title: EGC, PBS, Colon_MP, 2hr, rep3

value: Colon

value: EGC


title: HCT116_DMEM_24hr_Butyrate_rep2

status: Public on Jun 24 2025

type: SRA

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

country: USA

institute: Case Western Reserve University

description: Library name: Sample 30

library_source: transcriptomic

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: BSgenome.Hsapiens.UCSC.hg19 (version 1.4.3) and TxDb.Hsapiens.UCSC.hg19.knownGene (version 3.4.0)
Assembly: hg19
Supplementary files format and content: counts, bigwigs

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HCT-116 cells were grown in DMEM medium or human plasma like media (HPLM) with 10% fetal bovine serum and 1% penicillin/streptomycin. When cells were grown in HPLM, cells were washed in PBS and cultured in HPLM for at least three days prior to experiments. Caco-2 cells were grown in Eagle's Minimum Essential Medium supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 20% FBS, and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNA isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits following the manufacturer's protocol.

treatment_protocol: HCT-116 and Caco-2 cells were treated with different short chain fatty acids (SCFAs) or inhibitors for 6 or 24 hours prior to RNA isolation. For ChIP-seq experiments, cells were treated with 5 mM butyrate or 5 mM propionate for 24 hours prior to fixation.

tag: cell line

tag: cell type

value: Colorectal carcinoma

tag: genotype

value: Wild type

tag: treatment

value: 5 mM butyrate for 24 hours


title: whole animal, control strain exposed to DMSO, replicate 2

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

library_source: genomic

data_processing:
Raw data: original image data  from the high-throughput sequencing platform were transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contained sequences of reads and corresponding base quality.
Quality control: The sequencing error rate, the Qphred, the quality score (Phred) were calculated and the corresponding relationship between sequencing quality and Phred score in the base calling  was listed.
Sequencing Data Filtration:  Raw reades were removed if they paired reads contained adapter contaminations,  when they contained uncertain nucleotides in excess of 10% and / or the quality of nucleotides was poor (Q eqaul or less than 5).
Sequence Alignment : The sequencing data was aligned to the reference genome through BWA software and the mapping rate and coverage counted according to the alignment results.
Assembly: WBcel235
Supplementary files format and content: SNP detection was performed via ANNOVAR, including gene based annotation, region based annotation , filter based annotation etc.  SNP mutant frequency, InDel percentage in CDS and genome and SV annotations were also determined.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage in the presence or absence of benzo[a]pyrene.

extract_protocol:
Genomic DNA was extracted with QIAGEN genomic-tips (20/G) following the manufacturer’s protocol. The DNA quantity was measured using the Qubit 2.0 (Thermo Fisher) coupled with Qubit dsDNA HS assay kit (Thermo Fisher). The quality was assessed by gel electrophoresis loading 150 ng of sample into each well and separated for 40 minutes at 100 V.
Whole genome resequencing was based on  SBS (sequencing by synthesis) to identify the genetic variations in individual strains . The genomic DNA was randomly sheared into short fragments. The obtained fragments were end repaired, A-tailed and further ligated with Illumina adapter. The fragments with adapters were PCR amplified, size selected, and purified.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries  were sequenced on the Illumina platform, according to the library concentration.
Whole Genome Sequencing
Illumina NovaSeq PE150

treatment_protocol: L1 stage animals were exposed 48 hours at 20 ºC to benzo[a]pyrene supplemented to both the agar medium and the food source (E. coli OP50).

tag: tissue

value: whole animal

tag: strain

value: control

value: DMSO


title: EGC, PBS, Colon_MP, 2hr, rep4

city: Stanford

first: Julia

last: Kaltschmidt

state: CA

address: 288 Campus Drive

department: Neurosurgery

institute: Stanford University

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v.0.4.4, parameters: --paired --length 20 --phred33 --q 30). Trimmed sequences were aligned using STAR (v.2.5.3, default parameters). Multi-mapped reads were filtered.
Data visualization and analysis were performed using custom Rstudio scripts and the following Bioconductor packages: Deseq2 (Love at al. 2014), topGO, destiny and org.Mm.eg.db. Finally, we excluded pseudogenes and predicted genes from the count matrix to focus predominantly on well-annotated, protein-coding genes. In total, all the following analyses were performed on the same set of 21,076 genes.
Read quality control and counting were performed as previously described by Hahn et al (2023).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: EGC

extract_protocol:
RNA was isolated for sequencing using RNeasy Plus Micro Kit (Cat# 74034).
cDNA and library sytheses were performed in house using the Smart-seq2 protocol as described by Schaum et al (2020) and Iram et al (2022).

treatment_protocol: Lipopolysaccharide (LPS) from E. coli O111:B4 (Cat #tlrl-eblps) was purchased from Invivogen (San Diego, CA) and was reconstituted to 5mg/ml by homogenizing in 1ml of endotoxin-free water. Mice were randomly divided into a control group (phosphate-buffered saline - PBS), and treatment group (LPS), and received either a single IP injection of LPS (2mg/kg body weight) in PBS, or PBS alone. Mice were sacrificed 2 or 24 hours following PBS or LPS injection

tag: tissue (region)

tag: tissue (layer)

value: Myenteric Plexus

tag: Sex

value: Male

value: PBS

tag: timepoint

tag: mouse id


title: HCT116_DMEM_24hr_Butyrate_rep1

description: Library name: Sample 29


title: whole animal, control strain exposed to DMSO, replicate 1


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Static, rep 3, experiment 1.3

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Demultiplexed FASTQ files were quantified using Salmon v1.1.0
Salmon outputs were loaded into R via the tximeta package
Assembly: GRCh38, GENCODE version 30
Supplementary files format and content: A matrix of pseudocounts from Salmon collapsed to the gene level via tximeta with genes as rows and samples as columns exported to a comma separated values (csv) file.

extract_protocol:
Total RNA samples were assessed for concentration using a Qubit fluorometer (ThermoFisher Scientific, Waltham, MA) and for quality using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Up to one µg of total RNA was purified for mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolab Inc, Ipswich, MA).  Stranded RNA-Seq library construction was performed using the IDT xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA).  Library concentration was measured with a Qubit fluorometer and library size on an Agilent 4200 TapeStation (Agilent Technologies). Libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing. On average, approximately 30 million reads were generated from each sample.
The top channel of chip samples or a well from a 96 well plate were incubated with cold Accutase (STEMCELL Technologies) for 20 minutes at 37°C, then cells were extracted by flushing and washing with cold phosphate buffered saline (PBS), pelleted by centrifuge at 350 rcf, and frozen at -80°C. RNA was extracted from pellets using the RNeasy Micro Kit (Qiagen).
Various methods:  see SAMPLES "library construction protocol" section

value: iPSC-derived motor neuron cultures

value: CTR

value: Static


title: HCT116_DMEM_24hr_Vehicle_rep2

description: Library name: Sample 27

value: Equal volume sterile water for 24 hours


title: HCT116_DMEM_24hr_Butyrate_rep3

description: Library name: Sample 31


title: HCT116_DMEM_24hr_Vehicle_rep1

description: Library name: Sample 26


title: HCT116_DMEM_24hr_Vehicle_rep3

description: Library name: Sample 28


title: HCT116_DMEM_6hr_SCFAs_1to1to1_15mM_rep3

description: Library name: Sample 25

value: 15 mM acetate, butyrate, and propionate (5mM each) mix for 6 hours


title: whole animal, control strain exposed to 640 μM BaP, replicate 3

value: 640 μM BaP


title: whole animal, Cyp1A2 strain exposed to DMSO, replicate 2


title: HCT116_DMEM_6hr_SCFAs_1to1to1_15mM_rep2

description: Library name: Sample 24


title: EGC, PBS, Colon_MP, 2hr, rep1

value: Colon

value: Female


title: EGC, PBS, Colon_MP, 2hr, rep2

value: EGC


title: EGC, None, SI_SMP, rep6

value: Small Intestine

value: Submucosal Plexus


title: whole animal, control strain exposed to 640 μM BaP, replicate 2

value: whole animal


title: EGC, None, SI_SMP, rep5


title: HeLa cells, Sync-label Enrich, rep2

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

country: China

institute: Peking university

description:
2_HeLa_Sync_label_vs_Input_DESeq2_DEG.csv
HeLa_Sync-label_Input_Enrich_Reads_Count.txt
HeLa_Sync_Enrich_2

data_processing:
Raw reads were trimmed with Trim Galore!(v0.6.7) to remove low-quality bases and adapters and subsequently aligned to the Homo sapiens genome (Ensembl GRCh38.107) or Mus musculus (GRCm38.98) by HISAT2 (v2.2.1) with with ‘-rna-strandness RF’ parameters. After the low-quality reads were filtered out by SAMtools (v1.9), fragments mapped on the exons were processed using featureCounts (v2.0.2) to obtain the gene expression matrix. The R/Bioconductor package DESeq2 (v1.36.0) was used for data normalization and differential expression analysis.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: wildtype HeLa cells with Sync-label treatment

growth_protocol: HeLa and RAW264.7 cell lines were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
Cells grown in cell culture dishes at ~90% confluency were incubated with 50 nM photocatalyst in fresh medium at 37°C under 5% CO2 for 30 min, washed with PBS for three times, incubated with 50 µM QMPAB-2 in culture medium for 30 min and washed twice with PBS. After washing, cells were maintained in fresh medium at 37°C under 5% CO2 for 5 min and illuminated with blue LED (4 mW cm-2; λmax ∼460 nm) for 15 min at room temperature. Cells were placed about 5 cm from the light source. After illumination, cells were immediately collected using cell scraper and lysed with TRIzol reagent. Cellular total RNA purification was operated following the manufacture protocol by isopropanol precipitation.Total RNA was extracted using TRIzol reagent(Invitrogen).
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2(Takara). Labeled RNA was captured using Dynabeads MyOne Streptavidin C1 (Invitrogen).

value: HeLa

value: Human cervical cancer cells

value: WT

value: Sync-label+


title: HeLa cells, Sync-label Enrich, rep1

description:
2_HeLa_Sync_label_vs_Input_DESeq2_DEG.csv
HeLa_Sync-label_Input_Enrich_Reads_Count.txt
HeLa_Sync_Enrich_1


