title: 289-4.HTO.SamplePool.rs20765

description:
Library name: 20765
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Young mice AMs (10 mice) CD11C+CD11b- S1C

status: Public on Aug 12 2026

type: SRA

city: San Antonio

first: Larry

middle: S

last: Schlesinger

state: Texas

address: 8715, W Military Drive, Larry Schlesinger Laboratory, Texas Biomedical Research Institute

department: Host Pathogen Interactions program

country: USA

institute: Texas Biomedical Research Institute

description:
Library name: Sample 3 (S1C)
Mice Flow cytometry sorted BAL cells

library_source: transcriptomic

data_processing:
Raw sequencing reads were preprocessed using Trim Galore! to trim the adapters and low-quality sequences. Trimmed reads were mapped to the mouse mm10 reference genome using HISAT2.
Read counts for each sample were obtained using featureCounts. Differential gene expression analysis was carried out using  DESeq2.
The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR), and the shrunken log2 fold changes (LFCs) were calculated using the adaptive shrinkage (ash) estimator with an Empirical Bayes approach. Genes with FDR-adjusted p-value <0.05 and LFC of more than 1 or less than -1 were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: raw_counts.csv

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Alveolar macrophages (AMs) were isolated from both 10 young and 10 old mice. Cells were then stained and sorted by sorted into CD11c+ CD11b- populations from young and old mice, and CD11c- CD11b+ and CD11c+ CD11b+ populations from old mice using the BD FACSAria II flow cytometer flow cytometry using BV421 anti-CD11b (clone M1/70) and PE anti-CD11c (clone N418) antibodies. The post-sorted cells were then verified based on the gating strategy, and the purity of the populations was confirmed through gating.

extract_protocol:
Flowcytometry-sorted CD11c+ CD11b- AMs from young mice and CD11c+ CD11b-, CD11c-CD11b+, and CD11c+ CD11b+ AM populations from old mice were collected and washed at 250 x g for 10 min with 1% PBS. The RNA was isolated using TRIzol reagent (Invitrogen) and a Direct-zol RNA Microprep kit (Zymo Research) according to the manufacturer's instructions. The isolated RNA was quantified using the Qubit 4 Fluorimeter (Invitrogen), and its quality was assessed with the 4200 TapeStation System (Agilent). Samples with an RNA integrity number (RIN) higher than 7 were used for RNA-seq. RNA-seq libraries were prepared from 300 ng of total RNA using the NEB Next RNA Ultra Kit (Qiagen, Redwood City, CA) with poly(A) enrichment, and 50-bp single-read sequencing with approximately 25-30M reads per sample. The RNA sequencing was performed at the Genome Sequencing Facility (GSF) at UTHealth San Antonio using the HiSeq 3000 platform (Illumina).
Then RNA-seq libraries were prepared from 300ng of total RNA using the mRNA-seq library preparation and 50bp single read sequencing with about 25-30M reads per sample in the NEB Next RNA Ultra Kit (Qiagen, Redwood City, CA) with poly (A) enrichment.

tag: tissue

value: Lung

tag: cell line

value: Primary cells

tag: cell type

value: Alveolar macrophages

tag: age

value: 3 months Young mice

tag: treatment

value: CD11c+ CD11b- resident alveolar macrophages from young mice were isolated and flow cytometry sorted

tag: batch

value: Replicate batch-3


title: 289-1.GEX.SamplePool.rs20757

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

description:
Library name: 20757
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol: 10x Genomics 5' VDJ scRNA-seq

value: PBMC


title: 289-1.HTO.SamplePool.rs20756

description:
Library name: 20756
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-Seq, dissected germline, ESC420, TSR-2 control, rep 2

city: Austin

first: Elif

last: Sarinay Cenik

state: TX

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Library name: ESC-HSl-618
multimapping_fractional_counts_for_rRNA_expression.csv

data_processing:
Read trimming: Trim Galore! v0.6.10 used with default parameters.
Genome indexing: HISAT2 v2.2.1 used to build WBcel235 genome index with hisat2-build --seed 40.
Read mapping: HISAT2 v2.2.1 used with hisat2 -U --seed 40 --all, and all other default parameters.
Alignment sorting: Picard SortSam v3.1.1 used with -SORT_ORDER coordinate --CREATE_INDEX true.
Curated gene annotions: To quantify rDNA transcription, we manually curated “gene” annotations for the two unique internal transcribed spacers (ITS) and appended them to the WBcel235 annotation. See command: `echo -e 'I\tcurated_RMT\tgene\t15061160\t15062082\t.\t+\t.\tgene_id "5ETS"; gene_name "5ETS"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15063837\t15064300\t.\t+\t.\tgene_id "ITS1"; gene_name "ITS1"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15064454\t15064837\t.\t+\t.\tgene_id "ITS2"; gene_name "ITS2"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf echo -e 'I\tcurated_RMT\tgene\t15068356\t15069279\t.\t+\t.\tgene_id "3ETS"; gene_name "3ETS"; gene_source "curated_RMT"; gene_biotype "rRNA";' >> WBcel235_w_ITS.gtf`
Feature quantification: featureCounts v2.0.6 used with -a WBcel235_w_ITS.gtf -t gene -g gene_id -M -O --fraction.
Multi-mapping fractional counts were rounded for downstream analyses. We provided the fractional read counts as the processed data file.
Assembly: WBcel235
Supplementary files format and content: Comma-delimited file containing fractional counts of multi-mapping reads to the WBcel235 genome annotatation with additional curated rDNA loci including ITS regions (Wormbase identifiers from WBcel235). Note that reads were re-mapped separately for protein coding gene expression and ITS expression analyses (PCG expression: default hisat2 params and featureCounts -t exon -g gene; ITS expression: hisat2 --all and featureCounts -M --fraction).

organism: Caenorhabditis elegans

source_name: dissected germline

growth_protocol: Maintained and treated at 20°C on non-enriched plated seeded with OP50.

extract_protocol:
Dissected gonads were transferred to 1 mL of TRIzol, vortexed, then incubated for 5 minutes at room temperature. RNA was extracted by adding 200 µL of chloroform to the lysate, spinning for 10 minutes at 15,000 rpm, and isolating the supernatant. The isolated RNA was precipitated overnight at −20°C using 50 mM sodium acetate, 5 mM MgCl2, 15 mg/mL GlycoBlue™ Coprecipitant, and isopropanol.
RNA pellets were washed in 80% ethanol and processed with the SMARTer Stranded RNA-Seq kit. RNA was fragmented, converted to cDNA, and PCR amplified (1 min at 94°C; 15-17 cycles of 15 sec at 98°C, 15 sec at 55°C, 30 sec at 68°C). Libraries were purified using Agencourt AMPure XP beads, quantified with the Qubit™ dsDNA HS Assay Kit, and sequenced on a NovaSeq 6000 v1.5 SP flow cell.

treatment_protocol: Auxin (IAA) plates were prepared by diluting Alfa Aesar (#A10556) to 1 mM in NGM agar, while control plates contained an equivalent EtOH volume. Plates were poured, solidified, seeded with OP50, and incubated at 20°C overnight. Synchronized late L4 worms were transferred to control or auxin plates for 18 hours at 20°C.

value: dissected germline

tag: strain

tag: developmental stage

value: young adult

tag: Sex

value: hermaphrodite

value: EtOH control


title: Young mice AMs (10 mice) CD11C+CD11b- S1A

description:
Library name: Sample 1 (S1A)
Mice Flow cytometry sorted BAL cells

value: Replicate batch-1


title: RNA-Seq, dissected germline, ESC420, TSR-2 depletion via 1 mM IAA, rep 2

description:
Library name: ESC-HSl-613
multimapping_fractional_counts_for_rRNA_expression.csv

value: 1 mM auxin (IAA)


title: 278-4.TCR.SamplePool.rs20313

description:
Library name: 20313
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 278-2.TCR.32726.rs20307

description:
Library name: 20307
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived mature sc-islet (stage 6) 2 - gene barcode

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: PolyIII_S6_2_30KO
Village differentiation, H1 S6

library_source: transcriptomic single cell

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: feature counts as h5ad files

organism: Homo sapiens

extract_protocol: Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1, Illunmina NovaSeq 6000

value: ESC

tag: editing strategy

value: CRISPR/Cas9 method

tag: altered gene_symbol

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX26

tag: time

value: day 33

tag: model system

value: mature sc-islet (stage 6)

tag: parental cell_line


title: 278-4.HTO.SamplePool.rs20311

description:
Library name: 20311
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-Seq, dissected germline, ESC420, TSR-2 control, rep 1

description:
Library name: ESC-HSl-612
multimapping_fractional_counts_for_rRNA_expression.csv


title: 278-2.GEX.32726.rs20306

description:
Library name: 20306
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 278-2.HTO.32726.rs20305

description:
Library name: 20305
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 278-1.TCR.24957.rs20304

description:
Library name: 20304
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-Seq, dissected germline, ESC420, TSR-2 depletion via 1 mM IAA, rep 1

description:
Library name: ESC-HSl-606
multimapping_fractional_counts_for_rRNA_expression.csv


title: H1-derived immature sc-islet (stage 5) 2 - gene barcode

description:
Library name: PolyIII_S5_2_30KO
Village differentiation, H1 S5

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX24

value: day 18

value: immature sc-islet (stage 5)


title: E. coli 0.5x MIC Corramycin rep 3, 45 min

city: Saarbrücken

first: Franziska

last: Fries

state: Saarland

address: Campus E8 1

department: Microbial Natural Products

country: Germany

institute: Helmholtz Institute for Pharmaceutical Research Saarland

description:
Library name: Sample 24
Forward and reverse reads are denoted by R1 and R2.

data_processing:
Raw sequencing data was analyzed using Geneious Prime (version 2023.1.1). Reads were mapped to the reference sequence (NCBI NZ_CP009072.1 and NC_000962.3) and mRNA abundances were quantified as transcripts per million (TPM) prior to differential gene expression analysis with DESeq2.
Assembly: NCBI NZ_CP009072.1 (E. coli ATCC25922), NCBI NC_000962.3 (Mtb H37Rv)
Supplementary files format and content: csv files include raw transcript counts and normalized counts RPKM, TPM
Supplementary files format and content: xlsx files contain differential expression tables for the different samples, organized by organism (each with different sheets for the different conditions).

