title: WT, M31, HF+SD, 3W

first: Nancy

last: Carrasco

address: 2215 Garland Ave.

department: Molecular Physiology & Biophysics

institute: Vanderbilt University

description: Library name: 10687-JS-08

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 40-100 million uniquely mapped reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis using R version 4.1.0.
Assembly: mm39
Supplementary files format and content: comma separated text file containing raw counts for each sample
Supplementary files format and content: comma separated text file containing normalized counts for each sample

source_name: thyroid

growth_protocol: C57Bl/6J mice were placed on their respective diets (see experimental design/treatment protocol) at 8 weeks of age.

extract_protocol:
RNA was extracted using a hybrid method utilizing Trizol reagent and Qiagen RNeasy kit: The tissue samples were homogenized in the presence of 1 ml Trizol and 1.5 mm stainless steel bead, using the Qiagen TissueLyser II instrument for 2 min at 25 Hz, twice. Homogenized samples were incubated for 5 min at room temperature after which 200 ml chloroform was added, mixed well, and incubated for 3 min at room temperature. Samples were centrifuged at 10,000 x g at 4°C, after which the aqueous layer was transferred to a new tube and mixed with equal volume of 70%. The samples were loaded onto Qiagen RNAeasy column, and the samples were processed according to the protocol, including the optional on column DNAse treatment.  RNA was eluted in 35 µl of RNAse free water.
A Quality Control analysis was performed on the RNA samples using the Agilent Bioanalyzer to assess quality and an RNA Qubit assay was used to determine quantity.  Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit (NEB) (P/N: E7765L, NEB, Ipswich, MA) following the manufacturer’s instructions.  End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument. Next, prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturer's protocols. 150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50M reads per sample.  Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment. Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.

treatment_protocol: C57Bl/6J mice were placed on a high-fat diet and sucrose water, whereas control mice were given a chow diet. Thyroids were collected at two timepoints (3 weeks and 6 weeks).

value: thyroid

tag: age

value: WT

value: Overnutrition


title: ADT and HTO from dARC COG5 and uninfected clone from donor OM5334

status: Public on Feb 05 2026

type: SRA

city: New York

first: Alberto

last: Herrera

state: New York

department: Medicine

country: USA

institute: Weill Cornell Medicine

description:
Library name: BJ_clones_10_2_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

library_source: other

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Memory CD4+ T-cells (mCD4) were isolated from the PBMCs  of people with HIV (PWH) by negative selection using EasySep™ Human Memory CD4+ T Cell Enrichment Kit (STEMCELL Technologies), plated (10 cells/well, 96-well plates), and stimulated with irradiated allogeneic HIV-negative PBMCs (1x106/mL) in R10-100 with ARVs (RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, 1% HEPES buffer, 1% L-Glutamine supplemented with 100 Units/mL of IL-2, 1 µM Nevirapine, 1 µM Emtricitabine, 1 µM Tenofovir, 10 µM Enfuvirtide, and 10 µg/mL 10-1074 bNAb) with CD3 and CD28 antibodies for 21 days. Feeder PBMCs were depleted of CD8+ T-cells and NK cells using EasySep™ Human CD8 Positive Selection Kit II and EasySep™ Human CD56 Positive Selection Kit II (STEMCELL Technologies) before being co-cultured with mCD4 T-cells from PWH. At the end of stimulation cycle, p24 ELISA was performed on all plates. Cells from p24 ELISA-positive wells were plated in serial 3-fold dilution (96-well plates), stimulated at the same condition as aforementioned, and subjected to p24 ELISA after 21 days. After the second round of plating and ELISA, cells from p24 ELISA-positive wells were expanded under the same stimulation condition. Clonal purity of isolated infected populations was determined using IPDA and further serial dilution subs were performed as needed.

extract_protocol:
Following 2 weeks of rest from stimulation with  CD3 and CD28 antibodies and feeders in R10-100 with ARVs, cells were stained with DNA oligo-barcoded antibodies and loaded onto the 10x Chromium single-cell workflow (10X Genomics) as previously described61 with a few modifications. Approximately 0.05-0.3 x 106 cells per sample were resuspended in R10 media and incubated with the TotalSeq™-C Human Universal Cocktail (Biolegend) for 30 minutes at 4°C. In some cases, TotalSeq™-C hashing antibodies #1, #3 and #4 (Biolegend) were spiked into individual samples, which allowed for multiplexing of ARCs and uninfected clone combinations into the same 10X lane. After staining, cells were washed 3 times in R10 media, followed by centrifugation (400 × g for 5 minutes at 4°C) and supernatant aspiration. After the final wash, cells were resuspended in PBS and filtered through 70-µm cell strainers
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions (CG000330, revision G)

tag: tissue

value: peripheral blood

tag: cell type

value: CD4+ T cells

tag: adt

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)

tag: hto

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (dARC COG5), TotalSeq-C Hashtag 4 AGTAAGTTCAGCGTA (Uninfected clone)


title: WT, M19y, HF+SD, 3W

city: Nashville

state: TN

description: Library name: 10687-JS-06

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: strain

tag: treatment


title: WT, M20y, HF+SD, 3W

description: Library name: 10687-JS-07


title: TCR from dARC COG5 and uninfected clone from donor OM5334

description:
Library name: BJ_clones_10_2_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv

molecule: polyA RNA


title: WT, M7, HF+SD, 3W

description: Library name: 10687-JS-05


title: I618, PBMC before treatment, scTCR-seq

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
Library name: I618_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: TCR-Seq

molecule: other

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v1.1 or v2 (Dual Index) protocol (CG000208 or CG000331), 10x Genomics).

value: Peripheral Blood Mononuclear Cells

value: CD4+ T cell

tag: disease

value: Lung cancer


title: KPPC_takinib

city: ST LOUIS

first: KIAN

middle: HUAT

last: LIM

state: MO

address: 660 S. Euclid Avenue  Campus Box 8069, St. Louis

department: internal Medicine

institute: WashU

description:
Library name: Sample 2
10x genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcodes processing, gene counting and aggreegation were made using Cell Ranger software v2.1.1
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic cancer

extract_protocol:
Pancreatic tumors were harvested immediately after euthanasia cardiac punctured. Isolated fresh tumor tissues were washed with cold PBS, minced and dissociated to single-cell suspensions using enzymatic digestion buffer containing HBSS supplemented with 10% FBS, 2 mg/mL collagenase A (Roche), and 50 μg/mL DNase-I (Roche), for 45 minutes at 37°C with continuous rotation. Digested single-cell suspensions were filtered through 40-μm nylon strainers (Fisher Scientific) and cells were counted with using TC20 automated cell counter (Biorad). Single-cell suspensions were used for scRNAseq.
scRNAseq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6 week old KPPC mice treated with vehicle or Takinib (50mg/kg) for 14 days

value: Pancreatic cancer

tag: cell line

value: pancreas

value: tumor


title: MAP3K7fwt_KPPC_1

description:
Library name: Sample 3
10x genomics

treatment_protocol: scRNAseq analysis of 8 week-old KPPC WT, MAP3K7f/f   KPPC and MAP3K7f/wt KPPC mice

value: KPPC mice


title: mRNA from dARC COG5 and uninfected clone from donor OM5334

description:
Library name: BJ_clones_10_2_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: I628, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I628_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: CITE-seq

value: CD3+ T cell

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD127/TotalSeq-C0390 ; AntibodyAnti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: mRNA from dARC COG5 3 weeks and uninfected clone from donor OM5334

description:
Library name: BJ_clones_8_1_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: TCR from ARC Chr16 3 weeks andARC Chr16 5 months from donor OM5334

description:
Library name: BJ_clones_10_1_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment


title: I628, PBMC before treatment, scRNA-seq

description:
Library name: I628_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files


title: KPPC_WT

description:
Library name: Sample 1
10x genomics


title: I618, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I618_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: WT, M96, CD, 3W

description: Library name: 10687-JS-04

value: thyroid

value: Control


title: WT, M55, CD, 3W

description: Library name: 10687-JS-03

value: WT


title: ADT and HTO from ARC Chr16 3 weeks andARC Chr16 5 months from donor OM5334

description:
Library name: BJ_clones_10_1_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: peripheral blood

