title: Mouse_ID_74_32 wks drinking water

description:
Sample_ID_74
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_75_32 wks drinking water

status: Public on Apr 29 2024

type: SRA

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

country: USA

institute: US EPA

description:
Sample_ID_75
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

library_source: transcriptomic

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Excessive deviation of gene expression ranking in individual samples from the average was assessed by Spearman rank regression. Any sample that exhibited an R^2 value of less than 0.7 was excluded from further analysis (10 of 78 samples)
Count data was loaded into Partek Flow 10.0.22.0524 (build version 0, St. Louis, MO)
Raw gene counts were offset by 1.0, then normalized by media ratio. Genes with very low expression were eliminated from further analysis (those <3.4 (20%) geometric mean counts across all samples) as the final filter.
Differentially expressed genes from age-matched controls using DESeq2 (significance based on false discovery rate (FDR) ≤0.05)
Assembly: mm10
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv; aligned reads
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv; media ratio normalized counts, low quality samples removed
Supplementary files format and content: Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv; filtered genes (20% of lowest expressed genes by geometric mean across samples)

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: All procedures involving animal care were approved by an EPA Institutional Animal Care and Use Committee. Briefly, mice were received at age 21 days to the EPA AAALAC International accredited facility from Charles River Laboratories in Morrisville, NC, and acclimated for 7 days prior to treatment initiation. The animals were housed in polycarbonate cages in a laminar flow room and maintained under standard conditions (20 ± 2 C°; 40–60% relative humidity; 12 h light/dark cycle) and fed ad libitum Purina 5001 laboratory rodent diet (Purina Test Diets, St. Louis, MO). The study animals

extract_protocol:
Measurements were taken from direct lysates of archived mouse liver sections derived from FFPE blocks. Two to three sections of 15 µM from each sample block were closely trimmed to remove excess paraffin and placed into -20°C storage until shipment overnight on dry ice to the vendor (BioSpyder, Inc., Carlsbad, CA) for processing. There, liver was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos (DOs), with each pair of DOs targeting a single transcript within the mouse genome.
Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 2,205 Mus musculus target genes (TempO-Seq Mouse S1500+ surrogate attenuation panel, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads.

treatment_protocol: The target dose of 3.5 g/L (429 mg/kg-day) dichloroacetic acid (DCA; CAS 79-43-6, Aldrich, Milwaukee, WI) was based on the earlier carcinogenicity results observed in male mice, and is equivalent to 65 mg/kg-day in humans. The actual dose was estimated based on intake, body weight and water DCA concentrations, and the daily water concentration (ml/kg-day) by cage was measured every 4-5 weeks beginning with week 4. Drinking water stocks were prepared every 12-14 days and checked by ultraviolet absorption at 231nm to confirm DCA concentration (Beckman DU Series 600 spectrophotometer, Beckman Coulter, Brea, CA). The stock water pH was adjusted to 6.8-7.2 with NaOH, stored at 4-6°C and changed every 5-7 days, based on studies showing DCA to be stable over 1-2 weeks. As previously detailed, water consumption was initially 5-22% lower in the DCA drinking water groups, although by 52 weeks, water consumption was equivalent in all groups. The removal of DCA quickly returned water consumption to control levels, regardless of exposure length.

tag: strain

tag: Sex

value: male

tag: age

value: 4 wks

tag: tissue

value: liver

tag: time

value: 32 wks

tag: dose

value: CTL

tag: treatment

value: 32 wks drinking water


title: Patch cell Sample 690, Ghost, Chow diet

city: BORDEAUX

first: Carmelo

last: QUARTA

address: 146 rue Léo Saignat

country: France

institute: Inserm U1215

library_source: transcriptomic single cell

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.10 and Fastp v0.20.0 tools.
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR aligner v2.7.5a (parameters --outFilterType Normal --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNoverReadLmax 0.04 --outFilterMatchNmin 0 --outFilterMismatchNmax 10 --alignIntronMin 20 --alignIntronMax 0 --alignMatesGapMax 0 --quantMode GeneCounts --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample/Cell
Supplementary files format and content: tab-delimited text file includes normalized DESeq2 counts for each Sample/Cell

source_name: hypothalamus

extract_protocol:
At the end of the recording, each cell in the pipette was aspirated for 3 min. The pipette was then broken into an RNAse-free 200 µL Eppendorf tube containing the reaction mix from the SMART-Seq® Single Cell Kit (Takara, 634472).
cDNA synthesis was performed according to SMART-Seq® Single Cell Kit (Takara, 634472) and the manufacturer instructions, and libraries have been prepared with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).
scRNA-seq PATCH-seq

value: hypothalamus

tag: cell type

value: Ghost

tag: diet

value: Chow diet


title: Mouse_ID_81_57 wks drinking water

description:
Sample_ID_81
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks

value: 57 wks drinking water


title: Patch cell Sample 687, Ghost, Chow diet


title: Mouse_ID_70_10 wks drinking water

description:
Sample_ID_70
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv

value: 10 wks

value: 10 wks drinking water


title: Mouse_ID_73_32 wks drinking water

description:
Sample_ID_73
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 686, Pomc+, Chow diet

value: Pomc+


title: Mouse_ID_72_10 wks drinking water

description:
Sample_ID_72
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_71_10 wks drinking water

description:
Sample_ID_71
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_76_32 wks drinking water

description:
Sample_ID_76
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 689, Pomc+, Chow diet


title: Patch cell Sample 685, Pomc+, Chow diet


title: Patch cell Sample 684, Ghost, Chow diet


title: 293T_siGFP_rep3

type: RNA

city: Taipei

first: Hsiu-Ming

last: Shih

address: 128 Sec. 2, Academia Rd. Nankang,

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description:
293T_siGFP_rep3
Gene expression after 72hr transfection, ctrl for siHOTAIR_rep3.

hyb_protocol: Total Alexa fluor® 555 labeled cDNA 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 manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent SurePrint G3 Human GE 8x60K array for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028004_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities. These data were processed in Agilent GX 11.5 . Detailed information is as follows:
Threshold: 1.0
Log base: 2
Technology: Agilent.SingleColor.28004
Normalization: Shift to 75 percentile

label: Alexa fluor® 555

organism: Homo sapiens

source_name: 293T, GFP siRNA, 72hr

label_protocol: Using the Invitrogen SuperScript plus Indirect cDNA labeling System, we labeled 15ug total RNA with Alexa fluor® 555 and purified it using the purification module in the kit. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000.

growth_protocol: HEK293T cells were cultured in DMEM (high glucose, Gibco) supplemented with 10% fetal bovine serum (Gibco), 10 mM NaHCO3 (Sigma) and penicillin/streptomycin (Gibco).

extract_protocol: Total RNA was extracted by a commercial kit (NucleoSpin, Macherey-Nagel®). The concentration of RNA was quantified by a Nanodrop 2000 spectrophotometer (Thermo) and the quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In the HOTAIR experiment, siRNA oligonucleotides were targeted to HOTAIR or to GFP as a control. They were synthesized by Dharmacon. All transfections were performed by using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Three independent knockdown experiments were performed with HOTAIR. Total RNA was extracted after 3 days to perform microarray analysis.

tag: cell line

value: cultured human embryonic kidney cells

tag: sirna

value: siGFP


title: HTGTS_PC-9.hA3C_after rep2

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

library_source: genomic

data_processing:
HTGTS junction reads for each sample were recognized by designed barcode, primer and bait portion  as previously described (Mara Compagno et al., Nature 2017). The barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions. Briefly, we aligned sequences to the human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: hg38
Supplementary_files_format_and_content: HTGTS junctions; BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

molecule: genomic DNA

growth_protocol:
RPMI 1640 + 2mM Glutamine + 10% Fetal Bovine Serum (FBS)
PC-9 cells are grown in RPMI supplemented with 2 mM Glutamine and 10% FBS.

extract_protocol:
Rapid lysis buffer + 10ug/ml Proteinase K, at 56°C, overnight
Gennomic DNAs were extracte with Rapid lysis buffer containing 20 ug/ml of proteinase K overnight at 56°C.
Library was prepaired with the HTGTS methods previously described (Chiarle at al., Cell, 2011_PMID:21962511; Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells)
We induced DNA DSBs in intron 19 of ALK and we used linker forward primer and specific target reverse primers to capture functional fusions.

treatment_protocol:
100 nM osimertinib, every other day
Cells were treated with 100 nM of osimertinib every other day.

value: Non-small cell lung cancer

tag: genotype/variation

value: osimertinib


title: 293T_shluc_rep3

description:
293T_shluc_rep3
Gene expression after 72hr transfection, ctrl for 293T_shDaxx_rep3.

source_name: 293T, luc shRNA, 72hr

treatment_protocol: In order to knock down Daxx, HEK293T cells were transfected with a lentivirus plasmid constructed with a short hairpin RNA targeted to Daxx or to luciferase as a control. They were synthesized by Dharmacon. All transfections were performed by using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Three independent knockdown experiments were performed with Daxx. Total RNA was extracted after 3 days to perform microarray analysis.