organism: Escherichia coli

growth_protocol: E. coli ATCC25922 was grown overnight in cation-adjusted Mueller-Hinton broth (MHB2) at 37 °C with shaking. The next morning, the culture was sub-cultured 1:100 in fresh MHB2 and grown until log-phase, after which the culture was adjusted to an OD600 of 0.5. M. tuberculosis H37Ra was grown in Middlebrook 7H9 medium supplemented with 10% OADC until log-phase was reached. Single cells were prepared by syringing and the culture was adjusted to an OD600 of 0.5.

extract_protocol:
For E. coli, 500 µL of samples were centrifuged at 5,000 g, RT, 10 min. The supernatant was removed and pellets were dissolved in TE buffer (100 mM Tris, 1 mM EDTA, pH 8.0) containing 15 mg/mL lysozyme and 20 µL of proteinase K (Qiagen). Samples were mechanically disrupted with acid-washed glass beads (one spatula tip of sizes 150-212 µm, 212-300 µm and 425-600 µm, respectively) using the TissueLyser II (Qiagen) at a frequency of 1/s for 5 min. 700 µL QIAzol lysis reagent (Qiagen) were added and samples were disrupted for another two cycles with the TissueLyser II. Subsequently, total RNA was extracted using the RNeasy mini kit (Qiagen). For Mtb, 7 mL of samples were drawn and total RNA was extracted following a protocol consisting of mechanical disruption with the FastPrep machine (MP Biomedicals, Irvine, CA, USA) and extraction using the RNeasy mini kit (Qiagen).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Preparation Kit.

treatment_protocol: For E. coli, bacteria were treated with 0.125x, 0.25x or 0.5x MIC of corramycin, or DMSO (control) for either 15 min or 45 min. Each condition was performed in triplicates. For M. tuberculosis, bacteria were exposed to 0.5x, 1x or 2x MIC of corramycin, or DMSO (control) for either 6 h or 24 h. Each condition was performed in triplicates.

value: bacterial strain


title: 282-3.TCR.SamplePool.rs20298

description:
Library name: 20298
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.5x MIC Corramycin rep 2, 45 min

description:
Library name: Sample 23
Forward and reverse reads are denoted by R1 and R2.


title: 282-3.GEX.SamplePool.rs20297

description:
Library name: 20297
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 282-3.HTO.SamplePool.rs20296

description:
Library name: 20296
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.5x MIC Corramycin rep 1, 45 min

description:
Library name: Sample 22
Forward and reverse reads are denoted by R1 and R2.


title: H1-derived Pancretic progenitor 1 (stage 3) - gene barcode

description:
Library name: PolyIII_PP1_30KO
Village differentiation, H1 PP1

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX21

value: day 7

value: Pancretic progenitor 1 (stage 3)


title: 282-1.GEX.SamplePool.rs20291

description:
Library name: 20291
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 282-1.TCR.SamplePool.rs20292

description:
Library name: 20292
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived Definitive endoderm XM (stage 1) - gene barcode

description:
Library name: PolyIII_DE_30KO_XM
Village differentiation, H1 definitive endoderm

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX20

value: day 3

value: Definitive endoderm (stage 1)


title: 268-7.TCR.SamplePool.rs19824

description:
Library name: 19824
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 268-7.GEX.SamplePool.rs19823

description:
Library name: 19823
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived ESC (stage 0) - gene barcode

description:
Library name: PolyIII_ES_30KO
Village differentiation, H1 ESC

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX19

value: day -1

value: ESC (stage 0)


title: 268-7.HTO.SamplePool.rs19822

description:
Library name: 19822
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 268-5.TCR.SamplePool.rs19818

description:
Library name: 19818
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived mature sc-islet (stage 6) 2 - cell barcode

description:
Library name: LARRY_S6_2_30KO
Village differentiation, H1 S6

value: ESC

value: CRISPR/Cas9 method

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX18


title: 268-5.GEX.SamplePool.rs19817

description:
Library name: 19817
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 268-5.HTO.SamplePool.rs19816

description:
Library name: 19816
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived mature sc-islet (stage 6) 1 - cell barcode

description:
Library name: LARRY_S6_1_30KO
Village differentiation, H1 S6

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX17

value: day 33

value: mature sc-islet (stage 6)


title: 268-3.TCR.SamplePool.rs19812

description:
Library name: 19812
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.125x MIC Corramycin rep 2, 45 min

description:
Library name: Sample 17
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: 268-3.GEX.SamplePool.rs19811

description:
Library name: 19811
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived immature sc-islet (stage 5) 2 - cell barcode

description:
Library name: LARRY_S5_2_30KO
Village differentiation, H1 S5

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX16

value: day 18

value: immature sc-islet (stage 5)


title: 268-3.HTO.SamplePool.rs19810

description:
Library name: 19810
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: E. coli 0.125x MIC Corramycin rep 1, 45 min

description:
Library name: Sample 16
Forward and reverse reads are denoted by R1 and R2.


title: 268-2.TCR.SamplePool.rs19809

description:
Library name: 19809
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 268-2.GEX.SamplePool.rs19808

description:
Library name: 19808
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived Pancretic progenitor 2 (stage 4) - cell barcode

description:
Library name: LARRY_PP2_30KO
Village differentiation, H1 PP2

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX14

value: day 11

value: Pancretic progenitor 2 (stage 4)


title: H1-derived immature sc-islet (stage 5) 1 - cell barcode

description:
Library name: LARRY_S5_1_30KO
Village differentiation, H1 S5

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX15


title: E. coli control rep 3, 45 min

description:
Library name: Sample 15
Forward and reverse reads are denoted by R1 and R2.


title: 268-2.HTO.SamplePool.rs19807

description:
Library name: 19807
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli control rep 2, 45 min

description:
Library name: Sample 14
Forward and reverse reads are denoted by R1 and R2.


title: 268-1.GEX.SamplePool.rs19805

description:
Library name: 19805
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived Pancretic progenitor 1 (stage 3) - cell barcode

description:
Library name: LARRY_PP1_30KO
Village differentiation, H1 PP1

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX13

value: day 7

value: Pancretic progenitor 1 (stage 3)


title: 268-1.HTO.SamplePool.rs19804

description:
Library name: 19804
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 268-1.TCR.SamplePool.rs19806

description:
Library name: 19806
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli control rep 1, 45 min

description:
Library name: Sample 13
Forward and reverse reads are denoted by R1 and R2.


title: 261-5.TCR.SamplePool.rs19492

description:
Library name: 19492
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 289-1.TCR.SamplePool.rs20758

description:
Library name: 20758
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived Definitive endoderm XM (stage 1) - cell barcode

description:
Library name: LARRY_DE_30KO_XM
Village differentiation, H1 definitive endoderm

value: ESC

value: CRISPR/Cas9 method

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX12

value: day 3

value: Definitive endoderm (stage 1)


title: 261-5.GEX.SamplePool.rs19491

description:
Library name: 19491
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Young mice AMs (10 mice) CD11C+CD11b- S1B

description:
Library name: Sample 2 (S1B)
Mice Flow cytometry sorted BAL cells

value: Lung

value: Primary cells

value: Alveolar macrophages

value: 3 months Young mice

value: CD11c+ CD11b- resident alveolar macrophages from young mice were isolated and flow cytometry sorted

value: Replicate batch-2


title: E. coli 0.5x MIC Corramycin rep 3, 15 min

description:
Library name: Sample 12
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: RNA-Seq, dissected germline, ESC420, TSR-2 depletion via 1 mM IAA, rep 3

description:
Library name: ESC-HSl-619
multimapping_fractional_counts_for_rRNA_expression.csv

value: dissected germline

value: young adult

value: hermaphrodite

value: 1 mM auxin (IAA)


title: 278-4.GEX.SamplePool.rs20312

description:
Library name: 20312
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 261-5.HTO.SamplePool.rs19490

description:
Library name: 19490
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 261-4.TCR.SamplePool.rs19489

description:
Library name: 19489
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived ESC (stage 0) - cell barcode

description:
Library name: LARRY_ES_30KO
Village differentiation, H1 ESC

value: ESC

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX11

value: day -1

value: ESC (stage 0)


title: E. coli 0.5x MIC Corramycin rep 2, 15 min

description:
Library name: Sample 11
Forward and reverse reads are denoted by R1 and R2.


title: H1-derived mature sc-islet (stage 6) 1 - gene barcode

description:
Library name: PolyIII_S6_1_30KO
Village differentiation, H1 S6

value: CRISPR/Cas9 method

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX25

value: day 33

value: mature sc-islet (stage 6)


title: 261-4.GEX.SamplePool.rs19488

description:
Library name: 19488
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived mature sc-islet (stage 6) 2 - transcriptome library

description:
Library name: mRNA_S6_2_30KO
Village differentiation, H1 S6

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX10


title: 261-4.HTO.SamplePool.rs19487

description:
Library name: 19487
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.5x MIC Corramycin rep 1, 15 min

description:
Library name: Sample 10
Forward and reverse reads are denoted by R1 and R2.


title: 261-3.TCR.32726.rs19486

description:
Library name: 19486
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 278-1.GEX.24957.rs20303

description:
Library name: 20303
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H1-derived immature sc-islet (stage 5) 1 - gene barcode

description:
Library name: PolyIII_S5_1_30KO
Village differentiation, H1 S5

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX23

value: day 18

value: immature sc-islet (stage 5)


title: 278-1.HTO.24957.rs20302

description:
Library name: 20302
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 261-3.GEX.32726.rs19485

description:
Library name: 19485
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.25x MIC Corramycin rep 3, 15 min

description:
Library name: Sample 9
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: H1-derived Pancretic progenitor 2 (stage 4) - gene barcode

description:
Library name: PolyIII_PP2_30KO
Village differentiation, H1 PP2

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX22

value: day 11

value: Pancretic progenitor 2 (stage 4)


title: H1-derived mature sc-islet (stage 6) 1 - transcriptome library

description:
Library name: mRNA_S6_1_30KO
Village differentiation, H1 S6

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX9


title: H1-derived immature sc-islet (stage 5) 2 - transcriptome library

description:
Library name: mRNA_S5_2_30KO
Village differentiation, H1 S5

value: ESC

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX8


title: 261-3.HTO.32726.rs19484

description:
Library name: 19484
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: E. coli 0.25x MIC Corramycin rep 2, 15 min

description:
Library name: Sample 8
Forward and reverse reads are denoted by R1 and R2.