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 6, experiment 1.3

value: Flow


title: HeLa cells, Sync-label Input, rep2

description:
2_HeLa_Sync_label_vs_Input_DESeq2_DEG.csv
HeLa_Sync-label_Input_Enrich_Reads_Count.txt
HeLa_Sync_Input_2

source_name: wildtype HeLa cells without Sync-label treatment

value: Sync-label-


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Static, rep 2, experiment 1.3

value: iPSC-derived motor neuron cultures

value: CTR


title: HCT116_DMEM_6hr_SCFAs_1to1to1_15mM_rep1

description: Library name: Sample 23

value: Colorectal carcinoma

value: Wild type


title: whole animal, Cyp1A2 strain exposed to DMSO, replicate 1

value: DMSO


title: EGC, None, Colon_SMP, rep6

value: Colon


title: whole animal, Cyp1A2 strain exposed to DMSO, replicate 3


title: whole animal, Cyp1A2 strain exposed to 640 μM BaP, replicate 3

value: 640 μM BaP


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Static, rep 1, experiment 1.3

value: Static


title: EGC, None, SI_SMP, rep4

value: Small Intestine

value: EGC

value: Female


title: HeLa cells, Sync-label Input, rep1

description:
2_HeLa_Sync_label_vs_Input_DESeq2_DEG.csv
HeLa_Sync-label_Input_Enrich_Reads_Count.txt
HeLa_Sync_Input_1

value: HeLa


title: whole animal, control strain exposed to 640 μM BaP, replicate 1

value: whole animal

value: control


title: EGC, None, Colon_SMP, rep5

value: Submucosal Plexus


title: HeLa cells, CAT-seq Enrich, rep2

description:
HeLa_CAT-seq_vs_Input_DESeq2_DEG.csv.gz
HeLa_CAT-seq_Input_Enrich_Reads_Count.txt
HeLa_Single_Enrich_2

source_name: wildtype HeLa cells with CAT-seq treatment

value: Human cervical cancer cells

value: WT

value: CAT-seq+


title: HCT116_DMEM_6hr_SCFAs_1to1to1_5mM_rep2

description: Library name: Sample 21

value: 5 mM acetate, butyrate, and propionate (1.67 mM each) mix for 6 hours


title: EGC, None, Colon_SMP, rep4


title: whole animal, Cyp1A2 strain exposed to 640 μM BaP, replicate 2


title: HeLa cells, CAT-seq Enrich, rep1

description:
HeLa_CAT-seq_vs_Input_DESeq2_DEG.csv.gz
HeLa_CAT-seq_Input_Enrich_Reads_Count.txt
HeLa_Single_Enrich_1


title: HCT116_DMEM_6hr_SCFAs_1to1to1_5mM_rep1

description: Library name: Sample 20

value: Colorectal carcinoma


title: whole animal, Cyp1A2 strain exposed to 640 μM BaP, replicate 1


title: EGC, None, SI_MP, rep6

value: Myenteric Plexus


title: HeLa cells, CAT-seq Input, rep2

description:
HeLa_CAT-seq_vs_Input_DESeq2_DEG.csv.gz
HeLa_CAT-seq_Input_Enrich_Reads_Count.txt
HeLa_Single_Input_2

source_name: wildtype HeLa cells without CAT-seq treatment

value: CAT-seq-


title: HCT116_DMEM_6hr_Propionate_rep3

description: Library name: Sample 19

value: Wild type

value: 5 mM propionate for 6 hours


title: HCT116_DMEM_6hr_SCFAs_1to1to1_5mM_rep3

description: Library name: Sample 22


title: whole animal, Cyp1A1 strain exposed to DMSO, replicate 3

value: DMSO


title: EGC, None, Colon_MP, rep5

value: Colon


title: HCT116_DMEM_6hr_Butyrate_rep3

description: Library name: Sample 16

value: 5 mM  butyrate for 6 hours


title: EGC, None, SI_MP, rep5

value: Small Intestine

value: EGC

value: Female


title: HCT116_DMEM_6hr_Propionate_rep2

description: Library name: Sample 18


title: whole animal, Cyp1A1 strain exposed to DMSO, replicate 2

value: whole animal


title: EGC, PBS, WT, SI, 24hr, rep5

value: Gpr37WT; Plp1eGFP

value: PBS


title: HeLa cells, CAT-seq Input, rep1

description:
HeLa_CAT-seq_vs_Input_DESeq2_DEG.csv.gz
HeLa_CAT-seq_Input_Enrich_Reads_Count.txt
HeLa_Single_Input_1

value: HeLa

value: Human cervical cancer cells

value: WT


title: whole animal, Cyp1A1 strain exposed to DMSO, replicate 1


title: EGC, None, Colon_MP, rep4


title: EGC, None, SI_MP, rep4


title: CRTC3_KO rep3

city: Beiing

first: TAO

last: XING

state: Beiing

address: Beiing

institute: Peking University Cancer Hospital

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,then mapped to hg38 using TopHat.
fpkm were calculated using standard protocol
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol Reagent.Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1ug of total RNA  for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare for sequencing using Illumina protocols

value: liver cancer

value: KO


title: CRTC3_KO rep2


title: HCT116_DMEM_6hr_Butyrate_rep2

description: Library name: Sample 15

value: Colorectal carcinoma


title: HCT116_DMEM_6hr_Propionate_rep1

description: Library name: Sample 17

value: Wild type


title: whole animal, Cyp1A1 strain exposed to 640 μM BaP, replicate 3

value: 640 μM BaP


title: CRTC3_WT rep3


title: whole animal, Cyp1A1 strain exposed to 640 μM BaP, replicate 2


title: EGC, None, SI_SMP, rep2

value: Submucosal Plexus

value: Male


title: CRTC3_WT rep2


title: EGC, None, SI_SMP, rep1


title: HCT116_DMEM_6hr_Butyrate_rep1

description: Library name: Sample 14

value: 5 mM  butyrate for 6 hours


title: whole animal, Cyp1A1 strain exposed to 640 μM BaP, replicate 1


title: HCT116_DMEM_6hr_Acetate_rep2

description: Library name: Sample 12

value: 5 mM acetate for 6 hours


title: EGC, None, SI_SMP, rep3

value: Small Intestine

value: EGC


title: control strain exposed to 640 uM BaP, replicate 3

data_processing:
Raw data: riginal image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Novel gene prediction: Because transcriptome annotations are still incomplete, most RNA-seq studies will reveal novel genes and transcripts. The Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones.
Assembly: WBcel235
Supplementary files format and content: In the RNA-seq experiments, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments

extract_protocol:
The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: whole animal

value: control strain

value: exposed to 640 uM BaP


title: control strain exposed to 640 uM BaP, replicate 2


title: control strain exposed to 640 uM BaP, replicate 1


title: HCT116_DMEM_6hr_Vehicle_rep3

description: Library name: Sample 10

value: Equal volume sterile water for 6 hours


title: HCT116_DMEM_6hr_Acetate_rep3

description: Library name: Sample 13


title: EGC, None, Colon_SMP, rep2

value: Colon


title: EGC, None, SI_MP, rep3

value: Myenteric Plexus


title: Cyp1A2 strain exposed to 640 uM BaP, replicate 2

value: Cyp1A2 strain


title: CRTC3_WT rep1

value: liver cancer

value: WT


title: CRTC3_KO rep1

value: KO


title: EGC, None, SI_MP, rep2


title: Cyp1A2 strain exposed to 640 uM BaP, replicate 1


title: HepG2_IFN

data_processing:
Harvested the cells and extracted genomic DNA, which was further amplified, labeled with barcodes using NEBNext® High-Fidelity 2X PCR Master, and deep sequenced by Annoroad (Beijing, China) to assess the relative enrichment of sgRNA sequences.
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,The sgRNAs abundance as the readout of library screening was analyzed by Bowtie2 and the synergistic or suppressing impact on drug treatment was determined by DrugZ algorithm and NormZ scores.
Assembly: specify,tkov3_guide_sequence ，The Toronto human knockout pooled library (TKOv3) comprised of 70948 sgRNAs target-ing 18053 protein-coding genes was a gift from Jason Moffat (Addgene #125517)
Supplementary files format and content: counts
Supplementary files format and content: *_DrugZ.txt: Normalized Z-scores (NormZ) measured by DrugZ were used to identify genes associated with sensitization or resistance to IFN-γ.
Library strategy: CRISPR screen

extract_protocol:
DNA extraction from cells using QIAamp kit
labeled with barcodes using NEBNext® High-Fidelity 2X PCR Master

treatment_protocol:
The Toronto human knockout pooled library (TKOv3) comprised of 70948 sgRNAs target-ing 18053 protein-coding genes was a gift from Jason Moffat (Addgene #125517).
IFN-γ (50 ng/mL) or vehicle (control) for 14 days

value: ifn-gamma


title: HCT116_DMEM_6hr_Acetate_rep1

description: Library name: Sample 11

value: Colorectal carcinoma

value: Wild type


title: SK-HEP-1_day14

value: PBS


title: EGC, None, Colon_SMP, rep1

value: Submucosal Plexus

value: Male


title: SK-HEP-1_day0


title: HepG2_day14


title: EGC, None, Colon_MP, rep2

value: EGC


title: Cyp1A2 strain exposed to 640 uM BaP, replicate 3

value: whole animal


title: HepG2_day0


title: HCT116_DMEM_6hr_Vehicle_rep2

description: Library name: Sample 9


title: SK-HEP-1_IFN


title: HCT116_DMEM_6hr_Vehicle_rep1

description: Library name: Sample 8


title: HCT116_H3K27bu_ChIP

description: Library name: Sample 3

value: 5 mM butyrate for 24 hours


title: EGC, None, SI_MP, rep1

value: Small Intestine


title: control strain exposed to 40 uM BaP, replicate 2

value: control strain

value: exposed to 40 uM BaP


title: CTLs, Sync-label Enrich, rep1

description: CD8+ cytotoxic T lymphocytes with Sync-label treatment

data_processing:
Raw reads were trimmed with Trim Galore!(v0.6.7) to remove low-quality bases and adapters and subsequently aligned to the Homo sapiens genome (Ensembl GRCh38.107) or Mus musculus(GRCm38.98) by HISAT2 (v2.2.1) with with ‘-rna-strandness RF’ parameters.After the low-quality reads were filtered out by SAMtools (v1.9), fragments mapped on the exons were processed using featureCounts (v2.0.2) to obtain the gene expression matrix.The R/Bioconductor package DESeq2 (v1.36.0) was used for data normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

growth_protocol: Spleen were excised immediately after the mice (C57BL/6N) were sacrificed. Each spleen was transferred to a dish, and cut into small pieces with media (RPMI-1640 with 10% FBS) added to prevent drying. The tissue pieces with media were then transferred to a 40-µm cell drainer fitted on a 50-mL tube, and pressed through the cell drainer, while media was continuously added during the process. The collected cells were pelleted by centrifugation (300 g, 10 min), resuspended with 1 mL RBC (red blood cell) lysis buffer (eBioscience™, 00433357). The mixture was incubated at room temperature for 3 min to lyse red blood cells followed by the addition of 5 mL media (RPMI-1640 with 1% FBS). The cells were then pelleted from the mixture by centrifugation and resuspended in media (1 mL) for subsequent applications. Primary T cells were isolated from spleen lymphocytes using EasySepTM Mouse CD8+ T Cell Isolation Kit (STEMCELL technologies, 19853) according to the manufacturer’s protocol. In our cases, approximately 1 × 107 CD8+ naïve T lymphocytes with 90% purity (CD3-positive) were isolated per 108 spleen lymphocytes. NTLs or CTLs were cultured to over 50% confluence, and the culture medium was changed to RPMI-1640, followed by incubation at 37 °C with 5% CO2 for 24 h or specified duration and Iridium photocatalyst concentration was optimized to 20 nM to reduce background labeling noise.