tag: shRNA

value: shluc


title: 293T_siHOTAIR_rep1

description:
293T_siHOTAIR_rep1
Gene expression after 72hr transfection.

source_name: 293T, HOTAIR siRNA, 72hr

value: siHOTAIR


title: Mouse_ID_69_10 wks drinking water

description:
Sample_ID_69
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: male

value: 4 wks

value: liver


title: Mouse_ID_68_10 wks drinking water

description:
Sample_ID_68
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: CTL


title: HTGTS_PC-9.hA3C_after rep3


title: Mouse_ID_67_10 wks drinking water

description:
Sample_ID_67
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: Mouse_ID_64_78 wks DCA

description:
Sample_ID_64
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 78 wks

value: 78 wks DCA


title: 293T_siGFP_rep1

description:
293T_siGFP_rep1
Gene expression after 72hr transfection, ctrl for siHOTAIR_rep1.


title: HTGTS_PC-9.pMSCV_after rep3

value: pMSCV


title: 293T_siGFP_rep2

description:
293T_siGFP_rep2
Gene expression after 72hr transfection, ctrl for siHOTAIR_rep2.


title: 293T_shDaxx_rep3

description:
293T_shDaxx_rep3
Gene expression after 72hr transfection.

source_name: 293T, Daxx shRNA, 72hr

value: shDaxx


title: 293T_siHOTAIR_rep3

description:
293T_siHOTAIR_rep3
Gene expression after 72hr transfection.


title: 293T_shluc_rep2

description:
293T_shluc_rep2
Gene expression after 72hr transfection, ctrl for 293T_shDaxx_rep2.


title: Mouse_ID_65_78 wks DCA

description:
Sample_ID_65
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_66_78 wks DCA

description:
Sample_ID_66
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 673, Pomc+, High fat diet

value: hypothalamus

value: High fat diet


title: HTGTS_PC-9.hA3C_after rep1


title: Mouse_ID_62_78 wks DCA

description:
Sample_ID_62
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: Mouse_ID_63_78 wks DCA

description:
Sample_ID_63
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: Mouse_ID_60_57 wks DCA, 21 wks drinking water

description:
Sample_ID_60
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks DCA, 21 wks drinking water


title: Patch cell Sample 671, Ghost, High fat diet

value: Ghost


title: Mouse_ID_61_78 wks DCA

description:
Sample_ID_61
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: HTGTS_PC-9.pMSCV_after rep2


title: Mouse_ID_57_57 wks DCA, 21 wks drinking water

description:
Sample_ID_57
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: Mouse_ID_55_57 wks DCA, 21 wks drinking water

description:
Sample_ID_55
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: 293T_siHOTAIR_rep2

description:
293T_siHOTAIR_rep2
Gene expression after 72hr transfection.

value: cultured human embryonic kidney cells


title: Patch cell Sample 672, Pomc+, High fat diet

value: Pomc+


title: Patch cell Sample 668, Ghost, Chow diet

value: Chow diet


title: Mouse_ID_54_57 wks DCA

description:
Sample_ID_54
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks

value: 57 wks DCA


title: Patch cell Sample 667, Pomc+, Chow diet


title: Mouse_ID_52_57 wks DCA

description:
Sample_ID_52
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv

value: male


title: Mouse_ID_59_57 wks DCA, 21 wks drinking water

description:
Sample_ID_59
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 4 wks


title: Mouse_ID_58_57 wks DCA, 21 wks drinking water

description:
Sample_ID_58
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv

value: liver


title: HTGTS_PC-9.hA3C_before rep1

treatment_protocol: Cells were treated with 100 nM of osimertinib every other day.

value: Non-small cell lung cancer

value: No


title: Mouse_ID_49_57 wks DCA

description:
Sample_ID_49
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 666, Pomc+, Chow diet


title: Patch cell Sample 665, Pomc+, Chow diet


title: HTGTS_PC-9.pMSCV_before rep3


title: HTGTS_PC-9.pMSCV_after rep1

value: osimertinib


title: HTGTS_PC-9.pMSCV_before rep2

value: pMSCV


title: 293T_shluc_rep1

description:
293T_shluc_rep1
Gene expression after 72hr transfection, ctrl for 293T_shDaxx_rep1.

value: shluc


title: 293T_shDaxx_rep2

description:
293T_shDaxx_rep2
Gene expression after 72hr transfection.

value: shDaxx


title: Mouse_ID_48_32 wks DCA, 46 wks drinking water

description:
Sample_ID_48
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv

value: 78 wks

value: 32 wks DCA, 46 wks drinking water


title: Patch cell Sample 670, Pomc+, High fat diet

value: hypothalamus

value: High fat diet


title: HTGTS_PC-9.hA3C_before rep3


title: 293T_shDaxx_rep1

description:
293T_shDaxx_rep1
Gene expression after 72hr transfection.

value: cultured human embryonic kidney cells


title: Mouse_ID_56_57 wks DCA, 21 wks drinking water

description:
Sample_ID_56
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks DCA, 21 wks drinking water


title: Mouse_ID_53_57 wks DCA

description:
Sample_ID_53
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks


title: Mouse_ID_44_32 wks DCA, 46 wks drinking water

description:
Sample_ID_44
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_51_57 wks DCA

description:
Sample_ID_51
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks DCA


title: Patch cell Sample 669, Pomc+, Chow diet

value: Pomc+

value: Chow diet


title: Mouse_ID_50_57 wks DCA

description:
Sample_ID_50
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: male

value: 4 wks

value: liver


title: Mouse_ID_42_32 wks DCA

description:
Sample_ID_42
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 32 wks

value: 32 wks DCA


title: Mouse_ID_39_32 wks DCA

description:
Sample_ID_39
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_46_32 wks DCA, 46 wks drinking water

description:
Sample_ID_46
removed from final analysis
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv


title: Patch cell Sample 664, Ghost, Chow diet

value: Ghost


title: Patch cell Sample 659, Ghost, Chow diet


title: Mouse_ID_45_32 wks DCA, 46 wks drinking water

description:
Sample_ID_45
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: HTGTS_PC-9.hA3C_before rep2

value: Non-small cell lung cancer

value: No


title: Patch cell Sample 663, Pomc+, Chow diet


title: Mouse_ID_43_32 wks DCA, 46 wks drinking water

description:
Sample_ID_43
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 78 wks

value: 32 wks DCA, 46 wks drinking water


title: Patch cell Sample 662, Pomc+, Chow diet

value: hypothalamus


title: Patch cell Sample 657, Ghost, High fat diet

value: High fat diet


title: 1 year cerebellum from KO mouse 2 [177MTCB]

city: Philadelphia

first: Thomas

last: Roule

state: Pennsylvania

address: 3501 Civic Center Boulevard  5th Floor CTRB-5400

institute: CHOP

data_processing:
Reads were counted using FeatureCounts from the subread package (v2.0.1) with parameters: -p -C -O.
Differential gene expression analysis was performed with DEseq2 (V1.38.3) excluding genes with less than five reads, and all genes from chromosome X and Y. Differential expression was performed using a linear model and as factor the genotypes.
BigWig files were generated using bamCoverage from the deepTools suite with parameters: --normalizeUsing BPM --binSize 10.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file including read count values for each gene (.txt).
Supplementary files format and content: Coverage files in bigWig format (.bw).

source_name: cerebellum

extract_protocol:
Mouse brain tissue were dissected on ice, fast froze in liquid nitrogen, and stored in -80˚C until use. On the day of RNA extraction, 50mg to 100mg tissue from each sample was lysed in 1ml TRIzol (15596026, Invitrogen). Addition of 0.2ml chloroform (288306, Sigma-Aldreich) followed by centrifugation was performed to separate the solution into an aqueous phase and an organic phase. Isopropyl alcohol and 75% ethanol (111000200CSPP, Pharmco) was added in sequence to precipitate and wash the RNA pellets.
Library prep performed by Genewiz

value: cerebellum

value: mix

tag: genotype

value: Snx14 KO


title: 1 year cortex tissue from KO mouse 2 [177MTCX]

source_name: cortex

value: cortex


title: Patch cell Sample 661, Ghost, Chow diet

value: Chow diet


title: 1 year cortex tissue from control mouse 3 [474WTCX]

value: WT


title: Patch cell Sample 660, Pomc+, Chow diet

value: Pomc+


title: 1 year cortex tissue from KO mouse 1 [174MTCX]


title: Mouse_ID_47_32 wks DCA, 46 wks drinking water

description:
Sample_ID_47
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: male

value: 4 wks

value: liver


title: Mouse_ID_38_32 wks DCA

description:
Sample_ID_38
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 32 wks

value: 32 wks DCA


title: Mouse_ID_36_10 wks DCA, 68 wks drinking water

description:
Sample_ID_36
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 10 wks DCA, 68 wks drinking water


title: Mouse_ID_37_32 wks DCA

description:
Sample_ID_37
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: 1 year cortex from contorl mouse 1 [171HetCX]

