX_barcodes.tsv.gz, D1-GEX_features.tsv.gz, D1-GEX_matrix.mtx.gz, D1-TCR_filtered_contig_annotations.csv.gz
Supplementary files format and content: CellRanger-ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz
Library strategy: CITE-seq

source_name: T cells from a healthy donor

value: T cells from a healthy donor

value: T cells

value: unstimulated and antigen-stimulated


title: D14 LCL1 rep 2

description:
Library name: D14 LCL1 R2
M28

value: Kidney organoid

value: iPSCs (male)


title: D14 CTRL rep 2

description:
Library name: D14 CTRL R2
M21

value: DMSO control


title: Tumor, WT, rep 7


title: D14 LCL1 rep 1

description:
Library name: D14 LCL1 R1
M9


title: Tumor, WT, rep 6


title: iPSC, Spt16, ChIP_Hex_Rep2

first: Jia

institute: Rutgers University

value: SPT16 (Cell Signaling, 12191S)


title: D14 CL3 rep 1

description:
Library name: D14 CL3 R1
M5


title: DPSC-GFP, vivo, day21_1

city: Ann Arbor

first: Ririko

last: Tsuboi

state: MI

address: 1011 N.University, Rm 2420

department: Cariology, Restorative Sciences, Endodontics

institute: University of Michigan

description:
Library name: Sample7
10x Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.
Assembly: GRCh38
Supplementary files format and content: Vitro samples: h5 files
Supplementary files format and content: Vivo samples: tab-separated value files and matrix files

source_name: Dental pulp

growth_protocol: DPSCs were maintained in α-MEM supplemanted with 20% fatal bovine serum (FBS) and antibiotics in humidified atomosphere with 5% CO2 at 37℃

extract_protocol:
Virto sample; Cells were collected with trypsin and washed with PBS. Vivo sample; Implants were retrieved and digested in a solution of 3 mg/mL collagenase type I and 4 mg/mL dispase for 40 min at 37°C. DPSC-GFP were sorted by flow sorter. Collected cells were suspended in PBS with 0.04%BSA. The concentotation was 1000cells/µl.
Single cell suspensions were subjected to final cell counting on the Luna Fx7 Automated Cell Counter (LogosBio) and diluted to a concentration of 700 -1000 cells/ul. 3’ single cell libraries were generated using the 10x Genomics Chromium Controller and following the manufacturer’s protocol for 3’ V3.1 chemistry with NextGEM Chip G reagents (10x Genomics). Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (ThermoFisher). Pooled libraries were subjected to 150 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000).

treatment_protocol:
Vitro sample; Control was cultured in α-MEM with 5% FBS for 7 days, vasculogenic differentiation was induced with EGM2-MV supplemented with 50 ng/mL rhVEGF for 7days, neurogenic differentiation was induced with neural induction medium for 4 days and neural differentiation medium for 3days, odontoblast differentiation was induced α-MEM supplemented with 5% FBS and 10 μg/ml of dentin matrix proteins for 7 days.
Vivo sample; GFP transduced DPSCs (DPSC-GFP) were implanted subcutaneously in the dorsum of 5- to 7-week-old male immunodeficient mice. After 7 or 21 days, implants were retrieved and DPSC-GFP were sorted by flow sorter.

value: Dental pulp

value: dental pulp stem cells

value: GFP transduced

value: vivo


title: DPSC-GFP, vivo, day21_2

description:
Library name: Sample8
10x Genomics


title: Tumor, HS3ST1 KO, rep 10


title: Tumor, HS3ST1 KO, rep 9


title: iPSC, Spt16, ChIP_Con_Rep2

last: Fei

address: 604 Allison Rd

value: hiPSC

value: No


title: DPSC-GFP, vivo, day7_2

description:
Library name: Sample6
10x Genomics


title: Tumor, HS3ST1 KO, rep 8


title: iPSC, Spt16, ChIP_Con_Rep1

value: WT


title: D14 CL2 rep 1

description:
Library name: D14 CL2 R1
M4


title: Tumor, WT, rep 5


title: D14 CL2 rep 2

description:
Library name: D14 CL2 R2
M24


title: iPSC, NDF, ChIP_Hex_Rep2

value: antisera against hNDF


title: Tumor cells from P1

description:
Library name: P1-Tu
10X Genomics

value: Metastatic colorectal cancer

value: Tumor cells


title: DPSC-GFP, vivo, day7_1

description:
Library name: Sample5
10x Genomics


title: iPSC, Pol II, ChIP_Con_Rep1

value: RPB2 (GeneTex, GTX102535)


title: D14 CHIR-LDN rep 2

description:
Library name: D14 CHIR-LDN R2
M26

value: CHIR + LDN (day 11-12)


title: T cells from donor D1, unstimulated and stimulated, GEX

description:
Library name: D1-RNA
10X Genomics

value: T cells from a healthy donor

value: T cells

value: unstimulated and antigen-stimulated


title: Tumor, WT, rep 4

value: Tumor

value: Pancreatic ductal adenocarcinoma


title: DPSC, odontogenic diff., day7

description:
Library name: Sample4
10x Genomics

value: Dental pulp

value: odontogenic differentiation


title: D14 CTRL rep 1

description:
Library name: D14 CTRL R1
M1

value: Kidney organoid

value: iPSCs (male)