title: 261-1.TCR.24957.rs19480

description:
Library name: 19480
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 261-1.GEX.24957.rs19479

description:
Library name: 19479
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.25x MIC Corramycin rep 3, 45 min

description:
Library name: Sample 21
Forward and reverse reads are denoted by R1 and R2.


title: H1-derived immature sc-islet (stage 5) 1 - transcriptome library

description:
Library name: mRNA_S5_1_30KO
Village differentiation, H1 S5

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX7


title: E. coli 0.25x MIC Corramycin rep 1, 15 min

description:
Library name: Sample 7
Forward and reverse reads are denoted by R1 and R2.


title: PI, replicate 5, scRNAseq

city: Shanghai

first: Yiling

last: Yang

address: Fenglin Road

country: China

institute: Zhongshan Hospital, Fudan University

description: 10x Genomics

data_processing:
The raw sequencing data underwent preprocessing to construct gene expression profiles using CeleScope version 1.5.2 developed by Singleron Biotechnologies with standard settings. In summary, this process involved extracting and correcting barcodes and unique molecular identifiers (UMIs) from read one (R1), as well as removing adapter sequences and poly A tails from read two (R2). The cleaned R2 reads were then mapped to the human genome assembly GRCh38 transcriptome using STAR (v2.6.1b). Subsequently, uniquely mapped reads were annotated to exons using FeatureCounts (v2.0.1). Finally, successfully assigned reads sharing the same cell barcode, UMI, and gene identifier were aggregated to create a gene expression matrix suitable for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and  matrix files

source_name: gingival tissue

extract_protocol:
Following surgical procedures, freshly excised tissues were promptly placed in sCelLiveTM Tissue Preservation Solution (Singleron Bio Com, Nanjing, China) and refrigerated on ice within 30 minutes. Subsequently, the specimens were subjected to triple washing with Hanks Balanced Salt Solution (HBSS) and thereafter treated with 2 milliliters of sCelLiveTM Tissue Dissociation Solution (Singleron). This digestion process was carried out using the Singleron PythoN™ Automated Tissue Dissociation System (Singleron) at 37 °C for 15 mins. Following this, 2 milliliters of GEXSCOPE® red blood cell lysis buffer (Singleron) were introduced to lyse red blood cells, and the resulting mixture was incubated at 25 °C for an additional 10 minutes. Thereafter, the solution was centrifuged at 500 × g for 5 minutes and gently resuspended in PBS. Lastly, the samples were stained with trypan blue (Sigma, United States) and their cellular viability was assessed through microscopic examination.
Single-cell suspensions (1×105 cells/ml) with PBS (HyClone) were loaded into microfluidic devices using the Singleron Matrix® Single Cell Processing System (Singleron). Following this step, scRNA-seq libraries were constructed in accordance with the protocol specified by the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM and pooled for sequencing. Finally, the pooled libraries were subjected to high-throughput sequencing on an Illumina HiSeq X platform, utilizing 150 bp paired-end reads.

value: gingival tissue

tag: group

value: Peri-implantitis


title: H1-derived Pancretic progenitor 2 (stage 4) - transcriptome library

description:
Library name: mRNA_PP2_30KO
Village differentiation, H1 PP2

value: CRISPR/Cas9 method

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX6


title: 282-1.HTO.SamplePool.rs20290

description:
Library name: 20290
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 261-1.HTO.24957.rs19478

description:
Library name: 19478
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E. coli 0.25x MIC Corramycin rep 2, 45 min

description:
Library name: Sample 20
Forward and reverse reads are denoted by R1 and R2.


title: PI, replicate 4, scRNAseq

description: 10x Genomics


title: E. coli 0.125x MIC Corramycin rep 3, 15 min

description:
Library name: Sample 6
Forward and reverse reads are denoted by R1 and R2.


title: H1-derived Pancretic progenitor 1 (stage 3) - transcriptome library

description:
Library name: mRNA_PP1_30KO
Village differentiation, H1 PP1

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX5

value: day 7

value: Pancretic progenitor 1 (stage 3)


title: E. coli 0.125x MIC Corramycin rep 2, 15 min

description:
Library name: Sample 5
Forward and reverse reads are denoted by R1 and R2.


title: PI, replicate 1, scRNAseq

description: 10x Genomics


title: N, replicate 3, scRNAseq

description: 10x Genomics

value: natural teeth samples


title: E. coli 0.125x MIC Corramycin rep 1, 15 min

description:
Library name: Sample 4
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: N, replicate 2, scRNAseq

description: 10x Genomics


title: H1-derived ESC (stage 0) - transcriptome library

description:
Library name: mRNA_ES_30KO
Village differentiation, H1 ESC

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX3

value: day -1

value: ESC (stage 0)


title: N, replicate 1, scRNAseq

description: 10x Genomics


title: vdj_protein2

city: Cambridge

first: Darrell

middle: J.

last: Irvine

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description:
Library name: vdj_protein2
vdj_protein2

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1 and IgBLAST
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: BCR-Seq

source_name: Lymph node

extract_protocol:
FACS + 10x Genomics Chromium
10x Genomics 5` v3

value: Lymph node

value: CD4 binding site-specific B cells


title: E. coli control rep 2, 15 min

description:
Library name: Sample 2
Forward and reverse reads are denoted by R1 and R2.


title: vdj_dna2

description:
Library name: vdj_dna2
vdj_dna2


title: vdj_protein1

description:
Library name: vdj_protein1
vdj_protein1


title: H1-derived Definitive endoderm (stage 1) - gene barcode

description:
Library name: PolyIII_DE_30KO_ZN
Village differentiation, H1 definitive endoderm

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: 30_KO_DE_counts.h5ad
Supplementary files format and content: feature counts as h5ad files.

extract_protocol: 1000686 GEM-X Universal 3' Gene Expression v4, Illumina NovaSeq 6000

value: ESC

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX19

value: day 3

value: Definitive endoderm (stage 1)


title: vdj_dna1

description:
Library name: vdj_dna1
vdj_dna1


title: E. coli control rep 1, 15 min

description:
Library name: Sample 1
Forward and reverse reads are denoted by R1 and R2.


title: hto_protein2

description:
Library name: hto_protein2
hto_protein2

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1 and IgBLAST
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq


title: DNA from MASLD diet + 1xAza-TdC mouse-8

type: genomic

city: Daejeon

first: Hanyong

last: Go

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: KRIBB

hyb_protocol: Illumina Infinium Mouse Methylation BeadChip Kit protocol

scan_protocol: DNA was scanned using Illumina iSCAN system

data_processing: Mouse DNA methylation was analyzed using the MM285 array with preprocessing steps performed in the SEnsible Step-wise Analysis of Methylation data (SeSAMe, v1.20.0) package in R software (v4.4.0).

label: Cy3 and Cy8

molecule: genomic DNA

source_name: Liver

label_protocol: sodium bisulfite modification using EZ DNA Methylation-Gold kit (Zymo Research, Orange, CA)

extract_protocol: Genomic DNA was extracted from mouse liver tissue using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

value: Liver

tag: diet

value: MASLD diet


title: hto_dna2

description:
Library name: hto_dna2
hto_dna2


title: DNA from MASLD diet + 1xAza-TdC mouse-4

label: Cy3 and Cy7


description:
Library name: LP_ATAC-YY1-6h-2
library prep for ATAC-YY1-6h-2 derived from ADLI-0-0-052-3-12__OCM_108

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: .bed, .narrowPeak and unstranded.bw

extract_protocol:
Paired-end libaries
ATAC-sequencing

value: iPSC

value: Knock-in of inducible C-terminal degron

tag: condition

value: Auxin


title: gex_protein2

description:
Library name: gex_protein2
gex_protein2

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1 and IgBLAST
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

tag: tissue


description:
Library name: LP_ATAC-YY1-6h-1
library prep for ATAC-YY1-6h-1 derived from ADLI-0-0-052-3-12__OCM_108

tag: cell line


title: hto_dna1

description:
Library name: hto_dna1
hto_dna1

tag: cell type


title: gex_protein1

description:
Library name: gex_protein1
gex_protein1


title: DNA from MASLD diet + 1xAza-TdC mouse-2

label: Cy3 and Cy6


title: 1371-8.GEX.23824.rs102668

description:
Library name: 102668
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,PLN

value: Ilio-sacral LN,PLN


title: 1371-8.TCR.23824.rs102669

description:
Library name: 102669
Fig5.seurat.rds
Fig5.counts.rds


title: gex_dna2

description:
Library name: gex_dna2
gex_dna2


description:
Library name: LP_ATAC-YY1-24h-2
library prep for ATAC-YY1-24h-2 derived from ADLI-0-0-052-3-12__OCM_108


title: gex_dna1

description:
Library name: gex_dna1
gex_dna1


title: LR- liver sample-10

city: Hangzhou

first: Yiyuan

last: Chen

state: Zhejiang

address: Jiefang Road No.88

institute: The Second Affiliated Hospital, College of Medicine, Zhejiang University

description: Library name: Sample 20

data_processing:
Gene expression quantification was performed usingfeatureCounts (v1.5.0-p3) to calculate the number of reads mapped to each gene. Gene expressionlevels were normalized as FPKM (Fragments Per Kilobase of transcript per Million mapped reads)Differential expression analysis between two experimental conditions (with biological replicateswas performed using both DESeq2 (v1.20.0) and gdgek,(v3.22.5). For DESeq2, anegative binomialdistribution model was applied to estimate dispersion and test for significance. The resulting pvalues were adjusted for multiple testing using the Benjamini-Hochberg method. Genes withadjusted p-value < 0.05 were considered differentially expressed. In parallel, count data were alsonormalized using edgeR through a scaling factor, and differential expression was calculated usingexact tests. Significant genes were defined based on a corrected p-value < 0.05 and an absolute foldchange >2
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Format: Raw counts Content: Raw read counts for each gene (or transcript) across all samples.

