title: Neuro B5 | 021 | Tumour

status: Public on Apr 08 2026

city: Woolloongabba

first: Fernando

last: Guimaraes

state: QLD

address: 37 Kent Street

country: Australia

institute: Frazer Institute - University of Queensland

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: rawdata.csv: raw count data, normdata.csv: normalised count data (We performed quality control steps to all the samples, then removed samples with nuclei count < 200 and performed normalization of all samples that  passed the quality control steps.)
Library strategy: Spatial Transcriptomics

source_name: Neuroblastoma

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMx DSP WTA kit according to manufacture's construction

value: Neuroblastoma

value: Post-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

value: Staging  IV

tag: age dx_class

value: <12 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

value: amplified

tag: gender

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Death

tag: risk classification

value: High


title: 40-day exposed, 0.05 µM Mn

status: Public on Apr 03 2026

type: SRA

city: West Lafayette

first: Aaron

middle: B

last: Bowman

state: IN

address: 700 Mitch Daniels Blvd

department: School of Health Sciences

country: USA

institute: Purdue University

description: Library name: CD10-T40_005

library_source: transcriptomic single cell

data_processing:
FastQ raw reads went through quality control using FastQC, CellRanger (v6.1.2) pipeline, and empty droplet removal with DropletQC (0.0.0.9000) to create Seurat objects.
Assembly: hg38
Supplementary files format and content: Seurat object

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC-derived cortical culture

growth_protocol: An hiPSC line from a de-identified neurotypical male control (CD10) was maintained in mTeSR1 (Stem Cell Technologies, Cat# 85857, 85850) on Matrigel (Corning, Cat# 354277) coated 6-well plates. Before differentiation, hiPSCs were disassociated with Accutase (Innovative Cell Technologies, Inc., Cat# AT-104) and were subcultured into Matrigel coated plates with mTeSR1 supplied with 10 µM ROCK inhibitor Y-27632 (Selleckchem, Cat# S1049, dissolved in culture graded water, stock concentration 10 mM). Once the hiPSC culture reached 100% confluence, cortical neural induction was performed following a modified dual SMAD inhibition protocol as described previously (Joshi et al., 2019). Neural induction was initiated by switching from mTeSR1 to neuralization medium containing SMAD inhibitors SB431542 (Reprocell, Cat# 04-0010, dissolved in DMSO, stock concentration 20 mM, final concentration 10 µM) and LDN-193189 (Reprocell, Cat# 04-0074, dissolved in DMSO, stock concentration 2 mM, final concentration 0.4 µM). The neuralization medium is based on knockout DMEM/F12 (Gibco, Cat# 12660012) supplied with 15% v/v knockout serum replacement (Gibco, Cat# 10828028), 1X GlutaMAX (Gibco, Cat# 35050061), 1% (v/v) penicillin-streptomycin (Gibco, Cat# 15140122), 1X MEM non-essential amino acids (Gibco, Cat# 11140050), and 55 µM 2-mercaptoethanol (Sigma, Cat# M3148). During the 10-day induction phase, neuralization medium was gradually replaced by N2 medium while the concentration of SB431542 and LDN-193189 were maintained. The medium switch happened on induction Day 5, Day 7, and Day 9, when the ratio of neuralization medium and N2 medium moved from 3:1, to 1:1, and 1:3, respectively. N2 medium composed of DMEM/F-12 with GlutaMAX supplement (Gibco, Cat# 10565042), 4.5 g/L D-(+)-glucose (Thermo Scientific Chemicals, Cat# A16828), and 1X N2 supplement (Gibco, Cat# 17502048). On day 11, the culture medium was fully shifted to maintenance medium composed of 1:1 mixture of B27 neurobasal medium (Neurobasal medium (Gibco, Cat. #: 21103049) supplied with 1X B27 (Gibco, Cat. #: 17504044) and 1X GlutaMax (Gibco, Cat. #: 35050061)) and N-2 DMEM/F-12 medium (DMEM/F-12 with GlutaMax supplied with 1X N-2 (Gibco, Cat. #: 17502048), 1X MEM non-essential amino acid solution (Gibco, Cat. #: 11140050), 2% penicillin-streptomycin, and 100 µM 2-mecaptoethanol (CAS 60-24-2, Sigma-Aldrich, Cat. #: M3148) (Shi et al., 2012). The culture was maintained in this medium from day 11 onwards and replated by disassociating with Accutase (Innovative Cell Technologies, AT104) as needed.

extract_protocol:
Upon termination of either the exposure or the recovery phase, cultured cells were disassociated with Accutase and collected with DMEM/F12 (Gibco, Cat. #11320033) with 10% (v/v) fetal bovine serum (R&D Systems, Cat. #S11150) and 10 µM ROCK inhibitor Y-27632. Collected cell pellets were transferred into 50 mL conical tubes and gently triturated to ensure full disassociation. Cell suspensions were then centrifuged at 300 xg for 5 min and resuspended in DMEM/F12 with GlutaMax supplement (Gibco, Cat. #10565042) with 0.04% bovine serum albumin (BSA, Invitrogen, Cat. # AM2616) and 10 µM ROCK inhibitor Y-27632. A 70-µm strainer was used to remove clumps and cell counts were determined with Nexcelom Cellometer aiming for a final concentration of 1,000 cells/µL. Single cell suspension was transferred into low-binding Eppendorf tubes for 10X Chromium droplet preparation.
Libraries were prepared following instructions from 10X Genomics Chromium Gel Single Cell 3' protocol.

treatment_protocol: The day of neuralization initiation was counted as differentiation day 0 and Mn exposure was started upon full maturation of cortical neurons on differentiation day 110. MnCl2 was added to the culture media to achieve final concentrations of 0.05, 0.5, and 5 µM. An additional well with no MnCl2 was included as non-exposed control. The exposure was conducted for 40 consecutive days with medium refreshment interval of 72 hours. Upon exposure day 40, cultured cells either directly went into sample collections or switched into maintenance medium without Mn to recover for another 10 days before further assessments.

tag: cell type

value: hiPSC-derived cortical culture


title: HSG_RR_CD14_21

type: RNA

city: Monza

first: Jacopo

last: Ronchi

state: MB

address: Via Cadore 48

department: School of Medicine and Surgery

country: Italy

institute: University of Milano-Bicocca

description: monocytes from Female RR-MS patient

hyb_protocol: The labeled RNA was hybridized to the Affymetrix GeneChip miRNA 4.1 microarrays.

scan_protocol: Microarrays were scanned using the GeneAtlas™ Imaging Station.

data_processing: Raw CEL files were imported into the R environment and underwent normalization using the RMA algorithm, as implemented in the oligo R/Bioconductor package.

label: biotin

molecule: total RNA

source_name: Peripheral Blood

label_protocol: 1µg of total RNA was tagged with biotin using the FlashTag™ HSR RNA Labeling Kit for Affymetrix miRNA arrays (Genisphere LLC., Hatfield, PA, USA).

extract_protocol: The mirVana RNA isolation kit (Ambion, Inc., Austin, TX, USA) was used to extract total RNA from CD14+ monocytes, CD8+ T cells, and neutrophils, including small non-coding RNAs, in accordance with the manufacturer's protocol.

tag: tissue

value: Peripheral Blood

tag: age

tag: Sex

value: F

tag: condition

value: RR

value: Relapsing-Remitting Multiple Sclerosis

value: CD14+ monocytes

tag: hospital

value: HSG


title: A549ACE2_SARS2_infected_3

city: Taipei

first: Po-Chih

last: Wu

address: No.109, Ln. 130, Sec. 1, Academia Rd., Nangang Dist., Taipei City 115, Taiwan

country: Taiwan

institute: TFDA

description: Library name: Virus-3

library_source: transcriptomic

data_processing:
Filtered reads were aligned to the Homo sapiens reference genome (GENCODE GRCh38.p14 primary assembly) by using a STAR aligner.
Transcript abundance was quantified using Salmon
Differential gene expression analysis was conducted using the ‘DESeq2’ package in R software.
Assembly: GRCh38.p14
Supplementary files format and content: An CSV file includes original count matrix from DEseq2 for each sample.

growth_protocol: A549-ACE2 cells were maintained in Ham’s F-12 (Kaighn’s) medium supplemented with 10% (v/v) fetal bovine serum, 2 mM L-glutamine, and 200 μg/mL hygromycin B. Cultures were routinely tested and confirmed to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted from cell lysates using an EZ1 Advanced XL automated nucleic acid purification system (Qiagen, Hilden, Germany) with the EZ1&2 RNA Tissue Mini Kit (#959034, Qiagen), following the manufacturer’s instructions.
RNA sequencing libraries were prepared using an Illumina Stranded mRNA Prep library preparation kit (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instructions.

tag: cell line

tag: treatment


title: A549ACE2_SARS2_infected_2

description: Library name: Virus-2


title: 40-day exposed, 0 µM Mn control

description: Library name: CD10-T40_0


title: HSG_RR_CD14_19

description: monocytes from Female RR-MS patient


title: HSG_RR_CD14_23

description: monocytes from Female RR-MS patient


title: HSG_RR_CD14_18

description: monocytes from Male RR-MS patient

value: M


title: A549ACE2_SARS2_infected_1

description: Library name: Virus-1


title: A549ACE2_SARS2_infected_BAY20_3

description: Library name: V-B20-3


title: HSG_RR_CD14_22

description: monocytes from Male RR-MS patient


title: HSG_RR_CD14_16

description: monocytes from Female RR-MS patient


title: HSG_RR_CD14_13

description: monocytes from Female RR-MS patient


title: A549ACE2_SARS2_infected_BAY20_2

description: Library name: V-B20-2


title: HSG_RR_CD14_15

description: monocytes from Female RR-MS patient


title: HSG_RR_CD14_17

description: monocytes from Female RR-MS patient


title: HSG_RR_CD14_14

description: monocytes from Male RR-MS patient


title: A549ACE2_SARS2_infected_BAY20_1

description: Library name: V-B20-1


title: A549ACE2_SARS2_infected_BAY10_3

description: Library name: V-B10-3


title: A549ACE2_SARS2_infected_BAY10_2

description: Library name: V-B10-2


title: A549ACE2_SARS2_mock_3

description: Library name: Mock-3


title: A549ACE2_SARS2_infected_BAY10_1

description: Library name: V-B10-1


title: HSG_HC_NEU_9

description: neutrophils from Female HC

value: HC

value: Healthy Control

value: neutrophils


title: HSG_RR_CD14_12

description: monocytes from Female RR-MS patient


title: HSG_HC_NEU_8

description: neutrophils from Male HC


title: A549ACE2_SARS2_mock_1

description: Library name: Mock-1


title: HSG_RR_CD14_11

description: monocytes from Female RR-MS patient


title: Y3

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

country: China

institute: 川北医学院

description: Library name: sample9

data_processing:
Sequencing data quality control、Reference genome alignment、Quantification、Differential analysis、Enrichment analysis、Alternative splicing analysis、Variant calling
Assembly: GRCh38
Supplementary files format and content: File 'gene_count.xls': Tab-delimited text file constituting the raw gene expression count matrix. Rows represent genes (with gene identifiers in the first column), and columns represent individual libraries/samples (e.g., CK1, P1,Y1). The values are the raw read counts aligned to each gene, serving as the primary data for differential expression analysis.