value: DMSO control


title: DPSC, neurogenic diff., day7

description:
Library name: Sample3
10x Genomics

value: dental pulp stem cells

value: neurogenic differentiation


title: D14 CHIR-LDN rep 1

description:
Library name: D14 CHIR-LDN R1
M7

value: WT


title: iPSC, NDF, ChIP_Con_Rep2

value: antisera against hNDF

value: hiPSC

value: No


title: DPSC, vasculogenic diff., day7

description:
Library name: Sample2
10x Genomics

value: vasculogenic differentiation


title: Tumor, WT, rep 3


title: iPSC, NDF, ChIP_Hex_Rep1


title: iPSC, Spt16, ChIP_Hex_Rep1

value: SPT16 (Cell Signaling, 12191S)


title: iPSC, NDF, ChIP_Con_Rep1


title: D14 CHIR rep 1

description:
Library name: D14 CHIR R1
M2

value: CHIR (day 11-12)


title: Tumor, WT, rep 2


title: DPSC, control, day7

description:
Library name: Sample1
10x Genomics

value: control


title: Tumor, HS3ST1 KO, rep 7

value: Tumor


title: iPSC, Input


title: M8

description:
Library name: Sublibrary 8
Parse Biosciences SPLiT-seq

data_processing:
fastq files were demultiplexed and aligned to the genome using splitpipe from Parse Biosciences
Cell-gene count matricies were processed using Seurat v4 (described in text)
Assembly: Homo sapiens, hg38, Ensembl 105 annotation
Supplementary files format and content: .rds file of processed single-cells from kidney organoids from differentiation day 14, which include both control and distal-enriched cells.

extract_protocol:
6 individual organoids per timepoint were collected for FACS sorting for DRAQ5+, DAPI- single cells, and then fixed using the Parse Biosciences fixation protocol (Evercode Cell Fixation)
Parse Biosciences Evercode WT v2

treatment_protocol: distal-enriched kidney organoids were treated with LY29 from day 10 to day 12, and CHIR and LDN from day 11 to day 12

value: DD14 control and DE organoids


title: Tumor, HS3ST1 KO, rep 6

value: Pancreatic ductal adenocarcinoma


title: A549 cells treated with rhTR11B-biol rep 3

first: Shiyu

last: Qiu

state: Shanghai

address: West Huaihai Road

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: SAMPLE 6
Wr3

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to the reference genome using HISAT. FPKM 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.
Assembly: GRCh38
Supplementary files format and content: Certain tab-delimited text file includes RPKM values for each Sample.
Supplementary files format and content: Certain tab-delimited text file includes counts for each Sample.

source_name: lung

growth_protocol: A549 cells with certain treatments were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (PS) in humidified atomosphere with 5% CO2 at 37°C.

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

treatment_protocol: A549 cells were added and cultured with rhTR11B or PBS.

value: lung

value: A549 cells

value: lung adenocarcinoma cells

value: A549 cells were treated with rhTR11B


title: A549 cells treated with rhTR11B-biol rep 2

description:
Library name: SAMPLE 5
Wr2


title: Tumor, HS3ST1 KO, rep 5


title: M7

description:
Library name: Sublibrary 7
Parse Biosciences SPLiT-seq

value: Kidney organoid

value: iPSCs (male)


title: iPSC, Pol II, ChIP_Rep2

value: RPB2 (GeneTex, GTX102535)

value: WT


title: iPSC, Pol II, ChIP_Rep1

value: hiPSC


title: M6

description:
Library name: Sublibrary 6
Parse Biosciences SPLiT-seq


title: A549 cells treated with rhTR11B-biol rep 1

description:
Library name: SAMPLE 4
Wr1


title: iPSC, Spt16, ChIP_Rep2

value: No


title: A549 cells treated with PBS, NC-biol rep 3

description:
Library name: SAMPLE 3
W3

value: A549 cells were treated with PBS as negative control


title: Tumor, HS3ST1 KO, rep 4


title: M5

description:
Library name: Sublibrary 5
Parse Biosciences SPLiT-seq


title: iPSC, Spt16, ChIP_Rep1

value: SPT16 (Cell Signaling, 12191S)


title: iPSC, NDF, ChIP_Rep2

value: antisera against hNDF


title: D14 CHIR rep 2

description:
Library name: D14 CHIR R2
M22

value: CHIR (day 11-12)


title: A549 cells treated with PBS, NC-biol rep 2

description:
Library name: SAMPLE 2
W2


title: Tumor, WT, rep 1

value: Tumor


title: M2

description:
Library name: Sublibrary 2
Parse Biosciences SPLiT-seq

value: DD14 control and DE organoids


title: Tumor, HS3ST1 KO, rep 2

value: Pancreatic ductal adenocarcinoma


title: iPSC, NDF, ChIP_Rep1


title: A549 cells, TR11B-KO-biol rep 3

description:
Library name: SAMPLE 9
TBsg1-3

growth_protocol: A549 cells with certain genome edition were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (PS) in humidified atomosphere with 5% CO2 at 37°C.