value: spleen

value: CD8+ cytotoxic T lymphocytes

value: Sync-label+


title: HCT116_H3K9bu_ChIP

description: Library name: Sample 2


title: HCT116_Input_DNA_Propionate

description: Library name: Sample 7

value: 5 mM propionate for 24 hours


title: CTLs, Sync-label Input, rep2

description: CD8+ cytotoxic T lymphocytes without Sync-label treatment

value: WT

value: Sync-label-


title: Cyp1A1 strain exposed to 640 uM BaP, replicate 3

value: Cyp1A1 strain

value: exposed to 640 uM BaP


title: HCT116_Input_DNA_Butyrate

description: Library name: Sample 6

value: Colorectal carcinoma

value: Wild type


title: EGC, None, Colon_MP, rep3

value: Colon

value: Myenteric Plexus

value: Male


title: batch4etoh-2_S24

city: Chicago

first: Wenhe

last: Lin

state: Illinois

address: 920 E 58th St

institute: University of Chicago

description:
Library name: batch4_24
10X Genomics

library_source: transcriptomic single cell

data_processing:
We used CellRanger (7.0.0) to align samples to the human genome (GRCh38). We used Vireo to demultiplex samples by genotype and assign droplets to individuals 2 . We used a reference panel from 1000 Genomes Project Phase 3 3 for demultiplexing. We removed doublets and droplets that could not be confidently assigned to an individual. We removed individuals with fewer than 50 assigned cells. We further filtered cells to keep only those with less than 20% mitochondrial reads and with at least 750 genes expressed and at most 9000 genes detected.
Assembly: GRCh38-2020-A
Supplementary files format and content: tab-sepearated value files and matrix files

source_name: hetergenous

growth_protocol: HDCs were formed using a modified version of the STEMCELL Agrewell 400 protocol. We cultured iPSCs in E8 media with rock and synched lines up in each batch to desired density (50%-90% confluency). On the seeding day, we first prepared Aggrewell 400 24-well plates by pre-treating wells with anti-adherence rinsing solution (07010, STEMCELL), followed by rinsing with warm basal media DMEM/F12. iPSCs were dissociated into single cells and resuspended in Aggrewell EB Formation Medium (05893, STEMCELL) with ROCK inhibitor Y-27632 and Penicillin/Streptomycin. We counted cells and recorded viability twice using Countess II. Cells were seeded into each prepared well at a density of 1,000 cells per microwell (1.2x10^6 cells and 2mL per well). After 24 hours, we changed half of the media with fresh Aggrewell EB Formation Medium without ROCK inhibitor. After another 24 hours on day 2, we gently collected the aggregates and transferred them to an ultra-low attachment 6-well plate (CLS3471-24EA, Sigma) in prepared media for vehicle control or treatment groups. We maintained HDCs for an additional 19 days, replacing media with fresh prepared media every 48 hours.

extract_protocol:
HDCs were dissociated on day 21. We harvested HDCs following the STEMCELL Agrewell400 protocol. After rinsing HDCs with phosphate-buffered saline (Corning 21-040-CV), we dissociated them with AccuMax (STEMCELL 7921) at 37C. We gently pipetted HDCs up and down for 30s every 5 min until HDCs were completely dissociated. We then quenched the dissociation with warm E6 media. After spinning down, cells were resuspended in cold E6 media and strained them through a 40 mm strainer (Fisherbrand 22-363-547). We counted cells and measured viability using Trypan Blue and Countess II (AMQAF1000, invitrogen). We then mixed cells from each line for the same condition together in equal proportions, with one mixed suspension per condition. Each mixed suspension was counted again using hemocytometer to determine the final cell concentration. We adjusted the final concentration to 800-1,200 cells/ul for each mixed suspension. Cell suspensions remained on ice before loading to the 10X Chromium Controller.
We generated scRNA-seq libraries using Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (1000348, 10X Genomics).

treatment_protocol: For the chemical perturbations, we used concentration of 80mM, 0.6mM, 10uM for ethanol (BP2818500, Fisher Scientific), caffeine (C0750-5G, Sigma), and nicotine (N3876-5ML, Sigma) treatment, respectively. We prepared 10,000X stock solutions in non-denatured 200 proof ethanol (BP2818500, Fisher Scientific) and stored aliquots in -20C for all batches. Each time of changing media, we prepared fresh media by adding an aliquot of corresponding substance in basal media (E6 media (A1516401, ThermoFisher Scientific) with Penicillin/Streptomycin). For vehicle control, we used fresh basal media with 0.01% 200proof ethanol. To avoid sample swaps, we separated samples by condition with HDCs exposed to the same treatment in the same 6-well plate where individual lines were separated by well. Each well contained HDCs from one line and each 6-well plate contained six lines of HDCs in the same condition. Culture plates for ethanol treatment group were placed in a dedicated incubator that contained an open dish at the bottom with a solution of 80mM ethanol to create an equivalent concentration of ethanol atmosphere and prevent ethanol evaporation in the media.

value: hetergenous

value: multiplex

value: ethanol

tag: batch


title: Cyp1A2 strain exposed to 40 uM BaP, replicate 3

value: whole animal

value: Cyp1A2 strain

value: exposed to 40 uM BaP


title: CTLs, Sync-label Input, rep1

value: spleen

value: CD8+ cytotoxic T lymphocytes


title: HCT116_H3K27pr_ChIP

description: Library name: Sample 5

value: 5 mM propionate for 24 hours


title: control strain exposed to 40 uM BaP, replicate 3

value: control strain


title: batch4etoh-1_S19

description:
Library name: batch4_19
10X Genomics


title: Cyp1A1 strain exposed to 640 uM BaP, replicate 2

value: Cyp1A1 strain


title: Cyp1A1 strain exposed to 640 uM BaP, replicate 1

value: exposed to 640 uM BaP


title: batch4etoh-2_S23

description:
Library name: batch4_23
10X Genomics


title: NTLs, Sync-label Enrich, rep2

description: CD8+ naïve T lymphocytes with Sync-label treatment

value: CD8+ naive T lymphocytes

value: WT

value: Sync-label+


title: EGC, None, Colon_MP, rep1

value: Colon

value: Myenteric Plexus

value: EGC


title: siSMPLT

city: Montreal

first: Marc

middle: J

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

country: Canada

institute: Université de Montréal

description: Library name: siSMPLT

data_processing:
RNA-seq
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 37 (based on Ensembl 103)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 37
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: Colon

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: COLO 320DM

value: adenocarcinoma


title: batch4etoh-1_S18

description:
Library name: batch4_18
10X Genomics

value: hetergenous

value: multiplex

value: ethanol


title: CTLs, Sync-label Enrich, rep2

value: spleen


title: batch4etoh-2_S21

description:
Library name: batch4_21
10X Genomics


title: batch4etoh-2_S22

description:
Library name: batch4_22
10X Genomics


title: Cyp1A2 strain exposed to 40 uM BaP, replicate 1

value: whole animal

value: Cyp1A2 strain

value: exposed to 40 uM BaP


title: control strain exposed to 40 uM BaP, replicate 1

value: control strain


title: NTLs, Sync-label Enrich, rep1


title: batch4etoh-1_S20

description:
Library name: batch4_20
10X Genomics


title: HCT116_H3K9pr_ChIP

description: Library name: Sample 4

value: Colorectal carcinoma

value: Wild type

value: 5 mM propionate for 24 hours


title: HCT116_H3K4me3_ChIP

description: Library name: Sample 1


title: siL2

description: Library name: siL2


title: batch4caffeine-2_S16

description:
Library name: batch4_16
10X Genomics

value: caffeine


title: sino4

description: Library name: sino4

value: Colon


title: NTLs, Sync-label Input, rep1

description: CD8+ naïve T lymphocytes without Sync-label treatment

value: CD8+ naive T lymphocytes

value: WT

value: Sync-label-


title: Cyp1A1 strain exposed to 40 uM BaP, replicate 2

value: Cyp1A1 strain


title: Cyp1A2 strain exposed to 40 uM BaP, replicate 2


title: batch4caffeine-2_S15

description:
Library name: batch4_15
10X Genomics

value: hetergenous


title: siIDT

description: Library name: siIDT

value: COLO 320DM

value: adenocarcinoma


title: Cyp1A1 strain exposed to 40 uM BaP, replicate 1


title: siNT

description: Library name: siNT


title: Cyp1A1 strain exposed to 40 uM BaP, replicate 3


title: NTLs, Sync-label Input, rep2

value: spleen


title: control strain exposed to DMSO, replicate 3

value: whole animal

value: exposed to DMSO


title: HUDEP-2 MBD2Y178F Rep4

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description: Library name: HUDEP-2 MBD2Y178F Rep4

data_processing:
For HUDEP-2 RNA-seq, sequencing data was processed using the nf-core RNAseq workflow (v3.14) with the Kallisto pseudoaligner. Kallisto parameters were set with 100 bootstrap samples, and fragment length set to 75 with a standard deviation of 2 where single end reads were used.
Assembly: hg38
Supplementary files format and content: tsv abundance file - output from kallisto

