description: Library name: ROS1-N_delta_294-Flag_ros1-4_line1_Repeat_2

value: shoot


status: Public on Feb 03 2026

type: SRA

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

country: China

institute: Huazhong Agricultural University

description: Library name: ROS1-C_delta_146-Flag_ros1-4_line1_Repeat_1

library_source: genomic

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photoperiod. Shoots and roots of two-week-old plants and stems of four-week-old plants were collected for the indicated genotypes.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp reads, Annoroad Gene Technology).

tag: tissue

tag: genotype

value: ROS1-C_delta_146-Flag_ros1-4 line1

tag: chip antibody

value: Flag


title: D971A_E3-8-17-11_Flag_Repeat_1

description: Library name: D971A_E3-8-17-11_Flag_Repeat_1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak and broadpeak

value: ROS1D971A-Flag/ros1-4 #2


title: in_situ_ROS1D971A

description: Library name: in_situ_ROS1D971A

data_processing:
BatMeth2-pipel (v1.1)60 with the '-fastp' parameter was used to call the DNA methylation levels from the sequencing data, using the Arabidopsis genome (TAIR10)61 as the reference. For visualization, BedGraph files were converted to BigWig format using BatMeth2-bedGraphToBigWig (v1.1)
Assembly: Arabidopsis thaliana : TAIR10
Supplementary files format and content: bigwig

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, 69104). Bisulfite conversion of DNA was performed using the EpiTect Plus Bisulfite Kit (Qiagen, 59124), and bisulfite-treated DNA libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645), following the manufacturer’s instructions.
Llibraries were sequenced on an Illumina NovaSeq X Plus platform

value: in situ ROS1D971A


title: ROS1-Flag_knock-in_Repeat_2

description: Library name: ROS1-Flag_knock-in_Repeat_2

value: ROS1-Flag knock-in


title: DME-Flag/dme_Repeat_1

description: Library name: DME-Flag/dme_Repeat_1

value: DME-Flag/dme


title: Arabidopsis_shoot_drdd_Repeat_1

description: Library name: Arabidopsis_shoot_drdd_Repeat_1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-f BAMPE -B --nomodel --shift -100 --extsize 200 -q 0.01”
Assembly: Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \

extract_protocol:
The extracted nuclei were incubated with Tn5 transposase and tagmentation buffer according to the manufacturer’s instructions (Vazyme, TD501-01). After tagmentation, DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28004). PCR amplification of the library was performed for 10 cycles under the following conditions: 72 °C for 5 min, 98 °C for 30 s, followed by thermocycling at 98 °C for 10 s, 60 °C for 30 s, and 72 °C for 40 s, with a final extension at 72 °C for 5 min.
After PCR amplification, the libraries were purified using VAHTS DNA Clean Beads (Vazyme, N411) and sequenced on an Illumina NovaSeq X Plus platform.

value: drdd


title: D971A_E3-8-17-11

description: Library name: D971A_E3-8-17-11


title: Arabidopsis_shoot_ros1-4_Repeat 3

library_source: transcriptomic

data_processing:
The quality of the sequencing datasets was evaluated using FastQC
Fastp was used with “-l 15 -f 0 -t 0” parameters to filter out adapters and low-quality reads.
The filtered reads were aligned to the corresponding reference genome using Hisat2 with default parameters.
SAMtools with the parameter “-q 30” was used to remove low-quality mapped reads.
The normalization method employed in gene expression was EdgeR’s TMM (Trimmed Mean of M-values).
Assembly: Arabidopsis thaliana : TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include TMM values for each Sample

molecule: total RNA

extract_protocol:
Total RNA was isolated from the indicated tissues using the RNeasy Plant Mini Kit (QIAGEN, 74904). Library preparation was conducted using the RNA-seq Library Prep Kit for Illumina (Vazyme, NR606), following the manufacturer’s instructions.
Libraries were sequenced on an Illumina NovaSeq X Plus platform.