treatment_protocol: A549 cells were transfected with Lenti-CRISPR-V2 Empty plasmid or based OGT or TR11B KO plasmid.

value: lung

value: TR11B knockout

value: A549 cells were transfected with Lenti-CRISPR-V2 based TR11B-KO plasmid.


title: M1

description:
Library name: Sublibrary 1
Parse Biosciences SPLiT-seq


title: Tumor, HS3ST1 KO, rep 1


title: NDF-degron, MNase_Aux2h_Rep2

data_processing:
MNase-seq sequencing data were trimmed with Fastp (version 0.23.4) and Trim Galore! (version 0.6.7) Programs and aligned to the hg19 reference genome using Bowtie2 (version 2.5.3). Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools (version 1.15.1). The bam files generated by Bowtie2 were further analysis by Danpos (version 2.2.2), the wig files generated by Danpos were converted to bigwig files with UCSC Tool wigToBigWig. The nucleosome coverage an metagene profiles were further generated by Deeptools and normalized base on the reads of 2,437 transcriptionally inactive genes in cluster 4 (Figure 4c).
Assembly: hg19
Supplementary files format and content: bigWig

treatment_protocol: For auxin-inducible degron experiments, 0.5 mM 3-indoleacetic acid (IAA) (Sigma) or 0.1% (v/v) DMSO were added to the culture media of degron cells, for the specified duration.

value: NDF-degron

value: Auxin 2 hr


title: 12, chorionic girdle, 33

city: Olsztyn

first: Dawid

last: Tobolski

state: Warmińsko-mazurskie

address: Kazimierza Jaroszyka

department: Department of Large Animal Diseases and Clinic

country: Poland

institute: Institute of Veterinary Medicine, Warsaw University of Life Sciences

description: Library name: Sample 12

data_processing:
Quality control, FastQC v0.11.7
Filtering, Flexbar, 3.5.0
Alignment, Bismark v0.24.2
Reads counting, Htseq-count, 1.99.2
methylaition calling
Assembly: EquCab3.0 (110)
Supplementary files format and content: .bedGraph

organism: Equus caballus

source_name: chorionic girdle

extract_protocol:
Standard procedure of  DNeasy Blood & Tissue Kit (Qiagen)
Standard protocol of Ovation® RRBS Methyl-Seq System (NuGEN Technologies, San Carlos, CA, United States)

value: chorionic girdle

value: Day 33


title: A549 cells, TR11B-KO-biol rep 2

description:
Library name: SAMPLE 8
TBsg1-2

value: A549 cells

value: lung adenocarcinoma cells


title: A549 cells, TR11B-KO-biol rep 1

description:
Library name: SAMPLE 7
TBsg1-1


title: mm LCMV-cl13 Spleen_HTO

city: Melbourne

first: Daniel

last: Rawlinson

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

data_processing:
Alignment and quantification with CellRanger v7.0.0 multi function
Assembly: mm10-2020-A
Supplementary files format and content: .h5 files containing raw counts for both GEX and HTO assay across two experiments

source_name: Spleen

extract_protocol:
Cell populations were FACS sorted and labelled using Total-Seq antibody oligonucleotide cocktails
10x Chromium Single Cell 5’ Library and Gel Bead Kit v2

value: Spleen

value: Wild-type C57BL/6 mice

value: CD8+ T cell

value: wildtype + Klf2 KO

tag: disease state


title: 11, chorionic girdle, 33

description: Library name: Sample 11


title: mm LCMV-cl13 Spleen_GEX


title: 10, chorionic girdle, 33

description: Library name: Sample 10


title: NDF-degron, MNase_DMSO2h_Rep2

city: Piscataway

extract_protocol:
1 million iPSC cells per biological replicate were applied for MNase-seq. The MNase digestion time was optimized beforehand to yield ~80% mononucleosomes and ~20% dinucleosomes. The 140 – 180 bp fragments correspond to mono-nucleosomes were selected with 6% native gel for library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to kit instructions
MNase-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.

value: hiPSC

value: DMSO 2 hr


title: NDF-degron, MNase_Aux2h_Rep1


title: mm LCMV-docile LN&S_HTO

source_name: Lymph node & Spleen

value: Lymph node & Spleen

value: CD8+ T cell and DC

value: wildtype

value: LCMV docile


title: A549 cells, OGT-KO-biol rep 3

description:
Library name: SAMPLE 6
GTsg12-3

value: lung

value: OGT knockout

value: A549 cells were transfected with Lenti-CRISPR-V2 based OGT-KO plasmid.