growth_protocol: Human umbilical cord blood derived 2 (HUDEP2) cells were grown in serum free expansion medium (SFEM, StemSpan) supplemented with 50 ng/µL stem cell factor (In Vitro Technologies), 3 IU/mL erythropoietin (Lonza), 10 µM dexamethasone (Sigma-Aldrich), 1 µg/mL doxycycline (Sigma-Aldrich), and 0.5 mg/mL PSG. All cell cultures were incubated at 37°C in a water jacketed incubator with 5% CO2. CD34+ cells cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
HUDEP2 cells were harvested and washed in 1× PBS before lysis and RNA was isolated using TRI™ reagent (Sigma-Aldrich) according to the manufacturer’s instructions. RNA was purified using the RNeasy® Mini Kit and RNase-free DNase set (Qiagen) according to the manufacturer’s instructions. For CD34 cells, RNA samples were extracted with QIAGEN RNeasy micro Plus kit.
Stranded mRNA prep (Illumina) sequencing libraries were generated and RNA sequencing was performed by the Ramaciotti Centre for Genomics using NextSeq 1×75bp high output or NovaSeq 2x100bp flow cells (Illumina). For CD34 cells, RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CD34+ cell were electroporated with Cas9+ NT/UHRF1 gRNA1

value: erythroid progenitor cell line

value: MBD2 Y178F


title: batch4caffeine-2_S13

description:
Library name: batch4_13
10X Genomics

value: multiplex


title: control strain exposed to DMSO, replicate 2

value: control strain


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 2

city: Darlinghurst

first: Shabarni

last: Gupta

address: Precinct Loading Dock,, West Street (off Burton Street)

institute: Garvan Institute of Medical Researc

description: Library name: S7

data_processing:
The SpaceRanger Analysis Pipeline (v2.0.0, 10x Genomics) was used to align the sequencing reads (fastq) to a pre-built reference genome (10x Genomics) containing both the human and mouse genomes (GRCh38 + mm10) and gene expression quantified in each cell. Quality-control (QC) statistics were computed using the STutility package. Voxels with a library size < 3000 UMI were removed and remaining voxels manually curated to remove those that were disconnected from the main tissue section. Human and mouse genes were separated to create two datasets per sample, one measuring the expression of human genes at each voxel, pertaining to tumor cells, and the other measuring expression of mouse genes, pertaining to cells from the microenvironment. Genes were removed if they were detected in less than 10 voxels. Finally each dataset was filtered to remove voxels with low library diversity for a given genome (<1000 human genes detected, <300 mouse genes detected). After QC filtering, the human dataset comprised of 14,819 genes measured at 1170 and 1105 voxels for each tumor, while the mouse dataset comprised of 12,119 genes measured at 1150 and 1079 voxels in TX and TX section respectively. Remaining datasets were each normalized to 10,000 reads per voxel and log transformed. To correct for dropout (human dataset = 69.8% zeros, mouse dataset = 90.6% zeros) data was smoothed with the manifold smoothing method MAGIC. Cell-cycle phase assignment was performed using the CellCycleScoring function in Seurat (72) with previously defined S-phase and G2M-phase gene lists (71). Spatial plots throughout the manuscript were generated using STUtility.
Assembly: GRCh38 + mm10
Supplementary files format and content: .h5ad file with normalized cell counts, spatial coordinates of each cell, and relevant cell and sample-level metadata
Library strategy: Spatial Transcriptomics

organism:
Homo sapiens
Mus musculus

source_name: Primary tumour

extract_protocol:
Cryo-sectioning was done on OCT embedded and snap frozen tissue samples at 10um thickness and placed on cold Visium slide arrays. The sections were adhered by swiftly warming of the backside of the slide. The slides were then kept in -80°C less than 4 weeks before processing accordingly. In short, the slides were first warmed at 37°C for one minute and then immersed in pre-chilled methanol (VWR EU, 20847.307) for 30 minutes at -20°C for fixation. Staining with hematoxylin and eosin was carried out by one min of drying of the tissues with 500uL of isopropanol (Fisher Scientific, A461-1) followed by air drying until sections turned white. Around 1 mL of with Mayer’s hematoxylin (Agilent, S23309) was pipetted onto the slides and treated for four minutes. The slides were then washed in nuclease free water followed by a two-minute incubation with bluing buffer (Agilent, CS702), washed again and then counterstained with buffered eosin (Sigma-Aldrich, HT110216, 1:10 dilution in Tris-Acetic Acid Buffer). The slides were air dried for about 2 minutes and then warmed for 5 minutes at 37°C before mounting using 85percent Glycerol (Merck, 104094) and a coverslip. Bright field histology images were obtained using a 20X objective on Zeiss microscope using the Metafer VSlide system and the images were processed by the VSlide software. The images were extracted as jpgs for downstream analysis. After imaging, the coverslip and the remaining glycerol was washed off in Milli-Q water and the slides were attached in plastic cassettes included in the reagent kit and first subjected to 20 minutes of permeabilization at 37°C to let the mRNA reach the probes on the slide surface for binding. The protocol was then followed without deviations to create amplified libraries which in the end were individually indexed using the Dual Index Kit TT SetA, (PN-1000215, 10X Genomics), quality controlled on a BioAnalyzer instrument and concentrations were measured using Qubit DNA HS. The libraries were pooled equimolarly (2nM) and sequenced on the Nextseq 2000 (Illumina platform). To reach the appropriate read depth the recommended number of reads per ST spot were applied according to the protocol.
Spatial transcriptomics was conducted using 10X Visium Spatial Gene Expression Slide and Reagent Kit, 16 rxns (PN-1000184), according to the protocol detailed in document CG000239RevD for the TNBCs and CG000239RevE for the Xenografts, available in 10X Genomics demonstrated protocols.

value: Primary tumour


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 1

description: Library name: S5


title: batch4etoh-1_S17

description:
Library name: batch4_17
10X Genomics

value: ethanol


title: HUDEP-2 MBD2Y178F Rep3

description: Library name: HUDEP-2 MBD2Y178F Rep3


title: control strain exposed to DMSO, replicate 1


title: HUDEP-2 MBD2Y178F Rep5

description: Library name: HUDEP-2 MBD2Y178F Rep5


title: batch4caffeine-2_S14

description:
Library name: batch4_14
10X Genomics

value: caffeine


title: batch4caffeine-1_S12

description:
Library name: batch4_12
10X Genomics


title: HUDEP-2 MBD2Y178F Rep2

description: Library name: HUDEP-2 MBD2Y178F Rep2


title: HUDEP-2 WT Rep5

description: Library name: HUDEP-2 WT Rep5


title: batch4caffeine-1_S11

description:
Library name: batch4_11
10X Genomics


title: HUDEP-2 WT Rep4

description: Library name: HUDEP-2 WT Rep4


title: batch4caffeine-1_S10

description:
Library name: batch4_10
10X Genomics


title: Cyp1A1 strain exposed to DMSO, replicate 2


title: Cyp1A2 strain exposed to DMSO, replicate 2

value: Cyp1A2 strain


title: HUDEP-2 MBD2Y178F Rep1

description: Library name: HUDEP-2 MBD2Y178F Rep1


title: batch4caffeine-1_S9

description:
Library name: batch4_9
10X Genomics


title: Cyp1A2 strain exposed to DMSO, replicate 1


title: HUDEP-2 WT Rep1

description: Library name: HUDEP-2 WT Rep1

value: WT


title: batch4nicotine-2_S8

description:
Library name: batch4_8
10X Genomics

value: nicotine


title: 6068-KW-9

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

data_processing:
Reads aligned using BWA
Reads with mapping quality < 20 were removed using Samtools
Duplicates were removed & sorted by read-name using SortSam and MarkDuplicates
BAM files converted to BED files
1 kb windows made of PY79 genome using BEDtools
Counts in each window were quantified (annotateBed from BEDtools)
Normalized read counts by total number of reads and log2-transformed
Assembly: ASM49748v1
Supplementary files format and content: .txt files containing read counts in 1 kB windows for each sample

organism: Bacillus subtilis

source_name: whole cells

growth_protocol: OD=0.05 of WT cells were grown at 30C with shaking. Cells were collected once the densities reached OD=0.65-0.9.

extract_protocol: Genomic DNA extraction was performed.


title: batch4nicotine-2_S7

description:
Library name: batch4_7
10X Genomics


title: batch4nicotine-2_S5

description:
Library name: batch4_5
10X Genomics


title: Cyp1A2 strain exposed to DMSO, replicate 3


title: batch4nicotine-1_S2

description:
Library name: batch4_2
10X Genomics


title: Exp2_NTERT2G_TH2IL22_5

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

data_processing:
Preprocessing was performed using the seq2science rna-seq workflow (v0.9.5), performing the steps detailed below.
Reads were trimmed using fastp (v0.20.1, default settings).
Trimmed reads were mapped using STAR (v2.7.6a).
Read count extraction was performed using HTSeq-count (v0.12.4)
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text files include counts for each NHEK sample
Supplementary files format and content: tab-delimited text files include counts for each N/TERT-2G sample

source_name: Human epidermal equivalent

growth_protocol: NHEK were seeded to the transwell system for human epidermal equivalent (HEE) generation from the liquid nitrogen directly. N/TERT-2G were cultured in CnT-PR (CELLnTEC) in a humidified incubator with 5% CO2 at 37C. For HEEs cells were submerged in CnT-PR for 3 days and air exposed in CnT-PR-3D (CELLnTEC) for 8 days for NHEK and 10 days for N/TERT-2G.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. Total RNA Kit I (Omega Bio-Tek)
400ng of RNA per sample and the KAPA RNA HyperPrep kit with RiboErase (human/mouse/rat [HMR]) (Kapa Biosystems) were used. Fragmentation and priming was executed at 94°C for 6 min. A 1.5-μM stock (NEXTflex DNA barcodes; Bioo Scientific) was used for adapter ligation. Eight cycles of library amplification and a 0.8× bead-based cleanup. High-sensitivity DNA bioanalyzer (Agilent Technologies) was used to determine the library size, and to measure the library concentration the DeNovix double-stranded DNA (dsDNA) high-sensitivity assay was performed. Sequencing was done with the Illumina NextSeq 500 instrument and 42bp-paired end reads were generated.