title: Arabidopsis_shoot_ros1-4_Repeat 1


title: D971A_E3-8-7-6_Flag_Repeat_2

description: Library name: D971A_E3-8-7-6_Flag_Repeat_2

value: ROS1D971A-Flag/ros1-4 #1


title: Arabidopsis_shoot_rdd-2_Repeat_2

description: Library name: Arabidopsis_shoot_rdd-2_Repeat_2


title: D971A_E3-8-7-6_Flag_Repeat_1

description: Library name: D971A_E3-8-7-6_Flag_Repeat_1


title: D971A_E3-8-17-11_Flag_Repeat_2

description: Library name: D971A_E3-8-17-11_Flag_Repeat_2


title: Arabidopsis_shoot_nrpd1-3_Repeat 1


title: Arabidopsis_shoot_rdd-2_Repeat_1

description: Library name: Arabidopsis_shoot_rdd-2_Repeat_1


title: Arabidopsis_shoot_hda6_Repeat 1


title: D971A_E3_8_24_12_Flag_Repeat_1

description: Library name: D971A_E3_8_24_12_Flag_Repeat_1

value: ROS1D971A-Flag/ros1-4 #3


title: D971A_E3_8_24_12_Flag_Repeat_2

description: Library name: D971A_E3_8_24_12_Flag_Repeat_2


title: Arabidopsis_shoot_ros1-4_Repeat 2


title: D971A_E3_8_24_12

description: Library name: D971A_E3_8_24_12


title: Arabidopsis_shoot_Col-0_Repeat 1


title: Arabidopsis_shoot_hda6_Repeat 2


title: D971A_E3-8-7-6

description: Library name: D971A_E3-8-7-6


title: Arabidopsis_shoot_nrps1-3_ros1-4

value: nrps1-3 ros1-4


title: Arabidopsis_shoot_nrpd1-3_Repeat 3


title: Arabidopsis_shoot_ros1-4


title: Arabidopsis_stem_Col-0

source_name: stem

value: stem


title: Arabidopsis_shoot_hda6


title: Arabidopsis_shoot_Col-0_Repeat 3


title: Arabidopsis_shoot_hda6_Repeat 3


title: Arabidopsis_root_Col-0

source_name: root

value: root


title: Arabidopsis_shoot_sdg2-4_ros1-4_Repeat_2

value: sdg2-4 ros1-4


title: Arabidopsis_shoot_Col-0_Repeat 2


title: Arabidopsis_shoot_sdg2-4_ros1-4_Repeat_1


title: Arabidopsis_shoot_hda6_ros1-4

value: hda6 ros1-4


title: Arabidopsis_shoot_nrpd1-3


title: Arabidopsis_shoot_nrpd1-3_Repeat 2


title: Arabidopsis_shoot_ros1-4_Repeat_1


title: Arabidopsis_shoot_gcn5


title: Arabidopsis_shoot_gcn5_ros1-4

value: gcn5 ros1-4


title: NM450_043

status: Public on Feb 04 2026

type: genomic

city: Miaoli County

first: Shih-Sheng

last: Jiang

address: 35, Keyan Road, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: The bisulfite-converted DNA was hybridized to the Illumina HumanMethylation450/EPIC/EPIC v2.0 BeadChips according to the manufacturer’s Infinium HD protocol. Hybridization was performed at 48°C for 16 hours in a humidity-controlled chamber. Following hybridization, chips were washed using Illumina-supplied buffers to remove unbound DNA prior to extension.

scan_protocol: Arrays were scanned on the Illumina iScan System using default parameters. Images were processed using Illumina GenomeStudio Methylation Module software to extract signal intensities and compute methylation beta values. Quality control was performed using internal control probes.

data_processing: For NM450 (450K), NM850 (EPIC), and NM900 (EPICv2) samples, raw intensities were background-corrected, dye-bias-equalized, and functionally normalized using the ‘preprocessFunnorm’ function in the minfi R package. CpGs on sex chromosomes, containing SNPs (MAF ≥5%), in repetitive regions, or with poor detection p-values were removed. Three processed DNA methylation datasets were generated: NM450-114 (NM450 samples), NMC-47 (combined NM850 and NM900), and NMC-161 (combined NM450, NM850, and NM900), retaining CpGs common to the platforms within each dataset (373,275 CpGs for NM450-114; 558,115 CpGs for NMC-47; 298,801 CpGs for NMC-161). For each dataset, beta values were inverse-rank transformed to a standard normal distribution and regressed on confounders including sex, age, medical operation status, batch, top genotyping PCs, and top methylation PCs. The residuals were inverse-rank transformed again to produce the final processed DNA methylation data.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: lung

label_protocol: Genomic DNA (500 ng) underwent bisulfite treatment with the EZ DNA Methylation Kit (Zymo Research). Following conversion, samples were processed according to the Illumina Infinium HD Methylation Assay protocol, including amplification, fragmentation, and hybridization steps. Labeling was incorporated during the single-base extension step.