title: 9, chorionic girdle, 33

description: Library name: Sample 9

value: chorionic girdle


title: A549 cells, OGT-KO-biol rep 2

description:
Library name: SAMPLE 5
GTsg12-2


title: M3

description:
Library name: Sublibrary 3
Parse Biosciences SPLiT-seq

source_name: Kidney organoid

value: Kidney organoid

value: iPSCs (male)

value: WT

value: DD14 control and DE organoids


title: NDF-degron, MNase_DMSO2h_Rep1

value: NDF-degron


title: Tumor, HS3ST1 KO, rep 3

value: Tumor

value: Pancreatic ductal adenocarcinoma


title: 8, allantochorion, 42

description: Library name: Sample 8

source_name: allantochorion

value: allantochorion

value: Day 42


title: A549 cells treated with PBS, NC-biol rep 1

description:
Library name: SAMPLE 1
W1

value: A549 cells

value: lung adenocarcinoma cells

value: A549 cells were treated with PBS as negative control


title: iPSC, NDF-K, RNA_seq_Rep2

data_processing:
RNA-Seq sequencing data were trimmed and aligned to the hg19 reference genome and the ERCC Spike-in RNA annotation using Hisat2. Total reads from each gene were calculated using featureCounts. The standard curve for normalization was calculated as described in Schertzer et al. Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs. Bio Protoc 10, doi:10.21769/bioprotoc.3772 (2020). Statistics analysis was performed using JMP Pro (JMP Statistical Discovery).
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For RNA-seq, RNA was purified by TRIzol Reagent (Invitrogen), after DNase I treatment, 1 μg of RNA with ERCC RNA Spike-in Mix 1 was used for library construction.
The RNA-seq libraries were prepared with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB E7775S).

value: hiPSC

value: No


title: 7, allantochorion, 42

description: Library name: Sample 7


title: A549 cells, NC-biol rep 3

description:
Library name: SAMPLE 3
WT3

value: lung

value: A549 cells were transfected with Lenti-CRISPR-V2 Empty plasmid.


title: Wildtype LEC 72 hours post cataract surgery sample 3

city: Newark

first: Suhotro

last: Gorai

state: Delaware

address: 153 Courtney St

institute: University of Delaware

description:
72_hr_3
72H_RUNX_Cre_N_3_S120

data_processing:
Sequencing was performed by DNA Link USA, Inc
Aligned reads using HISAT2
Quanitified genes using htseq-count
Differential expression analysis was performed using edgeR
Assembly: Mus musculus GRCm39 Ensembl version 110
Supplementary files format and content: Gene level counts and Differential expression analysis results provided in an excel spreadsheet
Supplementary files format and content: Individual count files for each sample

source_name: lens capsule

extract_protocol:
RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104). (O’Neill, L. M., Wang, Y., & Duncan, M. K. (2023). Modeling Cataract Surgery in Mice. Journal of Visualized Experiments : JoVE, 202. https://doi.org/10.3791/66050)
Takara SMARTer Stranded Pico v2

value: lens capsule

value: lens epithelial cells (LEC)

value: wildtype

value: cataract surgery

value: 72 hour


title: iPSC, NDF-WT, RNA_seq_Rep2

value: NDF WT


title: Wildtype LEC 72 hours post cataract surgery sample 2

description:
72_hr_2
72H_RUNX_Cre_N_2_S119


title: 5, allantochorion, 42

description: Library name: Sample 5


title: 4, allantochorion, 33

description: Library name: Sample 4

value: Day 33


title: A549 cells, NC-biol rep 1

description:
Library name: SAMPLE 1
WT1

value: WT


title: Wildtype LEC 72 hours post cataract surgery sample 1

description:
72_hr_1
72H_RUNX_Cre_N_1_S118


title: iPSC, NDF-WT, RNA_seq_Rep1


title: Wildtype LEC zero hours post cataract surgery sample 3

description:
0_hr_3
0H_RUNX_Cre_N_3_S117

value: 0 hour


title: 3, allantochorion, 33

description: Library name: Sample 3

value: allantochorion


title: iPSC, NDF-K, Pro_seq_Rep2

data_processing:
PRO-Seq sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: PRO-Seq

extract_protocol:
For Pro-seq, cells were permeabilized and aliquoted with 1 million cells in 52 μL freeze buffer as described in Judd et al. A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq). bioRxiv, doi:10.1101/2020.05.18.102277.
Pro-seq was performed as described in Judd et al. A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq). bioRxiv, doi:10.1101/2020.05.18.102277.


title: Wildtype LEC zero hours post cataract surgery sample 2

description:
0_hr_2
0H_RUNX_Cre_N_2_S116


title: mm LCMV-docile LN&S_GEX

value: Lymph node & Spleen

value: Wild-type C57BL/6 mice

value: CD8+ T cell and DC

value: LCMV docile


title: Wildtype LEC zero hours post cataract surgery sample 1

description:
0_hr_1
0H_RUNX_Cre_N_1_S115


title: pHGG-3058 single nuclei, Long-read

description: Library name: pHGG-3058 single nuclei, Long-read

value: Brain

value: pediatric high-grade glioma cell line 7316-3058

value: Glioma cell


title: A549 cells, OGT-KO-biol rep 1

description:
Library name: SAMPLE 4
GTsg12-1

value: lung

value: A549 cells

value: lung adenocarcinoma cells

value: OGT knockout

value: A549 cells were transfected with Lenti-CRISPR-V2 based OGT-KO plasmid.