treatment_protocol: Cytokines were added in the last 72 hours in the following concentrations: IL-4 / IL-13 / IL-17A 50ng/mL and IL-22 10ng/mL

value: Human epidermal equivalent

value: Foreskin keratinocytes

value: TH2 + IL22

tag: treatment time

value: Day 7-10 ALI


title: batch4nicotine-1_S4

description:
Library name: batch4_4
10X Genomics

value: hetergenous


title: Exp2_NTERT2G_TH2IL17_2

value: TH2 + IL17


title: Exp2_NTERT2G_TH2IL22_4


title: HUDEP-2 WT Rep3

description: Library name: HUDEP-2 WT Rep3


title: 6068-KW-5


title: HUDEP-2 WT Rep2

description: Library name: HUDEP-2 WT Rep2


title: 6068-KW-7


title: Exp2_NTERT2G_TH2IL22_6


title: batch4nicotine-2_S6

description:
Library name: batch4_6
10X Genomics


title: Exp2_NTERT2G_TH2IL17_6


title: Cyp1A1 strain exposed to DMSO, replicate 1

value: whole animal

value: Cyp1A1 strain

value: exposed to DMSO


title: batch4nicotine-1_S3

description:
Library name: batch4_3
10X Genomics

value: multiplex


title: Exp2_NTERT2G_TH2IL17_5


title: batch4nicotine-1_S1

description:
Library name: batch4_1
10X Genomics


title: 6068-KW-8


title: Cyp1A1 strain exposed to DMSO, replicate 3


title: 6068-KW-6


title: 6068-KW-4


title: 6068-KW-2


title: batch3etoh-2_S22

description:
Library name: batch3_22
10X Genomics


title: 6068-KW-3


title: batch3etoh-1_S20

description:
Library name: batch3_20
10X Genomics


title: Exp2_NTERT2G_TH2_7


title: Exp2_NTERT2G_TH2_5


title: batch3etoh-1_S19

description:
Library name: batch3_19
10X Genomics


title: 6068-KW-1


title: Exp2_NTERT2G_Control_5

value: Control


title: batch3etoh-2_S23

description:
Library name: batch3_23
10X Genomics


title: Exp2_NTERT2G_Control_7


title: 6068-KW-15

description: KJW280 replicate 3 with 0.1% xylose induction

growth_protocol: OD=0.05 of WT cells were grown at 30C with shaking. Once the culture reached OD=0.2, treatment was administered. Cells were collected once the densities reached OD=0.65-0.9.

tag: replicate

value: ccrZ-, amyE::Pxyl-ccrZ-D166A-cat


title: batch3etoh-1_S18

description:
Library name: batch3_18
10X Genomics

value: ethanol


title: Exp2_NHEK38_TH2IL22_2

value: NHEK

value: Abdominal epidermal keratinocytes

value: Day 5-8 ALI


title: Exp1_NHEK38_TH2IL22_3


title: batch3caffeine-2_S16

description:
Library name: batch3_16
10X Genomics

value: caffeine


title: 6068-KW-12

description: KJW119 replicate 3 with 0.1% xylose induction

value: ccrZ-, amyE::Pxyl-ccrZ-cat


title: batch3caffeine-2_S15

description:
Library name: batch3_15
10X Genomics


title: batch3caffeine-2_S17

description:
Library name: batch3_17
10X Genomics


title: 6068-KW-14

description: KJW280 replicate 2 with 0.1% xylose induction


title: batch3caffeine-1_S14

description:
Library name: batch3_14
10X Genomics


title: 6068-KW-11

description: KJW119 replicate 2 with 0.1% xylose induction


title: Exp1_NHEK38_TH2IL22_1

value: Human epidermal equivalent


title: batch3etoh-2_S21

description:
Library name: batch3_21
10X Genomics


title: 6068-KW-10

description: KJW119 replicate 1 with 0.1% xylose induction


title: tumor case 40

type: genomic

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols.

data_processing: Raw data (CEL files) were processed using the R package EaCoN (v0.3.6-2) with SEQUENZA as segmentation algorithm. L2R files in CBS format were used as input for GISTIC (v2.0.23) to identify regions that are significantly amplified or deleted across all samples (confidence level 0.90, focal length cutoff 0.5, q-value threshold 0.1).

label: biotin

source_name: tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

value: tumor

tag: diagnosis

value: FL

tag: gender

value: male

tag: biopsy


title: batch3caffeine-1_S13

description:
Library name: batch3_13
10X Genomics

value: hetergenous


title: tumor case 35

value: MZL

value: female

value: Punch


title: Exp1_NHEK38_TH2IL17_1

tag: cell line

value: TH2 + IL17


title: batch3nicotine-2_S12

description:
Library name: batch3_12
10X Genomics

tag: cell type

value: multiplex

value: nicotine


title: Exp2_NHEK38_TH2IL17_3


title: Exp2_NHEK38_TH2_3


title: batch3nicotine-2_S11

description:
Library name: batch3_11
10X Genomics

tag: genotype


title: tumor case 34

value: Resect


title: Exp2_NTERT2G_Control_6

value: Foreskin keratinocytes

tag: treatment

value: Control


title: Exp1_NHEK38_TH2_2

tag: tissue

value: NHEK

value: Abdominal epidermal keratinocytes

value: Day 5-8 ALI


title: batch3nicotine-2_S10

description:
Library name: batch3_10
10X Genomics


title: 6068-KW-13

description: KJW280 replicate 1 with 0.1% xylose induction

tag: strain

value: ccrZ-, amyE::Pxyl-ccrZ-D166A-cat


title: tumor case 33

value: tumor


title: tumor case 32


title: batch3nicotine-1_S9

description:
Library name: batch3_9
10X Genomics


title: Exp1_NHEK38_TH2_1

value: Human epidermal equivalent


title: tumor case 31

value: male


title: batch3nicotine-1_S8

description:
Library name: batch3_8
10X Genomics

value: hetergenous


title: Exp2_NHEK38_Control_3


title: batch3nicotine-1_S7

description:
Library name: batch3_7
10X Genomics


title: Exp1_NHEK38_Control_2


title: tumor case 30

value: FL


title: batch3control-2_S5

description:
Library name: batch3_5
10X Genomics

value: control


title: tumor case 27

value: MZL

value: Punch


title: tumor case 29

value: female


title: batch3control-2_S6

description:
Library name: batch3_6
10X Genomics

value: multiplex


title: batch3control-1_S3

description:
Library name: batch3_3
10X Genomics


title: tumor case 28

value: Resect


title: Exp2_NHEK37_Control_4


title: Exp2_NHEK37_TH2IL22_3

value: TH2 + IL22


title: batch3control-1_S2

description:
Library name: batch3_2
10X Genomics


title: batch3control-2_S4

description:
Library name: batch3_4
10X Genomics


title: tumor case 24


title: batch3control-1_S1

description:
Library name: batch3_1
10X Genomics


title: tumor case 26


title: Exp2_NHEK37_TH2_4


title: tumor case 25


title: gmds +/- replicate3, 2 year

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

description: Instrument model: DNBSEQ-G99

data_processing:
Fastq files were align to the reference genome GRCz11 - danRer11 using STAR with default parameters.
Data analysis (raw counts) were conducted with Homer (http://homer.ucsd.edu/homer/ngs/rnaseq/) .
Assembly: GRCz11 - danRer11
Supplementary files format and content: tab-delimited text file of sequencing raw counts

organism: Danio rerio

source_name: eye

growth_protocol: Crispr generated gmds +/- mutant line were raised in the fish facility to 1 yr and 2 yrs old. Live fishes were ethaunized with tricane before dissection from the head to remove the 2 eyes from each animal using sterile forcepts and lab blade

extract_protocol:
Frozen eye tissue were grinded on dry-ice to powder and RNA extracted using RNAqueous Phenol-free Total RNA extraction kit and protocol form Thermofisher. 600ul of the lysis buffer used to extract total RNA. Total RNA extracted were further purified using Turbo DNA-free kit before library preparation. Starting concentration of total RNA is 500ng with RIN values not less than 7.
RNA libraries for RNAseq were prepared using NEBNext kit Poly(A) mRNA magnetic isolation protocol. Further library prepataion were done using using MGIEasy RNA Directional Library prep kit following manufacturer's protocol.
Library were sequenced using the DNBSEQ-G99 sequencing plateform.

treatment_protocol: Eye tissue were put in cyovials and flash freezed in liquid nitrogen, then stored on dy-ice in -80C simultenously for each group before RNA extraction.

value: eye

value: gmds +/-

tag: age

value: 2 year


title: Day_28_Vehicle_2

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

description: Library name: Vehicle I73T-2

data_processing:
RNA-SEQ Fastq files from paired end reads were trimmed, processed and evaluated for quality control using fastp. Resulting files were aligned against the mouse genome (mm10) using bowtie2 and quantified via featureCounts. Duplicate reads and chimeric fragments were flagged and excluded from the analysis.
scRNA-seq Fastq files were aligned to the mm10 reference genome using STARSolo
Downstream processing was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: tab seperated files

source_name: Lung

extract_protocol: scRNASeq Libraries were prepared using Illumina stranded total RNA accordine to manufacture instructions.  Total RNA for RNA-Seq was processed from cell pellets using the RNAeasy kit from Qiagen following manufacture instructions.