extract_protocol:
Extract RNA from tissues or cells.
Libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions, and sequencing was ultimately performed on an Illumina PE150platform.


title: Y2

description: Library name: sample8


title: Y1

description: Library name: sample7


title: A549ACE2_SARS2_mock_2

description: Library name: Mock-2


title: HSG_RR_CD14_10

description: lymphocytes from Male RR-MS patient


title: HSG_HC_NEU_7

description: neutrophils from Female HC


title: C6706 AKI, ::PompU-OueS-GBE1194, replicate 2

city: Memphis

first: Deepak

last: Balasubramanian

state: TN

address: 262 Danny Thomas Pl Rm D2037

department: Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

data_processing:
Demultiplexing, quality control and adapter trimming was performed with bcl-convert (v3.9.3). CLC Genomics Workbench (Qiagen) was used for subsequent data processing. Briefly, paired Illumina reads were mapped to the El Tor reference genome (GenBank AE003852.1- Chromosome I; AE003853.1- chromosome II) using the following settings to generate the transcripts per million bases (TPM) values: mismatch cost 2, insertion / deletion cost 3, length / similarity fraction 0.8, global strand specific alignment. Subsequent pairwise analysis between two datasets of interest (absolute fold change ≥ 2.0 filtered on average expression for FDR correction ≤ 0.01) were used for downstream analysis.
Assembly: Vibrio cholerae El Tor reference genome (GenBank AE003852.1- Chromosome I; AE003853.1- chromosome II)
Supplementary files format and content: Excel files containing read counts
Supplementary files format and content: Excel files containing TPM data

organism: Vibrio cholerae O1 biovar El Tor

source_name: bacterial cell

growth_protocol: AKI broth was used for virulence-inducing conditions (15 g l-1 BactoTM peptone, 4 g l-1 yeast extract, 5 g l-1 NaCl, 0.03% w/v sodium bicarbonate). Cells were grown for at 37 ˚C, initially static for 3.5 hrs followed by 4 hrs at 200 RPM before RNA isolation.

extract_protocol:
Total RNA was extracted using the DirectZol RNA miniprep kit, Zymo Research, following manufacturer instructions
DNase treatment, rRNA depletion, library preparation and Illumina NovaSeq 6000 sequencing (2x51 bp reads) was performed at SeqCenter, LLC (Pittsburgh, PA).

tag: strain

value: Strain C6706

value: bacterial cell

tag: genotype

value: AKI growth


title: P3

description: Library name: sample6


title: HSG_RR_NEU_13

description: neutrophils from Female RR-MS patient


title: HSG_HC_NEU_3

description: neutrophils from Female HC


title: HSG_HC_NEU_4

description: neutrophils from Female HC


title: P2

description: Library name: sample5


title: HSG_HC_NEU_5

description: neutrophils from Female HC


title: HSG_HC_NEU_15

description: neutrophils from Male HC


title: P1

description: Library name: sample4


title: CK3

description: Library name: sample3


title: CK2

description: Library name: sample2


title: Mock-treated T cells from Donor 4.

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

institute: SR-TIGET

description: Library name: S45_Mock_B2M_CD3D_TGFBR2_Donor4

library_source: genomic

data_processing:
Since amplicons were longer than read-length, reads were aligned to a 300 bp region centered on the sgRNA target site (±150 bp) using Bowtie2 in paired-end mode with default parameters
After that, original fastq files were subsetted to retain only reads mapping to the region of interest using the filterbyname module of the BBMap aligner (BBTools suite; sourceforge.net/projects/bbmap/)
The retained reads were subsequently analyzed with CRISPResso2 in paired-end or single-end mode. Trimmomatic software (http://www.usadellab.org/cms/?page=trimmomatic) was used to remove low quality bases (score < 30) and Illumina adapter sequences with the following options: --trim_sequences --trimmomatic_command trimmomatic --trimmomatic_options_string 'ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 MINLEN:100')
Paired-end reads were first merged using FLASH to generate a single contig, which was then aligned to the corresponding input amplicon reference. For samples in which merging was not possible due to low second-mate quality, amplicon length, or gRNA position, reads were instead aligned directly in single-end mode and modifications were quantified accordingly
The sgRNA sequence was provided to focus the analysis on the target region, and the quantification window was set to 20 bp on each side of the sgRNA cut site
Identified alleles were quantified by measuring the number of reads and their relative abundance among total read counts, considering only insertions and deletions. Substitutions were excluded from the analysis, as they are likely attributable to PCR or sequencing errors
Assembly: GRCh38
Supplementary files format and content: CRISPResso allele quantification table

molecule: genomic DNA

source_name: Blood

growth_protocol: B2M tdTomato K-562 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum, 1% L-glutamine, and 1% penicillin/streptomycin. Activated T cells were cultured in RPMI supplemented with 1% penicillin/streptomyci, 2% L-glutamine, 10% FBS, and 5 ng/ml of each IL-7 and IL-15. Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
gDNA extraction by Maxwell RSC Cultured cells DNA Kit (Promega), following provider indications.
Targeted genomic regions were amplified by PCR using locus-specific primers. A second round of PCR was performed to add full-length Illumina adapters and sample-specific barcodes.
Libraries were beads-purified, quantified, pooled at equimolar concentrations, and sequenced using an Illumina MiSeq platform in a paired-end mode generating 2x250 bp reads.

treatment_protocol: B2M tdTomato K-562 cells and activated T cells, post-Dynabeads removal, were nucleofected with poly-editor mRNA and gene-specific gRNAs.

value: Blood

value: T lymphocytes

value: Mock-treated


title: Mock-treated T cells from Donor 5.

description: Library name: S47_Mock_B2M_CD3D_TGFBR2_Donor5


title: T cells from Donor 5 treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2.

description: Library name: S46_Poly_B2M_CD3D_TGFBR2_Donor5

value: Poly-editing


title: CK1

description: Library name: sample1


title: HSG_HC_NEU_14

description: neutrophils from Female HC

value: Peripheral Blood


title: HSG_HC_NEU_10

description: neutrophils from Female HC

value: F


title: HSG_HC_NEU_12

description: neutrophils from Male HC


title: T cells from Donor 4 treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2

description: Library name: S44_Poly_B2M_CD3D_TGFBR2_Donor4


title: HSG_HC_CD8_8

description: lymphocytes from Male HC

value: CD8+ cells


title: HSG_HC_NEU_11

description: neutrophils from Female HC


title: HSG_HC_NEU_1

description: neutrophils from Female HC


title: HSG_HC_NEU_2

description: neutrophils from Female HC


title: HSG_HC_NEU_13

description: neutrophils from Female HC


title: HSG_HC_CD8_7

description: lymphocytes from Female HC


title: Mock-treated T cells from Donor 3.

description: Library name: S42_Mock_B2M_CD3D_TGFBR2_Donor3


title: HSG_HC_CD8_9

description: lymphocytes from Female HC


title: T cells from Donor 2 treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M

description: Library name: S37_Poly_AAVS1_B2M_Donor2


title: T cells from Donor 3  treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2

description: Library name: S43_Poly_B2M_CD3D_TGFBR2_Donor3


title: Mock-treated T cells from Donor 2.

description: Library name: S38_Mock_AVVS1_B2M_Donor2


title: HSG_HC_CD8_4

description: lymphocytes from Female HC


title: Mock-treated T cells from Donor 1.

description: Library name: S36_Mock_AAVS1_B2M_Donor1


title: HSG_HC_CD8_6

description: lymphocytes from Male HC


title: HSG_HC_CD8_3

description: lymphocytes from Female HC


title: Mock treated B2M tdTomato K-562 cells, replicate 1

description: Library name: S34_Mock_AAVS1_B2M_R1

source_name: K-562 B2M tdTomato

value: K-562 B2M tdTomato

value: lymphoblast cells

value: B2M tdTomato


title: B2M tdTomato K-562 cells treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M, replicate 2.

description: Library name: S32_Poly_AAVS1_B2M_R2


title: HSG_HC_CD8_14

description: lymphocytes from Female HC

value: HSG


title: T cells from Donor 1 treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M

description: Library name: S35_Poly_AAVS1_B2M_Donor1


title: B2M tdTomato K-562 cells treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M, replicate 1.

description: Library name: S31_Poly_AAVS1_B2M_R1


title: HSG_HC_CD8_12

description: lymphocytes from Male HC

value: M

value: HC


title: T cells from Donor 6 treated with a Cas9 targeting B2M

description: Library name: Cas9_B2M_Donor8

library_source: other

data_processing:
Reads quality was controlled with Fastqc v0.11.9, and low-quality reads and adapter sequences were trimmed using Trim_Galore v0.6.6. with the parameters --quality 20, --length 25, --paired, --rrbs
For samples containing an integrated cassette, custom references were generated using the reform function (https://github.com/gencorefacility/reform) by inserting cassette sequences (i.e., NY-ESO-1 TCR or PGK-GFP) into the corresponding target gene within the GRCh38 human reference genome
High-quality reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.064. Reads were aligned to both converted and unconverted versions of the reference genome using Bismark with the --local and the -X 600 parameters. Methylation calling was performed using the bismark_methylation_extractor script, selecting only those reads mapping to the original top or bottom strand based on the PCR primers
The methylation calls were loaded into the R environment and processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain CpGs located within the selected genomic regions (and to remove errors) and normalized using the normalizeCoverage function
Data from different samples were merged using the unite function, considering the positions covered in at least one replicate per condition. The percentage of methylation at each CpG was calculated using the percMethylation function
Assembly: GRCh38
Supplementary files format and content: Bismark coverage

molecule: other

growth_protocol: B2MtdTomato K-562 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum, 1% L-glutamine, and 1% penicillin/streptomycin. T cells were cultured in RPMI supplemented with 1% penicillin/streptomyci, 2% L-glutamine, 10% FBS, and 5 ng/ml of each IL-7 and IL-15. Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Genomic DNA extraction by Maxwell RSC Cultured cells DNA Kit (Promega) and bisufite conversion by EpiTect Bisulfite Kit, following provider indications.
Targeted genomic regions were amplified by PCR using locus-specific primers. A second round of PCR was performed to add full-length Illumina adapters and sample-specific barcodes.

treatment_protocol: Cell were nucleofected with Cas9 or poly-editor mRNA and gene-specific gRNAs


title: Mock-treated T cells from Donor 6

description: Library name: UT_B2M_CD3_TGFBR2_Donor6


title: Mock-treated T cells from Donor 5

description: Library name: UT_B2M_CD3_TGFBR2_Donor5


title: HSG_HC_CD8_13

description: lymphocytes from Female HC

value: Healthy Control


title: HSG_HC_CD8_10

description: lymphocytes from Female HC


title: T cells from Donor 5 treated with a Cas9 targeting B2M

description: Library name: Cas9_B2M_Donor7


title: T cells from Donor 6 treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2

description: Library name: Poly_B2M_CD3_TGFBR2_Donor6


title: HSG_HC_CD14_9

description: monocytes from Female HC

value: CD14+ monocytes


title: B2M tdTomato K-562 cells treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M, replicate 3.