extract_protocol: Tissue DNA was extracted from lung tissues using the QIAamp DNA Mini Kit (Qiagen Inc, USA). Bisulfite conversion of tissue DNA was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Inc, USA) according to the manufacturer’s instructions. DNA methylation of bisulfite-converted DNA was measured using the abovementioned platform, according to Illumina’s standard procedure in Genetech Biotech Co., Ltd.

value: lung

tag: age

tag: gender

value: Female

tag: smoking status

value: Non-smoking

tag: batch


title: Arabidopsis_shoot_nrpd1-3_Repeat_1

value: shoot


title: Arabidopsis_shoot_met1-9_Repeat_1


title: Arabidopsis_shoot_sdg2-4_Repeat_2


title: Arabidopsis_shoot_gcn5_ros1-4_Repeat_2


title: Arabidopsis_shoot_hda6_ros1-4_Repeat_2


title: Arabidopsis_shoot_hda6_Repeat_1


title: Arabidopsis_shoot_gcn5_ros1-4_Repeat_1


title: Arabidopsis_shoot_nrpd1-3_ros1-4_Repeat_2

value: nrpd1-3 ros1-4


title: Arabidopsis_shoot_hda6_Repeat_2


title: Arabidopsis_shoot_nrpd1-3_Repeat_2


title: Arabidopsis_shoot_nrpd1-3_ros1-4_Repeat_1


title: Arabidopsis_shoot_ros1-4_Repeat_2


title: Arabidopsis_stem_Col-0_Repeat_2


title: Arabidopsis_shoot_Col-0_Repeat_2


title: Arabidopsis_shoot_met1-9_Repeat_2


title: Arabidopsis_shoot_Col-0_Repeat_1


title: Arabidopsis_stem_Col-0_Repeat_1


title: Arabidopsis_shoot_sdg2-4_Repeat_1


title: Arabidopsis_shoot_hda6_ros1-4_Repeat_1


title: Arabidopsis_root_Col-0_Repeat_1


title: Arabidopsis_root_Col-0_Repeat_2


title: Arabidopsis_stem_ROS1-FLAG/ros1-4_Flag_Repeat_1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

value: Flag


title: Arabidopsis_shoot_sdg2-4_H3K4me3_Repeat_2


title: Arabidopsis_shoot_gcn5_Repeat_1


title: Arabidopsis_shoot_sdg2-4_H3K4me3_Repeat_1


title: Arabidopsis_shoot_ROS1-FLAG/ros1-4_hda6_Flag_Repeat_1

value: ROS1-FLAG/ros1-4 hda6


title: Arabidopsis_shoot_ros1-4_input_Repeat_1


title: Arabidopsis_shoot_ros1-4_H3K9ac_Repeat_2


title: Arabidopsis_stem_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_gcn5_Repeat_2


title: Arabidopsis_shoot_sdg2-4_ros1-4_H3K4me3_Repeat_2


title: Arabidopsis_shoot_ros1-4_H3K9ac_Repeat_1


title: Arabidopsis_shoot_sdg2-4_ros1-4_H3K4me3_Repeat_1


title: Arabidopsis_shoot_rChIP_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_nrps1-3_ros1-4_input_Repeat_2


title: Arabidopsis_shoot_rChIP_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_nrps1-3_ros1-4_input_Repeat_1


title: Arabidopsis_shoot_NRPD1-FLAG/nrpd1-3_ros1-4_Flag_Repeat_2

value: NRPD1-FLAG/nrpd1-3 ros1-4


title: Arabidopsis_shoot_NRPD1-FLAG/nrpd1-3_Flag_Repeat_2


title: Arabidopsis_shoot_nrpd1-3_input_Repeat_2


title: Arabidopsis_shoot_hda6_ros1-4_H3K9ac_Repeat_2


title: Arabidopsis_shoot_nrpd1-3_input_Repeat_1


title: Arabidopsis_shoot_ros1-4_H3K4me3_Repeat_2


title: Arabidopsis_shoot_DML3-FLAG/dml3-2_Flag_Repeat_2


title: Arabidopsis_shoot_eChIP_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_eChIP_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_ROS1-FLAG/ros1-4_hda6_Flag_Repeat_2