treatment_protocol: For scRNA-seq single cell suspensions were prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads. For flow cytometery RNA-seq single cell suspension were stainined with an antibody mix to identify AT2 cells and transitional AT2 cells. AT2 cells were identified as CD45-CD31-Epcam+CD104-MHCII hiCD51- and transitional At2 cells  CD45-CD31-Epcam+CD104-MHCII hiCD51+. Dead cells were excluded by Dapi staining. iAT2s were collected from matrigel dropplets via enzymatic digestion followed by immediate freezing of the cell pellets

value: Lung

value: Vehicle


title: Day 28_Metformin

description: Library name: Metformin I73T

value: Metformin


title: tumor case 23

value: tumor


title: Exp1_NHEK38_Control_1

value: Human epidermal equivalent

value: NHEK

value: Abdominal epidermal keratinocytes

value: Control


title: Day_28_Vehicle_1

description: Library name: Vehicle I73T-1


title: tumor case 22

value: MZL

value: male


title: gmds +/- replicate1, 2 year

description: Instrument model: DNBSEQ-G99


title: tumor case 21


title: tumor case 19

value: female

value: Punch


title: WT replicate3, 2 year

description: Instrument model: DNBSEQ-G99

value: WT


title: WT replicate2, 2 year

description: Instrument model: DNBSEQ-G99


title: tumor case 16

value: Resect


title: WT replicate1, 2 year

description: Instrument model: DNBSEQ-G99

value: eye


title: tumor case 18


title: gmds +/- replicate3, 1 year

description: Instrument model: DNBSEQ-G99

value: gmds +/-

value: 1 year


title: tumor case 15


title: gmds +/- replicate1, 1 year

description: Instrument model: DNBSEQ-G99


title: tumor case 13

value: FL


title: gmds +/- replicate2, 1 year

description: Instrument model: DNBSEQ-G99


title: WT replicate3, 1 year

description: Instrument model: DNBSEQ-G99


title: tumor case 12


title: tumor case 11


title: tumor case 10


title: tumor case 09


title: Healthy ExVivoBlood_exosomes_rep3

type: RNA

city: WuHan

first: xinghua

last: Liao

address: Wuhan University of Science and Technology, Hongshan District, Wuhan City, Hubei Province, China

description: Gene expression of exosomes in blood of TNBC patients

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Using feature extraction software 11.0.1.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid:012391_D_20060331) to analyze scanned images in order to obtain background-subtracted and spatially detrended processed signal intensities. The raw data is log-transformed, and the chip data is normalized to eliminate systematic errors.

source_name: Peripheral Blood, exosomes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Affymetrix) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Blood RNA Purification kit (TIANGEN, Beijing) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Blood samples were taken from TNBC patients and serum was separated after coagulation by centrifugation at 2000 g for 10 min at 4 °C. Serum samples were mixed with PBS in a 1:1 ratio. To isolate exosomes, they were centrifuged at 100,000 g for 90 min at 4 °C using ultracentrifuge.

value: exosomes from peripheral blood

tag: disease state

value: healthy


title: ICOS KO_2

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

description:
Library name: Sample_5
21079R-01-31V1_S65

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: sorted ILC2s


title: ICOS KO_3

description:
Library name: Sample_6
21079R-01-32V1_S66


title: ICOS KO_1

description:
Library name: Sample_4
21079R-01-30V1_S64


title: Healthy ExVivoBlood_exosomes_rep1

institute: Wuhan University of Science and Technology


title: ExVivoBlood_exosomes_rep3

value: patients diagnosed with triple negative breast cancer


title: ExVivoBlood_exosomes_rep2


title: sample1

city: Lyon

first: Gauthier

last: Toulouse

address: 8 avenue Rockfeller

country: France

institute: CNRS

description: Library name: Tomato_S10

data_processing:
The demulitplexing, barcodes processing, genes counting and aggregation were made using STARSolo (v2.7.9)
The data processing was made using Seurat (v5.0.1)
Assembly: GRCg6a.105
Supplementary files format and content: Tab-separated values and matrix files

organism: Gallus gallus

source_name: Limb

extract_protocol:
Chicken embryo somites were electroporated at E2.5 at the level of the forelimb with a plasmid coding for a constitutive nuclear dTomato and a mVenus under the control of a TCF/LEF-responding promoter. Embryos were screened for good electroporation 2 days later (E4.5). Nicely electroporated limb bud were dissected and digested with Dispase and Trypsin accoding to Ling et al. 2019, Nat. Cell Biol.). The single cell preparation was then shorted for the dTomato fluorescence and dTomato+ cells were submitted to 10x genomics single RNA-seq
Libraries were prepared according to 10x 3'expression V2 kit  & Illumina protocols

value: Limb

value: Myoblasts

tag: developmental stage


title: WT_3

description:
Library name: Sample_3
21079R-01-27V1_S63

value: BALB/C BYJ


title: ExVivoBlood_exosomes_rep1


title: WT_2

description:
Library name: Sample_2
21079R-01-26V1_S62


title: tumor case 07

value: tumor

value: MZL

value: male


title: Tgrp (T2test in scripts)

city: GIF-SUR-YVETTE

first: Jacques

last: Montagne

address: 1 AVENUE DE LA TERRASSE

data_processing:
cellranger-6.0.1
Assembly: dmel_r6.42
Supplementary files format and content: Tab separated values and matrix files

organism: Drosophila melanogaster

source_name: Tumor, group of 6

growth_protocol: Flies were raised on standard medium as described in the Material and Method section.

extract_protocol:
Tumors were dissected on ice in Ringer buffer, rinsed twice ice-cold Ringer baths and the extracellular matrix was digested by gentle pipetting for 3-5 minutes with 20µL 5X Trypsin (PAN BIOTECH P10-022100) twice diluted. Efficient digestion was promptly checked under fluorescent dissecting microscope. Consequently, for each sample, 1X Ringer buffer was added up to 1.5mL and each tube was filtered through 30µm filters (Sysmex CellTrics). Tubes were centrifugated for 4 minutes at 1000G, at 4°C; 1mL of supernatant was discarded and the same volume of fresh 1X Ringer buffer was added. A second centrifugation (4 minutes, 1000G, 4°C) was done and after carefully removing all supernatant, pellets were gently resuspended in 30µL 1X Ringer buffer for sequencing. The whole sample preparation procedure did not exceed 20 minutes.
Cell suspension was loaded into the Chromium Controller using a Chromium Next GEM Single Cell 3’ v3.1 kit (10x Genomics) to generate a droplet emulsion. cDNA was purified and libraries were prepared, according to the manufacturer’s recommendations. Single- cell libraries were sequenced on a NextSeq 2000 Instrument (Illumina) using a P2-100 cycles kit. FastQ files were analyzed using the Cell Ranger software (10X Genomics, version 6.0.1), including alignment, filtering and quantitation of reads on the Drosophila genome r6.42 and generation of feature-barcode matrices

treatment_protocol: Tumorous flies were heat-shocked at 37°C for 2-hrs 2-3 days after adult eclosion. At least 21-dpi flies were selected based on GFP fluorescence through the abdomens.

value: Tumor, group of 6

value: Tumor

value: yw,HS-flp, HS-mflp5; esg-gal4,UAS-flybow; FRT82B,Tub-Gal80 and yw,HS-flp; UAS-RasV12; FRT82B,Apc2N175K,ApcQ8

value: heat-shock at 37°C for 2-hrs 2-3 days after adult eclosion


title: Healthy ExVivoBlood_exosomes_rep2

value: female


title: tumor case 05

value: Resect


title: WT replicate2, 1 year

description: Instrument model: DNBSEQ-G99

value: eye

value: WT

value: 1 year


title: Tind6 (T1test in scripts)

source_name: Tumor, individual

value: Tumor, individual


title: tumor case 08

value: Punch


title: tumor case 06


title: Tind4 (JAMO80 in scripts)


title: WT replicate1, 1 year

description: Instrument model: DNBSEQ-G99


title: tumor case 04

value: FL


title: Tind3 (JAMO78 in scripts)


title: tumor case 03


title: tumor case 02


title: Tind2 (JAMO75 in scripts)


title: human iSP by LDN

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample10
10x Genomics

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 7.1.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: ventral stromal progenitor from human iPSC

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.


title: Tind1 (JAMO74 in scripts)


title: WT_1

description:
Library name: Sample_1
21079R-01-25V1_S61

value: lung

value: sorted ILC2s


title: Tind5 (JAMO81 in scripts)


title: CLDEcell-siNeg-72h

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

description: Gene expression after 72h transfection with siKrt15

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Microarray 8 x 60K Ver2.0 for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner G4900DA (Agilent Technologies) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 11.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CLDE cell, siNeg, 72h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop One Spectrophotometer.

growth_protocol: The mouse cervical loop-derived dental epithelial cell line CLDE was cultured in keratinocyte serum-free medium (Life Technologies, Carlsbad, CA, USA) in a humidified atmosphere containing 5% CO2 at 37℃ (Chiba et al. 2020b).

extract_protocol: Total RNA was extracted from CLDE cells using RNeasy Kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s instructions.

treatment_protocol: For RNA interference, CLDE cells were cultured until 80% confluency, and transfected with ON-TARGETplus non-targeting control siRNAs (siNeg, Horizon Discoveries, Cambridge, United Kingdom) and Krt15 mouse siRNA oligo duplex (siKrt15, Horizon Discoveries, Cambridge, United Kingdom) using Lipofectamine RNAiMax Reagent (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s protocol. Cells were harvested and analyzed at 72 h post-transfection.

value: dental epithelium

tag: treatment/time point

value: after 72h transfection with siKrt15


title: CLDEcell-mock-72h

description: Gene expression after 72h transfection with mock

source_name: CLDE cell, mock, 72h

value: cervical loop-derived dental epithelial cell line CLDE

value: after 72h transfection with mock


title: CLDEcell-siKrt15-72h

description: Gene expression after 72h transfection with siNeg

source_name: CLDE cell, siKrt15, 72h

value: after 72h transfection with siNeg


title: tumor case 01

value: tumor

value: male


title: human iSP by BMP4

description:
Library name: Sample11
10x Genomics

value: ventral stromal progenitor from human iPSC


title: donor 8, female, primary human macrophages CaptAvidin treated

status: Public on Jun 23 2025

first: Kara

last: Spiller

state: Pennsylvania

address: 3141 Chestnut Street, Bossone 718

institute: Drexel University

description: Library name: f4_M0_capt

data_processing:
Sequencing performed by Singulomics Corporation
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38/hg38
Supplementary files format and content: .xls file contains FPKM values for each sample

source_name: primary human macrophage

growth_protocol: Monocytes were cultured at 1x10^6 cells/mL in RPMI supplemented with 10% HS and 1% P/S on non-tissue-culture treated polystyrene plates (Corning). Monocytes were differentiated into unactivated macrophages by adding 20 ng/mL of macrophage colony-stimulating factor (M-CSF, Peprotech) for up to 7 days, with media changes on days 3 and 5.

extract_protocol:
Total RNA was extracted using the RNAqueous Micro Kit (invitrogen) according to the manufacturer’s protocol but heating the Elution Solution to 65°C.
mRNA was extracted using poly-T oligo-attached magnetic beads, then fragmented. cDNA was quantified using real-time PCR and fragment size was measured using a Bioanalyzer. The cDNA library was then constructed and analyzed with Qubit. Quantified libraries were then pooled and sequenced on Illumina platforms, based on sequencing by synthesis.