description: Library name: S33_Poly_AAVS1_B2M_R3


title: HSG_HC_CD14_7

description: monocytes from Female HC


title: HSG_HC_CD8_1

description: lymphocytes from Female HC


title: HSG_HC_CD14_4

description: monocytes from Female HC


title: Mock-treated T cells from Donor 4

description: Library name: UT_AAVS1_B2M_Donor4


title: T cells from Donor 5 treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2

description: Library name: Poly_B2M_CD3_TGFBR2_Donor5


title: HSG_HC_CD8_2

description: lymphocytes from Female HC


title: HSG_HC_CD8_15

description: lymphocytes from Male HC


title: HSG_HC_CD14_5

description: monocytes from Female HC


title: HSG_HC_CD14_8

description: monocytes from Male HC


title: T cells from Donor 3 treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M

description: Library name: Poly_AAVS1_B2M_Donor3


title: T cells from Donor 4 treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M

description: Library name: Poly_AAVS1_B2M_Donor4


title: T cells from Donor 4 treated with a Cas9 targeting AAVS1

description: Library name: Cas9_AAVS1_B2M_Donor4


title: HSG_HC_CD14_15

description: monocytes from Male HC


title: HSG_HC_CD14_2

description: monocytes from Female HC


title: Ox43, water, fecal, post

city: Stratford

first: Elizabeth

last: West

state: NJ

address: 2 Medical Center Dr

department: Neuroscience

institute: Rowan University School of Osteopathic of Medicine

description:
Library name: Ox43-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox43-SAD19

data_processing:
Fecal samples sent to Omega Bioservices (sister company to Omega Bio-tek) where data were analyzed with Illumina 16S Metagenomics App (Isis v2.5.35.6)
Assembly: Omega Bioservices utilized Greengenes taxonomic database (Illumina-curated version of May 2013 Greengenes)
Supplementary files format and content: csv files with bacteria count levels per sample (samples are per column) at genus and species levels
Supplementary files format and content: pdf file with aggregate summary containing sample information, species diversity results
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: Rattus norvegicus fecal sample

extract_protocol:
Fecal samples sent to Omega Bioservices (sister company to Omega Bio-tek) where they extracted DNA with mechanical homogenization and automated extraction
Fecal samples sent to Omega Bioservices (sister company to Omega Bio-tek) where they constructed the library using V3-V4 primers

value: Rattus norvegicus fecal sample

value: Long-Evans

value: female

value: Control (water)

tag: timepoint

value: Post


title: Ox43, water, fecal, pre

description:
Library name: Ox43-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox43-Pre-oxy

value: Pre


title: Mock treated B2M tdTomato K-562, replicate 2

description: Library name: Mock_AAVS1_B2M_R2

value: Mock-treated


title: Ox42, water, fecal, pre

description:
Library name: Ox42-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox42-Pre-oxy


title: Ox42, water, fecal, post

description:
Library name: Ox42-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox42-SAD19


title: T cells from Donor 3 treated with a Cas9 targeting AAVS1

description: Library name: Cas9_AAVS1_B2M_Donor3

value: Blood

value: T lymphocytes


title: HSG_HC_CD14_11

description: monocytes from Female HC

value: Peripheral Blood

value: F


title: HSG_HC_CD14_12

description: monocytes from Male HC


title: Ox39, water, fecal, post

description:
Library name: Ox39-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox39-SAD19


title: Unc13d untreated3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Library name: CAST-UT3-Unc13d-Tcells

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCm38 using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: mm10
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

organism: Mus musculus

source_name: T cells

extract_protocol:
Genomic DNA was isolated using the DNeasy blood & tissue kit (Machery-Nagel)
customized library prep, locus specific, CAST-Seq

value: T cells

value: Unc13d^jinx/jinx (mutant)

value: untreated

tag: batch


title: HSG_HC_CD14_10

description: monocytes from Female HC

value: HC

value: HSG


title: Ox38, water, fecal, pre

description:
Library name: Ox38-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox38-Pre-oxy


title: B2M tdTomato K-562 cells treated with a Cas9 targeting AAVS1, replicate 2

description: Library name: Cas9_AAVS1_B2M_R2

value: K-562 B2M tdTomato

value: lymphoblast cells

value: B2M tdTomato


title: Ox38, water, fecal, post

description:
Library name: Ox38-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox38-SAD19

value: Rattus norvegicus fecal sample

value: Long-Evans

value: female


title: HSG_HC_CD14_3

description: monocytes from Female HC

value: Healthy Control

value: CD14+ monocytes


title: HSG_HC_CD14_14

description: monocytes from Female HC


title: Ox39, water, fecal, pre

description:
Library name: Ox39-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox39-Pre-oxy

value: Control (water)

value: Pre


title: HSG_HC_CD14_1

description: monocytes from Female HC

value: Peripheral Blood


title: Ox36, water, fecal, pre

description:
Library name: Ox36-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox36-Pre-oxy

value: male


title: Mock treated  B2M tdTomato K-562, replicate 1

description: Library name: Mock_AAVS1_B2M_R1

value: Mock-treated


title: Unc13d untreated2

description: Library name: CAST-UT2-Unc13d-Tcells

value: T cells

value: Unc13d^jinx/jinx (mutant)


title: Ox36, water, fecal, post

description:
Library name: Ox36-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:Ox36-SAD19

value: Post


title: Unc13d untreated1

description: Library name: CAST-UT1-Unc13d-Tcells

value: untreated


title: Ox34, water, fecal, pre

description:
Library name: Ox34-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox34-Pre-oxy


title: B2M tdTomato K-562 cells treated with a Cas9 targeting AAVS1, replicate 1

description: Library name: Cas9_AAVS1_B2M_R1

value: K-562 B2M tdTomato


title: Ox34, water, fecal, post

description:
Library name: Ox34-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox34-SAD19


title: B2M tdTomato K-562 cells treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M, replicate 2

description: Library name: Poly_AAVS1_B2M_R2

value: lymphoblast cells

value: Poly-editing


title: CBE_Unc13d_g3 replicate 2

description: Library name: CAST-CBE-Unc13d-g3-2

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: B2M tdTomato K-562 cells treated with a poly-functional editor targeting AAVS1 and epi-silencing B2M, replicate 1

description: Library name: Poly_AAVS1_B2M_R1

value: B2M tdTomato


title: Ox32, water, fecal, pre

description:
Library name: Ox32-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox32-Pre-oxy

value: Rattus norvegicus fecal sample

value: Long-Evans


title: HSG_HC_CD14_13

description: monocytes from Female HC

value: F

value: HC

value: Healthy Control

value: CD14+ monocytes

value: HSG


title: Ox32, water, fecal, post

description:
Library name: Ox32-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox32-SAD19

value: male

value: Control (water)


title: CBE_Unc13d_g3 replicate 1

description: Library name: CAST-CBE-Unc13d-g3-1

value: T cells

value: Unc13d^jinx/jinx (mutant)


title: Ox30, water, fecal, pre

description:
Library name: Ox30-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:Ox30-Pre-oxy

value: Pre


title: Mock-treated T cells from Donor 2

description: Library name: Mock_TRAC_B2M_Donor2

value: Blood

value: T lymphocytes

value: Mock-treated


title: Ox26, water, fecal, post

description:
Library name: Ox26-SAD20
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox26-SAD20

value: female

value: Post


title: Mock-treated T cells from Donor 1

description: Library name: Mock_TRAC_B2M_Donor1


title: Cas9_Unc13d_g3 replicate 1

description: Library name: CAST-Cas9-Unc13d-g3-1

value: SpCas9 nuclease targeting Unc13d


title: Ox22, water, fecal, post

description:
Library name: Ox22-SAD20
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox22-SAD20

value: Rattus norvegicus fecal sample

value: Long-Evans


title: Ox22, water, fecal, pre

description:
Library name: Ox22-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox22-Pre-oxy


title: T cells from Donor 2 treated with a poly-functional editor targeting TRAC and epi-silencing B2M

description: Library name: Poly_TRAC_B2M_Donor2

value: Poly-editing


title: CBE_Unc13d_g2 replicate 2

description: Library name: CAST-CBE-Unc13d-g2-2

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: Ox19, water, fecal, pre

description:
Library name: Ox19-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox19-Pre-oxy


title: Ox26, water, fecal, pre

description:
Library name: Ox26-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox26-Pre-oxy


title: Ox30, water, fecal, post

description:
Library name: Ox30-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox30-SAD19


title: Ox19, water, fecal, post

description:
Library name: Ox19-SAD20
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox19-SAD20


title: Ox15, water, fecal, pre

description:
Library name: Ox15-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox15-Pre-oxy


title: T cells from Donor 1 treated with a poly-functional editor targeting TRAC and epi-silencing B2M

description: Library name: Poly_TRAC_B2M_Donor1


title: Ox15, water, fecal, post

description:
Library name: Ox15-SAD20
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox15-SAD20


title: Ox44, oxycodone, fecal, pre

description:
Library name: Ox44-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox44-Pre-oxy

value: Oxycodone


title: CBE_Unc13d_g2 replicate 1

description: Library name: CAST-CBE-Unc13d-g2-1


title: Ox44, oxycodone, fecal, post

description:
Library name: Ox44-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox44-SAD19


title: T cells from Donor 2 treated with a Cas9 targeting TRAC

description: Library name: Cas9_TRAC_B2M_Donor2


title: Ox41, oxycodone, fecal, post

description:
Library name: Ox41-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox41-SAD19


title: Poly-functional editors treated K-562 B2M tdTomato cells, replicate 3

description: Library name: Poly-edited K-562 B2MtdTomato_R3

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
High-quality remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0. reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local parameter and the methylation status was obtained using bismark_methylation_extractor script selecting only those reads mapping to the original top strand
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to only retain existing CpG in the promoter region (and remove any errors) and normalized using the normalizeCoverage function.
The information from the different samples were merged using the unite function considering the positions covered in at least one replicate per condition. The percentage of methylation at each CpG was calculated using the percMethylation function.
Assembly: GRCh38
Supplementary files format and content: Bismark coverage