title: Arabidopsis_shoot_ros1-4_input_Repeat_2


title: Arabidopsis_shoot_cutNC_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_cutN_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_cutNC_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_NRPD1-FLAG/nrpd1-3_ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_cutC_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_NRPD1-FLAG/nrpd1-3_Flag_Repeat_1


title: Arabidopsis_shoot_ros1-4_H3K4me3_Repeat_1


title: Arabidopsis_shoot_hda6_ros1-4_H3K9ac_Repeat_1


title: Arabidopsis_shoot_hda6_H3K9ac_Repeat_1


title: Arabidopsis_shoot_gcn5_ros1-4_H3K9ac_Repeat_2

value: gcn5  ros1-4


title: Arabidopsis_shoot_hda6_H3K9ac_Repeat_2


title: Arabidopsis_shoot_aChIP_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_Col-0_H3K4me1_Repeat_2


title: Arabidopsis_shoot_gcn5_H3K9ac_Repeat_2


title: Arabidopsis_root_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_gcn5_ros1-4_H3K9ac_Repeat_1


title: Arabidopsis_shoot_DML3-FLAG/dml3-2_Flag_Repeat_1


title: Arabidopsis_shoot_gcn5_H3K9ac_Repeat_1


title: Arabidopsis_shoot_DML2-FLAG/dml2-2_Flag_Repeat_2


title: Arabidopsis_shoot_DML2-FLAG/dml2-2_Flag_Repeat_1


title: Arabidopsis_shoot_cutN_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_cutCXXC_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_cutC_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: Arabidopsis_shoot_cutCXXC_ROS1-FLAG/ros1-4_Flag_Repeat_1


title: GC Day 0

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

country: USA

institute: NIAID

description: Library name: GC_D0

library_source: transcriptomic single cell

data_processing:
Data processed with BCL2fastq
Mapped to Mmul_10-2020 using cellranger 7.2.0
processed with Seurat v5
Assembly: Mmul_10-2020
Supplementary files format and content: Seurat files

organism: Macaca mulatta

source_name: bronchoalveolar lavage

extract_protocol:
Cells were resuspended in 100uL of live dead NIR 780 (Thermo Cat#L34994), diluted 1:1000 in PBS and incubated for 15 minutes. Cells were washed and stained with 50uL surface stain antibodies diluted in PBS + 1% FBS and incubated for 20 min at 4°C. Cells were washed 3 times with PBS + 1% FBS, before fixation with eBioscience Intracellular Fixation & Permeabilization Buffer Set (Thermo Cat# 88-8824-00) for 16 hours at 4°C. After fixation cells were washed with eBioscience Permeabilization Buffer, resuspended in 50uL intracellular stains diluted in Perm. Buffer, and stained for 30 min at 4°C. After staining cells were washed with Perm. Buffer 2x and resuspended in 180uL of PBS + 1% FBS + 0.05% Sodium Azide for analysis on the Cytek Aurora 5L.
Cryopreserved BAL cells were processed for scRNAseq using the 10X Genomics Chromium Single Cell 3′ kit (v3.1). Samples were then stained with unique TotalSeq-A hashtag antibodies (HTO) as per manufacturer’s (Biolegend) protocol. Equal number of cells from each sample were pooled and super-loaded on a 10X Genomics Next GEM chip and single cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate cDNA and HTO libraries were performed following 10X Genomics and Biolegend’s protocol respectively. Libraries were pooled and sequenced on an Illumina NovaSeq. Sequenced data was processed using cellranger (version 7.1.0) to demultiplex the libraries. The reads were aligned to mmul_10 genome to generate count tables. Sample batch effects were corrected using Harmony R package (version 1.2.3). The count tables were then further processed and analyzed using the Seurat (version 5.2.1) in R (version 4.4.1).

value: bronchoalveolar lavage

tag: cell type

value: mixed

tag: treatment

value: glucocorticoid immunosuppression


title: Control Day 13

description: Library name: Control_D10

value: Control


title: Arabidopsis_shoot_Col-0_H3K9me2_Repeat_2


title: Control Day 4

description: Library name: Control_D4


title: Kva-OM26, K24, R4

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

description:
Library name: 949_E4_K24
826_K24_txome.fa

data_processing:
Single-end strand-specific 65 bp reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 4.9 with options “-m 25 -q 30 -O 6 --trim-n --max-n 1”.
Gene expression quantification was performed using salmon version 1.9.0 with the “-l A” option. For each condition, a specific reference transcriptome was built concatenating both the genetic background's and the capsular region's fasta transcriptomes.
Assembly: Klebsiella pneumoniae
Supplementary files format and content: Tab delimited file generated by salmon and containing gene expression quantification.
Supplementary files format and content: Condition-specific transcriptome fasta file used by salmon to quantify gene expression.