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (ARC Chr16 3 weeks), TotalSeq-C Hashtag 4 AGTAAGTTCAGCGTA (ARC Chr16 5 months)


title: MAP3K7ff_KPPC

description:
Library name: Sample 2
10x genomics


title: M_SMN2

first: Oded

last: Regev

address: 215 Mercer St

institute: New York University

description:
Library name: M_SMN2
Transfected with a minimal construct for assessing speckle localization containing SMN2 exon 7

data_processing:
MinKNOW software version 24.11.10 was used to produce pod5 files.Output files were then basecalled using dorado version 0.8.2 using the super accuracy model dna_r10.4.1_e8.2_400bps_sup@v5.0.0 and the --no-trim option on one V100 GPU. The resulting BAM file was demultiplexed using dorado with options --kit-name SQK-PCB114-24 --no-trim. After converting the demultiplexed BAM files to FASTQ format, pychopper was used to orient the reads using option -k PCS111. Finally, oriented reads were aligned to the plasmid sequences using minimap2 with options -x splice --cs -uf -k14. Aligned reads were then visualized, manually inspected, and summarized using custom scripts. Reads aligning to the reverse strand were rare in all constructs and were ignored in the analysis since they are not predicted to bind to any of our FISH probes.
Assembly: Reads were aligned using minimap2 to each plasmid sequence, as well as to the GAPDH transcript sequence for normalization.
Supplementary files format and content: We used custom scripts to calculate summary statistics for each of the 40 samples, including full-length transcript reads counts, runaway transcription reads, cryptic splicing read counts, and cryptic transcription start site count.

source_name: HeLa Tet-On cells (TaKaRa)

growth_protocol: HeLa Tet-On cells (TaKaRa) were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) containing 4.5 g/L glucose. The medium was supplemented with 10% fetal bovine serum (FBS, Gibco), 1 mM sodium pyruvate (Gibco), and 50 U/mL penicillin-streptomycin (Gibco).

extract_protocol:
RNA extraction (QIAgen RNeasy minikit, 74116) was performed using a QIAcube following the manufacturer’s protocol.
Nanopore's PCR-cDNA Barcoding Kit (SQK-PCB114.24) was used. The protocol selects for polyadenylated transcripts by ligating an adapter at the 3'OH end of the RNA molecule and performs strand switching at the 5' end. Samples were barcoded using the provided adapters through 14 to 16 PCR cycles and pooled together in batches of 16.

treatment_protocol: Each sample was transfected with a different plasmid (name indicated by the sample name; sequence and plasmids available through AddGene), encoding a synthetic reporter with a tet-inducible promoter. Transfection was done using Lipofectamine 3000 reagent (Invitrogen) following the manufacturer's protocol. 22 h after transfection, the transfected reporter genes were induced for 2 h (doxycycline 2 μg/mL, Santa Cruz Biotechnology, sc-204734B) before extraction at 24 h post transfection. In Plad B and DMSO samples, cells were additionally treated with Pladienolide B (Plad B, 100 nM, Cayman Chemical, 445493-23-2) at 20 h post transfection (that is, 2 h before induction).

value: HeLa Tet-On cells (TaKaRa)

value: Plasmid transfection


title: I618, PBMC before treatment, scRNA-seq

description:
Library name: I618_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.

value: Peripheral Blood Mononuclear Cells


title: mRNA from ARC Chr16 3 weeks andARC Chr16 5 months from donor OM5334

description:
Library name: BJ_clones_10_1_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD4+ T cells


title: I541, PBMC before treatment, scTCR-seq

description:
Library name: I541_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Lung cancer


title: M_SMN1

description:
Library name: M_SMN1
Transfected with a minimal construct for assessing speckle localization containing SMN1 exon 7


title: M_COLQ_MUT

description:
Library name: M_COLQ_MUT
Transfected with a minimal construct for assessing speckle localization containing COLQ exon 16 (c.1244A>G)


city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: GA78104
4 samples (EHD-Flex2, EHD-Flex3, EHD-Flex4, EHD-Flex5) were multiplexed.

data_processing:
Libraries were sequenced on DNBSEQ-G400 platform in 100+100 or 43+100 base paired-end mode.
The DNBSEQ-G400 control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0 or 8.0.1, 10x Genomics) for the demultiplexing and UMI counting for each gene-cell (barcode) combination.
Assembly: GRCh38 (hg38)
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file including filtered UMI counts for each gene and cell barcode combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format file including raw UMI counts for each gene and cell barcode combination
Supplementary files format and content: feature_README.txt: tab delimited text file including the information for probe barcode to distinguish multiplexed samples

source_name: prostate cancer

extract_protocol:
Diagnostic prostate biopsy specimens were enzymatically dissociated into single-cell suspensions using collagenase-based digestion, followed by mechanical trituration and filtration to remove debris.
Single-cell RNA sequencing libraries were generated using the Chromium Single Cell Fixed RNA Profiling (Flex) platform and Chromium Human Transcriptome Probe Set v1.0.1 (10x Genomics) according to the manufacturer’s instructions.

value: prostate cancer


title: WT, M53, CD, 3W

description: Library name: 10687-JS-01


title: I541, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I541_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: WT, M35, HF+SD, 6W

description: Library name: 8915-JS-0008

value: Overnutrition


title: M_COLQ_WT

description:
Library name: M_COLQ_WT
Transfected with a minimal construct for assessing speckle localization containing COLQ exon 16


title: M_3HN5HN

description:
Library name: M_3HN5HN
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, HNRNP motif-rich region, 5' splice site, and a second HNRNP motif-rich region


title: WT, M54, CD, 3W

description: Library name: 10687-JS-02


title: EHD-Flex1

description: Library name: GA65242


title: I541, PBMC before treatment, scRNA-seq

description:
Library name: I541_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: WT, M34, HF+SD, 6W

description: Library name: 8915-JS-0007


title: HOS NXP800 6h, rep3

city: Nantes

first: Anaïs

last: Postec

address: 1 Rue Gaston Veil

country: France

institute: Nantes University

description: Library name: Sample 6

data_processing:
fastp (version 0.20.1) default parameters “--detect_adapter_for_pe”,  “-q 30”
STAR (version 2.7.5a) default parameters ” --twopassMode Basic”
htseq_count (version 0.12.4) default parameters “--order pos”, “ -s reverse” with GCF_000001405.40_GRCh38.p14 annotation
Assembly: hg38
Supplementary files format and content: Output from htseq_count

source_name: HOS-MNNG

extract_protocol:
NucleoSpin RNA Plus Kit (Macherey-Nagel)
DNBSEQ Eukaryotic Strand-specific mRNA library

value: HOS-MNNG

value: Osteosarcoma


title: M_3SR5SR

description:
Library name: M_3SR5SR
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, SR motif-rich region, 5' splice site, and a second SR motif-rich region


title: I530, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I530_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: CD4+ T cell


title: I530, PBMC before treatment, scTCR-seq

description:
Library name: I530_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: HOS NXP800 6h, rep1

description: Library name: Sample 4


title: WT, M5, HF+SD, 6W

description: Library name: 8915-JS-0005


title: M_HNSR

description:
Library name: M_HNSR
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region and an SR motif-rich region


title: HOS NXP800 6h, rep2

description: Library name: Sample 5


title: WT, M18, HF+SD, 6W

description: Library name: 8915-JS-0006


title: HOS DMSO 6h, rep2

description: Library name: Sample 2

value: DMSO


title: I530, PBMC before treatment, scRNA-seq

description:
Library name: I530_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.