title: H1-Btx

city: Zhengzhou City

first: Jingbo

last: Li

state: Henan Province

address: No. 6, Dongfeng Road

department: Department of Otorhinolaryngology

institute: Henan Province Hospital of Traditional Chinese Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellcosmo software v1.0.12(https://github.com/10KGenomics/CellCosmo)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood after treatment

extract_protocol:
Nuclei from frozen tissues were isolated using 10K Genomics nuclei isolation buffer with dounce homogenizer. The single nuclei suspensions were counted using lunaTM cell counter(Logos Biosystems), appropriate amount of nuclei were loaded onto a microfluidic chip of 10K Genomics 3’ single nuclei RNA kit v1.1，along with reverse transcription reagents, barcoding gel beads and droplet generation oil. The microfluidic chip was run on the 10K Genomics-Perseus™ single cell processing system to generate droplet emulsion, which is transferred to a thermal cycler to perform in drop reverse transcription. Barcoded cDNA was then purified from the emulsion using SPRI beads and PCR amplified. Sequencing libraries were prepared according to the manufacturer’s instructions of 10K Genomics Library Amp Kit and sequenced on Illumina NovaSeq 6000TM system in paired-end mode.
Sequencing libraries were prepared according to the manufacturer’s instructions of 10K Genomics Library Amp Kit and sequenced on Illumina NovaSeq 6000TM system in paired-end mode.

value: Blood after treatment

value: immunity cell


title: iPSC, NDF-WT, Pro_seq_Rep2

value: hiPSC

value: NDF WT

value: No


title: H2-Atx

description: 10X Genomics

source_name: Blood before treatment

value: Blood before treatment


title: H1-Atx

description: 10X Genomics


title: Wildtype LEC 5 day sample 3

description:
120_hr_3
7_S261

extract_protocol:
Lenses were dissected from mice and RNA extracted using SV Total RNA Isolation System (Invitrogen) (O’Neill, L. M., Wang, Y., & Duncan, M. K. (2023). Modeling Cataract Surgery in Mice. Journal of Visualized Experiments : JoVE, 202. https://doi.org/10.3791/66050)
SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian

value: lens capsule

value: lens epithelial cells (LEC)

value: wildtype

value: 5 day


title: A549 cells, NC-biol rep 2

description:
Library name: SAMPLE 2
WT2

value: WT

value: A549 cells were transfected with Lenti-CRISPR-V2 Empty plasmid.


title: iPSC, NDF-K, Pro_seq_Rep1


title: mouse Morula embryo - TMZ3

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

institute: wenzhou medical university

description: Library name: Sample12

data_processing:
Remove adapters from raw Cut&Tag data using fastp v 0.23.4
Cut-tag reads were aligned to the NCBI GRCm39 using Bowtie version 2.5.4
to create cut-tag coverage plots,the locations of the mapped cut-tag reads were extended to 50bp represent sequenced fragments,renormalizes and reformatted in the bigwig file format
Peaks were called using MACS v3.0.3 with the significance cut-off q-value <= 0.001
bigWig files were generated using deeptools v3.5.5
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse Morula embryo

growth_protocol: mouse embryos were maintained in KsOM and cultured in an incubator at 37°C with 5% CO₂

extract_protocol:
Cells were bound to concanavalin A-coated magnetic beads and permeabilized with the nonionic detergent digitonin
ChIP-seq libraries were prepared using Hyperactive® Universal CUT&Tag Assay Kit for Illumina.By using a primary antibody against H3K18ac, along with a corresponding secondary antibody and Protein A/G, the transposase fused to Protein A/G is precisely directed to cleave DNA sequences near the target protein. During the cleavage process, adaptor sequences are simultaneously added to both ends of the DNA fragments. The fragments were then amplified by 18 cycles of PCR to generate libraries suitable for high-throughput sequencing.

treatment_protocol: At the 2-cell stage,embryos were treated with 100uM TMZ(Merck)

value: mouse Morula embryo

value: TMZ inhibitor


title: Wildtype LEC 5 day sample 2

description:
120_hr_2
W_5_D_3_S260


title: iPSC, NDF-K, RNA_seq_Rep1


title: iPSC, NDF-K, NDF, Cut&Run_Clone22

data_processing:
CUT&RUN sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. Spike-in normalizations were performed as suggested by the manufacturer.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
For Cut&Run, 100, 000 live cells were prepared following the Cut&Run assay Kit (Cell Signaling Technology).
Cut&Run libraries were prepared with the CUT&RUN Assay Kit (Cell Signaling Technology 86652).