value: Het


title: HTGTS_PC-9.pMSCV_before rep1

value: Non-small cell lung cancer

value: pMSCV

value: No


title: Patch cell Sample 656, Ghost, High fat diet

value: hypothalamus

value: Ghost

value: High fat diet


title: 1 year cortex tissue from control mouse 2 [175HetCX]

value: cortex

value: mix


title: 1 year cerebellum from KO mouse 1 [174MTCB]

value: cerebellum

value: Snx14 KO


title: 1 year cerebellum from control mouse 3 [474WTCB]

value: WT


title: Patch cell Sample 655, Ghost, High fat diet


title: Mouse_ID_34_10 wks DCA, 68 wks drinking water

description:
Sample_ID_34
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: male

value: 4 wks

value: 78 wks


title: Mouse_ID_35_10 wks DCA, 68 wks drinking water

description:
Sample_ID_35
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: liver


title: Mouse_ID_28_10 wks DCA, 47 wks drinking water

description:
Sample_ID_28
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 57 wks

value: 10 wks DCA, 47 wks drinking water


title: Patch cell Sample 658, Pomc+, Chow diet

value: Pomc+

value: Chow diet


title: Mouse_ID_33_10 wks DCA, 68 wks drinking water

description:
Sample_ID_33
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 10 wks DCA, 68 wks drinking water


title: Mouse_ID_41_32 wks DCA

description:
Sample_ID_41
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 32 wks

value: 32 wks DCA


title: Mouse_ID_32_10 wks DCA, 68 wks drinking water

description:
Sample_ID_32
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_31_10 wks DCA, 68 wks drinking water

description:
Sample_ID_31
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 654, Pomc+, High fat diet

value: hypothalamus

value: High fat diet


title: Mouse_ID_40_32 wks DCA

description:
Sample_ID_40
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_26_10 wks DCA, 47 wks drinking water

description:
Sample_ID_26
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_29_10 wks DCA, 47 wks drinking water

description:
Sample_ID_29
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: 1 year cerebellum from control mouse 2 [175HetCB]

value: mix

value: Het


title: Mouse_ID_30_10 wks DCA, 47 wks drinking water

description:
Sample_ID_30
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 653, Ghost, High fat diet

value: Ghost


title: Mouse_ID_22_10 wks DCA, 22 wks drinking water

description:
Sample_ID_22
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 10 wks DCA, 22 wks drinking water


title: Mouse_ID_25_10 wks DCA, 47 wks drinking water

description:
Sample_ID_25
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: male


title: Mouse_ID_27_10 wks DCA, 47 wks drinking water

description:
Sample_ID_27
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 4 wks


title: 1 year cerebellum from contorl mouse 1 [171HetCB]

value: cerebellum


title: untreated controlgastric organoids [organoid-3]

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

country: Japan

institute: University of Tokyo

description: untreated Gastric organoids

data_processing:
Crude readings were subjected to quality control checks, after which the clean readings were aligned to the mouse genome reference sequences (GRCm38). The aligned reads were mapped and quantified using CLC Genomics Workbench software v7.5
Supplementary files format and content: Excel file that has total read counts, TPM, CPM, and RPKM of all genes in all cells

source_name: gastric organoids

growth_protocol: Gastric organoids were cultured in matrigel with standard culture medium, and at the first passage they were put on matrigel with growth factor-free, antibiotic-free medium

extract_protocol:
RNAs were extracted by Rneasy Mini kit
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn  of surface-bound oligos complementary to the library adapters. Each fragment is then amplified  into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the  templates are ready for sequencing.

treatment_protocol: Gastric organoids were incubated with bacteria for 4 hours

value: gastric organoid

value: untreated


title: Mouse_ID_21_10 wks DCA, 22 wks drinking water

description:
Sample_ID_21
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: liver


title: Mouse_ID_23_10 wks DCA, 22 wks drinking water

description:
Sample_ID_23
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: untreated control gastric organoids [organoid-2]

description: untreated Gastric organoids


title: Patch cell Sample 651, Pomc+, High fat diet

value: Pomc+


title: Mouse_ID_19_10 wks DCA, 22 wks drinking water

description:
Sample_ID_19
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_20_10 wks DCA, 22 wks drinking water

description:
Sample_ID_20
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 650, Pomc+, High fat diet


title: Mouse_ID_18_10 wks DCA

description:
Sample_ID_18
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 10 wks

value: 10 wks DCA


title: untreated control gastric organoids [organoid-1]

description: untreated Gastric organoids


title: Patch cell Sample 649, Ghost, High fat diet


title: Neisseria-treated gastric organoids [Ns-3]

description: Gastric organoids treated with Neisseria

value: Neisseria subflava


title: Mouse_ID_17_10 wks DCA

description:
Sample_ID_17
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_24_10 wks DCA, 22 wks drinking water

description:
Sample_ID_24
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv

value: 32 wks


title: Neisseria-treated gastric organoids [Ns-2]


title: Patch cell Sample 652, Ghost, High fat diet

value: hypothalamus


title: Neisseria-treated gastric organoids [Ns-1]


title: Mouse_ID_15_10 wks DCA

description:
Sample_ID_15
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 648, Ghost, High fat diet

value: High fat diet


title: Patch cell Sample 647, Pomc+, High fat diet


title: Mouse_ID_13_10 wks DCA

description:
Sample_ID_13
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_16_10 wks DCA

description:
Sample_ID_16
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Mouse_ID_14_10 wks DCA

description:
Sample_ID_14
Partek_TempOSeq_1500_2B_9404_BSCountData_Quantification.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Normalization_Normalized_counts.csv
Partek_TempOSeq_1500_2B_9404_BSCountData_Filter_features_Filtered_counts.csv


title: Patch cell Sample 644, Pomc+, High fat diet


title: Patch cell Sample 646, Ghost, High fat diet


title: Helicobacter-treated gastric organoids [Hp-3]

description: Gastric organoids treated with Helicobacter

value: Helicobacter pylori


title: Helicobacter-treated gastric organoids [Hp-2]


title: Patch cell Sample 645, Pomc+, High fat diet


title: Patch cell Sample 642, Pomc+, High fat diet


title: Helicobacter-treated gastric organoids [Hp-1]


title: Patch cell Sample 643, Ghost, High fat diet


title: Fusobacterium-treated gastric organoids [Fn-2]

description: Gastric organoidstreated with Fusobacterium

value: Fusobacterium nucleatum


title: Patch cell Sample 641, Pomc+, High fat diet


title: Patch cell Sample 640, Ghost, High fat diet

value: Ghost


title: ALA3

city: Bengbu City

first: Lin

last: Zhang

state: Anhui

address: 2600 Donghai Avenue

country: China

institute: Bengbu Medical College

data_processing:
Sequencing by illumina NovaSeq 6000（illumina，USA)
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing 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 Rnor_6.0 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
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: rn6
Supplementary files format and content: .elx file includes raw counts for each Samples
Supplementary files format and content: .elx file includes RPKM velues for each Samples

organism: Rattus norvegicus

source_name: Spinal Cord

extract_protocol:
Total RNA was extracted using trizol(Ambion/Invitrogen, USA) , Qubit2.0 Fluorometer for preliminary quantification and dilute the library to 1.5ng/ul
NEBNext® Ultra™ RNA Library Prep Kit for Illumina

value: Spinal Cord

value: WT

value: spinal cord injury + alpha-lipoic acid


title: Fusobacterium-treated gastric organoids [Fn-3]

description: Gastric organoids treated with Fusobacterium


title: Fusobacterium-treated gastric organoids [Fn-1]


title: AT2 organoid_scRNA

city: Cambridge

first: Kyungtae

last: Lim

email: kl492@cam.ac.uk, ktlim492@korea.ac.kr

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: 10X genomics

data_processing:
scRNA-seq data were mapped with STARsolo 2.7.10a using the GRCh38 reference distributed by 10X (3,0,0, derived fromEnsembl 93).
Cells were called by a customised EmptyDrops method from CellRanger 3.0.2 (distributed as emptydrops on PyPi).
The SNPs of the four donors were inferred from the bulk RNA-seq data using cellsnp-lite (--minMAF 0.1 –minCOUNT20). These SNPs were used to demultiplex the scRNA-seq data into four donors using souporcell (v2.5, -k 4 –known_genotypes $VCF).
All the codes were deposited at https://github.com/brianpenghe/2024_AT2_organoids - all the genotypes inferred
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: .h5ad

source_name: Fetal lung

growth_protocol: Cultured in alveolar type 2 differentiation medium (AT2 medium): Advanced DMEM/F12 supplemented with 1x GlutaMax, 1 mM HEPES and Penicillin/Streptomycin, 1X B27 supplement (without Vitamin A), 1X N2 supplement, 1.25 mM N-acetylcysteine, 50 nM Dexamethasone, 0.1 mM 8-Bromoadenosine 3’5’-cyclic monophosphate (cAMP), 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX), 50 μM DAPT, 100 ng/ml recombinant human FGF7, 3 μM CHIR99021, 10 μM A83-01, and 10 μM Y-27632. Medium was replaced every 2 days and cultures maintained for 2 weeks until the initial AT2 organoid colonies formed in the matrigel droplet. Organoids were typically passaged at a 1 to 3 ratio weekly by gently breaking into small fragments.