title: I520, PBMC before treatment, scTCR-seq

description:
Library name: I520_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: CD3+ T cell


title: I520, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I520_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: M_3HNSR

description:
Library name: M_3HNSR
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, an HNRNP motif-rich region, and an SR motif-rich region.


title: WT, M45, CD, 6W

description: Library name: 8915-JS-0003

value: thyroid

value: Control


title: M_HN5SR

description:
Library name: M_HN5SR
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region, 5' splice site, and an SR motif-rich region


title: HOS DMSO 6h, rep1

description: Library name: Sample 1


title: HOS DMSO 6h, rep3

description: Library name: Sample 3


title: WT, M43, CD, 6W

description: Library name: 8915-JS-0002

value: WT


title: M_3HN5SR

description:
Library name: M_3HN5SR
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, an HNRNP motif-rich region, 5' splice site, and an SR motif-rich region


title: WT, M48, CD, 6W

description: Library name: 8915-JS-0004


title: M_SRHN

description:
Library name: M_SRHN
Transfected with a minimal synthetic construct for assessing speckle localization containing an SR motif-rich region and an HNRNP motif-rich region


title: G47, PBMC before treatment, scTCR-seq

description:
Library name: G47_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: R40, PBMC before treatment, scRNA-seq

description:
Library name: R40_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000331), 10x Genomics).

value: Renal cancer


title: G47, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G47_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: I516, PBMC before treatment, scTCR-seq

description:
Library name: I516_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: M_3SRHN

description:
Library name: M_3SRHN
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, SR motif-rich region, and an HNRNP motif-rich region

value: HeLa Tet-On cells (TaKaRa)


title: WT, M22, CD, 6W

description: Library name: 8915-JS-0001


title: I516, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I516_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: E0771_R2_3

city: Houston

first: Xiang

last: Zhang

state: TEXAS

address: One Baylor Plaza, Alkek N1130

department: Breast Center

institute: Baylor College of Medicine

description:
Library name: E0771_R2_3
mouse 9; resistant E0771 cell line 2

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: mammary tumor

extract_protocol:
Tissues were minced and homogenized in 24-well plates using scalpels and pestles, with 0.5 ml of DMEM. Subsequently, 1 ml of tissue dissociation buffer was added, and the mixture was incubated at 37°C for 45 minutes. The dissociation solution was prepared by dissolving collagenase A (Sigma, 11088793001) in a mixture of 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to achieve a working concentration of 1 mg ml⁻¹. The resulting tissue suspension was filtered through a 70-μm strainer to ensure complete homogenization, and the strainer was rinsed with DMEM to recover any remaining single cells. The flow-through was then centrifuged at 500g for 5 minutes, and the supernatant was carefully decanted. In cases where red blood cells (RBCs) were present, a 1×RBC lysis buffer (1:10 dilution of 10× RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied and incubated at room temperature for 10 minutes. To halt and remove RBC lysis, 20 ml of DMEM was added, and the mixture was centrifuged at 450g for 5 minutes. The supernatant was discarded, and the cell pellet was washed with 10 ml of cold DMEM at 4°C. After another centrifugation at 500g for 5 minutes, the supernatant was removed, and the cells were resuspended in cold PBS (Sigma, D8537) containing 0.04% BSA. Finally, the cell suspension was passed through a 40-μm flowmi cell strainer to ensure uniformity.
Library construction follows CellPlex sample multiplexing protocal, for CellPlex multiplexed sample, we used 3' end sequencing protical, while we used 5' end sequencing for TotalSeqC multiplexed samples.

value: mammary tumor


title: I520, PBMC before treatment, scRNA-seq

description:
Library name: I520_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Peripheral Blood Mononuclear Cells


title: G47, PBMC before treatment, scRNA-seq

description:
Library name: G47_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Lung cancer


title: M_3SR5HN

description:
Library name: M_3SR5HN
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, SR motif-rich region, 5' splice site, and an HNRNP motif-rich region

value: Plasmid transfection


title: I516, PBMC before treatment, scRNA-seq

description:
Library name: I516_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.


title: G35, PBMC before treatment, scTCR-seq

description:
Library name: G35_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: M_SR5HN

description:
Library name: M_SR5HN
Transfected with a minimal synthetic construct for assessing speckle localization containing an SR motif-rich region, 5' splice site, and an HNRNP motif-rich region


title: E0771_R2_2

description:
Library name: E0771_R2_2
mouse 8; resistant E0771 cell line 2


title: E0771_R2_1

description:
Library name: E0771_R2_1
mouse 7; resistant E0771 cell line 2


title: I504, PBMC before treatment, scTCR-seq

description:
Library name: I504_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: E0771_R1_3

description:
Library name: E0771_R1_3
mouse 6; resistant E0771 cell line 1


title: M_3SR5, replicate 2

description:
Library name: M_3SR5_rep2
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, SR motif-rich region, and a 5' splice site (2nd replicate)


title: E0771_R1_2

description:
Library name: E0771_R1_2
mouse 5; resistant E0771 cell line 1


title: I504, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I504_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: G35, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G35_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: M_A5

description:
Library name: M_A5
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: G35, PBMC before treatment, scRNA-seq

description:
Library name: G35_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: M_A6

description:
Library name: M_A6
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: I354, PBMC before treatment, scTCR-seq

description:
Library name: I354_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: E0771_R1_1

description:
Library name: E0771_R1_1
mouse 4; resistant E0771 cell line 1


title: E0771_3

description:
Library name: E0771_3
mouse 3; naive E0771 cell


title: M_A3

description:
Library name: M_A3
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: G34, PBMC before treatment, scRNA-seq

description:
Library name: G34_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: I504, PBMC before treatment, scRNA-seq

description:
Library name: I504_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: G34, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G34_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: M_A4

description:
Library name: M_A4
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: G21, PBMC before treatment, scTCR-seq

description:
Library name: G21_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: G34, PBMC before treatment, scTCR-seq

description:
Library name: G34_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: E0771_1

description:
Library name: E0771_1
mouse 1; naive E0771 cell


title: I354, PBMC before treatment, scRNA-seq

description:
Library name: I354_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: G7, PBMC before treatment, scTCR-seq

description:
Library name: G7_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: M_A2

description:
Library name: M_A2
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: G21, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G21_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: M_A1

description:
Library name: M_A1
Transfected with a minimal synthetic construct for assessing speckle localization, part of A trajectory series (starting with M_3HN5 and ending in M_3SR5)


title: M_3HN5, replicate 2

description:
Library name: M_3HN5_rep2
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, an HNRNP motif-rich region, and a 5' splice site (2nd replicate)


title: I354, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I354_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: G7, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G7_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD127/TotalSeq-C0390 ; AntibodyAnti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: G21, PBMC before treatment, scRNA-seq

description:
Library name: G21_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: G7, PBMC before treatment, scRNA-seq

description:
Library name: G7_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: I664, PBMC before treatment, scTCR-seq

description:
Library name: I664_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: MCN_young_dARE_5

first: Ken

last: Lau

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

description:
Library name: 11579-PS-5
SPF-B facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 5