source_name: liver

extract_protocol:
Total RNA was extracted usingthe TRlzol® Reagent according to the manufacturer's protocol
RNA sequencing was performed usingthe lllumina Genome Analyzer Il platform (llumina, USA). Raw sequencing data in FASTQ format were first subjected to quality control. Adapter-containing reads, reads with more than 10%unknown nucleotides (N), and low-quality reads (defined as those in which over 50% of bases hadPhred scores <20) were removed using Trimmomatic (v0.39). Quality metrics including Q20, Q30,and GC content were calculated, and the resulting clean reads were used for all downstream analysesFor alignment, clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.0 .5). The aligned reads of each sample were assembled into transcripts using StringTie(v1.3.3b)in a reference-guided mode.

value: liver

tag: genotype

value: WT


title: DNA from MASLD diet + 0.1xAza-TdC mouse-4

label: Cy3 and Cy5

tag: treatment


title: DNA from MASLD diet + 0.1xAza-TdC mouse-3


title: LR- liver sample-8

description: Library name: Sample 18


description:
Library name: LP_ATAC-YY1-0h-2
library prep for ATAC-YY1-0h-2 derived from ADLI-0-0-052-3-12__OCM_108

value: DMSO


title: DNA from MASLD diet + 0.1xAza-TdC mouse-1


title: LR- liver sample-7

description: Library name: Sample 17


title: LR- liver sample-6

description: Library name: Sample 16


title: DNA from MASLD diet mouse-5


title: LR- liver sample-5

description: Library name: Sample 15


title: DNA from MASLD diet mouse-4


title: LR- liver sample-2

description: Library name: Sample 12


title: LR- liver sample-3

description: Library name: Sample 13


title: WT, 6mo, Rep2

city: Dallas

first: Ram

last: Madabhushi

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: WT2

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed to remove adapter sequences using Trimmomatic, and aligned to the mm10 (GRCm38.p6) reference genome using TopHat.
Aligned reads were processed by HTSeq-Count to obtain raw read counts, and deSeq2 (p < 0.05, log fold-change > 0.5 or < -0.5) was used to identify differentially regulated transcripts.
BamCoverage was used to convert aligned read files into BigWig signal tracks for visualization.
Assembly: mm10
Supplementary files format and content: tab delimited text file (Raw_Counts) includes raw counts for each sample
Supplementary files format and content: tab delimited text file (TPMs) includes calculated TPM values for each sample
Supplementary files format and content: bigwig files include merged, TPM-normalized RNA-seq signals for each genotype

source_name: Cortex

growth_protocol: Wild-type (Tdp2fl/fl, CAMKII:Cre negative) and Tdp2 conditional knockout (Tdp2fl/fl, CAMKII:Cre positive) mice were maintained in standard housing conditions until 6 months of age.

extract_protocol:
Fresh cortical tissue was dissected from 6-month old WT and Tdp2cKO mice, flash frozen in liquid nitrogen, and stored at -80°C. For RNA purification, samples were dissociated and lysed in 500µL Trizol using a manual homogenizer. RNA was extracted using a standard Trizol procedure, treated with DNase (NEB) for 1 hour at 37℃, and purified using an RNA clean and concentrator kit (Zymo).
The concentration and quality of purified RNA samples were assessed using an Agilent Tapestation 4200 both before and after library construction. Samples with a RIN score of 8 or higher were prepared for sequencing using a paired-end library preparation kit (Illumina) according to the manufacturer’s instructions.

value: Cortex

tag: age

value: 6 months


title: 1371-7.TCR.23824.rs102666

description:
Library name: 102666
Fig5.seurat.rds
Fig5.counts.rds

source_name: Liver,MesLN,PBMC,Spleen

value: Liver,MesLN,PBMC,Spleen


title: WT, 6mo, Rep3

description: Library name: WT3

tag: strain


title: LR- liver sample-1

description: Library name: Sample 11


title: DNA from MASLD diet mouse-3


title: LR+ liver sample-10

description: Library name: Sample 10


description:
Library name: LP_ATAC-TFDP1-24h-2
library prep for ATAC-TFDP1-24h-2 derived from ADLI-4-1-118-3-17__OCP_74G


title: DNA from SD diet mouse-5

value: Standard diet


description:
Library name: LP_ATAC-TFDP1-24h-1
library prep for ATAC-TFDP1-24h-1 derived from ADLI-4-1-118-3-17__OCP_74G


title: LR+ liver sample-7

description: Library name: Sample 7


title: LR+ liver sample-8

description: Library name: Sample 8


title: LR+ liver sample-6

description: Library name: Sample 6


title: DNA from SD diet mouse-3


description:
Library name: LP_ATAC-TFDP1-0h-1
library prep for ATAC-TFDP1-0h-1 derived from ADLI-4-1-118-3-17__OCP_74G


title: 1371-5.TCR.23824.rs102660

description:
Library name: 102660
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,MesLN,Spleen

value: Bone marrow,Colon,MesLN,Spleen


title: LR+ liver sample-5

description: Library name: Sample 5


title: LR+ liver sample-4

description: Library name: Sample 4


title: Bone marrow cells and bone cells, control littermates

city: Wuhan

first: Xin

last: Liu

address: Luojia Hill, Wuchang District

institute: Wuhan University

description:
Library name: Sample 1
10X Genomisc

data_processing:
Raw sequencing data were filtered and processed with Cellrange-7.0.0 (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) which includes: demultiplexing by cell barcodes and UMIs, spliced read alignment to the reference genome, and UMI-based gene expression quantification for each gene and cell. Potential doublets were identified and removed using the scDblFinder package (v1.12.0) for each sample.
Quality control was performed to filter low quality cells following the rules below: Cells with fewer than 200 detected genes were excluded, cells with extreme gene counts were filtered by removing those in the top and bottom 2% quantiles, cells with total UMI counts (nUMI) in the top or bottom 2% were discarded, cells with mitochondrial gene expression exceeding 20% of total reads were eliminated, and low-complexity cells by retaining only those with a log10(Genes per UMI) > 0.8 (novelty score) were excluded to ensure high-quality transcriptional profiles.
Raw count matrices were processed using Seurat (v4.3.0) in R (v4.2.3). For each sample, gene expression was normalized and variance stabilized via SCTransform, selecting 3,000 highly variable genes (HVGs) while excluding housekeeping genes, TCR/BCR, and immunoglobulin genes (IGV). Multiple samples were merged and batch-corrected using IntegrateData. Integrated data were centered and subjected to principal component analysis (PCA, 50 dimensions).
Clustering was performed using FindNeighbors and FindClusters. Nonlinear dimensionality reduction was conducted via Uniform Manifold Approximation and Projection (UMAP) for visualization. Automated annotation was performed using SingleR, PanglaoDB, and CellMarker. Manual refinement was applied based on canonical marker genes. FindAllMarkers function was applied in Seurat to detect DEGs among different clusters of the datasets. Pathway enrichment analysis was conducted by R package clusterProfiler (version 4.2.3).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Bones from wildtype mice

growth_protocol: Dmp1-Cre mediated conditional Mdm2 knockout in osteoocytes (Mdm2cKO). Mdm2cKO mice and the control littermates were sacrificed at 2-month old.

extract_protocol:
Bone marrow cells isolated through flushing, while cells from bone pieces were digested with 2.4 mg/mL collagenase I (Biosharp) and 5 mM EDTA alternately as previously described80,86. Specifically, periosteum cells were digested by collagenase I for two consecutive 15 minutes and cells were discarded. OLCs were digested according to the following steps: Collagenase I for two consecutive 15 minutes, EDTA for 20 minutes, Collagenase I for 20 minutes, EDTA for 20 minutes and finally Collagenase I for 20 minutes. All the digestion processes were performed on the shaker at 90 rpm, 37℃. Cells from five 2-month-old mice (3 males, 2 females) were pooled for each experimental group. Hematopoietic cell depletion was achieved using the Lineage Cell Depletion Kit (Miltenyi Biotec) according to the manufacturer`s instructions, followed by fluorescence-activated cell sorting to enrich CD45-; TER119-; CD71- cells by flow cytometry.
A single cell library was generated with Chromium Next GEM Single Cell 3ʹ Kit v3.1(10x Genomics) and sequenced on a Illumina NovaSeq 6000 system, targeting >30000 reads per cell for robust gene coverage.

value: Bones from wildtype mice

value: Bone marrow cells and bone cells

value: Wildtype


description:
Library name: LP_ATAC-TFDP1-0h-2
library prep for ATAC-TFDP1-0h-2 derived from ADLI-4-1-118-3-17__OCP_74G


title: LR+ liver sample-3

description: Library name: Sample 3


title: LR+ liver sample-2

description: Library name: Sample 2


description:
Library name: LP_ATAC-SSU72-6h-2
library prep for ATAC-SSU72-6h-2 derived from ADLI-4-3-93-3-4__OCP_74G


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL3

city: Berkeley

first: Michael

last: Rape

state: CA

address: 330F Li Ka Shing Center

department: MCB

institute: University of California Berkeley

description: Library name: FBXL14ΔCTE3_aHA

library_source: genomic

data_processing:
Pair-end reads were quality-checked with FastQC (version 0.12.1), trimmed with cutadapt (version 2.6) and aligned onto the human genome (hg38 assembly) using Bowtie2 (version 2.5.4).
Peaks were called with MACS3 (version 3.0.3)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: WTC11 iPSCs

extract_protocol:
DNA was purified using SPRIselect beads, washed with 85% ethanol and eluted in 0.1X TE Buffer.
Libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001). Library DNA size distribution was assessed using a Fragment Analyzer (Agilent). Final libraries were pooled and sequenced by QB3 Genomics, UC Berkeley, Berkeley, CA (RRID:SCR_022170) on an NextSeq P1 150PE (Illumina).