extract_protocol:
Single cell RNA libraries of four biological lines of AT2 organoids were generated using an 10X kit (10X genomics).
Library generation for 10x Genomics analysis performed following the Chromium Single Cell 5′ Reagents Kits (10x Genomics)
Single cell RNA seq was carried out according to 10x Chromium Single Cell 5’ Kits (v1), sequenced on a NovaSeq 6000 S4 Flowcell (paired-end (PE), 150-bp reads) to achieve an average of 80,000 PE reads per cell.

treatment_protocol: The fdAT2 organoids  were harvested individually and dissociated into single cells using TrypLE Express enzyme (Thermo Fisher Scientific, 12605010). The cell suspension was pooled, passed through a 45μm filter, pelleted, resuspended in 1ml of 0.04% BSA/PBS and counted. 5,000 cells per donor were pooled for single-cell RNA library preparation .

value: Fetal lung

value: AT2 organoid

value: 17, 21, 17, 20 post-conception week

value: AT2 medium

tag: pooled sample


title: Patch cell Sample 639, Pomc+, High fat diet

value: Pomc+


title: Sample_H3K27me3_shDaxx

description: the processd data obtained from this file is compared with the input(Input_D)

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.6.1 with the following confiuration "bwa aln -q 20"
Data were filtered if mapping quality is lower than 20.
peaks were called using SICER version 1.1 with the following setting: window size 200, gap size 600, FDR 0.01
The islands in two pairs of liraries were identified by SICER-df.sh and were compared with each other to determine the significant change.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using SICER

growth_protocol: HEK293T cells were cultured in DMEM (high glucose, Gibco) supplemented with 10 % fetal bovine serum (Gibco), 10 mM NaHCO3 (Sigma) and penicillin/streptomycin (Gibco).

extract_protocol: Cell lysis extracts were sonicated and immunoprecipitated with 5ug H3K27me3 antibody (Merk 07-449). DNA was purified and measured by Nano drop 2000 spectrophotometer (Thermo). Total 30ng of DNA was used for preparation the ChIP-Seq DNA library following by ChIP-Seq Sample Prep Kit (Illumina). Briefly, the kit converted the DNA overhangs into phosphorylated blunt ends, using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK). The 3' to 5' exonuclease activity of these enzymes removed 3' overhangs and the polymerase activity filled in the 5' overhangs. Subsequently, the protocol added an ‘A’ base to the 3' end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment (3' to 5' exo minus). This prepared the DNA fragments for ligation to the adapters, which have a single ‘T’ base overhang at their 3' end. After adaptor ligation, adequate DNA were selected from gel and subjected to PCR amplification. High throughput sequencing was performed by the Hiseq 2000 (Illumina) as manufacturer’s protocols.

treatment_protocol: In order to knock down Daxx, HEK293T subjected to be transfected with lentivirus plasmid constructed with sort hairpin RNA target to Daxx and luciferase, respectively.

value: HEK 293T

value: human embryonic kidney cells

tag: transfected with

value: shRNA specific to human Daxx

tag: passages

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: ALA2

tag: tissue


title: ALA1


title: Sample_H3K27me3_shluc

description: the processd data obtained from this file is compared with the input (Input_S)

value: shRNA specific to luciferase


title: CAF-EVs-rep2

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

data_processing:
Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text files include significant differential gene expression

source_name: CAFs

extract_protocol:
Cancer-associated fibroblasts (CAFs) and Primary normal fibroblasts (NFs) were isolated from pancreatic ductal carcinoma and paired non-cancerous tissues. Fibroblast populations were isolated by differential velocity adherent technique. Then the CAFs or NFs derived EVs were isolated and treated with Trizol and extract the total RNA
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), ribosomal RNA was removed from 1 μg total RNA using Ribo-off® rRNA Depletion Kit (Human/Mouse/Rat, Vazyme, cat.N406-01, Nanjing, China) and purified using VAHTS® RNA Clean Beads (Vazyme, cat. N412, Nanjing, China). VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, cat.NR604-02, Nanjing, China) was used for lncRNA library construction following the manufacturer's protocol. The enriched ncRNAs were segmented with FRAG/PRIME Buffer. The first cDNA strand was generated by reverse transcription starting from -3 ’ , and the second cDNA strand with U was synthesized using the first cDNA strand. Single- or dual-index adapters were ligated to the fragments with ligase, and size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). The ligated products were amplified with PCR by the following conditions: Incubated at 37 ° C for 10 minutes to remove the U containing antisense chain, initial denaturation at 98℃ for 10 sec; 12-14 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, extension at 72℃ for 30 sec, and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 290bp (±50 bp). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Illumina Corporation， San Diego，USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

value: CAFs

value: primary cancer-associated fibroblasts

value: EVs were isolated


title: Input_shDaxx

value: shRNA specific to Daxx


title: Patch cell Sample 638, Pomc+, High fat diet

value: hypothalamus

value: High fat diet


title: CAF-EVs-rep3


title: CAF-EVs-rep1


title: sham3

value: Spinal Cord

value: WT

value: sham operation


title: Patch cell Sample 637, Ghost, High fat diet

value: Ghost


title: NF-EVs-rep3

source_name: NFs

value: NFs

value: primary normal fibroblasts


title: sham2


title: NF-EVs-rep2


title: NF-EVs-rep1


title: Patch cell Sample 636, Ghost, Chow diet

value: Chow diet


title: Veh3

value: spinal cord injury + normal saline


title: sham1


title: Patch cell Sample 633, Ghost, Chow diet


title: hVICs-OM-SOLB1

city: Wuhan

first: Xing

last: Liu

state: Hubei

address: JieFang Avenue 1277

department: Cardiovascular Surgery

institute: Wuhan Union Hospital

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count.
Assembly: human NCBI genome build 36
Supplementary files format and content: excel file include RPKM value of each sample

molecule: polyA RNA

source_name: hVICs

growth_protocol: Noncalcified aortic valves were gently cut into small pieces and digested in 2 mg/ml Type I collagenase (Sigma-Aldrich, Saint Louis, MO) for 8 hours at 37 ℃ in 5% CO2. The separated primary hVICs were then cultured in high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco Laboratories, Gaithersburg, MD) in a humidified incubator with 5% CO2 at 37 ℃. For osteogenic differentiation, the cells were cultured with osteogenic medium (OM, Cyagen Biosciences, HUXMA-90021) to stimulate differentiation

extract_protocol:
Total RNA was isolated from the hVICs treated for 24 hours using Trizol reagent (Invitrogen, Carlsbad, CA). After solubilization, the addition of chloroform induces phase separation, wherein proteins are extracted to the organic phase, DNA settles at the interface, and RNA remains in the aqueous phase. Furthermore, we conducted a quality examination of all extracted RNAs using a NanoDrop spectrophotometer, only high-quality RNA samples (A260/280 ≥ 2.00) were selected for the subsequent experiments
Library preparation utilized the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Once the cells reached 70–80% confluence, they were treated. Treatment groups included OM (OM-treated group), OM plus SOLB (OM + SOLB treated group) (Selleck, Cat. No. S1848; SolB at 10 μM final concentration in OM)

value: hVICs

value: primary human valve interstitail cells

value: osteogenesis medium+Schisandrol B


title: Patch cell Sample 635, Ghost, Chow diet


title: hVICs-OM-SOLB2


title: Input_shluc

value: HEK 293T

value: human embryonic kidney cells

value: shRNA specific to luciferase


title: Patch cell Sample 632, Pomc+, Chow diet

value: Pomc+


title: Veh2


title: Patch cell Sample 631, Pomc+, Chow diet

value: hypothalamus


title: hVICs-OM-2

value: osteogenesis medium


title: Veh1

value: Spinal Cord


title: HL60 cell, Parental, Rep2

city: Hershey

first: Wei

last: Li

state: PA

address: 500 University Drive

institute: Penn State College of Medicine

data_processing:
Sequencing data were analyzed using Galaxy (https://usegalaxy.org/). Briefly, reads were trimmed and aligned to reference human genome and annotation files (GRCh38, build 38) using HISAT2. Difference of gene expression were detected by edgeR.
Assembly: human genome and annotation files (GRCh38, build 38)
Supplementary files format and content: Txt, normalized counts

source_name: HL-60 Cell line

growth_protocol: HL-60 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 (10-040-CV, Corning) supplemented with 10% FBS and 1% antibiotic–antimycotic solution at 37 °C with 5% CO2.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen) and total RNA was extracted by following the protocol from the manufacture.
RNA-seq libraries were prepared using the SMART-Seq mRNA HT kit (Takara Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

treatment_protocol: The protocol from (Breitman et al, 1980; Bunce et al, 1994; Collins, 1987) was used to differentiate HL-60 cells. In short, 3 × 105/ml cells were seeded in 100 mm cell culture dishes containing the RPMI listed above with 1 μM all-trans-retinoic acid (ARTA; R2625, Sigma), and 30 nM rhG-CSF for 24 days. Fresh media (3 mL) were added to HL-60 dishes every 4 days to maintain cell density of ~3 × 105/ml cells. After 24 days, differentiation status of the cells was confirmed using Ly6G for 32Dcl3cl3 cells and CD66b for HL-60 cells via flow cytometry.