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table.
NovaSeq:Technical read: Read1 - UMI/cell barcodes are positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - transcript
Assembly: Mouse: GRCm38.85
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: proximal colon

growth_protocol: primary cells

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)

value: proximal colon

value: primary cells

value: epithelial

value: Tnf(dARE/+)

value: SPF-B facility


title: I664, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I664_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: CD3+ T cell


title: M_noAG3SR5

description:
Library name: M_noAG3SR5
Transfected with a minimal synthetic construct for assessing speckle localization, derived from M_3SR5, with canonical AG dinucleotide removed


title: M_noBP3SR5

description:
Library name: M_noBP3SR5
Transfected with a minimal synthetic construct for assessing speckle localization, derived from M_3SR5, with branchpoint removed


title: MCN_young_dARE_4

description:
Library name: 11579-PS-3
SPF-B facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 4


title: G6, PBMC before treatment, scTCR-seq

description:
Library name: G6_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: G6, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G6_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: MCN_young_dARE_3

description:
Library name: 11579-PS-1
SPF-B facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 3


title: MCN_young_WT_3

description:
Library name: 11579-PS-2
SPF-B facility young wildtype proximal colon epithelial chelation, replicate 3


title: I664, PBMC before treatment, scRNA-seq

description:
Library name: I664_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: MCN_young_WT_4

description:
Library name: 11579-PS-4
SPF-B facility young wildtype proximal colon epithelial chelation, replicate 4


title: G6, PBMC before treatment, scRNA-seq

description:
Library name: G6_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: MCN_young_dARE_2

description:
Library name: 11339-PS-4
SPF-B facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 2


title: MCN_young_WT_2

description:
Library name: 11339-PS-3
SPF-B facility young wildtype proximal colon epithelial chelation, replicate 2


title: I559, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I559_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: G2, PBMC before treatment, scTCR-seq

description:
Library name: G2_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: I559, PBMC before treatment, scTCR-seq

description:
Library name: I559_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: MCN_young_WT_1

description:
Library name: 11339-PS-2
SPF-B facility young wildtype proximal colon epithelial chelation, replicate 1


title: M_3SRweak5

description:
Library name: M_3SRweak5
Transfected with a minimal synthetic construct for assessing speckle localization, derived from M_3SR5, with 5'ss weakened


title: M_HN5

description:
Library name: M_HN5
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region and a 5' splice site


title: I559, PBMC before treatment, scRNA-seq

description:
Library name: I559_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: M_weakPP3SR5

description:
Library name: M_weakPP3SR5
Transfected with a minimal synthetic construct for assessing speckle localization, derived from M_3SR5, with polypyrimidine weakened


title: G2, PBMC before treatment, scRNA-seq

description:
Library name: G2_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: G2, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: G2_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: M_3HN

description:
Library name: M_3HN
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site and an HNRNP motif-rich region


title: MCN_young_dARE_1

description:
Library name: 11339-PS-1
SPF-B facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 1


title: I554, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I554_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: I439, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I439_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: CD4+ T cell


title: I554, PBMC before treatment, scRNA-seq

description:
Library name: I554_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: M_3HN5

description:
Library name: M_3HN5
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, an HNRNP motif-rich region, and a 5' splice site


title: CONV_aged_WT_2

description:
Library name: 8880-PS-10
CONV facility wildtype proximal colon epithelial chelation, replicate 3

value: CONV facility (C. muridarum-positive)


title: I489, PBMC before treatment, scTCR-seq

description:
Library name: I489_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: I439, PBMC before treatment, scRNA-seq

description:
Library name: I439_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v1.1 kit. Captures 5' end of polyA+ transcripts.


title: I554, PBMC before treatment, scTCR-seq

description:
Library name: I554_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: I439, PBMC before treatment, scTCR-seq

description:
Library name: I439_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: CONV_aged_dARE_3

description:
Library name: 8880-PS-11
CONV facility aged Tnf(dARE/+) proximal colon epithelial chelation, replicate 3


title: M_HN3, PladB

description:
Library name: M_HN3_PladB
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region and a 3' splice site, 2h control DMSO treatment before induction

value: Plasmid transfection, Pladienolide B


title: Salmonella Typhimurium Δ5msr, mid log, biol rep 3

city: Bareilly

first: Manish

last: Mahawar

state: Uttar Pradesh

address: Izzatnagar

department: Division of Biochemistry

country: India

institute: Indian Veterinary Research Institute

description:
Library name: Sample 6
Column name in both Processed data files: msr5_3

data_processing:
Raw sequencing data generated by the Illumina platform were converted into FASTQ files containing sequence reads and corresponding quality scores through base calling.
Initial quality assessment of raw reads was performed using FastQC v0.11.9. rRNA reads were removed using SortMeRNA v4.3.6 against all eight provided rRNA databases.
Adapter sequences, low-quality bases (Q < 30), and short reads (<36 bp) were removed using fastp. Post-trimming quality checks were performed to confirm read quality improvement.
High-quality filtered reads were aligned to the Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 reference genome using HISAT2. Gene-level read counts were generated using HTSeq-count in union mode.
Low read counts (≤10 counts in at least four samples) were filtered out. Filtered read counts were normalized using the regularized log (rlog) transformation function of DESeq2.
Assembly: Reads were aligned to the Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 reference genome (Assembly: ASM694v2; Accession: GCF_000006945.2), downloaded from the NCBI genome repository.
Supplementary files format and content: tab-delimited text file contains gene-level raw read counts generated after alignment for all samples
Supplementary files format and content: Excel file contains filtered and normalized gene level expression data for all samples

source_name: whole cell

growth_protocol: S.Typhimurium wild-type and Δ5msr mutant strains were grown in LB broth media at 37°C/ 180 rpm until mid-logarithmic phase (OD₆₀₀ ≈ 1). Cultures (10 mL) were harvested by centrifugation, and bacterial pellets were immediately frozen and stored at −80 °C until further processing.

extract_protocol:
Frozen bacterial pellets from 10 mL cultures were subjected to RNA extraction using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA was quantified using a Qubit fluorometer, and RNA integrity was assessed using High Sensitivity RNA ScreenTape to determine RIN values.
A total of 1.2 µg of high-quality RNA was subjected to rRNA depletion using the NEBNext® rRNA Depletion Kit (Bacteria) following the manufacturer’s protocol. Double stranded cDNA libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina. Library construction involved RNA fragmentation, first-strand cDNA synthesis using random primers, second-strand cDNA synthesis, end repair, adapter ligation, removal of excess adapters using purification beads, PCR enrichment, and cleanup of PCR products. Final libraries were quantified using a Qubit fluorometer and assessed for fragment size distribution using High Sensitivity D1000 ScreenTape.

value: whole cell

value: msr_5 mutant


title: CONV_aged_dARE_4

description:
Library name: 8880-PS-12
CONV facility aged Tnf(dARE/+) proximal colon epithelial chelation, replicate 4


title: M_HN3

description:
Library name: M_HN3
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region and a 3' splice site

value: HeLa Tet-On cells (TaKaRa)


title: I489, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: I489_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Peripheral Blood Mononuclear Cells


title: CONV_aged_dARE_2

description:
Library name: 8880-PS-9
CONV facility aged Tnf(dARE/+) proximal colon epithelial chelation, replicate 2


title: M_5HN

description:
Library name: M_5HN
Transfected with a minimal synthetic construct for assessing speckle localization containing a 5' splice site and an HNRNP motif-rich region


title: Salmonella Typhimurium Δ5msr, mid log, biol rep 2

description:
Library name: Sample 5
Column name in both Processed data files: msr5_2