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene and the CTE gene region deleted from the FBXL14 gene

value: neural differentiation

value: day 4


description:
Library name: LP_ATAC-SSU72-6h-1
library prep for ATAC-SSU72-6h-1 derived from ADLI-4-3-93-3-4__OCP_74G

value: iPSC

value: Knock-in of inducible C-terminal degron

value: Auxin


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibody REPL2

description: Library name: FBXL14ΔCTE2_aIgG


title: Cryo-rep1

city: Ithaca

first: Ellie

last: Duan

state: New York

address: 507 Tower Rd., Ithaca, NY 14853, Ithaca, NY 1485

department: Animal Science

institute: Cornell University

description: Library name: Sample7

data_processing:
Raw sequencing FASTQ files were processed by trimming reads for low quality and adaptor sequences with TrimGalore (v0.6.0)61, which is a wrapper for cutadapt62 and fastQC. The reads were aligned using STAR (v2.7.0e)63 to the bovine reference genome (Bos_taurus/ARS-UCD1.2_GCA_002263795.2 reference genome). R packages limma64 and sva65 were used to remove batch effects in the three replicates, DESeq2 (v1.26.0)49 to identify differentially expressed genes (DEGs), and lfcshrink was used to generate normalized counts and statistical analysis of differential gene expression66. The DEGs were identified in the pair-wise manner using the criteria of Fold Change (FC) >2, Padj<0.05. Unsupervised hierarchical clustering analysis was applied to the whole DEG list and in a pair-wise manner using the ComplexHeatmap67 package in R. Functional analysis including Gene Ontology enrichment was performed and incorporated besides the clustering heatmap using ClusterGV68 in R. Finally, the intersections of DEGs among different conditions were plotted using UpsetR69 package in R.
Assembly: Bos_taurus/ARS-UCD1.2_GCA_002263795.2 reference genome
Supplementary files format and content: Raw read counts

organism: Bos taurus

source_name: Blastocyst embryo

extract_protocol:
RNA extracted and sent to the Cornell Bio-informatics facility for library preparation and sequencing. Total RNA extraction was performed using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) following the kit’s recommended protocol. Briefly, embryos were transferred to the extraction buffer and kept at 42 °C for 30 min on a pre-heated heater block and then centrifuged at 800 g for two min. Before loading the cell lysate into the purification column, the column was pre-conditioned by adding 250 μl of conditioning buffer, incubated for 5 min at room temperature and then centrifuged at 16,000 g for 1 min. To prepare the cell extract sample, 10 μl of ethanol was added to the cell extract and the mixture loaded into the purification column. 100 μl of Wash Buffer 1 was pipetted into the purification column and the column centrifuged for 1 min at 8,000 g. Then 100 μl of Wash Buffer 2 was pipetted into the purification column and the column centrifuged for 1 min at 8,000 g, followed by another 100 μl of Wash Buffer 2 and centrifugation for 2 min at 16,000 g. The purification column was then transferred to a new 0.5 ml microcentrifuge tube provided in the kit and 15 μl Elution Buffer was pipetted directly onto the membrane of the purification column. The column was incubated for 1 min at room temperature, centrifuged for 1 min at 1,000 g to distribute the Elution Buffer within the column, and then centrifuged for 1 min at 16,000 g to elute the RNA.
TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit HS dsDNA assay kit (Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Agilent) prior to pooling. Libraries were then sequenced on an Illumina instrument. At least 10M reads were generated per library.

value: Blastocyst embryo

value: Cryotop


description:
Library name: LP_ATAC-SSU72-24h-2
library prep for ATAC-SSU72-24h-2 derived from ADLI-4-3-93-3-4__OCP_74G


title: Nanuq-rep3

description: Library name: Sample6

value: Nanuq


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL2

description: Library name: FBXL14ΔCTE2_aHA


description:
Library name: LP_ATAC-SSU72-24h-1
library prep for ATAC-SSU72-24h-1 derived from ADLI-4-3-93-3-4__OCP_74G


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibody REPL1

description: Library name: FBXL14ΔCTE1_aIgG


title: CTR-rep3

description: Library name: Sample3

value: CTR


description:
Library name: LP_ATAC-SSU72-0h-2
library prep for ATAC-SSU72-0h-2 derived from ADLI-4-3-93-3-4__OCP_74G

value: DMSO


title: CTR-rep2

description: Library name: Sample2


title: PI, replicate 3, scRNAseq

description: 10x Genomics

value: gingival tissue

value: Peri-implantitis


title: H1-derived Definitive endoderm XM (stage 1) - transcriptome library

description:
Library name: mRNA_DE_30KO_XM
Village differentiation, H1 definitive endoderm

value: ESC

value: CRISPR/Cas9 method

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX4

value: day 3

value: Definitive endoderm (stage 1)


title: Bulk RNA-seq of brain endothelial cells STIM-2

status: Public on Aug 13 2026

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description:
Library name: STIM_2
RNA-seq

data_processing:
Adapter trimming was performed using fastp (v0.20.1) and reads were aligned to the GRCm39 reference genome using hisat2 (v2.1.0). To count reads overlapping genes, featureCounts v2.0.6 was used, and the output was loaded into R (v4.2.2) for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: counts table

source_name: Brain

growth_protocol: 6-week-old C57BL/6 mice mice were anesthetized with a ketamine/xylazine injection and perfused with 20ml of ice-cold PBS. Cortices were homogenized with GentleMACS tissue dissociator (Mylteni Biotech) in prewarmed DMEM supplemented with 2% Bovine Calf Serum (BCS, HyClone), 25µg/ml Liberase DL, 100µg/ml Dispase, 0.5mg/ml Papain, 10µg/ml DNase-I (all enzymes from Sigma) for 30 min at 37°C. After homogenization the cell suspension was filtered through a 70 μm strainer and myelin depletion was performed in 30% isotonic percoll (800g for 20 min at 4°C). Brain cell pellets were stained with anti-CD45-AlexaFluor 647 (1:200), anti-CD31-PE (1:100), and anti-Ly6C-APCCy7 (1:200) for 30 minutes on ice (all antibodies from Biolegend). DAPI was used for live/dead cells discrimination. The DAPI−CD45−CD31+Ly6C+ population was sorted on FACS Aria-III (BD Bioscience) using a 100 µm nozzle. Approximately 600,000 brain endothelial cells (BEC) per sample were sorted (two brains were pooled for each sample). BECs were collected into Endothelial Cell Medium (Cell Biologics, M1168), plated onto a Matrigel-coated 24-well plate and expanded for 12 days in Endothelial Cell Medium at 37°C with 5% CO2. Matrigel was removed using Cell Recovery Solution (Corning) prior to RNA extraction.

extract_protocol:
Cells were lysed in 450µl of lysis buffer for RNA extraction. The lysate was mixed by pipetting and briefly shaken for 1 minute at room temperature. Lysates were collected, and RNA was purified using the RNeasy Micro Kit (Qiagen 74004), following the manufacturer’s protocol. Purified RNA was stored at -80°C until analysis.
Library preparation was performed with 5-10ng of total RNA per sample. ds-cDNA was made using the low-input SMARTseq mRNA kit (Takarabio) according to manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Libraries were pooled and sequenced on an Illumina NovaSeqX Plus (2x150 sequencing recipe), targeting 50M reads per sample. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

treatment_protocol: On the day of the experiment, cells were incubated in serum-free medium for 2 hours prior to stimulation with recombinant mouse GAS6 (250 ng/mL; R&D Systems) and recombinant mouse IGF-I (200 ng/mL; PeproTech), or PBS as a control. After 6 hours stimulation, the medium was removed, and wells were washed with PBS.

value: Brain

value: Endothelial cells

value: Wild-type

value: IGF-1 + GAS6

tag: batch


title: H1-derived Definitive endoderm (stage 1) - cell barcode

description:
Library name: LARRY_DE_30KO_ZN
Village differentiation, H1 definitive endoderm

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX11


title: H1-derived Definitive endoderm (stage 1) - transcriptome library

description:
Library name: mRNA_DE_30KO_ZN
Village differentiation, H1 definitive endoderm

value: CARM1, CBX4, DPY30, EOMES, FEV, GCM1, HES1, HNF1A, HNF4A, INSM1, ISL1, JMJD6, MAFB, MEIS1, MEN1, NCOA5, NEUROG3, NKX6-1, NOTCH1, NOTCH2, ONECUT1, PAX6, PBX2, PDX1, RFX3, RFX7, RREB1, SIM1, SIX2, SIX3


title: X22093_MDM

city: Coventry

first: Jan

middle: Joris

last: Brosens

state: Warwickshire

address: Warwick Medical School

institute: University of Warwick

description: Library name: X22093_MDM

data_processing:
Sequence reads were aligned to Hg38 using STAR 2.5 and the number of reads in features was calculated using htseq-count (HTseq v2.0.0). Transcripts per million were calculated and used for differential gene expression analysis.
Differential expression analysis was performed in R (v4.5.1) using DESeq2 (Bioconductor; v1.48.1). Read counts were normalized with the median-of-ratios method, and outlier detection and dispersion estimation were performed with default DESeq2 functions. Genes were considered differentially expressed when they satisfied both thresholds: FDR-adjusted p<0.05 (Benjamini–Hochberg correction) and |log₂ fold-change|>1.
Assembly: Hg38
Supplementary files format and content: counts files .txt format

source_name: endometrium

growth_protocol: Endometrial biopsies were finely minced and digested enzymatically with 500µg/mL Collagenase Type Ia (Merck Life Science, C9891) and 100µg/mL DNase I (Lorne Laboratories LTD, LS002060) for 1 hour. After filtering through a 40µm cell sieve, stromal cells were cultured in growth medium (DMEM/F12 supplemented with 10% dextran-coated charcoal-stripped FBS, 2mM L-glutamine, 1nM b-estradiol (Merck Life Science, E2758), 2μg/mL recombinant human insulin (Merck Life Science, 91077C) and Antibiotic-Antimycotic. Growth factor-reduced Cultrex RGF Basement Membrane Extract, Type 2 (Biotechne) was added to freshly isolated endometrial gland fragments at a ratio of 1:20 (cell pellet: Cultrex). 20µL droplets were cured and overlaid with expansion medium (ExM: Advanced DMEM/F12 supplemented with N2, B27, 2mM L-glutamine, 500nM A83-01, 500ng/mL R-respondin-1, 10mM nicotinamide, 1.25mM N-acetyl-L-cysteine, 100ng/mL Noggin, 100ng/mL FGF-10, 50ng/mL HGF, 50ng/mL EGF and antibiotic-antimycotic) (Rawlings et al., 2021; Turco et al., 2017). 24 hours after stromal cells and gland organoids were established, assembloids were established as described previously (Rawlings et al., 2021).  Stromal cells and gland organoids were digested into a single cell suspension and mixed at a ratio of 1:1 (v/v) before adding ice-cold PureCol EZ Gel (Sigma-Aldrich) at a ratio of 1:20 (cell pellet: hydrogel). The suspension was aliquoted in 20μL droplets. Following polymerization, droplets were overlaid with ExM with 10nM b-estradiol.