value: HL-60 Cell line

value: promyeoloblasts

value: Parental


title: HL60 cell, Differentiation, Rep1

value: Differentiation


title: hVICs-OM-SOLB3


title: Patch cell Sample 630, Pomc+, Chow diet


title: HL60 cell, Parental, Rep1


title: hVICs-OM-1


title: F1290_male_induced

city: Bethesda

first: Luis

middle: A

last: Fernandez de Castro Diaz

state: Maryland

address: 30 Convent Drive

department: SDMHS

institute: NIDCR/NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a customized GRCm38 vM11 genome supplemented with SIRVs and commom mouse trnasgenes using STAR v2.5.2a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: mm10
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Bone marrow stromal cell

extract_protocol:
Bulk RNA was extracted from cultured cells using the TRIzol Reagent protocol without glycogen
Library preparation was performed according to the manufacturer’s instructions for the TruSeq stranded library kit v2. The libraries were then pooled and sequenced on a NovaSeq 6000 sequencer (Illumina) in paired-end mode, 151nt read length.

value: Bone marrow stromal cell

value: GNAS p.R201C

tag: Sex

value: male

value: Doxycycline hyclate 5 mg/mL


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siRELA, replicate2

city: boston

first: Yuanli

last: Zhen

address: 185 cambridge street

department: cancer center

institute: mgh

description:
siRELA-2
processed file_TPM_values

data_processing:
HiSeq Control Software (HCS) was used for image analysis and base calling. Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed (Illumina's bcl2fastq 2.17). Trimmomatic v.0.36 was used to trim sequence reads to remove adapter sequences and nucleotides with poor quality. STAR aligner v.2.5.2b was used to map the trimmed reads to the Homo sapiens reference genome (ENSEMBL).  DESeq2 was employed to compare expression between the sample.
Assembly: Homo sapiens reference genome (ENSEMBL)
Supplementary files format and content: gene names and TPM values of sicramble and siRELA with triplicates

growth_protocol: ICC13-7 cells were cultured in RPMI (Corning, 10-041-cv) supplemented with 10% fetal bovine serum (Gibco, 26140-079), and 1% penicillin/streptomycin (Gibco, 15140-122), used within 10 passages and tested regularly for mycoplasma

extract_protocol:
RNA was extracted from cells with  the Rneasy plus Mini Kit (QIAGEN) in accordance with the manufacturer-prescribed protocol.
RNA samples were quantified using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). RNA integrity was determined using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina was used based on the manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Cells were transfected with siscramble or siRELA

value: Intrahepatic cholangiocarcinoma

value: FGFR2-OPTN fusion

tag: treatment

value: siRELA


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siRELA, replicate1

description:
siRELA-1
processed file_TPM_values

tag: cell type


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siRELA, replicate3

description:
siRELA-3
processed file_TPM_values


title: F1342_male_induced


title: Sample_2_scRNAseq

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Department of Biomedical, Metabolic and Neural Sciences

country: Italy

institute: University of Modena and Reggio Emilia

description: 10x Genomics

data_processing:
Raw base call (BCL) files generated by NextSeq 550 sequencer were demultiplexed using Cell Ranger software to obtain FASTQ files
Alignment to the human reference genome (hg38), filtering and UMI counting are performed. The final output consists of two types of feature-barcode matrices, one in which features are represented by genes (RNA-seq data) and the other in which features are genomic regions (ATAC-seq data).
Assembly: hg38
Supplementary files format and content: Matrix files

molecule: nuclear RNA

source_name: sAML

extract_protocol:
CD34+ cells were purified from frozen BMMNCs. Then, nuclei were isolated following “Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing'' protocol by 10X Genomics. Briefly, cells were resuspended in a lysis buffer containing 0.01% Digitonin for 3 mins, washed twice, resuspended and diluted in Nuclei Buffer in order to load 6000 nuclei for each sample onto 10X cartridge; 1 U/𝜇L RNase inhibitor (Sigma-Aldrich, St.Louis, MO, USA) was added to all nuclei preparation buffers.
Libraries were prepared according to “Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing'' protocol by 10X Genomics and sequenced on an Illumina NextSeq 550 (service by Biodiversa s.r.l, Rovereto, Italy). All samples were subjected to 2x75bp paired-end sequencing.

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: disease state

value: secondary Acute Myeloid Leukemia


title: HL60 cell, Differentiation, Rep2

tag: cell line


title: Sample_1_scATACseq

description: 10x Genomics

library_source: genomic single cell

source_name: PMF

value: Primary Myelofibrosis


title: Hash labels, day 10 [SNU_D10_ST]

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer-Ingelheim

description:
SNU_D10_ST
10x Genomics

data_processing:
.fastq files for transcriptome, guide and label libraries were processed using STARsolo v2.7.10 (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md), which performs cell barcode demultiplexing, mapping to the reference and UMI collapsing.
STAR references for guide and label mapping were generated from .fastq files of guide and label libraries. We used empty droplets algorithm to differentiate between cells and empty drops with ambient RNA.
To assign gRNAs to individual cells we employed a binomial testing approach. For each cell-guide pair, we conducted a binomial test, wherein the count of successes corresponds to the specific gRNA's occurrences, the total number of trials being given by the total gRNA counts in that cell, and the gRNA's background frequency determining the success probability. We limited the maximum number of gRNAs per cell to 3 (for each cell the test was run for the 3 gRNAs with maximum counts).
Assembly: gencode v39
Supplementary files format and content: Tab-separated features, barcodes and expression matrix

growth_protocol: Cell lines were cultured in RPMI 1640 ATCC formulation supplemented with 10% FCS. The media of T47D was additionally supplemented with 0.2 U/ml bovine insulin.

extract_protocol:
Live cells were processed on 10X Genomics Chromium X platform and all subsequent steps were performed according to manufacturers instructions in CG000424 | Rev B Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (Dual Index)
Libraries were prepared according to manufacturers protocol CG000424 | Rev B Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (Dual Index)

treatment_protocol: Briefly, ~60 million cells were transduced with the lentiviral gRNA library at relatively low MOI (10-30% GFP positive cells 24h post-transduction in flow cytometry analysis) per cell line per replicate. Cells were selected with puromycin for two days resulting in >90% GFP positive cells. Selected cells were expanded in media without puromycin and passaged as needed while maintaining a 1000x representation of gRNAs.

tag: timepoint

value: day 10


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siscramble, replicate3

description:
siscramble-3
processed file_TPM_values

value: siscramble


title: hVICs-OM-3

value: hVICs

value: primary human valve interstitail cells

value: osteogenesis medium


title: Hash labels, day 5 [SNU_D5_ST]

description:
SNU_D5_ST
10x Genomics

value: day 5


title: Guide reads, day 5 [SNU_D5_sgRNA]

description:
SNU_D5_sgRNA
10x Genomics


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siscramble, replicate2

description:
siscramble-2
processed file_TPM_values


title: F1342_male_control

value: Bone marrow stromal cell


title: F1293_female_induced

value: GNAS p.R201C

value: female


title: F1162_male_induced

value: male

value: Doxycycline hyclate 5 mg/mL


title: Sample_1_scRNAseq

description: 10x Genomics


title: Guide reads, day 10 [SNU_D10_sgRNA]

description:
SNU_D10_sgRNA
10x Genomics


title: Transcriptome reads, day 10 [SNU_D10_GEX]

description:
SNU_D10_GEX
10x Genomics


title: Spleen_Treg_4

first: Adrian

last: Liston

description:
Spl4_T_S6
Spleen_T_3 in counts.txt

data_processing:
Following sequencing of purified tissue Treg and Tconv populations, the RNAseq data was processed using FastQC 18 for assessing read quality pre-and post-trimming, Trim Galore! 19 for trimming adapter sequences, and STAR aligner 20 for aligning to GENCODE 21 mouse primary assembly vM23, with the raw counts being generated by featureCounts 22. A combined report was generated using MultiQC 23. Raw counts were normalised using DESeq2 24, and global analysis using PCA, t-SNE 25,26 (perplexity parameter at ‘3’) and UMAP 27,28 was performed on the genes post minimum transcript per cell filtering of 0.01 transcripts per cell. Heatmaps were produced using Pearson correlation. Differential expression analysis was performed using the default DESeq2 analysis pipeline, but without using zero-centered Normal priors, log2 fold change shrinkage, outlier replacement using Cook’s distance or independent filtering. The selection criteria was absolute DESeq log2 beta ≥ 2 and adjusted p.value < 0.01. Gene set enrichment analysis was performed using GAGE 29 with the pathway visualisation done by Pathview 30. The script for the RNAseq analysis is available at https://github.com/AdrianListon/TissueTregs. The enriched profiles were compared using the clusterProfiler package 31.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen).RNA concentration and purity were determined using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity with a Bioanalyser 2100 (Agilent).
3′mRNA-seq library preparation and transcriptome analysis was performed by Lexogen (Austria) using the QuantSeq 3′mRNA-Seq Library Prep Kit for Illumina and QuantSeq data analysis workflow.