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: CONV_aged_dARE_1

description:
Library name: 8880-PS-8
CONV facility aged Tnf(dARE/+) proximal colon epithelial chelation, replicate 1


title: M_3SR5

description:
Library name: M_3SR5
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site, SR motif-rich region, and a 5' splice site


title: CONV_young_WT_3

description:
Library name: 8815-PS-11
CONV facility wildtype proximal colon epithelial chelation, replicate 1


title: M_HN3, DMSO

description:
Library name: M_HN3_DMSO
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region and a 3' splice site, 2h 100 nM Plad B treatment before induction

value: Plasmid transfection, DMSO


title: I489, PBMC before treatment, scRNA-seq

description:
Library name: I489_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Lung cancer


title: RE188, PBMC before treatment, scTCR-seq

description:
Library name: RE188_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: RE188, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE188_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: Salmonella Typhimurium Wild Type, mid log, biol rep 3

description:
Library name: Sample 3
Column name in both Processed data files: WT_3

value: Wild type


title: Salmonella Typhimurium Δ5msr, mid log, biol rep 1

description:
Library name: Sample 4
Column name in both Processed data files: msr5_1


title: CONV_aged_WT_1

description:
Library name: 8880-PS-7
CONV facility wildtype proximal colon epithelial chelation, replicate 2

value: proximal colon


title: M_SR5

description:
Library name: M_SR5
Transfected with a minimal synthetic construct for assessing speckle localization containing an SR motif-rich region and a 5' splice site

value: Plasmid transfection


title: Salmonella Typhimurium Wild Type, mid log, biol rep 2

description:
Library name: Sample 2
Column name in both Processed data files: WT_2


title: M_HN

description:
Library name: M_HN
Transfected with a minimal synthetic construct for assessing speckle localization containing an HNRNP motif-rich region


title: Salmonella Typhimurium Wild Type, mid log, biol rep 1

description:
Library name: Sample 1
Column name in both Processed data files: WT_1


title: RE188, PBMC before treatment, scRNA-seq

description:
Library name: RE188_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: M_SR3

description:
Library name: M_SR3
Transfected with a minimal synthetic construct for assessing speckle localization containing an SR motif-rich region and a 3' splice site


title: RE187, PBMC before treatment, scTCR-seq

description:
Library name: RE187_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: M_3SR

description:
Library name: M_3SR
Transfected with a minimal synthetic construct for assessing speckle localization containing a 3' splice site and an SR motif-rich region


title: CONV_young_dARE_6

description:
Library name: 8815-PS-8
CONV facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 2

value: primary cells

value: epithelial


title: M_5SR

description:
Library name: M_5SR
Transfected with a minimal synthetic construct for assessing speckle localization containing a 5' splice site and an SR motif-rich region


title: Replicate H62,  Wildtype, Ipsilateral tissue

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: H62ff1dpiDRGipsi

data_processing:
FASTQ files were processed with the NGS-Data-Charmer pipeline (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adapter trimming was performed, forllowed by alignment to the mm10 genome build using HISAT2, and duplicate alignments were removed using the Picard ‘MarkDuplicates’ module.
Assembly: mm39
Supplementary files format and content: Non-normalized gene expression counts are available in tab-delimited format in counts_exonic_matrix.txt. Normalized gene expression (in the form of Fragments Per Kilobase per Million) are available in tab-delimited format in fpkm_exonic_matrix.txt. Genome coverage tracks of de-duplicated reads are available in standard bigwig format.

source_name: Ipsi

extract_protocol:
RNA was collected using QIAGEN RNeasy plus mini kit.
Libraries were generated using the Illumina Stranded mRNA Library Prep Kit and sequenced on an Illumina NovaSeq X with a 2 × 150 bp paired-end configuration.

treatment_protocol: Ahr cKO (Ahr fl/fl Thy1CRE-ERT2/EYFP) or control (Ahr f/f or  f/+) male mice were injected with tamoxifen (once daily, 100 mg/kg i.p. for 5 consecutive days) at 17 weeks of age.  L4-L6 DRGs, both contralateral and ipsilateral were isolated from n=5 mice per group (DRGs from each mouse represents 1 sample) at 4 weeks post-tamoxifen treament. For the injury group, sciatic nerve transection lesion was performed on n=5 mice per group at 4 weeks post-tamoxifen treament and L4-L6 DRGs were isolated 1 day later.  DRGs were dissociated between ZT2 to 4 (ZT=0 when the light turns on in the mouse room).

value: Ipsi

value: DRG

value: FF

value: Spinal Cord Injury - 1dpi


title: CONV_young_dARE_5

description:
Library name: 8815-PS-7
CONV facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 1

value: Tnf(dARE/+)

value: CONV facility (C. muridarum-positive)


title: Replicate H65,  Wildtype, Ipsilateral tissue

description: Library name: H65ff1dpiDRGipsi


title: RE187, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE187_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: CD3+ T cell


title: Replicate H61, CRE genotype, Ipsilateral tissue

description: Library name: H61ffcre1dpiDRGipsi

value: CRE


title: M_SR

description:
Library name: M_SR
Transfected with a minimal synthetic construct for assessing speckle localization containing an SR motif-rich region

value: HeLa Tet-On cells (TaKaRa)


title: RE159, PBMC before treatment, scTCR-seq

description:
Library name: RE159_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Peripheral Blood Mononuclear Cells


title: Cranial bone with a defect at the center, Control

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Data were processed using the 10x Genomics Cell Ranger pipeline at default settings
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Calvaria

growth_protocol: Mice were kept under a 12-h light/dark cycle with food and water provided ad libitum. All procedures involving mice were approved by the Institutional Animal Care and Use Committee of The Johns Hopkins University under Protocol MO22M368.

extract_protocol:
Skulls were microdissected 7 d after defect creation.  Cranial bone with a defect at the center, with an approximate edge length of 3mm, was minced and subjected to six sequential enzymatic digestions with a mixture containing collagenase type I (1 mg/ml; Worthington Biochemical Corporation, Lakewood, NJ, USA, LS004197) and collagenase type II (1 mg/ml; Worthington Biochemical Corporation, LS004177).  Cell fractions (from sequential digestions 1 to 6) were collected and resuspended in red blood cell lysis buffer (37°C for 5 min). Digestions were subsequently filtered through 40-μm sterile strainers. Cells were then washed in PBS and resuspended in HBSS at a concentration of ~1000 cells/μl.
for all samples, 10x Genomics Chromium standard protocol

treatment_protocol: 2 samples were analyzed comparing mRNA from mice. One is a control group which received intraperitoneal injection of vehicle control (10% DMSO). The other is a GA group which received intraperitoneal injection of gambogic amide. gambogic amide (GA)  was used to activate TrkA. Mice received intraperitoneal (IP) injection of either 100 μL vehicle control (10% DMSO) or GA (1.2 mg/kg in 10% DMSO). Treatment began 24h prior to calvarial injury, and continued daily thereafter for 1 week.