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and biisufite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of B2M and TET2 were amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina

treatment_protocol: Cell were nucleofected with ETR mRNA and gRNA trageting the promoter of B2M or TET2

value: K-562 B2M tdTomato

value: lymphoblast cells

value: B2M tdTomato

value: B2M epi-silencing


title: Cas9_Unc13d_g2 replicate 2

description: Library name: CAST-Cas9-Unc13d-g2-2

value: T cells

value: Unc13d^jinx/jinx (mutant)


title: Cas9_Unc13d_g3 replicate 2

description: Library name: CAST-Cas9-Unc13d-g3-2


title: CBE_Unc13d_g1 replicate 2

description: Library name: CAST-CBE-Unc13d-g1-2


title: Ox41, oxycodone, fecal, pre

description:
Library name: Ox41-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox41-Pre-oxy

value: Pre


title: T cells from Donor 1 treated with a Cas9 targeting TRAC

description: Library name: Cas9_TRAC_B2M_Donor1

value: Blood

value: T lymphocytes


title: Cas9_Unc13d_g2 replicate 1

description: Library name: CAST-Cas9-Unc13d-g2-1


title: Ox40, oxycodone, fecal, pre

description:
Library name: Ox40-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox40-Pre-oxy

value: female


title: CBE_Unc13d_g1 replicate 1

description: Library name: CAST-CBE-Unc13d-g1-1


title: Mock treated K-562 B2M tdTomato cells, replicate 3

description: Library name: Mock K-562 B2MtdTomato_R3

value: Mock


title: Ox40, oxycodone, fecal, post

description:
Library name: Ox40-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox40-SAD19

value: Post


title: Poly-functional editors treated K-562 B2M tdTomato cells, replicate 2

description: Library name: Poly-edited K-562 B2MtdTomato_R2


title: Ox37, oxycodone, fecal, pre

description:
Library name: Ox37-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox37-Pre-oxy

value: Rattus norvegicus fecal sample


title: Ox37, oxycodone, fecal, post

description:
Library name: Ox37-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox37-SAD19

value: Long-Evans


title: Ox35, oxycoodone, fecal, post

description:
Library name: Ox35-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox35-SAD19

value: male


title: Ox35, oxycoodone, fecal, pre

description:
Library name: Ox35-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox35-Pre-oxy


title: Cas9_Unc13d_g1 replicate 1

description: Library name: CAST-Cas9-Unc13d-g1-1

value: SpCas9 nuclease targeting Unc13d


title: HSC untreated

description: Library name: CAST-Lei-UT-HSC

value: untreated


title: Cas9_Unc13d_g1 replicate 2

description: Library name: CAST-Cas9-Unc13d-g1-2


title: Ox33, oxycodone, fecal, post

description:
Library name: Ox33-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox33-SAD19

value: Oxycodone


title: Mock treated K-562 B2M tdTomato cells, replicate 2

description: Library name: Mock K-562 B2MtdTomato_R2

value: K-562 B2M tdTomato

value: lymphoblast cells


title: Ox31, oxycodone, fecal, pre

description:
Library name: Ox31-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:Ox31-Pre-oxy


title: Ox33, oxycodone, fecal, pre

description:
Library name: Ox33-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox33-Pre-oxy


title: Poly-functional editors treated K-562 B2M tdTomato cells, replicate 1

description: Library name: Poly-edited K-562 B2MtdTomato_R1

value: B2M tdTomato

value: B2M epi-silencing


title: Mock treated K-562 B2M tdTomato cells, replicate 1

description: Library name: Mock K-562 B2MtdTomato_R1


title: Ox29, oxycodone, fecal, post

description:
Library name: Ox29-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox29-SAD19


title: Ox31, oxycodone, fecal, post

description:
Library name: Ox31-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox31-SAD19


title: CBE-HSC-d14 replicate 2

description: Library name: CAST-Lei-CBE-HSC-d14-r2

source_name: HSCs

value: HSCs

value: Unc13d^jinx/jinx (mutant)

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: CBE-HSC-d14 replicate 1

description: Library name: CAST-Lei-CBE-HSC-d14-r1


title: Ox29, oxycodone, fecal, pre

description:
Library name: Ox29-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:Ox29-Pre-oxy

value: Pre


title: Ox12, oxycodone, fecal, post

description:
Library name: Ox12-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox12-SAD19

value: female


title: CBE-T cells-d14 replicate 2

description: Library name: CAST-Lei-CBE-T cells-d14-r2

value: T cells


title: T cells from Donor 4 treated with ETRs targeting TET2

description: Library name: TET2 silencing

value: Blood

value: T lymphocytes

value: TET2 epi-silencing


title: Ox11, oxycodone, fecal, post

description:
Library name: Ox11-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox11-SAD19

value: Rattus norvegicus fecal sample

value: Long-Evans

value: Post


title: Mock treated T cells from Donor 3

description: Library name: Mock B2M_Donor 3

value: Mock


title: Ox12, oxycodone, fecal, pre

description:
Library name: Ox12-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox12-PO

value: Oxycodone


title: CBE-HSC-d7 replicate 2

description: Library name: CAST-Lei-CBE-HSC-d7-r2


title: Ox16, oxycodone, fecal, post

description:
Library name: Ox16-SAD20
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox16-SAD20

value: male


title: Mock treated T cells from Donor 4

description: Library name: Mock TET2


title: T cells from Donor 3 treated with a tripartite ETR targeting B2M

description: Library name: B2M silencing tripartite ETR_Donor 3


title: Ox11, oxycodone, fecal, pre

description:
Library name: Ox11-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox11-PO


title: CBE-T cells-d14 replicate 1

description: Library name: CAST-Lei-CBE-T cells-d14-r1


title: Ox10, oxycodone, fecal, post

description:
Library name: Ox10-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox10-SAD19


title: Ox10, oxycodone, fecal, pre

description:
Library name: Ox10-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox10-PO


title: Mock treated T cells from Donor 2

description: Library name: Mock B2M_Donor 2


title: Ox9, oxycodone, fecal, pre

description:
Library name: Ox9-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox9-PO


title: Ox16, oxycodone, fecal, pre

description:
Library name: Ox16-Pre-oxy
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox16-Pre-oxy


title: Ox9, oxycodone, fecal, post

description:
Library name: Ox9-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox9-SAD19


title: T cells from Donor 3 treated with ETRs targeting B2M

description: Library name: B2M silencing ETR combination_Donor 3


title: CBE-HSC-d7 replicate 1

description: Library name: CAST-Lei-CBE-HSC-d7-r1


title: Ox8, oxycodone, fecal, post

description:
Library name: Ox8-SAD21
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox8-SAD21


title: Ox7, oxycodone, fecal, pre

description:
Library name: Ox7-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox7-PO


title: Ox8, oxycodone, fecal, pre

description:
Library name: Ox8-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox8-PO


title: Ox6, oxycodone, fecal, post

description:
Library name: Ox6-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox6-SAD19


title: CBE-T cells-d7 replicate 1

description: Library name: CAST-Lei-CBE-T cells-d7-r1,


title: CBE-T cells-d7 replicate 2

description: Library name: CAST-Lei-CBE-T cells-d7-r2


title: Ox7, oxycodone, fecal, post

description:
Library name: Ox7-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox7-SAD19


title: T cells from Donor 2 treated with ETRs targeting B2M

description: Library name: B2M ETR silencing _Donor 2


title: Mock treated T cells from Donor 1

description: Library name: Mock B2M_Donor 1


title: Ox4, oxycodone, fecal, pre

description:
Library name: Ox4-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox4-PO


title: Jinx-HSC-UT

description: Library name: CAST-Jinx-HSC-UT

value: untreated


title: Ox4, oxycodone, fecal, post

description:
Library name: Ox4-SAD21
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:Ox4-SAD21


title: T cells from Donor 2 treated with a tripartite ETR targeting B2M

description: Library name: B2M silencing tripartite ETR_Donor 2

value: B2M epi-silencing


title: Ox6, oxycodone, fecal, pre

description:
Library name: Ox6-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox6-PO


title: T cells from Donor 2 treated with a poly-functional editor targeting B2M and AAVS1

description: Library name: B2M Poly-functional_Donor 2


title: Jinx-HSC replicate 1

description: Library name: CAST-Jinx-HSC-BE1

value: HSCs


title: T cells from Donor 1 treated with a poly-functional editor targeting B2M and AAVS1

description: Library name: B2M Poly-functional_Donor 1


title: Ox3, oxycodone, fecal, pre

description:
Library name: Ox3-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox3-PO


title: MEFs-UT

description: Library name: CAST-UT-MEFs

source_name: MEF CF1

value: MEF CF1

value: CF-1 mouse embryos


title: Ox1, oxycodone, fecal, pre

description:
Library name: Ox1-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox1-PO

value: Pre


title: Ox2, oxycodone, fecal, post

description:
Library name: Ox2-SAD21
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox2-SAD21


title: Ox3, oxycodone, fecal, post

description:
Library name: Ox3-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox3-SAD19


title: Testic cells,rep5

city: beijing

first: KehKooi

last: Kee

address: 30 Shuangqing Road

institute: Tsinghua University

description:
Library name: NOA5
10x Genomics

data_processing:
Raw reads were demultiplexed and mapped to the reference genome  using the 10X Genomics Cell Ranger pipeline (cellranger 4.0.0; default parameters).
Assembly: GRCh38
Supplementary files format and content: Processed data are provided in the MEX (Matrix Exchange) format, which is the standard output of the 10X Genomics Cell Ranger pipeline. Each sample has three files: barcodes.tsv.gz (contains cell barcode sequences), features.tsv.gz (contains gene identifiers and symbols), and matrix.mtx.gz (contains the count matrix in sparse matrix format). These files together constitute the gene expression matrix of all single cells, suitable for downstream analysis with tools like Seurat or Scanpy.

source_name: Testis, NOA

extract_protocol:
Human testis samples were minced with sterilized scissors after washing three times with PBS.Then were digested in 1 mg/ml collagenase type IV at 37C for 15 min. During the process of digestion, the tissues were pipetted up and down once in every seven minutes.The digestion process was stopped with DMEM (containing 10% FBS).The cell suspension was filtered through 40-mm nylon mesh. After centrifugation, the cells were suspended in DMEM (containing 10% FBS) for further sample selection.
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3.1 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina  NovaSeq 6000  according to the manufacturer’s instructions (Illumina).

value: Testis, NOA

value: Testic cells,rep5

value: human Testic cells,rep5

value: NOA


title: Bone marrow-derived MSC, healthy control, male, 44 yeas age, cell passage number = P2

city: Porto Salvo

first: Isabel

middle: Bogalho

last: Martins

address: Instituto Superior Técnico - Campus Taguspark Av. Prof. Doutor Cavaco Silva