treatment_protocol: Perfusion, tissue digestion

value: Spleen

value: Treg

value: WT


title: FGFR2-fusion+ intrahepatic cholangiocarcinoma, siscramble, replicate1

description:
siscramble-1
processed file_TPM_values

value: Intrahepatic cholangiocarcinoma

value: FGFR2-OPTN fusion


title: F1290_male_control


title: sample2: zebrafish strain AB, BaP

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% .
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

source_name: Whole-larvae treated from 3 to 6 dpf with benzo[⍺]pyrene (1 μM)

extract_protocol:
Total RNA was extracted from 4 pooled biological replicates using NZYol (NZYTech, Lisbon, Portugal).
200 ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

treatment_protocol: Zebrafish larvae were exposed to 1 μM BaP or 0.1% DMSO from 3 to 6 dpf

tag: strain

value: AB

value: Wild type

tag: age

value: Larvae of 6 dpf

value: Whole-larvae

value: BaP (1 uM)


title: Sample_2_scATACseq

description: 10x Genomics

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: secondary Acute Myeloid Leukemia


title: Transcriptome reads, day 5 [SNU_D5_GEX]

description:
SNU_D5_GEX
10x Genomics

value: day 5


title: sample1: zebrafish strain AB, DMSO

source_name: Whole-larvae treated from 3 to 6 dpf with DMSO (0.1%)

tag: genotype


title: Spleen_Treg_3

description:
Spleen3_T_S5
Spleen_T_2 in counts.txt


title: F1162_male_control

value: Bone marrow stromal cell

value: GNAS p.R201C


title: F1293_female_control

value: female


title: Spleen_Treg_2

description:
Spleen2_T_S4
Spleen_T_1 in counts.txt

value: Spleen


title: Sun-7R-3

city: Shanghai

first: Jie

last: Wang

address: No.168, Changhai Rd., Yangpu District

department: Department of Urology

institute: Changhai Hospital, Naval Medical University(Second Military Medical University)

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human renal cancer cells

growth_protocol: Sun-7C and Sun-7R were routinely generated  (100mm3 culture dish ) on 1640 medium

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: sunitinib-resistant


title: Choroid plexus brain organoids, HIV+CD11b

city: San Francisco

first: Warner

last: Greene

address: 1650 Owens St

institute: Gladstone institutes

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger software (Version V3.1.0)
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: stem cell derived choroid plexus brain organoids

extract_protocol:
Briefly, 8 or more  organoids per condition (mock and HIV infection) were washed twice with DPBS without ions. A single-cell suspension was generated using neural dissociation kit (Miltenyi Biotec) and gentleMACS™ dissociator according to manufacturer’s protocol. Microglia were enriched using CD11b magnetic microbeads (Miltentyi Biotec). Cells were resuspended in an appropriate volume of 0.04% BSA in PBS. Viability and cell numbers were assessed before being subjected to the 10X RNA-sequencing protocol.
Single-cell suspensions per condition were loaded into a Chromium Next GEM Chip G, with a target output of 5000~10000 cells per channel. The chip was then loaded onto a chromium controller v3.1 (l0X Genomics), for single-cell GEM generation and barcoding. For the six loaded channels, GEM generation, barcoding, cDNA amplification and library preparation were performed using the Single-cell 3′ Gel Bead and Library v3.1 kit (10X Genomics) in the BSL3. Amplified cDNA and final libraries were evaluated on a Bioanalyzer for quality control and sequenced together on lllumina NovaSeq 6000 platform.

value: iPSC

value: HIV + CD11b


title: Sun-7R-2


title: Spleen_NoTreg_1

description:
SPL1_NT_S3
Spleen_NT_1 in counts.txt

value: Tconv

value: WT


title: Sun-7R-1


title: Choroid plexus brain organoids, Mock+CD11b

description: 10x Genomics

value: stem cell derived choroid plexus brain organoids

value: Mock medium+ CD11b


title: Sun-7C-3

value: control


title: Choroid plexus brain organoids, A12_HIV

description: 10x Genomics

value: HIV


title: PP_Treg_2

description:
PP_2T_S1
PeyersPatches_T_2 in counts.txt

value: Peyer's patch

value: Treg


title: PP_Treg_3

description:
PP_3T_S26
PeyersPatches_T_3 in counts.txt


title: RNAPII_JMURTK2_Mock_CP_24h

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

data_processing:
Raw sequencing data were trimmed using fastp version 0.12.4 35 and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5, with parameters –k 1
Prior to all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard-tools version 2.26.11 (Li et al., 2009).
CPM values in the genome tracks were calculated by subtracting those in the input tracks as the background value of each cell.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCompare command from deepTools version 3.5.1 include CPM counts for each sample.
Library strategy: CUT&RUN

extract_protocol:
Cells were suspended in 1 x Wash Buffer and attached to concanavalin A beads, permeabilized with 100 μL of Antibody Binding Buffer containing digitonin.
Libraries were created by Takara Bio using the ThruPLEX DNA-Seq Kit (Takara, R400674) and amplified for 16 cycles under the following conditions: denaturation at 98°C for 20 s, followed by annealing and extension at 72°C for 50 s. The samples were sequenced by Takara Bio using the NovaSeq 6000 platform (Illumina), with 150 bp paired end reads.


title: H3R26C, DMSO

city: Pittsburgh

first: Benjamin

middle: Alexander

last: Nacev

address: 5117 Centre Avenue, Suite 2.6b

department: Medicine

institute: University of Pittsburgh

data_processing:
Basecalling was done by Illumina RTA v.3.4.4
FASTQ files were first processed using CellRanger V6 with the mouse genome and transcript reference data (refdata-gex-mm10-2020-A) supplied by 10X genomics. The output from CellRanger was then analyzed using the Seurat R package version 4.
Assembly: MM10
Supplementary files format and content: CellRanger feature, barcode and count matrices

extract_protocol:
Cells were washed with PBS and dissociated using TrypLE Express, which was quenched with Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum. The cells were collected by centrifugation and resuspended in 0.04% BSA in PBS. The cells were passed through a 70 µm cell strainer.
50,000 cells were submitted to the Memorial Sloan Kettering Integrative Genomics Operation core facility for further processing and sequencing on a 10X genomics platform

value: mesenchymal progenitor cells

value: DMSO


title: H3WT, 5-aza


title: H3R26C, 5-aza


title: PP_Treg_1

description:
PP_1T_S21
PeyersPatches_T_1 in counts.txt


title: Choroid plexus brain organoids, A1_Mock

description: 10x Genomics

value: Mock medium


title: H3WT, DMSO


title: RNA_JMURTK2_Mock_NT2_24h

data_processing:
Raw sequencing data were trimmed using trim-galore version 0.6.5-1 and mapped to the hg38 genome using HISAT2 version 2.2.1.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1 include CPM counts for each sample.

extract_protocol:
RNA was collected using the RNeasy Mini Kit (Qiagen).
Library preparation for RNA-seq samples was performed in the Rhelixa using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).


title: PP_NoTreg_2

description:
PP_2NT_S22
PeyersPatches_NT_1 in counts.txt


title: Sun-7C-2


title: Sun-7C-1


title: WT_CD45_pos

city: Saint Louis

first: Sheila

last: Stewart

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4/v5 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary fat pad

extract_protocol:
FVB background MMTV-PyMT+/INK-ATTAC- (WT) and MMTV-PyMT+/INK-ATTAC+ (INK+)  mice were weaned and recruited to studies by 28-30 days of age. Administration of AP20187 (10 mg/kg, 3 doses/week) was delivered through intra peritoneal inections . By 7 weeks of age, tumor-bearing mammary fat pads were digested to single cell suspension, staied, and sorted into CD45+ and CD45- populations. Samples from 2 mice were pooled for each sample.
FVB background MMTV-PyMT+ mice were weaned and recruited to studies by 28-30 days of age. Administration of ABT737 (25 mg/kg/week) or vehicle (Veh) was delivered through intra peritoneal inections . By 7 weeks of age, tumor-bearing mammary fat pads were digested to single cell suspension, staied, and sorted into CD45+ and CD45- populations. Samples from 2 mice were pooled for each sample.
Immune cells: Live/DEAD- CD45+ cells were sorted; Non-immune cells: Live/DEAD- CD45- cells were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Immune Cells