organism: Klebsiella pneumoniae

source_name: bacterial cells

growth_protocol: Overday culture was started in minimal medium supplemented with 0.2% of glucose from freshly plated colonies and incubated at 37°C until OD600 reached ~0.6-0.8.

extract_protocol:
RNA was extracted using the Macherey Nagel Trizol (ref:740971.250) according to the manufacturer’s instructions and treated with DNase I provided in the kit. RNA concentration, quality, and integrity from four independent replicates were checked using the Invitrogen Qubit and the Agilent 2100 Bioanalyzer system.
cDNA libraries were prepared from 1–3 µg of total RNA using the Illumina Total RNA Library Preparation Kit (Illumina, USA), following the manufacturer’s protocol. To facilitate rRNA depletion, Ribo-Zero Plus Microbiome probes (Illumina) were used. Index barcodes were added by PCR for 13 cycles. Unbound adaptors and index primers were re-moved via purification with AMPure XP magnetic beads (Beckman Coulter, USA). The final libraries displayed an electrophoretic size distribution ranging from 250 to 900 bp, with a predominant peak at approximately 400 bp, as assessed on a 3500 Fragment Analyzer (Agilent Technologies, USA). Sequencing was performed on a NextSeq 2000 system using a P3 50-cycle flow cell (Illumina) to generate 67-nt single-end, dual-indexed reads.