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Técnico (IST)

description:
Library name: CM78
column name in counts_all_samples.txt: CM78

data_processing:
Raw sequencing reads were generated in FASTQ format using Illumina DRAGEN FASTQ Generation v3.8.4, followed by quality assessment with FastQC (v 0.12.1). Reads were aligned to the GRCh38 human reference genome using STAR (2.7.11a --- 2023/08/15 ::: STARdiploid) and mapping statistics were recorded. After BAM file processing, gene counts were generated using the GenomicFeatures and GenomicAlignments BioConductor packages within R (v 4.2.3, RStudio). Hierarchical clustering and different gene expression analysis (DGE) was then performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: counts_all_samples.txt include raw counts for each sample

source_name: Bone marrrow

growth_protocol: 10% fetal bovine serum MSC qualified + Dulbecco's Modified Eagle Medium (DMEM) + 1% Andibiotic Antimycotic (Sigma-Aldrich)

extract_protocol:
RNA extraction was performed by using High Pure RNA Isolation Kit (Roche) according to the manufacturer’s protocol and RNA was quantified in NanoDrop® (Thermo Fisher Scientific). Quality control (QC) of RNA samples was then performed with Fragment Analyzer™ (Agilent Technologies) and analyzed with ProSize data analysis software 4.0.2.7.
Full-length complementary DNAs (cDNAs) were generated following the SMART-Seq2 protocol as described by Picelli, 2014. Quality control of cDNA was performed with Fragment Analyzer™ (Agilent Technologies) and ProSize data analysis software 4.0.2.7. All samples passed QC. Library preparation was performed following the Nextera library preparation protocol (Nextera® XT DNA Library Preparation kit, Illumina), as previously described by Baym, 2015. Libraries were confirmed by Fragment Analyzer™ (Agilent Technologies) and then sequenced in NextSeq2000 (Illumina). 100 bp single-end reads were obtained. For this experiment, a yield of about 25 million reads per sample was requested.

treatment_protocol: Selected bone marrow-derived mesenchymal stromal cells, previously isolated from bone marrow (BM) samples by an erythrocyte sedimentation method (HetaSep™, STEMCELL Technologies), were expanded in Dulbecco's Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) MSC-qualified (Thermo Fisher Scientific) at a cell density of 3000 cells/cm2. Medium changes where performed each 72h and cells were harvested at 70% confluence.

value: Bone marrrow

value: mesenchymal stromal cells

tag: subject status

value: healthy control

value: 44 yeas age

tag: cell passage_number

value: DMEM 10%FBS


title: Tcells-UT

description: Library name: CAST-UT-mouseT-cells

value: T cells

value: Unc13d^jinx/jinx (mutant)


title: Bone marrow-derived MSC, healthy control, male, 11 yeas age, cell passage number = P2

description:
Library name: CM11
column name in counts_all_samples.txt: CM11

value: male

value: 11 yeas age


title: Ox2, oxycodone, fecal, pre

description:
Library name: Ox2-PO
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv: Ox2-PO

value: Rattus norvegicus fecal sample

value: Long-Evans

value: Oxycodone


title: HSC-UT

description: Library name: CAST-UT-HSCs

source_name: HSCc

value: HSCc

value: untreated


title: Testic cells,rep3

description:
Library name: NOA3
10x Genomics

value: Testis, NOA

value: Testic cells,rep3

value: human Testic cells,rep3


title: Jinx-HSC replicate 2

description: Library name: CAST-Jinx-HSC-BE2

value: HSCs

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: Bone marrow-derived MSC, aplastic anemia, male, 35 years age, cell passage number = P4

description:
Library name: AM87
column name in counts_all_samples.txt: AM87

value: Bone marrrow

value: mesenchymal stromal cells

value: aplastic anemia

value: 35 years age


title: Ox1, oxycodone, fecal, post

description:
Library name: Ox1-SAD19
Column name in Species_Level_Aggregate_counts.csv and Genus_Level_Aggregate Counts.csv:  Ox1-SAD19

value: Post


title: MEFs-Cas9 replicate 1

description: Library name: CAST-Cas9-d6-Rep1-MEFs

value: MEF CF1

value: CF-1 mouse embryos

value: SpCas9 nuclease targeting Unc13d


title: MEFs-Cas9 replicate 2

description: Library name: CAST-Cas9-d6-Rep2-MEFs


title: Testic cells,rep4

description:
Library name: NOA4
10x Genomics

value: Testic cells,rep4

value: human Testic cells,rep4

value: NOA


title: Bone marrow-derived MSC, aplastic anemia, male, 7 years age, cell passage number = P5

description:
Library name: AM15
column name in counts_all_samples.txt: AM15

value: male

value: 7 years age

value: DMEM 10%FBS


title: MEFs-CBE replicate 2

description: Library name: CAST-CBE-d6-Rep2-MEFs


title: Bone marrow-derived MSC, healthy control, female, 4 yeas age, cell passage number = P5

description:
Library name: CF18
column name in counts_all_samples.txt: CF18

value: healthy control

value: female

value: 4 yeas age


title: Testic cells,rep2

description:
Library name: NOA2
10x Genomics

value: Testis, NOA

value: Testic cells,rep2

value: human Testic cells,rep2


title: iUB optoRET organoid, GDNF+ light+ rep3

city: Philadelphia

first: Ronald

last: Canlla

state: Pennsylvania

address: 107 Towne Building

institute: University of Pennsylvania

description:
Library name: MSDMXS_24
column names in MSDMXS-expression-matrix.tsv: MSDMXS_24_cpm, MSDMXS_24_count

data_processing:
Quality of the resulting fastq files was assessed using FastQC v0.12.1.
Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1.
PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0.
Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32.
Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated text file containing gene-level raw counts and normalized expression values. Rows represent genes and columns represent samples

source_name: kidney organoid

growth_protocol: Human iPSC-derived ureteric bud (iUB) organoids were maintained in appropriate differentiation media under standard culture conditions at 37°C and 5% CO2

extract_protocol:
Day 12 iUB or day 11 iUB-optoRET organoids were extracted from Matrigel droplets using 600 µl of chilled Cell Recovery Solution (#354253, Corning) on ice for 20-30 min and were triturated approximately every 5 min. Organoids from each group were pooled into a single 15 ml conical tube, washed briefly in 1x DPBS, and placed in DNA/RNA shield (#R1100, Zymo). All sample preparation areas were pre-cleaned with RNaseZAP (#R2020, Sigma) before handling.
Libraries were prepared using a commercial service (Plasmidsaurus). In brief, total RNA per sample was subject to mRNA capture, reverse transcription, and second strand synthesis. This was followed by tagmentation and Illumina library indexing and amplification.

value: kidney organoid

value: MAFB:mTagBFP2/GATA3:mCherry human iPSC-derived ureteric bud organoids

value: ureteric bud epithelial cells

value: optoRET-expressing; MAFB:mTagBFP2/GATA3:mCherry reporter line


title: Bone marrow-derived MSC, aplastic anemia, male, 15 years age, cell passage number = P6

description:
Library name: AM08
column name in counts_all_samples.txt: AM08

value: Bone marrrow

value: mesenchymal stromal cells

value: aplastic anemia

value: 15 years age


title: iUB optoRET organoid, GDNF+ light+ rep2

description:
Library name: MSDMXS_20
column names in MSDMXS-expression-matrix.tsv: MSDMXS_20_cpm, MSDMXS_20_count


title: iUB optoRET organoid, GDNF- light-, rep3

description:
Library name: MSDMXS_21
column names in MSDMXS-expression-matrix.tsv: MSDMXS_21_cpm, MSDMXS_21_count


title: MEFs-CBE replicate 1

description: Library name: CAST-CBE-d6-Rep1-MEFs

value: MEF CF1

value: CF-1 mouse embryos

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: CB46923 treatment C

city: Singapore

first: John

last: Ouyang

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

description: Library name: CB46923_C

data_processing:
The demultiplexed reads were aligned against GRCh38 reference genome using Alevin via salmon 1.5.2.53,54 The single-cell data were loaded into count matrices, and all 45 samples were merged using Seurat v4.1.55 Cells that expressed 500 to 6,702 (top 2% of entire dataset) genes and contained less than 20% of transcripts mapping to mitochondrial genes were retained. Subsequently, 5,000 cells were subsampled from each day and condition (13 day-conditions in total), with the exception of Day3-C, which is comprised of 2,151 cells, and Day0, where we subsampled 15,000 cells. This resulted in a total of 72,151 cells.
Assembly: GRCh38
Supplementary files format and content: Seurat Object containing all samples

source_name: Cord Blood

extract_protocol:
UCB-CD34+ were cultured respectively in Stemspan-AOF media supplemented in cytokine cocktails with and without C7 respectively as described previously for 3, 7 and 11 days. Harvested cells were then resuspended into single-cell suspensions into 1000-6000 cells/ul to be loaded into Chromium microfluidic chips with targeted cell recovery of 10,000 using the Chromium Controller (10x Genomics, USA).
Single-cell RNA-seq libraries were prepared according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10 X Genomics, USA; PN-1000268). Captured libraries were sequenced on the Novaseq 6000 sequencer analyzer at PE150 and sequencing depth of 20,000 read pairs per cell (Novogene, China).

value: Cord Blood

value: Primary Cells

value: HSPCs

value: normal

value: condition C


title: CB46923 uncultured

description: Library name: CB46923_Unc

value: untreated


title: Testic cells,rep1

description:
Library name: NOA1
10x Genomics

value: Testis, NOA

value: Testic cells,rep1

value: human Testic cells,rep1

value: NOA


title: Tcells-Cas9 replicate 2

description: Library name: CAST-Cas9-d3-Rep2-mouseTcells

value: T cells

value: Unc13d^jinx/jinx (mutant)

value: SpCas9 nuclease targeting Unc13d


title: Bone marrow-derived MSC, aplastic anemia, male, 12 years age, cell passage number = P3

description:
Library name: AM10
column name in counts_all_samples.txt: AM10

value: Bone marrrow

value: mesenchymal stromal cells

value: aplastic anemia

value: male

value: 12 years age

value: DMEM 10%FBS


title: iUB optoRET organoid, GDNF- light+, rep2

description:
Library name: MSDMXS_19
column names in MSDMXS-expression-matrix.tsv: MSDMXS_19_cpm, MSDMXS_19_count

value: kidney organoid

value: MAFB:mTagBFP2/GATA3:mCherry human iPSC-derived ureteric bud organoids

value: ureteric bud epithelial cells

value: optoRET-expressing; MAFB:mTagBFP2/GATA3:mCherry reporter line


title: CB46923 treatment D

description: Library name: CB46923_D

value: Cord Blood

value: Primary Cells

value: HSPCs

value: normal

value: condition D


title: iUB optoRET organoid, GDNF+ light-, rep3

description:
Library name: MSDMXS_22
column names in MSDMXS-expression-matrix.tsv: MSDMXS_22_cpm, MSDMXS_22_count


title: iUB optoRET organoid, GDNF+ light-, rep2

description:
Library name: MSDMXS_18
column names in MSDMXS-expression-matrix.tsv: MSDMXS_18_cpm, MSDMXS_18_count


title: HSR_T1D_CD8_9

description: lymphocytes from Male T1D patient

value: Peripheral Blood

value: M

value: Type 1 Diabetes

value: CD8+ cells

value: HSR


title: iUB optoRET organoid, GDNF- light+, rep3

description:
Library name: MSDMXS_23
column names in MSDMXS-expression-matrix.tsv: MSDMXS_23_cpm, MSDMXS_23_count


title: Tcells-Cas9 replicate 1

description: Library name: CAST-Cas9-d3-Rep1-mouseTcells

value: T cells

value: Unc13d^jinx/jinx (mutant)