value: Mammary fat pad

value: FVB MMTV-PyMT

value: 7 weeks old


title: H3K27ac_JMURTK2_Mock_CP_24h


title: RNA_JMURTK2_Mock_CP2_24h


title: WT_CD45_neg

description: 10x Genomics

value: Non-immune cells


title: Pancreas_Treg_6

description:
Pan_6_T_S34
Pancreas_T_3 in counts.txt

value: Pancreas


title: Pancreas_Treg_5

description:
Pan_5_T_S32
Pancreas_T_2 in counts.txt


title: Pancreas_Treg_1

description:
Pan_1_T_S30
Pancreas_T_1 in counts.txt


title: Veh_CD45_neg

description: 10x Genomics


title: BRD4_JMURTK2_Mock_CP_24h


title: Pancreas_NoTreg_5

description:
Pan_5_NT_S31
Pancreas_NT_1 in counts.txt

value: Tconv


title: Ear_Lmajor_S2W2

city: Philadelphia

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
The raw reads were mapped to the mouse reference transcriptome (Ensembl; Mus musculus) using Kallisto
All subsequent analyses were carried out using the statistical computing environment R, in RStudio and Bioconductor
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Assembly: Ensembl; Mus musculus version 108
Supplementary files format and content: The processed gene expression matrix file is represented as log2 counts per million (CPM)

source_name: Bulk ears from C57BL/6 L. major-infected mice colonized with S. epidermidis (S2W)

growth_protocol: C57BL/6 mice were topically colonized with 10^8 S. epidermidis every day for a total of five applications and then intradermally infected with 2 x 10^6 L. major parasites. Staphylococcus epidermidis strain Tu3298 expressing a fluorescent protein mCherry (S2W) was a gift of Dr. Tiffany Scharschmidt (UCSF).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Cat #74106) according to the manufacturer’s instructions
Poly(A)+-enriched cDNA libraries Illumina TruSeq Stranded mRNA library prep workflow (QIAGEN, Cat #74106) and Ribo-Zero Gold rRNA depletion (Illumina, Cat # MRZG12324) was used to remove ribosomal content

treatment_protocol: Mice were colonized once per week for the duration of the experiment. At 5 weeks post-infection, lesions were obtained for bulk RNA-seq.

value: bulk Skin-Ear


title: Ear_Lmajor4

source_name: Bulk ears from C57BL/6 L. major-infected mice

value: Lmajor


title: Ear_Lmajor2


title: Ear_Lmajor_S2W5


title: Ear_Lmajor3


title: INK_CD45_pos

description: 10x Genomics


title: INK_CD45_neg

description: 10x Genomics


title: Ear_Lmajor1


title: Fibrous dysplasia_6

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25 human genome using STAR v2.5.2a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.01  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCh38.v25 human genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCh38.v25 human genome
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Femur

value: Femur

value: Bone marrow stromal cell

value: GNAS p.R201H

value: Male


title: LN_Treg_6

description:
LN_6_T_S33
LymphNode_T_2 in counts.txt

value: Lymph node

value: Treg

value: WT


title: Fibrous dysplasia_5

value: Female


title: ABT_CD45_pos

description: 10x Genomics

value: Immune Cells


title: LN_Treg_7

description:
LN_7_T_S35
LymphNode_T_3 in counts.txt


title: LN_Treg_10

description:
LN_10_T_S37
LymphNode_T_1 in counts.txt


title: Ear_S2W5

source_name: Bulk ears from C57BL/6 mice colonized with S. epidermidis (S2W)


title: CTCF_JMURTK2_Mock_CP_24h


title: ABT_CD45_neg

description: 10x Genomics

value: Mammary fat pad


title: Veh_CD45_pos

description: 10x Genomics

value: FVB MMTV-PyMT


title: Fibrous dysplasia_3


title: LN_NoTreg_8

description:
LN_8_NT_S36
LymphNode_NT_1 in counts.txt


title: osn_veh_3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of gene and counts per million matrix including all samples

source_name: Primary mouse mammary fibroblasts line

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini kit.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

treatment_protocol:
Mouse mammary fibroblasts line was derived from the mammary fat pad of a healthy B6 mouse.
For DNA damage-induced senescence (dsn) samples, MMFs at 50-60% confluence were treated with vehicle (H2O) or doxorubicine (100 nM) for 24 hours. Media was refreshed every 3 days. Vehicle group was split routinely to maintain healthy cell density. Cells were lysed for RNA collection on day 7.
For oxidative stres damage-induced senescence (osn) samples, MMFs at 50-60% confluence were treated with vehicle (H2O) or hydrogen peroxide (750 uM) for 2 hours and were allowed to recover for 48 hours. The drug treatment was repeated for two more times. Vehicle group was split routinely to maintain healthy cell density. Cells were lysed for RNA collection on day 6.

value: Primary mouse mammary fibroblasts line

tag: time


title: Fibrous dysplasia_2

value: GNAS p.R201C


title: Ear_S2W3


title: Lung_Treg_6

description:
Lungs_6_T_S38
Lung_T_3 in counts.txt

value: Lung


title: osn_veh_2


title: Fibrous dysplasia_1


title: Ear_S2W1


title: Fibrous dysplasia_4


title: osn_veh_1


title: Lung_Treg_1

description:
Lung_1_T_S12
Lung_T_1 in counts.txt


title: Healthy donor_4

source_name: Iliac crest

value: Iliac crest

value: Wild-type


title: osn_h2o2_1


title: Liver_Treg_4

description:
Liv4_T_S10
Liver_T_3 in counts.txt

value: Liver


title: Healthy donor_6


title: osn_h2o2_3


title: Lung_NoTreg_5

description:
Lungs_5_NT_S39
Lung_NT_1 in counts.txt

value: Tconv


title: Ear_Naive3

source_name: Bulk ears from C57BL/6 mice

value: bulk Skin-Ear

value: naive


title: Ear_Naive1


title: osn_h2o2_2


title: Healthy donor_3

value: Bone marrow stromal cell


title: Healthy donor_5

value: Male


title: Liver_Treg_3

description:
Liver3_T_S9
Liver_T_2 in counts.txt

value: Treg


title: Ear_S2W4


title: bulk ears from RAG-/- L. braziliensis-infected mice + CD8 T cells (rep2)

description:
wk5_cd8_2
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

data_processing:
Samples were sequenced on an Illumina NextSeq 500 to produce 75–base pair single-end reads. The raw reads were mapped to the mouse reference transcriptome (Ensembl; Mus musculus) using Kallisto
All subsequent analyses were carried out using the statistical computing environment R, in RStudio and Bioconductor
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Differentially expressed genes (2-fold and 5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Assembly: Ensembl; Mus musculus version 96
Supplementary files format and content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary files format and content: Tab-delimited text filtered (for genes detected at <1 CPM in at least 3 samples), normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method)
Supplementary files format and content: Tab-delimited text file with study design

growth_protocol: Rag1-/- mice were infected withL. braziliensis(strain MHOM/BR/01/BA788) and subsequently reconstituted with CD8+ T cells alone or CD8+ and CD4+ T cells or did not receive any T cells. 5 weeks post-infection, mice were euthanized, and ears were collected in RNAlater

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Poly(A)+-enriched cDNA libraries Illumina TruSeq Stranded mRNA library were prepared. Ribo-Zero Gold rRNA depletion (Illumina) was used to remove ribosomal content
[sample quality control]  Quality assessment and quantification of RNA preparations and libraries were carried out using an Agilent 4200 TapeStation and Qubit 3, respectively.

value: ears + CD8 T cells

value: RAG-/-

tag: infection

value: L. braziliensis

tag: animal age

value: 6 weeks

value: female


title: dsn_veh_2

value: Primary mouse mammary fibroblasts line


title: Healthy donor_2


title: Ear_Naive4


title: Liver_Treg_1

description:
LIVER1T_S2
Liver_T_1 in counts.txt

value: WT


title: dsn_veh_3


title: bulk ears from RAG-/- L. braziliensis-infected mice + CD8 T cells (rep1)

description:
wk5_cd8_1
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt


title: Healthy donor_1


title: Liver_NoTreg_2

description:
Liver2_NT_S8
Liver_NT_1 in counts.txt


title: Lung_Treg_5

description:
Lungs_5_T_S40
Lung_T_2 in counts.txt

value: Lung


title: Ear_Naive5


title: bulk ears from RAG-/- L. braziliensis-infected mice + CD4 and CD8 T cells (rep3)

description:
wk5_cd4cd8_3
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

value: ears + CD4 and CD8 T cells


title: dsn_veh_1


title: LPL_NoTreg_3

description:
LPL_3NT_S24
LaminaPropriaLymphocyte_NT_1 in counts.txt

value: Small intestinal LPL


title: 31_vcaf

source_name: cancer associated fibroblasts

extract_protocol:
Tumors were collected from 3 10-week-old FVB background MMTV-PyMT mice and then digested with 2 mg/mL Collagenase I and 2 U/mL Dnase. The cells were stained and suject to sorting to isolate each CAF population as described bellow. Sorted cells were directly collected into lyses buffer as instructed by Qiagen RNeasy Micro kit. RNA was further purified following the kit's protocol.
icaf: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C+; m2cafneg: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146-, PDGFRa+, NCAM-; m2cafpos: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146-, PDGFRa+, NCAM+; vCAF: icaf: LIVE/DEAD-, CD45/CD31/EPCAM-, PDGFRb+, Ly6C-, CD146+, PDGFRa-
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