value: antisera against hNDF


title: 1, allantochorion, 33

description: Library name: Sample 1

value: allantochorion

value: Day 33


title: Wildtype LEC 5 day sample 1

description:
120_hr_1
W_5_D_1_S259


title: iPSC, NDF-WT, Pro_seq_Rep1


title: mouse Morula embryo - TMZ2

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample11


title: mouse Morula embryo - TMZ1

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample10


title: iPSC, NDF-WT, NDF, Cut&Run


title: Wildtype LEC zero hour sample 3

description:
0_hr_3
W_0_hr_3_S258

value: 0 hour


title: mouse Morula embryo - Control3

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample9


title: 2, allantochorion, 33

description: Library name: Sample 2


title: Wildtype LEC zero hour sample 1

description:
0_hr_1
W_0_hr_1_S256


title: NDF-degron, NDF, Cut&Run_Aux1h_Rep2

value: NDF-degron

value: Auxin 1 hr


title: mouse Morula embryo - Control2

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample8


title: H2-Btx

description: 10X Genomics

value: Blood after treatment

value: immunity cell


title: Splenic pDC, WT, HTO

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
RNA library sequenced reads were aligned to Mus musculus reference genome (mm10/GRCm38) using CellRanger (10X Genomics). UMI correction was performed to handle PCR duplications. Quality control was then performed by calculating the number of genes, UMIs and the proportion of mitochondrial genes for each cell using iCellR R package (v1.2.1) (https://github.com/rezakj/iCellR). Cells were filtered out if they did not meet the following quality control thresholds:
-Ratio of reads mapping to mitochondrial/nuclear < 0.1
-Minimum number of genes > 500
-Maximum number of genes < 5000
Then the gene-cell matrix was normalized based on ranked geometric library size factor (ranked GLSF) using iCellR.
Assembly: mm10
Supplementary files format and content: CSV file contains single cell raw counts for all genes by cell.
Library strategy: CITE-Seq

molecule: protein

extract_protocol:
Nucleic acids were extracted from single cells according to the 10x Genomics Single Cell Genomics Protocol (v2).
The cDNA fraction was converted into a 3’ tag gene expression library according to the 10x Genomics Single Cell Genomics Protocol (v2).

value: Spleen

value: Plasmacytoid dendritic cell


title: mouse Morula embryo - Control1

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample7


title: NDF-degron, NDF, Cut&Run_DMSO1h_Rep2

value: hiPSC

value: DMSO


title: mouse 8-Cell embryo - TMZ3

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample6

source_name: mouse 8-Cell embryo

value: mouse 8-Cell embryo


title: Splenic pDC, WT, RNA

value: WT


title: NDF-degron, NDF, Cut&Run_Aux1h_Rep1


title: Splenic pDC, WT, ADT


title: NDF-degron, NDF, Cut&Run_DMSO1h_Rep1


title: mouse 8-Cell embryo - TMZ1

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample4


title: mouse 8-Cell embryo - TMZ2

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample5


title: NDF-degron, NDF, Cut&Run_DMSO_Rep2


title: iPSC, NDF-K, NDF, Cut&Run_Clone20

value: No


title: Wildtype LEC zero hour sample 2

description:
0_hr_2
W_0_hr_2_S257

value: lens capsule

value: lens epithelial cells (LEC)

value: wildtype


title: NDF-degron, NDF, Cut&Run_Aux2h_Rep2

value: antisera against hNDF

value: Auxin 2 hr


title: Splenic pDC, WT, RNA

description:
Gene Expression
filtered_feature_bc_matrix.h5

data_processing:
cellranger arc v2.0 was used to generate counts tables for both assays
Counts were QC'd using standard Signac and Seurat workflow including for ATAC: 3000 < atac peak region fragments < 20000; percent reads in peaks > 15%; percent of reads falling into blacklist regions < 10%; nucleosome signal < 4 (ratio of nucleosome-bound : nucleosome-freee fragments);TSS  > 2 (ratio of fragments falling to TSS regions : TSS-flanking regions)
RNA QC: 1000 < read counts < 25000; percent of reads mapping to mitochondrial genome < 20%
ATAC reads were normalized via TF-IDF; RNA reads normalized using SCTransform
Assembly: mm10
Supplementary files format and content: .h5 counts object and comma-separated metadata produced by cellranger arc
Library strategy: 10X Multiome (snATAC + snRNA)

extract_protocol:
We followed the 10X Genomics protocol for nuclei isolation with a lysis time of 4 minutes.
Libraries were constructed as per the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User GuideCG000338 Rev F


title: NDF-degron, NDF, Cut&Run_Aux2h_Rep1


title: pDC-C, WT, CpG-A, rep2

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The FASTQ files were further processed using Seq-N-Slide pipeline.
The sequencing reads were adapter and quality trimmed with Trimmomatic and then aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The FeatureCounts program was utilized to generate counts for each gene based on the number of aligned reads that overlap its exons.
These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Assembly: mm10/GRCm38
Supplementary files format and content: CSV file contains raw counts for all genes and samples.

extract_protocol:
RNA was purified from cells using RNeasy Micro kit w/ gDNA Eliminator column (QIAgen Cat# 74034).
Low input Clontech SMART- Seq HT with Nxt HT

value: Sca1+ CD69+ pDC

value: CpG-A


title: mouse 8-Cell embryo - Control1

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample1


title: mouse 8-Cell embryo - Control2

address: 瓯海区茶山街道温州医科大学

description: Library name: Sample2


title: pDC-C, WT, CpG-A, rep3


title: NDF-degron, NDF, Cut&Run_DMSO_Rep1

value: NDF-degron


title: NDF-degron, Spt16, ChIP_Aux2h_Rep3

data_processing:
ChIP-Seq sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. Spike-in normalizations were performed as suggested by the manufacturer.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, after quenching and lysis, chromatin was sonicated with a Covaris S220 focused-ultrasonicator.
ChIP-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.