treatment_protocol: Appropriate doses of soluble biotin or avidin variants were added directly to the media (RPMI + 10% HS + 1% P/S + M-CSF) for macrophages from 8 donors (4 male and 4 female) on day 6 of culture and cultured for 24 hours.

value: primary human macrophage

tag: Sex

value: female

value: CaptAvidin


title: donor 7, female, primary human macrophages avidin treated

description: Library name: f3_M0_avidin

value: avidin


title: donor 7, female, primary human macrophages control

description: Library name: f3_M0


title: gmds +/- replicate2, 2 year

description: Instrument model: DNBSEQ-G99

value: eye

value: gmds +/-

value: 2 year


title: donor 6, male, primary human macrophages streptavidin treated

description: Library name: m4_M0_strep

value: streptavidin


title: donor 8, female, primary human macrophages control

description: Library name: f4_M0


title: donor 7, female, primary human macrophages streptavidin treated

description: Library name: f3_M0_strep


title: donor 6, male, primary human macrophages control

description: Library name: m4_M0


title: donor 6, male, primary human macrophages avidin treated

description: Library name: m4_M0_avidin


title: Exp2_NHEK37_TH2IL17_4

value: Human epidermal equivalent

value: NHEK

value: Abdominal epidermal keratinocytes

value: TH2 + IL17

value: Day 5-8 ALI

tag: batch


title: WT

description: Library name: WT

value: Lung

value: WT

value: Vehicle


title: donor 5, female, primary human macrophages streptavidin treated

description: Library name: f2_M0_strep


title: donor 5, female, primary human macrophages CaptAvidin treated

description: Library name: f2_M0_capt


title: donor 4, male, primary human macrophages low dose of biotin

description: Library name: m3_M0_bio_lo

value: male

value: low dose biotin


title: donor 4, male, primary human macrophages high dose of biotin

description: Library name: m3_M0_bio_hi

value: primary human macrophage

value: high dose biotin


title: donor 4, male, primary human macrophages streptavidin treated

description: Library name: m3_M0_strep


title: donor 3, male, primary human macrophages high dose of biotin

description: Library name: m2_M0_bio_hi


title: donor 5, female, primary human macrophages avidin treated

description: Library name: f2_M0_avidin

value: female

value: avidin


title: donor 3, male, primary human macrophages avidin treated

description: Library name: m2_M0_avidin


title: Amniotic fluid A10149

city: Shenzhen

first: xiaojin

last: luo

state: China (Mainland)

address: 6 Ailong Road SHENZHEN

institute: Longgang District maternity & Child Heal

description: Hybridized to Cytoscan750K

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CHAS 4.3.0) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CHAS 4.3.0. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Amniotic fluid

extract_protocol: Genomic DNA is extracted from prenatal specimens or aborted tissue using the Qiagen DNA Blood mini kit. The quality and quantity of DNA were evaluated by spectrophotometer and agarose gel electrophoresis.

value: Female


title: donor 4, male, primary human macrophages CaptAvidin treated

description: Library name: m3_M0_capt

value: CaptAvidin


title: donor 5, female, primary human macrophages control

description: Library name: f2_M0


title: donor 2, male, primary human macrophages streptavidin treated

description: Library name: m1_M0_strep

value: streptavidin


title: donor 6, male, primary human macrophages CaptAvidin treated

description: Library name: m4_M0_capt


title: donor 3, male, primary human macrophages CaptAvidin treated

description: Library name: m2_M0_capt


title: donor 3, male, primary human macrophages control

description: Library name: m2_M0


title: donor 3, male, primary human macrophages streptavidin treated

description: Library name: m2_M0_strep


title: donor 1, female, primary human macrophages high dose of biotin

description: Library name: f1_M0_bio_hi


title: Amniotic fluid A12042

description: Hybridized to Cytoscan750K


title: donor 3, male, primary human macrophages low dose of biotin

description: Library name: m2_M0_bio_lo


title: Amniotic fluid CMA230075

description: Hybridized to Cytoscan750K


title: donor 1, female, primary human macrophages streptavidin treated

description: Library name: f1_M0_strep


title: donor 1, female, primary human macrophages control

description: Library name: f1_M0


title: donor 2, male, primary human macrophages control

description: Library name: m1_M0


title: donor 1, female, primary human macrophages CaptAvidin treated

description: Library name: f1_M0_capt


title: human kidney biopsy, disease, sample 5

first: Katalin

last: Susztak

address: 12-123 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Renal, Electrolyte, and Hypertension Division, Department of Medicine

institute: University of Pennsylvania, Perelman School of Medicine

description:
Library name: KRAD70
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation of raw fastq files was performed using cellranger-6.0.1 (include introns = True).
Initial data processing and quality control was performed using Seurat 4.0.2. Cells were filtered based on mitochondrial genes (< 15%) and nCounts/nFeatures (> 300).
Doublets were identified using DoubletFinder 2.0.
Ambient RNA correction was performed using SoupX 1.5.0.
Final sample merging, integration, data cleaning, and cell type annotation was performed in Scanpy 1.9 using scVI 0.19.0 for integration in an iterative clustering approach (see our manuscript for more details).
Assembly: Mouse: mm10-3.0.0. Human: hg19-3.0.0
Supplementary files format and content:
Raw counts after final filtering in matrix format (.csv).
Human: Filtered matrix after Cell ranger (.h5)
Additional metadata including cell type annotation (.csv)

source_name: Kidney

extract_protocol:
Mouse: Nuclei were extracted using a lysis buffer composed of Tris-HCl, NaCl, MgCl2, 10% NP40, and an RNAse inhibitor (40 U/ul). Frozen mouse kidney was finely chopped into 1-2 mm segments using a razor blade in 500 µl of the lysis buffer. This minced tissue was then placed into a gentleMACS C tube and homogenized with 1 ml of lysis buffer in a gentleMACS homogenizer using the Multi_E_01 and Multi_E_02 programs for 30 seconds. The homogenate was then passed through a 40 µm strainer (08-771-1, Fisher Scientific) and the strainer was rinsed with 2 ml of wash buffer (PBS 1X + 10% BSA (50 mg/ml) + RNAse inhibitor (40 U/ul)). The nuclei were spun down at 500xg for 5 minutes at 4°C, and the resulting pellet was re-suspended in wash buffer and filtered again through a 40 µm Flowmi cell strainer (BAH136800040-50EA, Sigma Aldrich). The quality of the nuclei was assessed, and their number was counted. Following the manufacturer's instructions, 10,000 to 30,000 cells (varied per sample) were loaded into the Chromium Controller using a Chromium Next GEM chip G Single Cell Kit to create single-cell gel beads in an emulsion.
Human: Nuclei were extracted using a lysis buffer composed of Tris-HCl, NaCl, MgCl2, 10% NP40, and an RNAse inhibitor (40 U/ul). Frozen biopsy tissue weighing 1-3 mg was finely chopped into 1-2 mm segments using a razor blade in 500 µl of the lysis buffer. This minced tissue was then placed into a gentleMACS C tube and homogenized with 1 ml of lysis buffer in a gentleMACS homogenizer using the Multi_E_01 and Multi_E_02 programs for 30 seconds. The homogenate was then passed through a 40 µm strainer (08-771-1, Fisher Scientific) and the strainer was rinsed with 2 ml of wash buffer (PBS 1X + 10% BSA (50 mg/ml) + RNAse inhibitor (40 U/ul)). The nuclei were spun down at 500xg for 5 minutes at 4°C, and the resulting pellet was re-suspended in wash buffer and filtered again through a 40 µm Flowmi cell strainer (BAH136800040-50EA, Sigma Aldrich). The quality of the nuclei was assessed, and their number was counted. Following the manufacturer's instructions, 10,000 to 30,000 cells (varied per sample) were loaded into the Chromium Controller (10X Genomics, PN-120223) using a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to create single-cell gel beads in an emulsion.
Mouse: Library was generated following the manufacturer's instructions (Chromium Next GEM Single Cell 3′ GEM Kit v2) for synthesizing cDNA and preparing the library. The libraries underwent quality control with the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) prior to sequencing.
Human: The Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and the Single Index Kit T Set A (10X Genomics, PN-120262) were used as per the manufacturer's guidance for synthesizing cDNA and preparing the library. The libraries underwent quality control with the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) prior to sequencing.

value: Kidney


title: donor 2, male, primary human macrophages avidin treated

description: Library name: m1_M0_avidin


title: Amniotic fluid A10728

description: Hybridized to Cytoscan750K


title: Amniotic fluid A12066

description: Hybridized to Cytoscan750K


title: Amniotic fluid A12018

description: Hybridized to Cytoscan750K


title: Amniotic fluid A12044

description: Hybridized to Cytoscan750K


title: donor 1, female, primary human macrophages avidin treated

description: Library name: f1_M0_avidin


title: human kidney biopsy, disease, sample 2

description:
Library name: KRAD34
10X Genomics


title: Amniotic fluid A9092

description: Hybridized to Cytoscan750K


title: human kidney biopsy, disease, sample 4

description:
Library name: KRAD60
10X Genomics


title: human kidney biopsy, disease, sample 1

description:
Library name: KRAD31
10X Genomics


title: Amniotic fluid A8827

description: Hybridized to Cytoscan750K


title: human kidney biopsy, disease, sample 3

description:
Library name: KRAD46
10X Genomics


title: Amniotic fluid A11398

description: Hybridized to Cytoscan750K


title: Tumor_042_S83

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description: Library name: Tumor_042_S83