value: FVB MMTV-PyMT

value: cancer associated fibroblasts

value: No teatment

value: 10 weeks old


title: bulk ears from RAG-/- L. braziliensis-infected mice + CD4 and CD8 T cells (rep2)

description:
wk5_cd4cd8_2
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt


title: TGFβ 3

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

data_processing:
RNA-Seq fastq files were processed using Trim-galore
Sequences were aligned using Star aligner
Aligned result files were counted using featureCounts
DEG analysis was carried out with edgeR package
Assembly: GRCh38
Supplementary files format and content: minruidata_rawcount.csv, csv, read count result matrix

source_name: Human dermal fibroblasts

growth_protocol: Human dermal fibroblasts were isolated and cultured in Dulbecco’s modified Eagle’s medium-Ham’s F-12 (DMEM/F-12) containing 10% fetal bovine serum (FBS); Before an experiment, dermal fibroblasts were serum-starved in DMEM/F-12 medium containing 0.1% FBS overnight.

extract_protocol:
Total RNA was isolated with the NucleoSpin RNA II extraction system (Macherey-Nagel, Düren, Germany)
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Dermal fibroblasts were incubated for 48 h with TGFβ (10 ng/ml, #100-21C, PeproTech, Hamburg, Germany), with or without recombinant Adropin34-76 (#032-35, Phoenix Pharmaceuticals, Burlingame, CA, USA) dissolved in sterile distilled water at concentration of 100 ng/ml.

value: Human dermal fibroblasts

value: TGFBeta


title: dsn_doxo_1


title: LPL_Treg_3

description:
LPL_3T_S23
LaminaPropriaLymphocyte_T_3 in counts.txt

value: Treg


title: TGFβ treatment with Adropin34-76 2


title: bulk ears from RAG-/- L. braziliensis-infected mice (rep2)

description:
wk5_naive_2
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

value: ears


title: LPL_Treg_2

description:
LPL_2T_S17
LaminaPropriaLymphocyte_T_2 in counts.txt


title: TGFβ 2


title: 31_m2cafpos


title: Vehicle 3

value: Vehicle


title: Kidney_Treg_3

description:
Kid3_T_S27
Kidney_T_2 in counts.txt

value: Kidney


title: bulk ears from RAG-/- L. braziliensis-infected mice (rep1)

description:
wk5_naive_1
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

value: RAG-/-

value: L. braziliensis

value: 6 weeks


title: bulk ears from RAG-/- naïve mice (rep2)

description:
wk5_nocells_2
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

source_name: bulk ears from RAG-/- naïve mice

value: control

value: female


title: dsn_doxo_2

value: Primary mouse mammary fibroblasts line


title: dsn_doxo_3


title: 31_icaf


title: Kidney_NoTreg_6

description:
Kid6_NT_S28
Kidney_NT_1 in counts.txt

value: Tconv

value: WT


title: TGFβ treatment with Adropin34-76 3


title: Vehicle 2


title: Kidney_Treg_1

description:
Kid1_T_S29
Kidney_T_1 in counts.txt


title: Kidney_Treg_5

description:
Kid5_T_S11
Kidney_T_3 in counts.txt


title: TGFβ 1


title: bulk ears from RAG-/- naïve mice (rep3)

description:
wk5_nocells_3
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt


title: LPL_Treg_1

description:
LPL_1T_S16
LaminaPropriaLymphocyte_T_1 in counts.txt

value: Small intestinal LPL


title: TGFβ treatment with Adropin34-76 1


title: bulk ears from RAG-/- L. braziliensis-infected mice (rep3)

description:
wk5_naive_3
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt


title: bulk ears from RAG-/- L. braziliensis-infected mice + CD4 and CD8 T cells (rep1)

description:
wk5_cd4cd8_1
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

value: ears + CD4 and CD8 T cells


title: 31_m2cafneg

value: FVB MMTV-PyMT

value: cancer associated fibroblasts

value: No teatment

value: 10 weeks old


title: 30_vcaf


title: H3R26C_replicate_3

data_processing:
Transcript abundance was determined using Salmon (v0.8.1) and the GENCODE reference transcript sequences
Transcript counts from Salmon were imported into R with the tximport R Bioconductor package (v1.20), and differentially expressed genes were determined with the DESeq2 R Bioconductor package (v1.32)
Assembly: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary files format and content: genome wide tracks as bigwig files

extract_protocol:
RNA was  extracted using the RNAeasy kit (Qiagen) with on column DNAase I digestion per manufacturer instructions.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit (New England Biolabs) with polyA selection according to the manufacturer instructions.

value: mesenchymal progenitor


title: 30_m2cafneg


title: bulk ears from RAG-/- naïve mice (rep1)

description:
wk5_nocells_1
SacramentoAmorim2024_counts_raw.txt
SacramentoAmorim2024_filtered_normalized_cpmlog2.txt
SacramentoAmorim2024_studyDesign.txt

value: ears


title: IEL_Treg_2

description:
IEL_2T_S19
IntraEpithelialLayer_T_2 in counts.txt

value: Small intestinal IEL

value: Treg


title: H3R26C_replicate_2


title: Input-3

first: Minrui

state: Shanghai

address: 12 Wulumuqi Zhong Road

institute: Fudan University

data_processing:
1. Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4)
2. Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality
3. The clean reads were mapped to the human genome (assembly human genome hg38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software
4. PCR duplicates were removed using Picard (v2.22.2-0)
5. Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff
6. Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10)
7. Pearson correlation coefficient between biological replicates was calculated using deeptools (v3.4.3) multiBamSummary with default parameters
8. TSS heatmap was generated using deeptools (v3.4.3) computeMatrix reference-point (parameters: -a 5000 -b 5000 --skipZeros )
9. Differential analysis based on detected peaks between group C (or group AT) and group T was performed using R package DESeq2 (v1.26.0) with default parameters
10. Motif analysis based on detected peaks was performed using homer findMotifsGenome.pl (v4.10) with default parameters
11. The resulting histograms (genomic ‘signal maps’) were stored in bigWig files using deeptools (v3.4.3) bamCoverage (parameters: --normalizeUsing RPKM --extendReads 200 --ignoreForNormalization chrX chrY --ignoreDuplicates)
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Dermal fibroblasts (1 × 10^7 cells) were fixed with 1% formaldehyde at room temperature for 10 minutes, quenched with 125 mM glycine and harvested.
ChIP-seq assays, including purification of the enriched DNA, were performed using the ChIP-IT High Sensitivity Kit (#53040, Active Motif, Carlsbad, CA, USA). In brief, chromatin was isolated by adding lysis buffer and fragmented by sonication. DNA was sheared to an average length of 200–500 bp with a EpiShear probe sonicator (#53051, Active Motif, Carlsbad, CA, USA). The input DNA was purified with PCR Purification Kit (#28104, QIAGEN Miami, FL, USA).

value: Human dermal fibroblasts

tag: chip-seq antibody


title: 30_m2cafpos


title: Vehicle 1

value: Vehicle


title: Input-2


title: 30_icaf


title: Input-1


title: 27_vacf


title: AT-3

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-608, Novus Biologicals)


title: H3R17C_replicate_3


title: AT-2

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-607, Novus Biologicals)


title: H3R26C_replicate_1


title: Blood_Treg_5

address: Tennis Court Road

institute: University of Cambridge

description:
Blood5_T_S14
Blood_T_3 in counts.txt

value: Blood


title: H3R17C_replicate_2


title: 27_m2cafpos


title: 27_m2cafneg


title: Blood_Treg_4

description:
Blood_4_T_S13
Blood_T_2 in counts.txt


title: H3R17C_replicate_1


title: AT-1

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-606, Novus Biologicals)


title: 27_icaf


title: Blood_Treg_2

description:
Blood2_T_S7
Blood_T_1 in counts.txt

value: WT


title: IEL_Treg_3

description:
IEL_3T_S25
IntraEpithelialLayer_T_3 in counts.txt


title: IEL_Treg_1

description:
IEL_1T_S18
IntraEpithelialLayer_T_1 in counts.txt


title: H3R8C_replicate_3


title: T-3

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-605, Novus Biologicals)

value: TGFb


title: Blood_NoTreg_5

description:
Blood5_NT_S15
Blood_NT_1 in counts.txt

value: Tconv


title: H3R8C_replicate_2


title: H3R8C_replicate_1


title: T-2

value: antibodies against GLI1 (polyclonal, rabbit, #NB600-604, Novus Biologicals)


title: IEL_NoTreg_2

description:
IEL2NT_S20
IntraEpithelialLayer_NT_1 in counts.txt