extract_protocol:
Assembloid cultures were washed with PBS before digestion with 500µg/ml collagenase I for 10 min at 37°C with regular manual shaking. Samples were washed twice in PBS and cell pellets were snap frozen at -80°C. RNA extraction was performed using the RNeasy Micro Kit (Qiagen Manchester, UK) according to the manufacturer’s instructions. RNA concentration and purity were determined using a NanoDrop ND-1000 and all RNA samples were stored at –80°C until use.
After RNA from all assembloids have been extracted, quality control was performed on the Agilent 2100 Bioanalyzer using Total RNA Nano chips (Agilent Technologies, Stockport, UK), and libraries were prepared using TruSeq RNA library preparation V2 kits (Illumina, Cambridge, UK). Samples were sequenced on a NextSeq 500 (Illumina), using 75 cycle high output cartridge and 42bp paired end reads.

treatment_protocol: Assembloids were grown in ExM with E2 for 4 days, followed by a 4-day decidual time course. To induce decidualization, ExM was replaced with minimal decidualization medium (MDM) containing 1nM beta-estradiol, 1μM medroxyprogesterone acetate (MPA) and 0.5mM 8-bromo-cAMP. For Poly(I:C) treatment, assembloids were pretreated with 1μg/mL Poly(I:C) (High MW, VacciGradeTM, vac-pic, InvivoGen) after 2 days of ExM with E2 (Day -2) and continued upon decidual induction. Poly(I:C) treatment was continued in MDM for 4 days (Fig 1A).

value: endometrium

tag: patientid

value: stromal and epithelial cell assembloid co-culture

value: decidualised control (Dec) - 22093


title: SUDHL4 - CC282_50 - D2 - rep3

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: 7357-CH-0156

data_processing:
We used featureCounts 2.0.6 to count the number of reads on gene level.
Assembly: GRCh38
Supplementary files format and content: readcount on gene level

source_name: cell line

extract_protocol:
Cells for RNAseq were prepared according to instructions from Discovery Life Sciences.
Five million cells per sample were collected, washed, fixed, and stored at -80 C prior to shipping to Discovery Life Sciences where downstream RNAseq was carried out.

value: cell line


title: LR- liver sample-9

description: Library name: Sample 19

value: liver

value: WT


description:
Library name: LP_ATAC-YY1-24h-1
library prep for ATAC-YY1-24h-1 derived from ADLI-0-0-052-3-12__OCM_108

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

value: Auxin


description:
Library name: LP_ATAC-YY1-0h-1
library prep for ATAC-YY1-0h-1 derived from ADLI-0-0-052-3-12__OCM_108

tag: altered gene_symbol

value: DMSO


title: X22089_PolyIC_PolyIC

description: Library name: X22089_PolyIC_PolyIC

value: polyIC+decidualised (Dec+P) - 22089


description:
Library name: LP_ATAC-SMARCD1-6h-1
library prep for ATAC-SMARCD1-6h-1 derived from ADLI-0-0-053-09__OCM_108

tag: time


title: LR- liver sample-4

description: Library name: Sample 14


description:
Library name: LP_ATAC-TFDP1-6h-2
library prep for ATAC-TFDP1-6h-2 derived from ADLI-4-1-118-3-17__OCP_74G

tag: model system


description:
Library name: LP_ATAC-TFDP1-6h-1
library prep for ATAC-TFDP1-6h-1 derived from ADLI-4-1-118-3-17__OCP_74G

tag: parental cell_line


title: X22089_ExM

description: Library name: X22089_ExM

value: undifferentiated control (NT) - 22089


title: WT cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL2

description: Library name: WT2_aHA

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene

value: neural differentiation

value: day 4


title: Cyro-rep3

description: Library name: Sample9

value: Blastocyst embryo

value: Cryotop


title: X22085_MDM

description: Library name: X22085_MDM

value: endometrium

value: stromal and epithelial cell assembloid co-culture

value: decidualised control (Dec) - 22085


title: DNA from SD diet mouse-4

value: Liver

value: Standard diet


title: Cryo-rep2

description: Library name: Sample8


title: Nanuq-rep1

description: Library name: Sample4

value: Nanuq


title: X22085_ExM

description: Library name: X22085_ExM

value: undifferentiated control (NT) - 22085


title: Immortalized endometrial stromal cells treated with 2nM 1,25(OH)2D3 2

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Library name: Calcitriol_THESC2

data_processing:
Reads were trimmed of adapter sequences using Trim Galore with default settings except for specifying Illumina adapter sequences and paired-end validation.
Assembly: hg38 genome
Supplementary files format and content: merged files contain merged peaks in bed format for each condition
Supplementary files format and content: bigwig files contain non-normalized bed files for each sample.

source_name: T-HESC

growth_protocol: The cells were cultured and distributed into a 6-well plate in DMEM/F12 containing 10% v/v fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
The cells were lysed with Greenleaf lysis buffer (10 mM Tris-Cl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and ddH2O up to final volume)
The lysed cells were tagmented by Tn5 transposase, amplified using PCR, and purified by AMPure XP beads.

treatment_protocol: The cells were treated either with vehicle or 1,25(OH)2D3 containing 2% v/v charcoal-stripped fetal bovine serum.

value: T-HESC

value: Endometrial Stromal Cells

value: calcitriol


title: Immortalized endometrial stromal cells treated with 2nM 1,25(OH)2D3 3

description: Library name: Calcitriol_THESC3


description:
Library name: LP_ATAC-SMARCD1-0h-2
library prep for ATAC-SMARCD1-0h-2 derived from ADLI-0-0-053-09__OCM_108

value: iPSC

value: Knock-in of inducible C-terminal degron

value: DMSO


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibody REPL3

description: Library name: FBXL14ΔCTE3_aIgG

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene and the CTE gene region deleted from the FBXL14 gene

value: neural differentiation


title: Hematopoietic, (NC06,CH05,CH03)

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
Library name: HM_2
10x Genomics Single Cell 3’ V3

data_processing:
Raw FASTQ files were processed using CellRanger version 8.0.1 (10X Genomics). RNA counts were generated by aligning to the GRCh38 (hg38) reference using SC3Pv3 or SC3Pv4 for 10Xv3 or 10Xv4 3’ pair end sequencing respectively. HTO counts were generated using the same method, by aligning to their respective barcodes.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts

source_name: Bone Marrow

extract_protocol:
Niche fraction - Digested cell suspension were depleted for hematopoietic cells using automated magnetic cell separation system (AUTOMACS). Cells were stained with biotin anti-human CD45 and biotin anti-human glycophorin A (Biolegend).  Depleted fraction was stained for 1 hour at 4 degrees with the following antibodies: CD45-BUV395 (BD), GlyA-FITC (Biolegend), CD38-PECy7 (Biolegend), CD34-APCCy7 (Biolegend), NGFR-AF647 (Biolegend) and CD31-PE (Biolegend) and FVS575V was used for dead cell exclusion. Cells were sorted on a BD Aria Fusion. Two populations were sorted: CD45-GlyA-CD38-  niche fraction and CD45lowCD34+ HSPC fraction. Niche fraction was resuspended in PBS + 0.04% BSA and loaded into the 10x Genomics Chip G or X.  Hematopoietic fraction - Frozen mononuclear cell fractions were thawed using X-VIVO medium (Lonza) supplemented with 50% FBS and 110 mg/mL DNase. The suspension was centrifuged at 1200 rpm for 8 mins, cells were resuspended in RPMI with 10% FBS and counted. 4-5x106 MNC cells were resuspended in staining buffer (2% BSA,0.01% Tween in PBS) in conical bottom polypropylene FACS tubes. Cells were incubated with Fc Blocking reagent at a dilution of 1:10 (FcX, BioLegend) for 10 minutes on ice. After FcX block incubation, 0.1ug (per 1x106 cells) of unique TotalSeq™-B Hashing antibody (Biolegend) was added and incubated for 30 minutes on ice. Cells were washed 5 times with 1 ml Staining buffer (2%BSA/0.01%Tween, PBS), spined at 4˚C for 5 minutes at 350g. After the final wash, cells were resuspended in FACS buffer (PBS 2% FBS) and stained with the following antibodies: Lineage cocktail-FITC, CD45-PECy7, CD34-APCCy7 for 1 hour at 4 degrees. DAPI was used for dead cell exclusion. Cells were filtered and sorted on a BD Aria Fusion. Three hematopoietic populations were sorted: Mature cells (Lineage+), committed progenitors (Lineage-CD45+) and hematopoieitc progenitors (Lineage-CD45lowCD34+).  Samples were pooled evenly for two library preparations: Mature library (Mature cells and committed progenitors) and HSPC library. Pooled samples were delivered to the Princess Margaret Genomics Center (PMGC) for single cell sequencing preparation using the 10X platform.
We used Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chromium GEM-X Single Cell 3', Library & Gel Bead Kit v4 and followed the protocol as provided by 10x Genomics. Sorted HSPC fraction was frozen until further use.