value: bacterial cells

tag: background

tag: serotype

tag: replicate


title: Kva-OM26, K24, R3

description:
Library name: 949_E3_K24
826_K24_txome.fa


title: Arabidopsis_shoot_Col-0_H3K9ac_Repeat_2


title: Control Day 7

description: Library name: Control_D7


title: Arabidopsis_shoot_Col-0_H3K9me2_Repeat_1


title: Arabidopsis_shoot_Col-0_H3K9ac_Repeat_1


title: Arabidopsis_shoot_Col-0_H3K4me3_Repeat_2


title: Arabidopsis_shoot_Col-0_H3K27me3_Repeat_2


title: Arabidopsis_shoot_Col-0_H3K4me3_Repeat_1


title: Kva-OM26, K2, R4

description:
Library name: 872_E4_K2
826_K2_txome.fa


title: Arabidopsis_shoot_Col-0_H3K4me1_Repeat_1


title: Arabidopsis_shoot_aChIP_ROS1-FLAG/ros1-4_Flag_Repeat_2


title: Arabidopsis_shoot_Col-0_H3K27me3_Repeat_1


title: Kva-OM26, K1, R2

description:
Library name: 871_E2_K1
826_K1_txome.fa


title: Kva-OM26, K1, R1

description:
Library name: 871_E1_K1
826_K1_txome.fa


title: Kva-OM26, K2, R1

description:
Library name: 872_E1_K2
826_K2_txome.fa


title: Arabidopsis_root_ROS1-FLAG/ros1-4_Flag_Repeat_2

value: root


title: Kva-OM26, dCap, R3

description:
Library name: 856_E3_dCap
826_WT_txome.fa

value: dCap


title: GC Day 13

description: Library name: GC_D10


title: GC Day 4

description: Library name: GC_D4


title: Kva-OM26, WT, R1

description:
Library name: 826_E1_WT
826_WT_txome.fa

value: WT


title: Preinfection GC

description: Library name: GC_Pre


title: GC Day 7

description: Library name: GC_D7


title: Kva-OM26, dCap, R1

description:
Library name: 856_E1_dCap
826_WT_txome.fa


title: Control Day 0

description: Library name: Control_D0


title: Kpn CIP 52.145, K3, R4

description:
Library name: 909_E4_K3
55_K3_txome.fa

value: Kpn CIP 52.145


title: Kpn CIP 52.145, K3, R1

description:
Library name: 909_E1_K3
55_K3_txome.fa


title: Kpn CIP 52.145, K2, R3

description:
Library name: 882_E3_K2
55_K2_txome.fa


title: Kpn CIP 52.145, K3, R2

description:
Library name: 909_E2_K3
55_K3_txome.fa


title: Kpn CIP 52.145, K3, R3

description:
Library name: 909_E3_K3
55_K3_txome.fa


title: Preinfection Control

description: Library name: Control_Pre


title: Kpn CIP 52.145, K1, R2

description:
Library name: 870_E2_K1
55_K1_txome.fa


title: Kpn CIP 52.145, K1, R3

description:
Library name: 870_E3_K1
55_K1_txome.fa


title: Kva-OM26, K24, R1

description:
Library name: 949_E1_K24
826_K24_txome.fa


title: Kva-OM26, K2, R3

description:
Library name: 872_E3_K2
826_K2_txome.fa


title: Kpn CIP 52.145, K24, R4

description:
Library name: 859_E4_K24
55_K24_txome.fa


title: Kpn CIP 52.145, K24, R2

description:
Library name: 859_E2_K24
55_K24_txome.fa


title: Kva-OM26, K2, R2

description:
Library name: 872_E2_K2
826_K2_txome.fa


title: Kpn CIP 52.145, dCap, R2

description:
Library name: 821_E2_dCap
55_WT_txome.fa


title: Kpn CIP 52.145, dCap, R4

description:
Library name: 821_E4_dCap
55_WT_txome.fa


title: Kpn CIP 52.145, WT, R2

description:
Library name: 55_E2_WT
55_WT_txome.fa


title: Kva-OM26, K1, R3

description:
Library name: 871_E3_K1
826_K1_txome.fa


title: Kpn CIP 52.145, WT, R4

description:
Library name: 55_E4_WT
55_WT_txome.fa


title: Kpn ST45, K24, R4

description:
Library name: 793_E4_K24
51_WT_txome.fa

value: Kpn ST45


title: Kpn ST45, K24, R2

description:
Library name: 793_E2_K24
51_WT_txome.fa


title: Kpn ST45, K24, R1

description:
Library name: 793_E1_K24
51_WT_txome.fa


title: Kva-OM26, dCap, R4

description:
Library name: 856_E4_dCap
826_WT_txome.fa


title: Kva-OM26, WT, R3

description:
Library name: 826_E3_WT
826_WT_txome.fa


title: Kva-OM26, dCap, R2

description:
Library name: 856_E2_dCap
826_WT_txome.fa


title: Kpn ST45, K3, R3

description:
Library name: 792_E3_K3
51_K3_txome.fa


title: Kva-OM26, WT, R2

description:
Library name: 826_E2_WT
826_WT_txome.fa


title: Kpn ST45, K3, R2

description:
Library name: 792_E2_K3
51_K3_txome.fa


title: Kpn CIP 52.145, K2, R2

description:
Library name: 882_E2_K2
55_K2_txome.fa