value: SpCas9 nuclease targeting Unc13d


title: iUB optoRET organoid, GDNF- light-, rep2

description:
Library name: MSDMXS_17
column names in MSDMXS-expression-matrix.tsv: MSDMXS_17_cpm, MSDMXS_17_count

value: kidney organoid


title: CB46923 treatment A

description: Library name: CB46923_A

value: condition A


title: Mock-treated T cells from Donor 3

description: Library name: UT_AAVS1_B2M_Donor3

value: Blood

value: T lymphocytes

value: Mock-treated


title: CB46923 treatment B

description: Library name: CB46923_B

value: Cord Blood

value: Primary Cells

value: condition B


title: iUB optoRET organoid, GDNF- light+, rep1

description:
Library name: MSDMXS_15
column names in MSDMXS-expression-matrix.tsv: MSDMXS_15_cpm, MSDMXS_15_count

value: MAFB:mTagBFP2/GATA3:mCherry human iPSC-derived ureteric bud organoids

value: ureteric bud epithelial cells

value: optoRET-expressing; MAFB:mTagBFP2/GATA3:mCherry reporter line


title: iUB optoRET organoid, GDNF+ light+ rep1

description:
Library name: MSDMXS_16
column names in MSDMXS-expression-matrix.tsv: MSDMXS_16_cpm, MSDMXS_16_count


title: iUB optoRET organoid, GDNF- light-, rep1

description:
Library name: MSDMXS_13
column names in MSDMXS-expression-matrix.tsv: MSDMXS_13_cpm, MSDMXS_13_count


title: Tcells-CBE replicate 2

description: Library name: CAST-CBE-d3-Rep2-mouseTcells

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: CB49916 uncultured

description: Library name: CB49916_Unc

value: HSPCs

value: normal

value: untreated


title: Tcells-CBE replicate 1

description: Library name: CAST-CBE-d3-Rep1-mouseTcells

value: T cells

value: Unc13d^jinx/jinx (mutant)


title: HSC-Cas9 replicate 2

description: Library name: CAST-Cas9-d3-Rep2-HSCs

value: HSCs

value: SpCas9 nuclease targeting Unc13d


title: iUB optoRET organoid, GDNF+ light-, rep1

description:
Library name: MSDMXS_14
column names in MSDMXS-expression-matrix.tsv: MSDMXS_14_cpm, MSDMXS_14_count

value: kidney organoid


title: iUB organoid, GDNF++, rep3

description:
Library name: MSDMXS_11
column names in MSDMXS-expression-matrix.tsv: MSDMXS_11_cpm, MSDMXS_11_count

value: GDNF++


title: iUB organoid, RETi+, rep3

description:
Library name: MSDMXS_12
column names in MSDMXS-expression-matrix.tsv: MSDMXS_12_cpm, MSDMXS_12_count

value: RETi+


title: CB49916 treatment D

description: Library name: CB49916_D

value: Cord Blood

value: condition D


title: HSC-CBE replicate 2

description: Library name: CAST-CBE-d3-Rep2-HSCs


title: iUB organoid, GDNF+, rep3

description:
Library name: MSDMXS_10
column names in MSDMXS-expression-matrix.tsv: MSDMXS_10_cpm, MSDMXS_10_count

value: GDNF+


title: iUB organoid, GDNF-, rep3

description:
Library name: MSDMXS_9
column names in MSDMXS-expression-matrix.tsv: MSDMXS_9_cpm, MSDMXS_9_count

value: MAFB:mTagBFP2/GATA3:mCherry human iPSC-derived ureteric bud organoids

value: GDNF-


title: HSC-CBE replicate 1

description: Library name: CAST-CBE-d3-Rep1-HSCs


title: CB49916 treatment A

description: Library name: CB49916_A

value: Primary Cells

value: condition A


title: iUB organoid, RETi+, rep2

description:
Library name: MSDMXS_8
column names in MSDMXS-expression-matrix.tsv: MSDMXS_8_cpm, MSDMXS_8_count

value: ureteric bud epithelial cells


title: HSC-Cas9 replicate 1

description: Library name: CAST-Cas9-d3-Rep1-HSCs


title: iUB organoid, GDNF++, rep2

description:
Library name: MSDMXS_7
column names in MSDMXS-expression-matrix.tsv: MSDMXS_7_cpm, MSDMXS_7_count


title: CB49916 treatment B

description: Library name: CB49916_B

value: HSPCs

value: normal

value: condition B


title: CB49916 treatment C

description: Library name: CB49916_C

value: condition C


title: iUB organoid, GDNF-, rep2

description:
Library name: MSDMXS_5
column names in MSDMXS-expression-matrix.tsv: MSDMXS_5_cpm, MSDMXS_5_count


title: UNC13D_UT

description: Library name: 2nd-UT-BM

source_name: bone marrow

value: bone marrow

value: Unc13d^jinx/jinx (mutant)

value: untreated


title: CB49847 uncultured

description: Library name: CB49847_Unc


title: iUB organoid, RETi+, rep1

description:
Library name: MSDMXS_4
column names in MSDMXS-expression-matrix.tsv: MSDMXS_4_cpm, MSDMXS_4_count

value: kidney organoid


title: UNC13D_1870_replicate 2

description: Library name: 3rd-1-Rep2-BM

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: iUB organoid, GDNF-, rep1

description:
Library name: MSDMXS_1
column names in MSDMXS-expression-matrix.tsv: MSDMXS_1_cpm, MSDMXS_1_count


title: CB49847 treatment C

description: Library name: CB49847_C

value: Cord Blood


title: iUB organoid, GDNF+, rep2

description:
Library name: MSDMXS_6
column names in MSDMXS-expression-matrix.tsv: MSDMXS_6_cpm, MSDMXS_6_count


title: iUB organoid, GDNF++, rep1

description:
Library name: MSDMXS_3
column names in MSDMXS-expression-matrix.tsv: MSDMXS_3_cpm, MSDMXS_3_count

value: GDNF++


title: Recurrent synovial sarcoma, thigh (resection specimen)

city: Niigata City

first: Tomohiro

last: Miyazaki

address: 1-757 Asahimachi-Dori, ChuoKu

department: Orthopedics

country: Japan

institute: Niigata University Graduate School of Medical and Dental Sciences

description: Library name: r24

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using RNA-seq aligner STAR (Version 2.7.11b).
Structural variants and gene fusions were identified using Arriba (Version 2.5.1).
Assembly: hg38
Supplementary files format and content: [Sample_ID]_fusions.tsv: A tab-separated values (TSV) file containing the list of gene fusions identified by Arriba.
Supplementary files format and content: [Sample_ID]_fusions.pdf: A PDF file providing visual representations (fusion plots) of the identified gene fusions.

source_name: Thigh subcutaneous tumor

extract_protocol:
Approximately 100 mg of tumor specimen was homogenized and total RNA was extracted using an acid guanidinium thiocyanate-phenol-chloroform (AGPC) method with chloroform phase separation and isopropanol precipitation.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and  NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Thigh subcutaneous tumor


title: iUB organoid, GDNF+, rep1

description:
Library name: MSDMXS_2
column names in MSDMXS-expression-matrix.tsv: MSDMXS_2_cpm, MSDMXS_2_count

value: MAFB:mTagBFP2/GATA3:mCherry human iPSC-derived ureteric bud organoids

value: GDNF+


title: CB49847 treatment D

description: Library name: CB49847_D

value: Primary Cells

value: condition D


title: UNC13D_1838_replicate 1

description: Library name: 2nd-1838-Rep1-BM


title: neoantigen peptide44 reactive T cells from FT,TCR

city: Oxford

first: luyao

last: wang

state: Oxfordshire

address: MRC Weatherall Institute of Molecular Medicine (Oxford University & John Radcliffe Hospital)

country: United Kingdom

institute: University of oxford

description:
Library name: P44_TCR_11642
10x Genomics

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v7.0, 10X Genomics).
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: Matrix Market (MTX) count matrix (matrix.mtx.gz): UMI counts per gene (rows) by cell barcode (columns), generated by CellRanger 7.0. Feature annotation (features.tsv.gz): gene identifiers and names corresponding to matrix rows.Barcode list (barcodes.tsv.gz): cell barcode sequences corresponding to matrix columns.Filtered contig annotations (*_filtered_contig_annotations.csv): A comma-separated values (CSV) table produced by Cell Ranger, containing, for each cell barcode, the high-confidence TCR contig calls. Columns include barcode, contig_id, high_confidence (TRUE/FALSE), chain (e.g. TRA/TRB), full_length (TRUE/FALSE), productive (TRUE/FALSE), cdr3 (amino acid), cdr3_nt (nucleotide), v_gene, d_gene, j_gene, etc.
Library strategy: TCR-Seq

source_name: fallopian tube (FT)

extract_protocol:
Following tissue enzymatic dissociation of tissues, single-cell suspensions were subjected to antibody staining with anti-EPCAM, anti-CD56, anti-CD3 and anti-CD103. Cells were purified by fluorescence-activated cell sorting (FACS) on SONY MA400 cell sorter equipped with four lasers (405 nm, 488 nm, 561 nm and 638nm). A 100-μm nozzle running at 70 psi and 90 kHz was used as the setup for each sort session.
TRM-like and circulating T cells were sorted from 4 different HGSOCs for scRNA-seq analysis. Single-cell RNA-sequencing was performed using the 10X Genomics Chromium. A single-cell suspension derived from dissociated tissue was sorted. The cell suspension was loaded onto the 10X Genomics Chromium Single Cell Controller at a concentration of 700~1000 cells per microliter in order to encapsulate between 5000 and 12,500 cells per sample. Briefly, the single cells, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs) and then reverse transcription of poly-adenylated mRNA was performed inside each droplet. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium Next GEM Single Cell v2 and V(D)J Reagent Kits. 25,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the NovaSeq X Plus instrument. Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v7.0 software.