value: Calvaria

value: primary

value: Cranial defect cells

value: IP injection of 100 μL vehicle control (10% DMSO)


title: Cranial bone with a defect at the center, GA

description: 10x Genomics

value: IP injection of 100 μL GA (1.2 mg/kg in 10% DMSO)


title: CONV_young_dARE_7

description:
Library name: 8815-PS-9
CONV facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 3

value: proximal colon

value: primary cells


title: RE187, PBMC before treatment, scRNA-seq

description:
Library name: RE187_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Lung cancer


title: Sham neurobots, Rep 4

city: Boston

first: Haleh

last: Fotowat

state: MA

address: 201 Brookline Ave

institute: Wyss Institute

description: Library name: NN4

data_processing:
Clean reads were extracted from FASTQ files, removing reads with adapter contamination, when uncertain nucleotides constitute more than 10 percent of either read (N > 10%), and when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
The index to the reference genome (Xenopus laevis version 10.1) was built using Hisat2 v2.0.5 and clean reads were aligned to the reference. The mapped reads of each sample were assembled using StringTie (v1.3.3b) and FeatureCounts v1.5.0-p3  was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0) and the resulting p-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Assembly: Xenopus laevis version 10.1
Supplementary files format and content: Excel file that includes a gene count table
Supplementary files format and content: Excel file that includes FPKM normalized count table

organism: Xenopus laevis

source_name: Tissue excised from the animal hemisphere of a Nieuwkoop and Faber stage 9 Xenopus laevis embryo (animal caps)

extract_protocol:
This protocol involves extracting RNA from high-lipid tissue using an automated homogenization method followed by a filtration column. The process involves grinding the tissue into fine powder in liquid nitrogen, adding a lysis solution to the tissue powder, vortexing, and centrifugation to isolate the lysate. The RNA is then purified and concentrated using a filtration column, followed by a series of washing steps.
Low-input eukaryotic mRNA library preparation (non-directional)


title: Replicate H62,  Wildtype, Contralateral tissue

description: Library name: H62ff1dpiDRGcontra

source_name: Contra

value: Contra

value: DRG


title: RE159, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE159_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: Sham neurobots, Rep 2

description: Library name: NN2

value: Tissue excised from the animal hemisphere of a Nieuwkoop and Faber stage 9 Xenopus laevis embryo (animal caps)


title: Replicate H65,  Wildtype, Contralateral tissue

description: Library name: H65ff1dpiDRGcontra

value: FF

value: Spinal Cord Injury - 1dpi


title: EZH2_CR_CBX2_KO_rep1

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: GFP CUT&RUN

library_source: genomic

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed, and reads were trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates.
Assembly: mm10
Supplementary files format and content: Bigwig files contain coverage at 100 bp windows genome-wide  calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads), 2800000000 was a number chosen arbitrarily in the range of total mapped base pairs in M. musculus genome.

molecule: genomic DNA

source_name: mESC CBX2fl/fl-HaloTag EZH2-GFP

extract_protocol:
The CUT&RUN of CBX2 in CBX2fl/fl-HaloTag was performed using a CUTANA™ ChIC/CUT&RUN Kit (EpiCypher). Cells were harvested, split to a single-cell suspension, counted, and 0.5 x 10^6 cells were used in each reaction, and reactions were run in duplicate. Cells were washed with PBS, then Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor), and bound to activated ConA beads for 10 minutes. Supernatant was removed from beads, 50 μL Antibody Buffer ((20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor, 0.1% Digitonin, 2 mM EDTA) with 1:50 Anti-HaloTag® (polyclonal) (Promega) or 1:200 Anti-GFP (monoclonal) (Invitrogen) was added, and cells were gently vortexed to thoroughly resuspend beads before overnight incubation at 4°C on a nutator. The following day, the Antibody buffer was removed with the tubes on a magnetic stand and cells were washed twice with pAG-MNase Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 x EDTA-free protease Inhibitor, 0.1% Digitonin). After the washes, 50 μL pAG-MNase Buffer + 2.5 μL pAG-MNase was added to each reaction, tubes were then vortexed to mix and incubated at RT for 10 minutes. Supernatant was removed and each reaction was washed twice with 200 μL pAG-MNase Buffer. Afterwards 2 mM CaCl2 in pAG-MNase Buffer was added to activate pAG-MNase for chromatin digestion, beads were vortexed to resuspend, and tubes were then incubated at 4°C on a nutator for 2 hours. Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 50 μg/mL Glycogen) + E. coli spike-in was added following digestion and tubes were gently vortexed to mixed then placed in a preheated thermocycler set to 37°C. Reactions were then purified and eluted from included columns, then quantified using a Qubit.   Genome-wide H3K27me3 domain changes were profiled using the CUT&Tag protocol adapted from EpiCypher. Cells were harvested via 0.25% trypsin-EDTA solution and counted using 0.4% trypan blue stain and Countess automated cell counter. A single-cell suspension was prepared by washing cells with cold 1x PBS and resuspending 1.0 x 106 cells in 1 mL cold nuclear extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton x-100, 20% glycerol, & 0.5 mM spermidine), then incubated on ice for 10 minutes to isolate nuclei. Biomag Plus Concanavalin A beads were activated with two washes of cold bead activation buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, & 1 mM MnCl22). After activation, beads were added to aliquots of 0.1 x 106 isolated nuclei and incubated at room temperature for 10 minutes. Nuclei:bead samples were resuspended in 50 µL cold Antibody150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, & protease inhibitors) followed by the addition of 0.5 µg of anti-H3K27me3 (#9733S, Cell Signaling Technology). To facilitate primary antibody binding, samples were incubated on nutator at room temperature for 1 hour. Samples were resuspended in 50 µL Digitonin150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors) followed by the addition of 0.5 µg CUTANA anti-rabbit secondary antibody (#13-1047, EpiCypher). Samples were then incubated on nutator at room temperature for 1 hour to facilitate binding, followed by two washes with 200 µL cold Digitonin300 buffer (20 mM HEPES-KOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors). The tagmentation reaction was performed by resuspending samples in 50 µL cold Tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, & protease inhibitors) and incubating at 37°C in thermocycler for 1 hour. Samples were washed with 50 µL TAPS buffer (10 mM TAPS pH 8.5 & 0.2 mM EDTA) then resuspended in 5 µL SDS Release buffer (10 mM TAPS pH 8.5 & 0.1% SDS) to quench the tagmentation reaction and release adaptor-tagged DNA fragments into solution.
For CUT&RUN, following end repair and adaptor ligation, 1X SPRIselect beads were used to wash prepped DNA and PCR was ran for 15 cycles of denaturation and annealing/extension. The PCR settings were: Initial Denaturation at 98°C for 30 Seconds, Denaturation at 98°C for 10 seconds, Annealing/extension at 65°C for 75 seconds, Final Extension at 65°C for 5 minutes. Following PCR, 1X SPRIselect beads were used to wash amplified library-prepped DNA and each eluted product was ran on a Tapestation (Agilent) for fragment analysis before multiplexing and PE150 sequencing.  For CUT&Tag, After incubating samples at 58°C in thermocycler for 1 hour, 15 µL SDS Quench buffer (0.67% Triton x-100), 2 µL i5 universal primer (EpiCypher), 2 µL i7 barcoded primer (EpiCypher), 0.005 ng Escherichia coli spike-in DNA (made in-house), and 25 µL NEBNExt High Fidelity 2x PCR Master Mix were added to each sample for library construction with the following PCR protocol: 5 minutes at 58°C, 5 minutes at 72°C, 45 seconds at 98°C, 14 cycles of 15 seconds at 98°C and 10 seconds at 60°C, with a final extension for 1 minute at 72°C. Libraries were checked for quality using the Qubit dsDNA HS Assay kit and TapeStation High Sensitivity DNA assay kit and then sequencing was performed using Novaseq 6000 (Novogene) to generate 150 bp paired-end reads.