value: SPT16 (Cell Signaling, 12191S)


title: pDC-C, WT, CpG-A, rep1


title: iPSC, NDF-K, Spt16, ChIP_Rep2


title: Porphyromonas gingivalis replicate 2

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description:
Library name: PG.R2
In the PETRI-seq script, the barcode sequences were renamed as the individual cell ID such as EX16_bc1_9_bc2_9_bc3_94 on the fly, so there are no logs or intermediate files for the information about the actual barcode sequences for each cell ID.

data_processing:
The raw reads were processed using the PETRI-Seq computational pipeline scripts (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/)
Assembly: The processed reads were aligned Porphyromonas gingivalis w83 genome (Refseq: GCF_002892595.1).
Supplementary files format and content: The raw read counts for each gene and each single cell were formatted as a matrix file.

organism: Porphyromonas gingivalis

source_name: w83 strain

growth_protocol: P. gingivalis W83 was cultivated anaerobically at 37°C Brain Heart Infusion broth containing 5 mg/L hemin and 1 mg/L vitamin K1.

extract_protocol:
Bacterial cells were fixed with 4% formaldehyde in PBS, permeabilized with lysozyme treatment, and processed for RNA extraction using a modified PETRI-seq protocol. RNA integrity was maintained with RNase inhibitors throughout the procedure.
Single-cell transcriptomes were captured using PETRI-Seq, which employs iterative split-pool barcoding to tag transcripts at the single-cell level. The resulting cDNA libraries underwent second-strand synthesis, tagmentation using the Nextera XT DNA Library Preparation Kit, and PCR amplification. Libraries were purified, quantified, and sequenced on an Illumina NextSeq platform.

value: w83 strain


title: pDC-A, Ifnar1-KO, rep3

value: Spleen

value: Sca1- CD69- pDC


title: Porphyromonas gingivalis replicate 3

description:
Library name: PG.R3
In the PETRI-seq script, the barcode sequences were renamed as the individual cell ID such as EX16_bc1_9_bc2_9_bc3_94 on the fly, so there are no logs or intermediate files for the information about the actual barcode sequences for each cell ID.


title: NDF-degron, Spt16, ChIP_DMSO2h_Rep3

value: hiPSC

value: DMSO 2 hr


title: iPSC, NDF-K, Spt16, ChIP_Rep1


title: Porphyromonas gingivalis replicate 1

description:
Library name: PG.R1
In the PETRI-seq script, the barcode sequences were renamed as the individual cell ID such as EX16_bc1_9_bc2_9_bc3_94 on the fly, so there are no logs or intermediate files for the information about the actual barcode sequences for each cell ID.


title: pDC-A, Ifnar1-KO, rep2


title: iPSC, NDF-WT, Spt16, ChIP_Rep2

value: NDF WT


title: Splenic pDC, WT, ATAC

description:
Peaks
filtered_feature_bc_matrix.h5

value: Plasmacytoid dendritic cell

value: WT


title: pDC-A, Ifnar1-KO, rep1


title: 564Igi B cell V(D)J

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

description: Library name: 100-B-VDJ

data_processing:
Data were aligned with reference genome refdata-cellranger-mm10-3.0.0 with  CellRanger version 3.0.2.
Assembly: mm10
Supplementary files format and content: matrix output from CellRanger

extract_protocol:
total splenocytes were purified as for flow cytometry, followed by negative selection with biotinylated Ter-119, anti-biotin microbeads, and magnetic separation (Miltenyi).
Following single-cell separation on the 10x Chromium system and cDNA generation, libraries were generated using the 5’mRNA and V(D)J kits, then sequenced using PE100 sequencing on DNBSEQ.

value: 564Igi heterozygous (B6.129S4(Cg)-Igktm1(Igk564)Tik Ightm1(Igh564)Tik/J)


title: 564Igi T cell V(D)J

description: Library name: 100-T-VDJ


title: pDC-C, WT, rep2


title: pDC-C, WT, rep3


title: iPSC, NDF-K, NDF, ChIP

value: No


title: iPSC, NDF-WT, Spt16, ChIP_Rep1


title: iPSC, NDF-WT, NDF, ChIP


title: WT T cell V(D)J

description: Library name: 85-T-VDJ


title: pDC-C, WT, rep1


title: WT B cell V(D)J

description: Library name: 85-B-VDJ


title: pDC-B, WT, rep3

value: Sca1+ CD69- pDC


title: Spt16-degron, NDF, ChIP_Aux4h_Rep1

value: antisera against hNDF

value: Auxin 4 hr


title: pDC-B, WT, rep2


title: T cells from donor D1, unstimulated and stimulated, feature barcode (FB)

description:
Library name: D1-FB
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-multi software (v7.1.0 ) for CITEseq (5' RNA, FB and TCR) or Cell-Ranger ATAC software (v2.1.0)
Assembly: scRNAseq (GRCh38-2020-A) scTCRseq(GRCh38-alts-ensembl-7.1.0) scATACseq (GRCh38-r107)
Supplementary files format and content: CellRanger output files: D1-GEX_barcodes.tsv.gz, D1-GEX_features.tsv.gz, D1-GEX_matrix.mtx.gz, D1-TCR_filtered_contig_annotations.csv.gz
Supplementary files format and content: CellRanger-ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz
Library strategy: CITE-seq