title: Kpn ST45, K3, R1

description:
Library name: 792_E1_K3
51_K3_txome.fa


title: Kpn CIP 52.145, K2, R4

description:
Library name: 882_E4_K2
55_K2_txome.fa


title: Kpn ST45, K1, R4

description:
Library name: 790_E4_K1
51_K1_txome.fa


title: Kpn CIP 52.145, K24, R1

description:
Library name: 859_E1_K24
55_K24_txome.fa


title: Kpn CIP 52.145, K24, R3

description:
Library name: 859_E3_K24
55_K24_txome.fa


title: Kpn CIP 52.145, dCap, R1

description:
Library name: 821_E1_dCap
55_WT_txome.fa


title: Kpn CIP 52.145, WT, R3

description:
Library name: 55_E3_WT
55_WT_txome.fa


title: Kpn ST45, dCap, R3

description:
Library name: 711_E3_dCap
51_WT_txome.fa


title: Kpn ST45, K1, R2

description:
Library name: 790_E2_K1
51_K1_txome.fa


title: Kpn CIP 52.145, K1, R4

description:
Library name: 870_E4_K1
55_K1_txome.fa


title: Kpn ST45, K24, R3

description:
Library name: 793_E3_K24
51_WT_txome.fa


title: Kpn ST45, K3, R4

description:
Library name: 792_E4_K3
51_K3_txome.fa


title: Kpn ST45, WT, R3

description:
Library name: 51_E3_WT
51_WT_txome.fa


title: Kpn ST45, WT, R1

description:
Library name: 51_E1_WT
51_WT_txome.fa


title: Kpn BJ1, K3, R4

description:
Library name: 784_E4_K3
26_K3_txome.fa

value: Kpn BJ1


title: Kpn BJ1, K24, R2

description:
Library name: 785_E2_K24
26_K24_txome.fa


title: Kpn BJ1, K24, R1

description:
Library name: 785_E1_K24
26_K24_txome.fa


title: Kpn CIP 52.145, WT, R1

description:
Library name: 55_E1_WT
55_WT_txome.fa


title: Kpn ST45, K2, R4

description:
Library name: 791_E4_K2
51_K2_txome.fa


title: Kpn ST45, K2, R3

description:
Library name: 791_E3_K2
51_K2_txome.fa


title: Kpn ST45, K2, R2

description:
Library name: 791_E2_K2
51_K2_txome.fa


title: Kpn BJ1, K3, R2

description:
Library name: 784_E2_K3
26_K3_txome.fa


title: Kpn ST45, K2, R1

description:
Library name: 791_E1_K2
51_K2_txome.fa


title: Kpn BJ1, K2, R4

description:
Library name: 783_E4_K2
26_WT_txome.fa


title: Kpn ST45, K1, R3

description:
Library name: 790_E3_K1
51_K1_txome.fa


title: Kpn ST45, K1, R1

description:
Library name: 790_E1_K1
51_K1_txome.fa


title: Kpn BJ1, K2, R3

description:
Library name: 783_E3_K2
26_WT_txome.fa


title: Kpn ST45, dCap, R4

description:
Library name: 711_E4_dCap
51_WT_txome.fa


title: Kpn BJ1, K2, R1

description:
Library name: 783_E1_K2
26_WT_txome.fa


title: Kpn ST45, dCap, R2

description:
Library name: 711_E2_dCap
51_WT_txome.fa


title: Kpn BJ1, dCap, R4

description:
Library name: 752_E4_dCap
26_WT_txome.fa


title: Kpn ST45, dCap, R1

description:
Library name: 711_E1_dCap
51_WT_txome.fa


title: Kpn ST45, WT, R2

description:
Library name: 51_E2_WT
51_WT_txome.fa


title: Kpn ST45, WT, R4

description:
Library name: 51_E4_WT
51_WT_txome.fa


title: Kpn BJ1, K3, R3

description:
Library name: 784_E3_K3
26_K3_txome.fa


title: Kpn BJ1, WT, R3

description:
Library name: 26_E3_WT
26_WT_txome.fa


title: Kpn BJ1, dCap, R3

description:
Library name: 752_E3_dCap
26_WT_txome.fa


title: Kpn BJ1, dCap, R2

description:
Library name: 752_E2_dCap
26_WT_txome.fa


title: Kpn BJ1, K24, R4

description:
Library name: 785_E4_K24
26_K24_txome.fa


title: Kpn BJ1, K3, R1

description:
Library name: 784_E1_K3
26_K3_txome.fa


title: Kpn BJ1, WT, R1

description:
Library name: 26_E1_WT
26_WT_txome.fa


title: Kpn BJ1, K2, R2

description:
Library name: 783_E2_K2
26_WT_txome.fa


title: Kpn BJ1, K1, R4

description:
Library name: 782_E4_K1
26_K1_txome.fa


title: Kpn BJ1, K1, R3

description:
Library name: 782_E3_K1
26_K1_txome.fa


title: Kpn BJ1, K1, R2

description:
Library name: 782_E2_K1
26_K1_txome.fa


title: Kpn BJ1, WT, R4

description:
Library name: 26_E4_WT
26_WT_txome.fa


title: Kpn BJ1, dCap, R1

description:
Library name: 752_E1_dCap
26_WT_txome.fa


title: WT2 (F2_alpha), RNA-seq_H_E9-5_WT_rep2

city: Bern

first: Ali

last: Hashemi Gheinani

address: Murtenstrasse 35, Department for BioMedical Research, Functional Urology