value: Bone Marrow

tag: disease state

value: Mixed

tag: Sex

tag: compartment

value: Hematopoietic


title: WT cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL1

description: Library name: WT1_aHA

value: HA tag appended to the loci of the TLE1 gene

value: day 4


title: CTR-rep1

description: Library name: Sample1

tag: tissue

value: Blastocyst embryo

value: CTR


title: Immortalized endometrial stromal cells treated with 2nM 1,25(OH)2D3 1

description: Library name: Calcitriol_THESC1

tag: cell line

value: T-HESC


title: Hematopoietic, (NC02,CH06, NC07, CH04)

description:
Library name: HM_4
10x Genomics Single Cell 3’ V4


title: PI, replicate 2, scRNAseq

description: 10x Genomics

data_processing:
The raw sequencing data underwent preprocessing to construct gene expression profiles using CeleScope version 1.5.2 developed by Singleron Biotechnologies with standard settings. In summary, this process involved extracting and correcting barcodes and unique molecular identifiers (UMIs) from read one (R1), as well as removing adapter sequences and poly A tails from read two (R2). The cleaned R2 reads were then mapped to the human genome assembly GRCh38 transcriptome using STAR (v2.6.1b). Subsequently, uniquely mapped reads were annotated to exons using FeatureCounts (v2.0.1). Finally, successfully assigned reads sharing the same cell barcode, UMI, and gene identifier were aggregated to create a gene expression matrix suitable for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and  matrix files

value: gingival tissue

tag: group

value: Peri-implantitis


title: Meloidogyne incognita-infected Moneymaker tomato roots tissue sections of day 7

city: Qingdao

first: Lijun

last: Jiang

state: Shandong

address: 11#, Keyuan Jing 4 Road

department: Chinese Academy of Agricultural Sciences

institute: Tobacco Research Institute

description:
Library name: M-7d
frozen embedding spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using Illumina BCL Convert to generate FQSTQ files
Sequencings were aligned to Moneymaker tomoto genome to gene expression count using BSTMatrix with default parameters
Gene expression in level 6 of Refseq coding genes were quantified using BSTMatrix with default parameters
Assembly: Moneymaker tomato
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: barcodes_pos.tsv.gz: list of barcodes' position
Library strategy: Spatial transcriptomics

organism: Solanum lycopersicum

source_name: Root

growth_protocol: The Moneymaker tomato plants were grown in the artifical climate chamber until 4-6 leaf size

extract_protocol:
The galls were collected and OCT embedded on the third, fifth, seventh day after inoculated with Meloidogyne incognita,  15μm frozen sections were cut with pre-cooled cryostat
Spatial trasncriptome sequencing libraries were constructed by Illumina NovaSeq 6000

treatment_protocol: Each plant was inoculated with 5000 Meloidogyne incognita pre-parasitic second-stage juveniles

value: Root

value: Meloidogyne incognita-inoculated


title: Nanuq-rep2

description: Library name: Sample5

value: Nanuq


description:
Library name: LP_ATAC-SMARCC1-6h-2
library prep for ATAC-SMARCC1-6h-2 derived from ADLI-0-0-056-01__OCM_108

tag: cell type

value: iPSC

value: Knock-in of inducible C-terminal degron

tag: condition

value: Auxin


title: Immortalized endometrial stromal cells treated with vehicle1

description: Library name: Vehicle_THESC1

value: Endometrial Stromal Cells

tag: treatment

value: vehicle


title: E. coli control rep 3, 15 min

description:
Library name: Sample 3
Forward and reverse reads are denoted by R1 and R2.

data_processing:
Raw sequencing data was analyzed using Geneious Prime (version 2023.1.1). Reads were mapped to the reference sequence (NCBI NZ_CP009072.1 and NC_000962.3) and mRNA abundances were quantified as transcripts per million (TPM) prior to differential gene expression analysis with DESeq2.
Assembly: NCBI NZ_CP009072.1 (E. coli ATCC25922), NCBI NC_000962.3 (Mtb H37Rv)
Supplementary files format and content: csv files include raw transcript counts and normalized counts RPKM, TPM
Supplementary files format and content: xlsx files contain differential expression tables for the different samples, organized by organism (each with different sheets for the different conditions).

extract_protocol:
For E. coli, 500 µL of samples were centrifuged at 5,000 g, RT, 10 min. The supernatant was removed and pellets were dissolved in TE buffer (100 mM Tris, 1 mM EDTA, pH 8.0) containing 15 mg/mL lysozyme and 20 µL of proteinase K (Qiagen). Samples were mechanically disrupted with acid-washed glass beads (one spatula tip of sizes 150-212 µm, 212-300 µm and 425-600 µm, respectively) using the TissueLyser II (Qiagen) at a frequency of 1/s for 5 min. 700 µL QIAzol lysis reagent (Qiagen) were added and samples were disrupted for another two cycles with the TissueLyser II. Subsequently, total RNA was extracted using the RNeasy mini kit (Qiagen). For Mtb, 7 mL of samples were drawn and total RNA was extracted following a protocol consisting of mechanical disruption with the FastPrep machine (MP Biomedicals, Irvine, CA, USA) and extraction using the RNeasy mini kit (Qiagen).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Preparation Kit.

value: bacterial strain


description:
Library name: LP_ATAC-SSU72-0h-1
library prep for ATAC-SSU72-0h-1 derived from ADLI-4-3-93-3-4__OCP_74G

value: DMSO


title: hto_protein1

description:
Library name: hto_protein1
hto_protein1

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1 and IgBLAST
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

value: Lymph node

value: CD4 binding site-specific B cells


title: X22093_PolyIC_PolyIC

description: Library name: X22093_PolyIC_PolyIC

value: endometrium

value: stromal and epithelial cell assembloid co-culture

value: polyIC+decidualised (Dec+P) - 22093


description:
Library name: LP_ATAC-SMARCC1-6h-1
library prep for ATAC-SMARCC1-6h-1 derived from ADLI-0-0-056-01__OCM_108


title: tup11/12/php5-d cells under  glucose starved condition

city: Hachioji-shi

first: Yusuke

last: Tsuruta

state: Tokyo

address: Minamiosawa 1-1

department: Department of Chemistry, Graduate School of Science,

country: Japan

institute: Tokyo Metropolitan University

description:
Library name: tupphp5_glu_minus
non-strand-specific

data_processing:
RNA-seq reads were subjected to adapter-trimming and filtering using fastp (-q 20 -l 20 -3). Trimmed reads were aligned to the S. pombe genome (ASM294v2.30) using HISAT2. Properly paired alignments were extracted using SAMTools (samtools view -f 2). Reads mapped to each gene were counted using featureCounts. Gene annotation data that were available on January 4, 2025, were downloaded from PomBase. Only protein coding genes were considered. The read counts were normalized using Transcripts Per Million (TPM).
Assembly: ASM294v2.30
Supplementary files format and content: tab-delimited text file includes TPM normalized counts.

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

extract_protocol:
The total RNA was purified as described in R T Elder et al. (doi: 10.1073/pnas.80.9.2432).
The libraries were non-strand-specific and were prepared using poly(A) selection

value: S. pombe cell culture

tag: genotype

value: glucose starved condition


title: WT cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibodyREPL3

description: Library name: WT3_aIgG

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene

value: neural differentiation

value: day 4


title: Meloidogyne incognita-infected Moneymaker tomato roots tissue sections of day 3

description:
Library name: M-3d
frozen embedding spatial transcriptomics sequencing

value: Root

value: Meloidogyne incognita-inoculated


title: tup11/12/php5-d cells under glucose rich condition

description:
Library name: tupphp5_glu_plus
non-strand-specific

value: glucose rich condition


city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

description:
Library name: LP_ATAC-SMARCC1-24h-2
library prep for ATAC-SMARCC1-24h-2 derived from ADLI-0-0-056-01__OCM_108

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: .bed, .narrowPeak and unstranded.bw

value: iPSC

value: Knock-in of inducible C-terminal degron

value: Auxin


title: FBXL14ΔCTE cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL1

description: Library name: FBXL14ΔCTE1_aHA

value: HA tag appended to the loci of the TLE1 gene and the CTE gene region deleted from the FBXL14 gene


title: WT cells expressing endogenously HA-tagged TLE1 probed with anti-HA antibody REPL3

description: Library name: WT3_aHA


title: X22093_ExM

description: Library name: X22093_ExM

value: endometrium

value: undifferentiated control (NT) - 22093


title: tup11/12-d cells under glucose starved condition

description:
Library name: tup_glu_minus
non-strand-specific


description:
Library name: LP_ATAC-SMARCD1-6h-2
library prep for ATAC-SMARCD1-6h-2 derived from ADLI-0-0-053-09__OCM_108


description:
Library name: LP_ATAC-SMARCC1-24h-1
library prep for ATAC-SMARCC1-24h-1 derived from ADLI-0-0-056-01__OCM_108


title: FPBC patient 28

city: Santa Monica

first: Melanie

last: Goldfarb

address: 2200 Santa Monica blvd

department: Surgical Oncology

institute: Saint Johns Cancer Institute

description:
DNA from breast cancer FFPE tissue
JW-SBC-43

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC 850K Beadchip using standard Illumina protocol

scan_protocol: The array was scanned with the iScan system from Illumina according to the manufacturer's guidelines.