value: mESC CBX2fl/fl-HaloTag EZH2-GFP

value: 48 hours of 1.0 uM 4-Hydroxytamoxifen


title: EZH2_CR_CBX2_KO_rep2

description: GFP CUT&RUN


title: Sham neurobots, Rep 1

description: Library name: NN1


title: RE159, PBMC before treatment, scRNA-seq

description:
Library name: RE159_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell


title: Replicate H96,  Wildtype, Contralateral tissue

description: Library name: H96ff1dpiDRGcontra


title: Replicate H97,  Wildtype, Contralateral tissue

description: Library name: H97ff1dpiDRGcontra


title: RE106, PBMC before treatment, scTCR-seq

description:
Library name: RE106_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: CONV_young_dARE_8

description:
Library name: 8815-PS-10
CONV facility young Tnf(dARE/+) proximal colon epithelial chelation, replicate 4

value: epithelial

value: Tnf(dARE/+)

value: CONV facility (C. muridarum-positive)


title: RE106, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE106_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: EZH2_CR_CBX2_WT_rep2

description: GFP CUT&RUN


title: Biobots, Rep 3

description: Library name: XB3


title: EZH2_CR_CBX2_WT_rep1

description: GFP CUT&RUN


title: Replicate H63,  Wildtype, Contralateral tissue

description: Library name: H63ff1dpiDRGcontra


title: CBX2_CR_rep2

description: HaloTag CUT&RUN

source_name: mESC CBX2fl/fl-HaloTag

value: mESC CBX2fl/fl-HaloTag


title: Replicate H100, CRE genotype, Contralateral tissue

description: Library name: H100ffcre1dpiDRGcontra

value: CRE


title: Biobots, Rep 2

description: Library name: XB2


title: RE97, PBMC before treatment, scTCR-seq

description:
Library name: RE97_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: RE97, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE97_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: Biobots, Rep 1

description: Library name: XB1


title: H3K27me3_D6_rep2

description: H3K27me3 CUT&Tag in CBX2 WT cells

value: 144 hours of 1.0 uM 4-Hydroxytamoxifen


title: Replicate H99, CRE genotype, Contralateral tissue

description: Library name: H99ffcre1dpiDRGcontra


title: Replicate H95, CRE genotype, Ipsilateral tissue

description: Library name: H95ffcre1dpiDRGipsi

value: Ipsi


title: Replicate H64, CRE genotype, Ipsilateral tissue

description: Library name: H64ffcre1dpiDRGipsi


title: RE97, PBMC before treatment, scRNA-seq

description:
Library name: RE97_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Lung cancer


title: RE106, PBMC before treatment, scRNA-seq

description:
Library name: RE106_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: RE89, PBMC before treatment, scTCR-seq

description:
Library name: RE89_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: Sham neurobots, Rep 3

description: Library name: NN3


title: RE89, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE89_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: H3K27me3_D4_rep2

description: H3K27me3 CUT&Tag in CBX2 WT cells

value: 96 hours of 1.0 uM 4-Hydroxytamoxifen


title: Biobots, Rep 4

description: Library name: XB4


title: H3K27me3_D4_rep1

description: H3K27me3 CUT&Tag in CBX2 WT cells


title: Replicate H63, Wildtype, Ipsilateral tissue

description: Library name: H63ff1dpiDRGipsi

value: DRG


title: Neurobots, Rep 2

description: Library name: NB2

value: Tissue excised from the animal hemisphere of a Nieuwkoop and Faber stage 9 Xenopus laevis embryo (animal caps)


title: Replicate H64, CRE genotype, Contralateral tissue

description: Library name: H64ffcre1dpiDRGcontra

value: Contra


title: Neurobots, Rep 4

description: Library name: NB4


title: RE89, PBMC before treatment, scRNA-seq

description:
Library name: RE89_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: H3K27me3_D6_rep1

description: H3K27me3 CUT&Tag in CBX2 WT cells


title: Neurobots, Rep 1

description: Library name: NB1


title: Smoker S201725, follow-up

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: S201725-2

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 38 (GRCh38) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Genes were filtered for analysis based on counts per million (CPM) reads mapped across all samples. Genes with CPM counts greater than 1 in more than 10% of the total number of patients were used in subsequent analyses. CPM was calculated using the calcNormFactors and cpm functions from the edgeR package (version 4.4.1).
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 61860 x 36 matrix of "expected_count" values computed by RSEM

source_name: Bronchial brushing

extract_protocol:
Total RNA was isolated from bronchial brushings using the miRNAs Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit (Illumina, San Diego, CA).

value: Bronchial brushing

tag: subject id

tag: flowcell

value: AAAYGHHHV

tag: median tin

tag: smoking status

value: smoker

tag: visit

value: follow-up

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: Sex

value: male


title: H3K27me3_D2_rep2

description: H3K27me3 CUT&Tag in CBX2 WT cells

value: 48 hours of 1.0 uM 4-Hydroxytamoxifen


title: Neurobots, Rep 3

description: Library name: NB3

tag: tissue


title: Multiome1, scATAC-seq

description:
Library name: Multiome1_ATAC
10x Genomics Multiome scATAC-seq

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger ARC (v2.0.2, 10x Genomics) with the reference genome GRCh38 (version 2020-A-2.0.0, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file generated by Cell Ranger ARC. Contains filtered gene expression matrix (genes × barcodes) for nuclear RNA.
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: simple text version of HDF5 file descrived above, in tab-separated values(tsv) and matrix(mtx) format.
Supplementary files format and content: atac_fragments.tsv.gz: tab-separated values(tsv) file listing all Tn5 transposition events (fragments) identified in scATAC-seq data generated by Cell Ranger ARC.

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Single Cell Multiome ATAC + Gene Expression kit protocol (CG000338, Rev F), 10x Genomics).

value: Peripheral Blood Mononuclear Cells

tag: disease state

tag: cell type

value: CD4+ T cell

tag: library type

value: ATAC


title: Replicate H97, Wildtype, Ipsilateral tissue

description: Library name: H97ff1dpiDRGipsi

value: Ipsi

tag: genotype

value: FF

value: Spinal Cord Injury - 1dpi


title: H3K27me3_D2_rep1

description: H3K27me3 CUT&Tag in CBX2 WT cells

value: mESC CBX2fl/fl-HaloTag


title: Replicate H96, Wildtype, Ipsilateral tissue

description: Library name: H96ff1dpiDRGipsi

value: DRG


title: Smoker S201724, baseline

description: Library name: S201724

value: baseline

value: Hispanic or Latino

tag: age


title: P8 PBMC pre-operative, scTCR-seq

description:
Library name: P8_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Lung cancer

value: CD3+ T cell

value: TCR


title: H3K27me3_D0_rep2

description: H3K27me3 CUT&Tag in CBX2 WT cells


title: Multiome1, snRNA-seq

description:
Library name: Multiome1_GEX
10x Genomics Multiome snRNA-seq

molecule: nuclear RNA

value: mRNA


title: H3K27me3_D0_rep1

description: H3K27me3 CUT&Tag in CBX2 WT cells


title: Smoker S201717, baseline

description: Library name: S201717

value: Bronchial brushing

value: AAAYGHHHV

value: smoker

value: Black or African American

value: Non-Hispanic

value: female


title: Replicate H100, CRE genotype, Ipsilateral tissue

description: Library name: H100ffcre1dpiDRGipsi

value: Ipsi

value: CRE

tag: treatment


title: Smoker S201725, baseline

description: Library name: S201725-1

value: White

value: male


title: Replicate H99, CRE genotype, Ipsilateral tissue

description: Library name: H99ffcre1dpiDRGipsi

value: DRG

value: Spinal Cord Injury - 1dpi


title: CBX2_CR_rep1

description: HaloTag CUT&RUN

value: mESC CBX2fl/fl-HaloTag


title: Smoker S201712, baseline

description: Library name: S201712

value: baseline


title: Replicate H95, CRE genotype, Contralateral tissue

description: Library name: H95ffcre1dpiDRGcontra

value: Contra


title: Smoker S201707, baseline

description: Library name: S201707


title: P8 TIL, scTCR-seq

description:
Library name: P8_TIL_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