extract_protocol:
Dissociated tumor cells were labeled with EpCAM antibody (BD Bioscience). EpCAM+ live cells were sorted by FACS and subjected to single-cell ATAC sample preparation. Live PBL samples were also sorted for single-cell ATAC sample preparation.
Libraries were prepared according to manufactures' instruction (single-cell 5' immune profiling and single-cell ATAC) (10X Genomics)

value: T cells from a healthy donor

value: T cells

value: unstimulated and antigen-stimulated


title: Spt16-degron, NDF, ChIP_Aux4h_Rep2


title: pDC-B, WT, rep1


title: WT gene expression

description: Library name: 85-5_expression


title: Spt16-degron, NDF, ChIP_DMSO4h_Rep1

value: DMSO 4 hr


title: Spt16-degron, NDF, ChIP_DMSO4h_Rep2


title: pDC-A, WT, rep2


title: pDC-A, WT, rep1


title: Replicate 2, AVP-flox;Cre, Tamoxifen

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description: Library name: Sample 6

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 113). Transcript per million (TPM) and expected counts were generated by RSEM. Computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 113
Supplementary files format and content: RNA_rawTPM.txt

source_name: Kidney

growth_protocol: Mice were maintained in NHLBI/NIH mouse facicility

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMART-Seq HT Kit (Takara Bio). cDNA was generated using 1 ng of total RNA with 11 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

value: Kidney

value: IMCD

value: AVP-flox; Cre

value: Tamoxifen


title: CD45+GFP+ plaque cells

city: New York

first: Fang

department: Medicine

institute: Columbia University Irving Medical Center

description:
10X Genomics
HF02

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v3.0.1.
The outputs of Cell Ranger were analyzed using Seurat 4.3.0.1 in R.
Samples were filtered based on the number of genes per cell (> 800 and < 6000), number of Unique Molecular Identifiers (< 20000), and percentage of mitochondrial genes (< 5%).
Differential expressing genes among clusters were performed using the MAST 1.26.0 test with min.pct threshold as 0.1.
Genes with an absolute fold change > 1.5 and Bonferroni-corrected P < 0.05 were defined as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: HF01_barcodes.tsv.gz: list of barcode for HF01
Supplementary files format and content: HF01_features.tsv.gz: list of gene IDs for HF01
Supplementary files format and content: HF01_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for HF01
Supplementary files format and content: HF02_barcodes.tsv.gz: list of barcode for HF02
Supplementary files format and content: HF02_features.tsv.gz: list of gene IDs for HF02
Supplementary files format and content: HF02_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for HF02

source_name: atherosclerotic plaque cells

extract_protocol: Samples were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 (mouse samples) according to the manufacturer's instructions by Single Cell Analysis Core at the JP Sulzberger Columbia Genome Center.

value: atherosclerotic plaque cells

value: LysMCre+/-, LipaTg/wt, Ldlr-/-


title: NDF-degron, Pol II, ChIP_Aux2h_Rep2

value: RPB2 (GeneTex, GTX102535)

value: hiPSC

value: NDF-degron

value: Auxin 2 hr


title: NDF-degron, Pol II, ChIP_Aux2h_Rep1


title: Replicate 3, AVP-flox;Cre, Tamoxifen

description: Library name: Sample 7


title: 564Igi gene expression

description: Library name: 100-5_expression

value: Spleen

value: 564Igi heterozygous (B6.129S4(Cg)-Igktm1(Igk564)Tik Ightm1(Igh564)Tik/J)


title: Replicate 1, AVP-flox;Cre, Tamoxifen

description: Library name: Sample 5


title: NDF-degron, Pol II, ChIP_DMSO2h_Rep2

value: DMSO 2 hr


title: Replicate 4, AVP-flox, Tamoxifen

description: Library name: Sample 4

value: AVP-flox


title: NDF-degron, Pol II, ChIP_DMSO2h_Rep1


title: PM, Lipa overexpression, replicate 2

description:
Element Biosciences AVITI sequencer
LipaTg2

data_processing:
Raw sequencing reads were mapped to the mouse genome version GRCm39 (M33) using Salmon (version 1.10.2) to obtain transcript abundance counts. MultiQC was used to generate quality control reports based on Salmon read mapping results.
The transcript-level count information was summarized to the gene level using tximport (version 1.28.0).
Differential expression was assessed using DESeq2 (version 1.40.0). Genes with an absolute fold change > 1.5 and false discovery rate (FDR)-adjusted P value < 0.05 were considered as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld

source_name: PM

extract_protocol:
Total RNAs were extracted from PMs (female mice: 3 Ctl and 3 LipaTg) using the Quick-RNA miniprep plus kit (Zymo).
With a minimum of 150 ng input RNA, strand-specific, poly(A)+ libraries were prepared and sequenced at 20 million 100-bp paired-end reads per sample.

value: PM

value: Female


title: Replicate 3, AVP-flox, Tamoxifen

description: Library name: Sample 3


title: NDF-degron, Spt16, ChIP_Aux2h_Rep2

value: SPT16 (Cell Signaling, 12191S)


title: CD45+GFP- plaque cells

description:
10X Genomics
HF01

value: LysMCre-/-, LipaTg/wt, Ldlr-/-