data_processing:
Data normalization and quality control were performed using the R package ChAMP (v.2.36.0). Batch effects were tested and corrected using the ComBat function in ChAMP, and probes with a detection p-value above 0.01 were excluded. Probes targeting non-CG dinucleotides, single nucleotide polymorphisms, and chromosome Y were removed from downstream analyses
processed value definition: Beta-values, corrected for batch effect from the different sample origin and other potential batches in the arrays

source_name: Breast Cancer

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from 10-15 um thick tissue sections by microdissection with a needle. Genomic DNA was isolated using the Quick-DNA FFPE Miniprep kit (#D3067; Zymo Research, CA.). Genomic DNA was quantified by Qubit® 3.0 Fluorometer (Q33216; Thermo Fisher Scientific, CA). Genomic DNA was converted with Sodium bisulfite using EZ DNA Methylation-Direct (#D5021, Zymo Research, CA), following the manufacturer's recommendations

tag: batcharray

value: Array 2

value: Breast Cancer

tag: age at diagnosis

tag: breast cancer subtype

value: Female

tag: tumor histology

value: Invasive ductal carcinoma

tag: grade

value: Grade II (moderate/intermediate)


title: WT cells under nitrogen starved condition

description:
Library name: WT_N_minus
non-strand-specific

value: S. pombe cell culture

value: WT

value: nitrogen starved condition


description:
Library name: LP_ATAC-SMARCD1-24h-2
library prep for ATAC-SMARCD1-24h-2 derived from ADLI-0-0-053-09__OCM_108

tag: editing strategy

tag: altered gene_symbol

tag: time

tag: model system


description:
Library name: LP_ATAC-SMARCC1-0h-2
library prep for ATAC-SMARCC1-0h-2 derived from ADLI-0-0-056-01__OCM_108

value: DMSO

tag: parental cell_line


title: WT cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibodyREPL2

description: Library name: WT2_aIgG

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene

value: neural differentiation

value: day 4


title: X22089_MDM

description: Library name: X22089_MDM

tag: tissue

tag: patientid

value: stromal and epithelial cell assembloid co-culture

value: decidualised control (Dec) - 22089


title: FPBC patient 26

description:
DNA from breast cancer FFPE tissue
JW-SBC-41

tag: Sex


description:
Library name: LP_ATAC-SMARCB1-6h-2
library prep for ATAC-SMARCB1-6h-2 derived from ADLI-4-0-048-3-02__OCP_74G

tag: cell line

tag: cell type

value: iPSC

value: Knock-in of inducible C-terminal degron

value: Auxin


title: Act37-Liq

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

description: Library name: 1004-L

data_processing:
A custom FASTA database was generated containing all of the coding sequences (CDS) from reference genome GAS ATCC 12344 and CDS from HG316453.2, NC_002737.2, NC_006086.1, NC_007296.2, NC_008021.1, NC_008022.1, and NC_008024.1 that could not be found in the ATCC strain using BWA MEM v0.7.17 (49). Raw RNA-seq reads were aligned to this custom database using BWA MEM. The expression level of gene features (CDS regions from the reference) were quantitated using FeatureCounts v2.0.3 (55) as raw read counts of the stranded libraries. Differential analysis of quantitated gene features as compared with treatment (acute vs carrier) or sampling method (liquid vs swab) was performed using the software package edgeR (56, 57) on raw sequence counts. Prior to analysis, the data were filtered to remove any features that had less than 5 total counts summed across all samples. Data were normalized as counts per million and an additional normalization factor was computed using the trimmed mean of M-values (TMM) algorithm. Statistical tests were performed using the “exactTest” function in edgeR. Adjusted p-values (q-values) were calculated using the Benjamini-Hochberg false discovery rate (FDR) correction. Significant gene features were determined based on an FDR threshold of 0.05 (5%).
Assembly: Custom database, see above.
Supplementary files format and content: Tab delimited text file containing the counts for each gene (CDS) in the custom reference database for each sample.

molecule: cytoplasmic RNA

organism: Streptococcus pyogenes

source_name: Cultured bacteria

growth_protocol: For liquid samples, overnight cultures of GAS strains were grown in THY medium. In the morning, cultures were diluted 1:10 in fresh THY medium and grown at 37 °C static until the OD600 reached 0.4-0.6. Cells were then spun down and resuspended in 500 µL DNA/RNA Shield (Zymo) before storage at -80 °C until extraction. Swab samples were processed directly from -80C flash frozen swabs.

extract_protocol:
For liquid samples, pellets were resuspended in 200 µL lysis solution (TRIzol Max Bacterial Enhancement Reagent (ThermoFisher 16122012) which had been pre-heated to 95 °C mixed with 1 mg/mL lysozyme and 50 U/mL mutanolysin) and moved to a MagMAX prime bead beating tube (ThermoFisher A58155). For swabs, 500 µL DNA/RNA Shield was added to frozen swabs and then vortexed for 30-60 seconds. The tubes containing the swabs were then sonicated in a sonicator bath for 5 minutes to help with removing adherent cells. Following sonication, swabs were again vortexed for 30-60 seconds  and then the tubes were spun down for 5 minutes at 4 °C. The supernatant and swab were removed and the resulting pellet resuspended in 200 µL lysis solution and moved to MagMAX bead beating tubes as above. All samples were placed in an OMNI Bead Ruptor 12 (Omni International, 19-050A) and beat twice for 4 minutes each with a 30 second break in between. The mixtures were then incubated at 37 °C for 30 minutes to allow additional enzymatic lysis and then incubated at 95 °C for 5 minutes. RNA was then collected using the TRIzol Max Bacterial RNA Isolation kit (ThermoFisher 16096-040) per manufacturer’s instructions including the phase separation and RNA precipitation steps. RNA pellets were air dried and resuspended in 45 µL DEPC-treated water. The Turbo DNA-free kit (ThermoFisher AM1907) was used per manufacturer’s instructions to remove any remaining DNA in the sample. The final RNA quantity and quality were measured on a NanoDrop One. Depletion of eurkaryotic RNA was done on the RNA from the swab samples using the MICROEnrich kit (ThermoFisher AM1901) per manufacturer’s instructions. The final precipitation step was skipped and the samples were taken immediately into the MICROBExpress kit protocol (ThermoFisher AM1905) per manufacturer’s instructions to remove bacterial rRNA. For liquid cultures, bacterial rRNA was removed using the same MICROBExpress kit using 2-10 µg starting RNA in 15 µL or less volume.
RNA-seq libraries for samples sequenced on the Novaseq X: Libraries were prepared in house using the NEB Next Ultra II Directional RNA library prep kit (NEB E7765) per the manufacturer’s protocol for purified mRNA. mRNA input amounts ranged from 1-100 ng total. Briefly, rRNA depleted RNA in was first fragmented at 94°C for 10 minutes with random primers. First and then second strand cDNA was synthesized, followed by cDNA purification using SPRIselect beads. Ends were prepped and NEBNext adaptors were ligated to cDNA strands. Samples were again purified using SPRIselect beads, followed by PCR enrichment of adaptor ligated DNA using unique indexed forward and reverse primers. Samples were purified once more using SPRIselect beads, and library quality was analyzed using a NanoDrop, Qubit and Tapestation.  RNA-seq libraries for samples sequenced on the HiSeq 2500 were prepared in house using the Kapa Stranded RNASeq Library Preparation kit (KK8400) per manufacturers instructions for purified mRNA with input range of 10-100 ng total. RNA was fragmented at 94°C for 6 minutes with random primers. Illumina adapters were ligated and library quality analyzed using NanoDrop, Qubit, and Tapestation.

value: Cultured bacteria


title: X22085_PolyIC_PolyIC

description: Library name: X22085_PolyIC_PolyIC

value: endometrium

tag: treatment

value: polyIC+decidualised (Dec+P) - 22085


title: LR+ liver sample-1

description: Library name: Sample 1

data_processing:
Gene expression quantification was performed usingfeatureCounts (v1.5.0-p3) to calculate the number of reads mapped to each gene. Gene expressionlevels were normalized as FPKM (Fragments Per Kilobase of transcript per Million mapped reads)Differential expression analysis between two experimental conditions (with biological replicateswas performed using both DESeq2 (v1.20.0) and gdgek,(v3.22.5). For DESeq2, anegative binomialdistribution model was applied to estimate dispersion and test for significance. The resulting pvalues were adjusted for multiple testing using the Benjamini-Hochberg method. Genes withadjusted p-value < 0.05 were considered differentially expressed. In parallel, count data were alsonormalized using edgeR through a scaling factor, and differential expression was calculated usingexact tests. Significant genes were defined based on a corrected p-value < 0.05 and an absolute foldchange >2
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Format: Raw counts Content: Raw read counts for each gene (or transcript) across all samples.

value: liver

tag: genotype


title: Car12-Swab1

description: Library name: 351-S

source_name: Oropharyngeal swab

value: Oropharyngeal swab


description:
Library name: LP_ATAC-SMARCD1-24h-1
library prep for ATAC-SMARCD1-24h-1 derived from ADLI-0-0-053-09__OCM_108

tag: condition


title: LR+ liver sample-9

description: Library name: Sample 9

source_name: liver

value: WT


title: Immortalized endometrial stromal cells treated with vehicle3

description: Library name: Vehicle_THESC3

value: T-HESC

value: Endometrial Stromal Cells

value: vehicle


title: Act28-Swab1

description: Library name: 1000-S


title: WT cells expressing endogenously HA-tagged TLE1 probed with unspecific IgG antibodyREPL1

description: Library name: WT1_aIgG

value: WTC11 iPSCs

value: iPSCs

value: HA tag appended to the loci of the TLE1 gene


title: Immortalized endometrial stromal cells treated with vehicle2

description: Library name: Vehicle_THESC2


description:
Library name: LP_ATAC-SMARCD1-0h-1
library prep for ATAC-SMARCD1-0h-1 derived from ADLI-0-0-053-09__OCM_108

value: DMSO


title: FPBC patient 23

description:
DNA from breast cancer FFPE tissue
JW-SBC-38

tag: batcharray

value: Array 2

value: Breast Cancer

tag: age at diagnosis

value: Female

value: Invasive ductal carcinoma

value: Grade III (poorly differentiated)


title: tup11/12/php5-d cells under nitrogen starved condition

description:
Library name: tupphp5_N_minus
non-strand-specific

value: S. pombe cell culture

value: nitrogen starved condition


title: Meloidogyne incognita-infected Moneymaker tomato roots tissue sections of day 5

description:
Library name: M-5d
frozen embedding spatial transcriptomics sequencing

value: Root

value: Meloidogyne incognita-inoculated


title: tup11/12-d cells under nitrogen starved condition

description:
Library name: tup_N_minus
non-strand-specific


description:
Library name: LP_ATAC-SMARCB1-24h-1
library prep for ATAC-SMARCB1-24h-1 derived from ADLI-4-0-048-3-02__OCP_74G

value: iPSC

value: Knock-in of inducible C-terminal degron

value: Auxin