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor


title: Tumor_210_S50

description: Library name: Tumor_210_S50


title: Tumor_076_S88

description: Library name: Tumor_076_S88


title: Tumor_043_S80

description: Library name: Tumor_043_S80


title: Amniotic fluid A10107

description: Hybridized to Cytoscan750K


title: donor 2, male, primary human macrophages high dose of biotin

description: Library name: m1_M0_bio_hi


title: Normal_225_S124

description: Library name: Normal_225_S124

source_name: Tumor (adjacent normal)

value: Tumor (adjacent normal)


title: Amniotic fluid A9790

description: Hybridized to Cytoscan750K


title: Tumor_006_S122

description: Library name: Tumor_006_S122


title: Amniotic fluid A9244

description: Hybridized to Cytoscan750K


title: Amniotic fluid A11288

description: Hybridized to Cytoscan750K


title: Amniotic fluid A10124

description: Hybridized to Cytoscan750K


title: Tumor_225_S79

description: Library name: Tumor_225_S79


title: Normal_217_S83

description: Library name: Normal_217_S83


title: Amniotic fluid A8580

description: Hybridized to Cytoscan750K


title: Tumor_217_S82

description: Library name: Tumor_217_S82


title: Normal_212_S77

description: Library name: Normal_212_S77


title: donor 1, female, primary human macrophages low dose of biotin

description: Library name: f1_M0_bio_lo


title: Tumor_212_S74

description: Library name: Tumor_212_S74


title: Tumor_186_S101

description: Library name: Tumor_186_S101


title: Normal_206_S89

description: Library name: Normal_206_S89


title: Tumor_200_S98

description: Library name: Tumor_200_S98


title: Normal_176_S113

description: Library name: Normal_176_S113


title: Normal_177_S123

description: Library name: Normal_177_S123


title: Amniotic fluid A8370

description: Hybridized to Cytoscan750K


title: Tumor_206_S104

description: Library name: Tumor_206_S104


title: Amniotic fluid A9008

description: Hybridized to Cytoscan750K


title: Amniotic fluid A12072

description: Hybridized to Cytoscan750K


title: Tumor_176_S78

description: Library name: Tumor_176_S78


title: Tumor_162_S77

description: Library name: Tumor_162_S77


title: Tumor_158_S97

description: Library name: Tumor_158_S97


title: Normal_158_S65

description: Library name: Normal_158_S65


title: Amniotic fluid A12058

description: Hybridized to Cytoscan750K


title: Normal_162_S7

description: Library name: Normal_162_S7


title: Tumor_177_S76

description: Library name: Tumor_177_S76


title: Normal_157_S53

description: Library name: Normal_157_S53


title: Tumor_146_S114

description: Library name: Tumor_146_S114


title: Normal_146_S66

description: Library name: Normal_146_S66


title: Tumor_145_S62

description: Library name: Tumor_145_S62


title: Tumor_139_S58

description: Library name: Tumor_139_S58


title: Normal_145_S88

description: Library name: Normal_145_S88


title: Normal_139_S22

description: Library name: Normal_139_S22


title: Tumor_172_S109

description: Library name: Tumor_172_S109


title: Amniotic fluid A9022

description: Hybridized to Cytoscan750K


title: Tumor_138_S71

description: Library name: Tumor_138_S71


title: Tumor_138_S53

description: Library name: Tumor_138_S53


title: Normal_172_S120

description: Library name: Normal_172_S120


title: Tumor_137_S65

description: Library name: Tumor_137_S65


title: Normal_132_S27

description: Library name: Normal_132_S27


title: Tumor_128_S87

description: Library name: Tumor_128_S87


title: Tumor_132_S74

description: Library name: Tumor_132_S74


title: Normal_135_S28

description: Library name: Normal_135_S28


title: Tumor_135_S84

description: Library name: Tumor_135_S84


title: Normal_138_S72

description: Library name: Normal_138_S72


title: Tumor_157_S115

description: Library name: Tumor_157_S115


title: Normal_137_S29

description: Library name: Normal_137_S29


title: Tumor_124_S113

description: Library name: Tumor_124_S113


title: Tumor_118_S42

description: Library name: Tumor_118_S42


title: Normal_124_S24

description: Library name: Normal_124_S24


title: Normal_118_S112

description: Library name: Normal_118_S112


title: Normal_128_S64

description: Library name: Normal_128_S64


title: Tumor_084_S52

description: Library name: Tumor_084_S52


title: Normal_084_S68

description: Library name: Normal_084_S68


title: Tumor_081_S112

description: Library name: Tumor_081_S112


title: Normal_081_S15

description: Library name: Normal_081_S15


title: Normal_070_S10

description: Library name: Normal_070_S10


title: Tumor_070_S67

description: Library name: Tumor_070_S67


title: Normal_074_S69

description: Library name: Normal_074_S69


title: Tumor_074_S36

description: Library name: Tumor_074_S36


title: Tumor_067_S44

description: Library name: Tumor_067_S44


title: Normal_067_S84

description: Library name: Normal_067_S84


title: Normal_061_S18

description: Library name: Normal_061_S18


title: Tumor_061_S34

description: Library name: Tumor_061_S34


title: Tumor_052_S103

description: Library name: Tumor_052_S103


title: Normal_052_S126

description: Library name: Normal_052_S126


title: Normal_200_S111

description: Library name: Normal_200_S111


title: Tumor_050_S102

description: Library name: Tumor_050_S102


title: Normal_050_S106

description: Library name: Normal_050_S106


title: Tumor_045_S81

description: Library name: Tumor_045_S81


title: Tumor_047_S125

description: Library name: Tumor_047_S125


title: Tumor_036_S100

description: Library name: Tumor_036_S100


title: Normal_036_S4

description: Library name: Normal_036_S4


title: Lymph node metastasis_1, MDA-MB-231 xenograft model, Mouse 43978

description:
Library name: S8
10X Genomics

data_processing:
The cellranger count pipeline (version 3.0.2) was used for alignment, filtering, barcode counting, and UMI counting from FASTQ files
Assembly: hg19 + mm10
Supplementary files format and content: h5ad file with normalized cell counts and relevant cell and sample-level metadata

source_name: Lymph node metastasis

extract_protocol:
Post-euthanasia, organs were harvested, washed in cold 1× PBS to remove blood, and either processed immediately or minced into small fragments and cryopreserved in 5% DMSO-FBS in liquid nitrogen. For immediate processing, tissues were finely minced using stacked blades in 100–200 µL FV media until a homogenous paste was obtained, then transferred to 15 mL Falcon tubes containing 4.5 mL FV media (5% FBS added fresh) and kept on ice.  Enzymatic dissociation was initiated with 500 µL Collagenase-Hyaluronidase (C-H) per tube, incubated at 37°C on a rotating wheel for 40 minutes. At 15–20 minutes, tissues were mechanically disrupted using 5 mL serological pipettes. Dissociation efficiency was assessed using a 96-well plate, and tubes were returned to the wheel for another 15–20 minutes. After final pipetting, reactions were stopped by placing tubes on ice and adding cold FACS buffer (2% FBS in PBS), followed by centrifugation at 1300 rpm for 6 minutes.  Red blood cell lysis was performed using 1.5 mL freshly prepared RBL buffer (1:10 in Buxter water), incubated for 2 minutes, then stopped with FACS buffer and centrifuged. Pellets were resuspended in 10 mL FACS buffer with 50 µL DNase and filtered through pre-wetted 40 µm strainers to collect single-cell suspension 1 (SCS1).  Filters were inverted and flushed with 12 mL FACS media to recover retained tissue, centrifuged, resuspended in 100 µL DNase, and treated with 1–2 mL TEG trypsin at 37°C for up to 2 minutes using a cut P1000 tip. Trypsin was neutralized with FACS buffer, and cells were centrifuged and resuspended in 10 mL FACS buffer + 100 µL DNase, then filtered through activated 40 µm strainers to yield SCS2.  Both SCS1 and SCS2 were centrifuged (1300 rpm, 6 minutes), combined in 2 mL FACS buffer, and a 50–100 µL aliquot was reserved as an unstained control. Remaining cells were pelleted and stained with 1 mL of pre-titrated antibody solution, incubated at 4°C for 40 minutes with gentle shaking, washed twice, and resuspended in 500 µL FACS buffer for sorting. GFP-expressing MDA-MB-231 cells were sorted and processed for scRNA-seq following 10x Genomics protocols.
Single-cell suspensions were processed using the Chromium Controller (10x Genomics) and the Single Cell 3′ Reagent Kits v2 (PN-120237), following the manufacturer’s instructions (10x Genomics, CG00052, Rev F). Cells were encapsulated into nanoliter-scale Gel Bead-in-Emulsions (GEMs), where cell lysis and reverse transcription occurred, barcoding each cDNA molecule with a unique 10x barcode and UMI. Following GEM-RT incubation, emulsions were broken and cDNA was purified using Silane Dynabeads. Amplified cDNA was enzymatically fragmented and processed through end repair, A-tailing, adaptor ligation, and indexing PCR using sample-specific barcodes (Chromium i7 Sample Index Plate, PN-220103). Libraries were quality controlled using Bioanalyzer or TapeStation, quantified, and sequenced on an Illumina platform using a paired-end 2×150 bp configuration, with Read 1 containing 26 bp (barcode + UMI), i7 index of 8 bp, and Read 2 of 98 bp.

value: Lymph node metastasis


title: Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43979

description:
Library name: S16
10X Genomics


title: Liver metastasis, MDA-MB-231 xenograft model, Mouse 43979

description:
Library name: S14
10X Genomics

source_name: Liver metastasis

value: Liver metastasis


title: Lung metastasis, MDA-MB-231 xenograft model, Mouse 43979

description:
Library name: S15
10X Genomics

source_name: Lung metastasis

value: Lung metastasis


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 43978

description:
Library name: S20
10X Genomics

source_name: Primary tumour

value: Primary tumour


title: Liver metastasis_1, MDA-MB-231 xenograft model, Mouse 43978

description:
Library name: S10
10X Genomics


title: Liver metastasis_2, MDA-MB-231 xenograft model, Mouse 43978

description:
Library name: S11
10X Genomics


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 43979

description:
Library name: S21
10X Genomics


title: Lung metastasis, MDA-MB-231 xenograft model, Mouse 43975

description:
Library name: S6
10X Genomics


title: Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43975

description:
Library name: S7
10X Genomics


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 43973

description:
Library name: S18
10X Genomics


title: Liver metastasis, MDA-MB-231 xenograft model, Mouse 43975

description:
Library name: S5
10X Genomics


title: Primary tumour, MDA-MB-231 xenograft model, Mouse 43975

description:
Library name: S19
10X Genomics


title: Lung metastasis, MDA-MB-231 xenograft model, Mouse 43973

description:
Library name: S4
10X Genomics


title: Normal_047_S92

description: Library name: Normal_047_S92


title: Normal_045_S105

description: Library name: Normal_045_S105


title: Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43973

description:
Library name: S2
10X Genomics


title: Liver metastasis, MDA-MB-231 xenograft model, Mouse 43973

description:
Library name: S3
10X Genomics