value: fallopian tube (FT)

value: CD3+CD103+tissue-resident memory-like T cells (TRMLs)


title: UNC13D_1870_replicate 1

description: Library name: 3rd-1-Rep1-BM


title: Primary synovial sarcoma, thigh (resection specimen)

description: Library name: p21

source_name: Thigh soft tissue tumor

value: Thigh soft tissue tumor


title: CB49847 treatment B

description: Library name: CB49847_B

value: HSPCs

value: normal

value: condition B


title: neoantigen peptide43 reactive T cells from FT,TCR

description:
Library name: P43_TCR_11642
10x Genomics


title: CB49847 treatment A

description: Library name: CB49847_A

value: condition A


title: CD3+ T cells from PBMC, biological replicate 4,TCR

description:
Library name: PBMC_TCR_11657
10x Genomics

source_name: PBMC

value: PBMC

value: CD3+ T cells


title: tumor organoid reactive T cells from FT,TCR

description:
Library name: Org_TCR_11642
10x Genomics


title: CD3+ T cells from PBMC, biological replicate 3,TCR

description:
Library name: PBMC_TCR_11642
10x Genomics


title: CB49636 uncultured

description: Library name: CB49636_Unc

value: untreated


title: CB49636 treatment D

description: Library name: CB49636_D

value: Cord Blood


title: Aldosterone-treated DVC, GEM-X chemistry, replicate 2

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

description:
Library name: ALDO_GEMX_rep2
10X GEM-X

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; version 9.0.1) and using the mm10-2020-A mouse assembly.
Assembly: mm10-2020-A mouse assembly
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5

source_name: Dorsal Vagal Complex

extract_protocol:
Hsd11b2-IRES-Cre mice aged 5-10 weeks received bilateral stereotaxic injections of Cre-dependent AAV-H2b-mCherry into the NTS. After 2 weeks of recovery, mice were sacrificed between 9:00 am – 12:00 pm by rapid decapitation immediately after removal from the home cage. Brains were extracted and chilled in DMEM/F12 media slush (Thermo Fisher Scientific). Brains were then placed dorsal side up in a chilled stainless steel brain matrix (Stoelting, Wood Dale, IL) and 1 mm coronal sections of the caudal medulla were collected. Tissue from the caudal medulla was placed in chilled RNAprotect solution (QIAGEN, Aarhus, Denmark) and then the Dorsal Vagal Complex was microdissected under a fluorescent stereoscope. During dissections, tissue was pooled according to treatment (vehicle or aldosterone). All pooled samples were incubated overnight at 4°C in RNAprotect®. RNAprotect solution was then removed from sample tubes the following day before storing samples at -80°C.
Each sample underwent nuclear dissociation and purification procedures before being incubated with NucBlue (Thermo fisher scientific). After incubation, nuclei were flow sorted together into RT Reagent B (10x Genomics) using a Cytek Aurora CS cell sorter with a 70 μm nozzle to remove poor quality nuclei, enrich for mCherry positive nuclei, and count the number of nuclei per sample. Sorted nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell 3’ GEM-X chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Gene expression libraries for 'Rep 2' were sequenced on an Illumina NovaSeq 6000 sequencer (Read1 - 28, i7 = 10, i5 = 10, Read2 = 90). Gene expression libraries for 'Rep 3' were sequenced on an AVITI24 (Element Biosciences) (Rep 2) sequencer using a 150-cycle kit with the following sequencing configuration: i7 = 10, i5 = 10, Read1 = 29, Read2 =91.

treatment_protocol: Mice were treated with either vehicle or aldosterone for 24 hours before tissue collection

value: Dorsal Vagal Complex

value: 24hr ALDO

value: mixed


title: CD3+ T cells from PBMC, biological replicate 2,techinical replicate2,TCR

description:
Library name: PBMC_TCR_11641_2
10x Genomics


title: CD3+ T cells from PBMC, biological replicate 2,techinical replicate1,TCR

description:
Library name: PBMC_TCR_11641_1
10x Genomics


title: Vehicle-treated DVC, GEM-X chemistry, replicate 2

description:
Library name: Veh_GEMX_rep2
10X GEM-X

value: 24hr vehicle


title: TRMs from Omentum tumor, biological replicate 3,TCR

description:
Library name: OM_TCR_11642
10x Genomics

source_name: Omentum tumor

value: Omentum tumor


title: Aldosterone treated DVC, male, Epi Multiome chemistry, GEX, replicate 1

description: Library name: MaleA_GEX

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; cellranger-arc-2.0.2) and using the mm10-2020-A mouse assembly.
Assembly: mm10-2020-A
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5

extract_protocol:
Hsd11b2-IRES-Cre mice aged 5-10 weeks received bilateral stereotaxic injections of Cre-dependent AAV-H2b-mCherry into the NTS. After 2 weeks of recovery, mice were sacrificed between 9:00 am – 12:00 pm by rapid decapitation immediately after removal from the home cage. Brains were extracted and chilled in DMEM/F12 media slush (Thermo Fisher Scientific). Brains were then placed dorsal side up in a chilled stainless steel brain matrix (Stoelting, Wood Dale, IL) and 1 mm coronal sections of the caudal medulla were collected. Tissue from the Dorsal Vagal Complex was microdissected under a fluorescent stereoscope, frozen on dry ice, and pooled according to sex and treatment (vehicle or aldosterone). All pooled samples were stored dry at -80°C.
Each sample underwent nuclear dissociation and purification procedures before being incubated with NucBlue (Thermo fisher scientific). After incubation, a portion of the nuclei were added to a collection tube with ATAC Buffer B (10X Genomics). Subsequently, mCherry+ nuclei were flow sorted into the same collection tube using a FACS Aria cell sorter with a 70 μm nozzle to remove poor quality nuclei and count the number of nuclei per sample. Pooled nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell Multiome ATAC + Gene Expression was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Gene expression and ATAC libraries were sequenced on an Illumina NovaSeq 6000 sequencer with the following sequencing configurations: GEX - Read1 - 28, i7 = 10, i5 = 10, Read2 = 90, ATAC - Read1 = 50, i7 = 8, i5 = 24, Read2 = 49..

value: male

tag: library type

value: mRNA


title: CB49636 treatment B

description: Library name: CB49636_B

value: Primary Cells


title: CB49636 treatment C

description: Library name: CB49636_C

value: condition C


title: CD3+ T cells from PBMC, biological replicate 1,TCR

description:
Library name: PBMC_TCR_11640
10x Genomics


title: Aldosterone treated DVC, male, Epi Multiome chemistry, ATAC, replicate 1

description: Library name: MaleA_ATAC

library_source: genomic single cell

value: ATAC


title: Aldosterone treated DVC, female, Epi Multiome chemistry, ATAC, replicate 1

description: Library name: FemaleA_ATAC

value: female


title: TRMs from Omentum tumor, biological replicate 1,TCR

description:
Library name: OM_TCR_11640
10x Genomics

value: CD3+CD103+tissue-resident memory-like T cells (TRMLs)


title: TRMs from Omentum tumor, biological replicate 2,TCR

description:
Library name: OM_TCR_11641
10x Genomics


title: CB49636 treatment A

description: Library name: CB49636_A

value: HSPCs

value: normal

value: condition A


title: TRMs from Omentum tumor, biological replicate 4,TCR

description:
Library name: OM_TCR_11657
10x Genomics


title: CB48726 uncultured

description: Library name: CB48726_Unc

value: untreated


title: TRMs from FT, biological replicate 4,TCR

description:
Library name: FT_TCR_11657
10x Genomics

value: fallopian tube (FT)


title: Vehicle treated DVC, male, Epi Multiome chemistry, ATAC, replicate 1

description: Library name: MaleV_ATC

value: Dorsal Vagal Complex


title: TRMs from FT, biological replicate 2,TCR

description:
Library name: FT_TCR_11641
10x Genomics


title: TRMs from FT, biological replicate 1,TCR

description:
Library name: FT_TCR_11640
10x Genomics


title: CB48726 treatment D

description: Library name: CB48726_D

value: Cord Blood

value: condition D


title: tumor organoid reactive T cells from FT,GEX

description:
Library name: Org_GEX_11642
10x Genomics

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v7.0, 10X Genomics).
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: Matrix Market (MTX) count matrix (matrix.mtx.gz): UMI counts per gene (rows) by cell barcode (columns), generated by CellRanger 7.0. Feature annotation (features.tsv.gz): gene identifiers and names corresponding to matrix rows.Barcode list (barcodes.tsv.gz): cell barcode sequences corresponding to matrix columns.Filtered contig annotations (*_filtered_contig_annotations.csv): A comma-separated values (CSV) table produced by Cell Ranger, containing, for each cell barcode, the high-confidence TCR contig calls. Columns include barcode, contig_id, high_confidence (TRUE/FALSE), chain (e.g. TRA/TRB), full_length (TRUE/FALSE), productive (TRUE/FALSE), cdr3 (amino acid), cdr3_nt (nucleotide), v_gene, d_gene, j_gene, etc.


title: CB48726 treatment C

description: Library name: CB48726_C


title: neoantigen peptide43 reactive T cells from FT,GEX

description:
Library name: P43_GEX_11642
10x Genomics


title: Aldosterone treated DVC, female, Epi Multiome chemistry, GEX, replicate 1

description: Library name: FemaleA_GEX

value: 24hr ALDO


title: Vehicle treated DVC, male, Epi Multiome chemistry, GEX, replicate 1

description: Library name: MaleV_GEX

value: 24hr vehicle


title: TRMs from FT, biological replicate 3,TCR

description:
Library name: FT_TCR_11642
10x Genomics


title: CB48726 treatment B

description: Library name: CB48726_B

value: condition B


title: CD3+ T cells from PBMC, biological replicate 3,GEX

description:
Library name: PBMC_GEX_11642
10x Genomics

value: PBMC

value: CD3+ T cells


title: Vehicle treated DVC, female, Epi Multiome chemistry, GEX, replicate 1

description: Library name: FemaleV_GEX

value: mRNA


title: CD3+ T cells from PBMC, biological replicate 4,GEX

description:
Library name: PBMC_GEX_11657
10x Genomics


title: Vehicle treated DVC, female, Epi Multiome chemistry, ATAC, replicate 1

description: Library name: FemaleV_ATAC

value: ATAC


title: neoantigen peptide44 reactive T cells from FT,GEX

description:
Library name: P44_GEX_11642
10x Genomics


title: CD3+ T cells from PBMC, biological replicate 2,techinical replicate2,GEX

description:
Library name: PBMC_GEX_11641_2
10x Genomics


title: CB48726 treatment A

description: Library name: CB48726_A

value: Primary Cells


title: CD3+ T cells from PBMC, biological replicate 2,techinical replicate1,GEX

description:
Library name: PBMC_GEX_11641_1
10x Genomics


title: Tlr5 wildtype + ABX/TLR5-agonist/bleomycin Rep S08

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

description: Library name: N734SE2RepS08

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by trim_galore
The raw reads were filtered by removing adaptor sequences, contamination and low-quality reads. Cleaned reads were mapped to mouse mm10 using STAR aligner
Subread featureCounts was applied for gene quantification based on the mouse refGene gene annotation available from UCSC Genome Browser website
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count from featureCounts and RPKM normalized counts for each sample

source_name: lung

extract_protocol:
Animals were euthanized 36-hours post treatment, lungs were collected and digested as described in Sakamachi et al., 2025 (manuscript provisionally accepted). Briefly, alveolar type II cells were sorted, and RNA was isolated using the NucleoSpin RNA kit for RNA purification (Macherey-Nagel, Catalog# 740955.50). Each sample is comprised by a pool of 3 animals.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Following Barkauskas et al., 2013: SPC-Cre.ERT2 x ROSA-TOMATO mice were injected with Tamoxifen (0.25 mg/10 g to 2.5 mg/10 g body weight) by intraperitoneal administration, every other day for up to 4 treatments to induce TOMATO expression in SPC+ cells. Animals were rested for two-weeks following the final tamoxifen administration prior to bleomycin administration. Animals were treated with Bleomycin, TLR5-agonist/bleomycin, or antibiotics (ABX)/TLR5-agonist/bleomycin, as described in Sakamachi et al., 2025.