source_name: Tumor-infiltrating lymphocyte (TIL)

value: Tumor-infiltrating lymphocyte (TIL)

value: Lung cancer

value: erythrocyte-removed TIL

value: TCR


title: P8 PBMC pre-operative, scRNA-seq

description:
Library name: P8_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

value: mRNA


title: Replicate H6, CRE genotype, Contralateral tissue

description: Library name: H61ffcre1dpiDRGcontra


title: WT Schwann cells, replicate 3

description: Library name: PB1-WT-M3

data_processing:
FASTQ file preprocessing, quality control, and alignment to the mouse mm10 genome were done using the NGS-Data-Charmer pipeline. Adaptor trimming was performed with Trim-Galore (v0.6.5), and reads were aligned using Bowtie2 (v2.4.1). Duplicates were removed with SAMtools (v1.10), and gene expression was quantified using Feature Counts with the GENCODE vM25 annotation.
Assembly: mm10
Supplementary files format and content: Tab-separated counts file, "counts_exonic_matrix.txt", contains the non-normalized gene expression values. Tab-separated counts file, "fpkm_exonic_matrix.txt", contains the normalized gene expression values in Fragments Per Kilobase per Million (FPKM).

source_name: dorsal root ganglion

growth_protocol: For Schwann cell (SC) culture, WT and PB1KO DRGs were isolated from adult mice and placed into DMEM/F12 solution on ice, washed twice with ice-cold HBSS-HEPES buffer, and incubated in 0.6% collagenase at 37°C for 45 minutes. After washing with HBSS-HEPES, mixed cells were plated onto plates coated with poly-L-lysine and laminin. To enrich Schwann cells, the dissociated mixed cell cultures were cultured in SC medium containing 2 µM forskolin, 10 nM neuregulin, 10% FBS, 1% non-essential amino acids, and 4% ascorbic acid in DMEM high glucose Glutamax. Through the use of specialized medium and after passaging, there were almost no neurons remaining in the culture. Fibroblasts were removed by magnetic cell separation using anti-Thy1 antibody, and the medium was changed every 2 days. Cells were passaged at 80% confluence, with purity exceeding 80% at passages 3 to 5.

extract_protocol:
Total RNA from WT and PB1KO SCs was isolated using an RNeasy Micro kit (Qiagen) following instructions for on-column DNase digestion. RNA quality and concentrations were determined using an Agilent Bioanalyzer (Agilent RNA 6000 Pico, 5067-1513).
For library construction using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), the protocol follows the TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E. This procedure begins with RNA isolation, followed by mRNA enrichment using poly(A) selection. The mRNA is then fragmented, reverse transcribed into cDNA, and adapter-ligated. After amplification, the library is purified, and its quality and quantity are assessed before sequencing.

value: dorsal root ganglion

value: Schwann cell

value: WT


title: S14_no_2

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

description: Library name: Sample 6

data_processing:
Read trimming and clipping were done with cutadapt. The resulting trimmed reads were consolidated into FASTA format. Read filtering, read mapping, nucleotide-wise coverage calculations, and genome feature-wise read quantification were performed using READemption2 version2.0.4 and the short-read mapper Segemehl version 0.3.4, applying an accuracy threshold of 95%. The references employed included the Escherichia coli K-12 substr. DH10B genome (accession number NC_010473.1) and the T6 phage that was resequenced in the present study. The uniquely aligned reads were utilized to conduct the coverage calculations.
Assembly: Escherichia coli K-12 substr. DH10B genome (accession number NC_010473.1)
Supplementary files format and content: wiggle

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Cultures of bacteria expressing either empty vector or Septu EcB88, which were grown overnight, were diluted 100-fold in fresh LB medium with 100 μg/ml of chloramphenicol and 1 mM CaCl₂.

extract_protocol:
Total RNA was extracted using the hot phenol method. The aqueous phase was precipitated with 2 volumes of ice-cold ethanol and 1/30 volume of 3 M NaOAc (pH 6.5) for 2 h at -20°C. The pellet was washed with ice-cold 75% ethanol and resuspended in sterilized water. Then the extracted RNA was treated with DNase followed by phenol:chloroform:isoamyl alcohol extraction. The aqueous phase was precipitated again with 2.5 volumes of ice-cold ethanol and 1/30 volume of 3 M NaOAc (pH 6.5) for 2 h at -20°C. The pellet was washed with 75% ethanol and resuspended in sterilized water.
cDNA library preparation followed by sequencing was conducted by Filgen, Inc. and Arraystar Inc.. RNA samples were pretreated to eliminate specific modifications that might impede the process (deacylation of 3’–aminoacyl RNA, removal of 3’–cP (2’,3’–cyclic phosphate), phosphorylation of 5’–OH, and demethylation of m1A and m3C ). Library preparation was executed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs). The procedural workflow incorporated 3’–adapter ligation, 5’–adapter ligation, cDNA synthesis, PCR amplification, and size selection of PCR products ranging from 134 to 160 bp.

treatment_protocol: Upon reaching OD600 of 0.5, phages were added into the culture at a multiplicity of infection (MOI) of 10. After 30 min post-infection, a stop solution (95% v/v ethanol and 5% v/v water-saturated phenol (pH > 7.0)) was added to the culture and then immediately stored at -80°C.

value: bacterial cell

tag: strain

tag: infection

value: no infection


title: P8 PBMC pre-operative, Feature Barcoding(ADT)

description:
Library name: P8_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

source_name: Peripheral Blood Mononuclear Cells

value: ADT

tag: adt

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: S14_T6_2

description: Library name: Sample 8

value: T6 phage infection


title: S14_T6_1

description: Library name: Sample 7


title: P8 TIL, Feature Barcoding(ADT)

description:
Library name: P8_TIL_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: S14_no_1

description: Library name: Sample 5


title: WT Schwann cells, replicate 1

description: Library name: PB1-WT-M1


title: Nonsmoker NS201723, baseline

description: Library name: NS201723

value: Bronchial brushing

tag: subject id

tag: flowcell

value: AAAYGHHHV

value: nonsmoker

value: baseline

value: Black or African American

value: Non-Hispanic

value: female


title: P8 TIL, scRNA-seq

description:
Library name: P8_TIL_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Tumor-infiltrating lymphocyte (TIL)

value: Lung cancer

value: erythrocyte-removed TIL


title: WT Schwann cells, replicate 2

description: Library name: PB1-WT-M2

value: dorsal root ganglion

value: Schwann cell


title: P7 PBMC pre-operative, Feature Barcoding(ADT)

description:
Library name: P7_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell


title: Nonsmoker NS201719, baseline

description: Library name: NS201719

tag: median tin

tag: smoking status

value: Declined/Not Available

value: Hispanic or Latino

value: male


title: cont_no_2

description: Library name: Sample 2

value: bacterial cell

value: no infection


title: Smoker S201701, baseline

description: Library name: S201701

value: Bronchial brushing

value: AAAYGHHHV

value: smoker

tag: visit

tag: race


title: Nonsmoker NS201722, baseline

description: Library name: NS201722

value: nonsmoker

value: baseline

value: Black or African American

tag: ethnicity

value: Non-Hispanic

tag: Sex


title: PB1 knockout Schwann cells, replicate 2

description: Library name: PB1-KO-M2

tag: tissue


title: PB1 knockout Schwann cells, replicate 3

description: Library name: PB1-KO-M3

tag: cell type


title: P7 PBMC pre-operative, scTCR-seq

description:
Library name: P7_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: TCR-Seq

tag: disease state

value: Lung cancer

tag: library type

value: TCR


title: cont_T6_1

description: Library name: Sample 3

tag: genotype

value: T6 phage infection