value: lung

value: alveolar type II epithelial cells

value: Tlr5 wildtype

value: Sftpc-CreERT2 x Rosa26R-tdTm


title: CD3+ T cells from PBMC, biological replicate 1,GEX

description:
Library name: PBMC_GEX_11640
10x Genomics


title: CB46894 uncultured

description: Library name: CB46894_Unc

value: HSPCs

value: normal

value: untreated


title: Tlr5 wildtype + ABX/TLR5-agonist/bleomycin Rep S06

description: Library name: N734SE2RepS06


title: CB46894 treatment D

description: Library name: CB46894_D

value: Cord Blood


title: TRMs from Omentum tumor, biological replicate 4,GEX

description:
Library name: OM_GEX_11657
10x Genomics

value: Omentum tumor

value: CD3+CD103+tissue-resident memory-like T cells (TRMLs)


title: CB46894 treatment C

description: Library name: CB46894_C

value: condition C


title: TRMs from Omentum tumor, biological replicate 3,GEX

description:
Library name: OM_GEX_11642
10x Genomics


title: CB46894 treatment B

description: Library name: CB46894_B

value: condition B


title: Tlr5 wildtype + ABX/bleomycin Rep S11

description: Library name: N734ControlRepS11

value: bleomycin


title: CB46894 treatment A

description: Library name: CB46894_A

value: condition A


title: TRMs from FT, biological replicate 3,GEX

description:
Library name: FT_GEX_11642
10x Genomics

value: fallopian tube (FT)


title: Tlr5 wildtype + ABX/bleomycin Rep S02

description: Library name: N734ControlRepS02


title: TRMs from FT, biological replicate 2,GEX

description:
Library name: FT_GEX_11641
10x Genomics


title: Tlr5 wildtype + ABX/TLR5-agonist/bleomycin Rep S01

description: Library name: N734SE2RepS01


title: TRMs from Omentum tumor, biological replicate 2,GEX

description:
Library name: OM_GEX_11641
10x Genomics


title: TRMs from FT, biological replicate 1,GEX

description:
Library name: FT_GEX_11640
10x Genomics


title: TRMs from Omentum tumor, biological replicate 1,GEX

description:
Library name: OM_GEX_11640
10x Genomics


title: Tlr5 wildtype + ABX/bleomycin Rep S04

description: Library name: N734ControlRepS04


title: TRMs from FT, biological replicate 4,GEX

description:
Library name: FT_GEX_11657
10x Genomics


title: UNC13D_1838_replicate 2

description: Library name: 2nd-1838-Rep2-BM

value: bone marrow

value: Unc13d^jinx/jinx (mutant)

value: evoCDA1-BE4max cytosine base editor targeting Unc13d


title: CB42988 uncultured

description: Library name: CB42988_Unc

value: Primary Cells


title: OM_B9_15d_Rep1

city: Seoup

first: Dong Woo

last: Lee

address: 174, Yulgok-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Human PDLSC cultured in OM with BMP9 treatment for 15 day, replicate 1

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: Human PDLSC (periodontal ligament stem cell)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: PDLSCs were maintained in α-MEM supplemented with 10% FBS at 37°C in a 5% CO2 humidified incubator.  For the OM group, osteogenic medium (containing β-glycerophosphate, ascorbic acid, dexamethasone) was used.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: NT: no additional treatment , B2: BMP2 (concentration 8nM) , B9: BMP9 (concentration 8nM) Cells were incubated for 1, 7, or 15 days depending on the group.

value: human periodontal ligament stem cells derived from adult donors

value: Normal

value: 28 year old


title: Tlr5 wildtype + TLR5-agonist/bleomycin RepS06

description: Library name: N110SE2RepS06

value: lung

value: alveolar type II epithelial cells

value: Tlr5 wildtype

value: Sftpc-CreERT2 x Rosa26R-tdTm


title: OM_B9_15d_Rep2

description: Human PDLSC cultured in OM with BMP9 treatment for 15 day, replicate 2


title: CB42988 treatment D

description: Library name: CB42988_D

value: Cord Blood

value: HSPCs

value: normal

value: condition D


title: CB42988 treatment B

description: Library name: CB42988_B

value: condition B


title: Tlr5 wildtype + bleomycin S05

description: Library name: N110ControlRepS05

value: bleomycin


title: Tlr5 wildtype + TLR5-agonist/bleomycin Rep S04

description: Library name: N110SE2RepS04


title: CB42988 treatment C

description: Library name: CB42988_C

value: condition C


title: Tlr5 wildtype + bleomycin Rep S03

description: Library name: N110ControlRepS03


title: Tlr5 wildtype + TLR5-agonist/bleomycin Rep S02

description: Library name: N110SE2RepS02


title: Tlr5 wildtype + bleomycin Rep S01

description: Library name: N110ControlRepS01


title: CB42988 treatment A

description: Library name: CB42988_A

value: condition A


title: OM_B2_7d_Rep2

description: Human PDLSC cultured in OM with BMP2 treatment for 7 day, replicate 2


title: GM_NT_15d_Rep1

description: Human PDLSC cultured in GM with no treatment for 15 day, replicate 1


title: CB42557 treatment D

description: Library name: CB42557_D


title: OM_B9_7d_Rep1

description: Human PDLSC cultured in OM with BMP9 treatment for 7 day, replicate 1


title: CB42557 uncultured

description: Library name: CB42557_Unc

value: untreated


title: OM_B2_15d_Rep2

description: Human PDLSC cultured in OM with BMP2 treatment for 15 day, replicate 2


title: OM_NT_7d_Rep2

description: Human PDLSC cultured in OM with no treatment for 7 day, replicate 2


title: LCMV Clone 13, Day 21, sgCtrl, ATAC

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description:
Library name: scMulti_Cl13D21_P14_sgCtrl_ATAC
10x scMultiome-seq ATAC library

data_processing:
FASTQ generation and alignment to mouse mm10 genome were performed using Cell Ranger ARC (10x Genomics) with the default settings.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: filtered_feature_bc_matrix.h5; atac_fragments.tsv.gz; atac_fragments.tsv.gz.tbi

source_name: Spleen

extract_protocol:
P14 CD8 T cells were sorted from spleens of LCMV Cl13-infected mice at day 21 p.i. Cells from 3-4 mice per condition were pooled (about 100,000 total). Nuclei were extracted per 10x protocol (CG000365).
scMultiome libraries were generated using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Libraries were constructed per manufacturer's instructions (CG000338).

value: Spleen

value: P14 CD8 T cells

value: CRISPR sgCtrl


title: GM_NT_15d_Rep2

description: Human PDLSC cultured in GM with no treatment for 15 day, replicate 2

value: human periodontal ligament stem cells derived from adult donors

value: Normal

value: 28 year old


title: CB42557 treatment C

description: Library name: CB42557_C

value: Primary Cells


title: OM_B2_7d_Rep1

description: Human PDLSC cultured in OM with BMP2 treatment for 7 day, replicate 1


title: OM_NT_15d_Rep1

description: Human PDLSC cultured in OM with no treatment for 15 day, replicate 1


title: LCMV Clone 13, Day 21, sgCtrl, GEX

description:
Library name: scMulti_Cl13D21_P14_sgCtrl_GEX
10x scMultiome-seq GEX library

molecule: nuclear RNA


title: OM_NT_15d_Rep2

description: Human PDLSC cultured in OM with no treatment for 15 day, replicate 2


title: OM_B2_15d_Rep1

description: Human PDLSC cultured in OM with BMP2 treatment for 15 day, replicate 1


title: CB42557 treatment B

description: Library name: CB42557_B


title: CB42557 treatment A

description: Library name: CB42557_A


title: LCMV Clone 13, Day 21, sgKlf3, GEX

description:
Library name: scMulti_Cl13D21_P14_sgKlf3_GEX
10x scMultiome-seq GEX library

value: CRISPR sgKlf3


title: OM_B9_7d_Rep2

description: Human PDLSC cultured in OM with BMP9 treatment for 7 day, replicate 2


title: GM_NT_7d_Rep2

description: Human PDLSC cultured in GM with no treatment for 7 day, replicate 2


title: LCMV Clone 13, Day 21, sgKlf3, ATAC

description:
Library name: scMulti_Cl13D21_P14_sgKlf3_ATAC
10x scMultiome-seq ATAC library


title: CB42389 uncultured

description: Library name: CB42389_Unc

value: Cord Blood


title: OM_NT_1d_Rep2

description: Human PDLSC cultured in OM with no treatment for 1 day, replicate 2


title: LCMV Clone 13, Day 21, sgKlf2, ATAC

description:
Library name: scMulti_Cl13D21_P14_sgKlf2_ATAC
10x scMultiome-seq ATAC library

value: CRISPR sgKlf2


title: GM_NT_1d_Rep2

description: Human PDLSC cultured in GM with no treatment for 1 day, replicate 2


title: CB42389 treatment D

description: Library name: CB42389_D

value: HSPCs

value: normal


title: GM_NT_7d_Rep1

description: Human PDLSC cultured in GM with no treatment for 7 day, replicate 1


title: WTR9

description: Library name: Sample 106

data_processing:
Paired-end sequencing of the hypervariable V3-V4 region of the 16S rRNA gene was performed with Read 1 (TATGGTAATTGTGTGCCAGCMGCCGCGGTAA), Read 2 (AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT), and Index Primers (ATTAGAWACCCBDGTAGTCCGGCTGACTGACT) using an Illumina MiSeq instrument (Illumina) to produce 250 base-paired reads.
Bioinformatics analysis of bacterial 16S rRNA amplicon data was conducted using the Quantitative Insights into Microbial Ecology (QIIME2 (qiime2-2022.11; 1) pipeline.
Statistical analysis done with DEseq2 (v 1.38.3)
The dada2 algorithm was used to generate amplicon sequence variants (ASVs) with empirically determined trimming settings for each analysis.
Taxonomic classification was done using the SILVA version 138 database formatted for QIIME2 (https://docs.qiime2.org/2024.10/data-resources/)
Assembly: mm10
Supplementary files format and content: OTU table in text format, sample IDs and readcounts for each sample
Library strategy: 16S rRNA-seq

extract_protocol:
Lungs were excised from animals under sterile conditions and were collected into DNA extraction buffer containing ATL buffer and proteinase K (Qiagen) and shaken in a FastPrep Instrument (MP Biomedicals) at 5.0ms-1 for 30s. Following bead-beating, genomic DNA (gDNA) was extracted using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with the manufacturer protocol.
The PCR amplification of the target region was performed using 515F (GTGYCAGCMGCCGCGGTAA) and 806R (GGACTACNVGGGTWTCTAAT) 16S primers. Amplicons were then purified using NGS clean-up and size-select (Macherey-Nagel) in accordance with the manufacturer protocol.

treatment_protocol: Animals were treated with Bleomycin, TLR5-agonist/Bleomycin, or ABX/Bleomycin. Some animals receieved fecal microbiota transfer (FMT).

value: lung

value: male

value: wild-type

value: FMT recipient