department: DBMR

country: Switzerland

institute: University of Bern

description:
Library name: Sample 2
F

data_processing:
Sequencing quality was monitored with the Illumina Sequencing Analysis Viewer (version 2.4.7), and base call files were demultiplexed and converted to FASTQ format using bcl2fastq v2.20.
RNA-seq reads were aligned to the mouse reference genome assembly GRCm39.110 (mm39) using STAR (version 2.7.9a).
Gene-level read counts (in .csv format) were obtained with the featureCounts function from the Subread package (version 2.0.1).
Analysis of differentially expressed genes (DEGs) was performed using the DESeq2 package (version 1.30.1) within Bioconductor.
Assembly: GRCm39.110 (mm39)
Supplementary files format and content: csv file listing normalized read counts (FPKM)

organism: Mus musculus

source_name: embryonic heart

extract_protocol:
Stage-matched embryonic hearts were micro-dissected and collected in RNAlater (Sigma, R0901). Total RNA was extracted using the Qiagen RNeasy Micro Kit (Cat. No. 74004).
Per replicate, RNA quantity and integrity were evaluated using a Qubit 4.0 Fluorometer with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32855) and a Fragment Analyzer System with the Fragment Analyzer RNA Kit (Agilent, DNF-471), respectively.
Sequencing libraries were generated from 300 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020595) in combination with TruSeq RNA UD Indexes (Illumina, 20022371), according to the manufacturer’s protocol. Pooled libraries were quantified using a Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Fisher Scientific, Q32854) and assessed for fragment size distribution on an Agilent Fragment Analyzer with the HS NGS Fragment Kit (Agilent, DNF-474). Equimolar amounts of each library were then pooled and sequenced in paired-end mode on an Illumina NovaSeq 6000 platform using the NovaSeq 6000 SP Reagent Kit v1.5 (300 cycles; Illumina, 20028400).

value: embryonic heart

tag: cell line

value: wildtype


title: MUT1 (F1A), RNA-seq_H_E9-5_H2-URIdd_rep1

description:
Library name: Sample 4
F

value: H2-URI d/d


title: Kpn BJ1, K1, R1

description:
Library name: 782_E1_K1
26_K1_txome.fa


title: Kpn BJ1, WT, R2

description:
Library name: 26_E2_WT
26_WT_txome.fa


title: MUT3 (M2A), RNA-seq_H_E9-5_H2-URIdd_rep3

description:
Library name: Sample 6
M


title: dyW/dyW AAV9-Spc/CBh-DL 5

city: Basel

first: Eleonora

last: Maino

address: Spitalstrasse 41

department: Biozentrum

institute: University of Basel

description: Library name: dyW_DL_35716

data_processing:
FASTQ files were aligned to the indexed mouse transcriptome mm10 using Salmon with the flags validateMappings, seqBias and gcBias.
Assembly: GRCm38/mm10
Supplementary files format and content: Salmon output quant.sf file, contains plain-text, tab-separated

molecule: polyA RNA

source_name: TA muscle

extract_protocol:
total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen)
Libraries were prepared using the TruSeq stranded mRNA library kit (Illumina) starting from 200 ng of RNA.

value: TA muscle

value: dyW/dyW

tag: Sex

value: male


title: dyW/dyW 6

description: Library name: dyW_CTRL_19582

value: non-injected

value: female


title: dyW/dyW AAV9-Spc/CBh-DL 2

description: Library name: dyW_DL_39345


title: MUT2 (F2A), RNA-seq_H_E9-5_H2-URIdd_rep2

description:
Library name: Sample 5
F


title: dyW/dyW 5

description: Library name: dyW_CTRL_15800


title: WT1 (F1_alpha), RNA-seq_H_E9-5_WT_rep1

description:
Library name: Sample 1
F


title: dyW/dyW AAV9-Spc/CBh-DL 1

description: Library name: dyW_DL_39336


title: dyW/dyW 1

description: Library name: dyW_CTRL_39298


title: WT3 (M1_alpha), RNA-seq_H_E9-5_WT_rep3

description:
Library name: Sample 3
M


title: dyW/dyW 2

description: Library name: dyW_CTRL_16389


title: wild-type 6

description: Library name: WT_CTRL_27095

value: wild-type


title: AAV9-Spc/CBh-DL 2

description: Library name: WT_DL_35714

value: wild-type/dyW


title: dyW/dyW AAV9-Spc/CBh-DL 6

description: Library name: dyW_DL_35721


title: dyW/dyW AAV9-Spc/CBh-DL 3

description: Library name: dyW_DL_35673


title: dyW/dyW AAV9-Spc/CBh-DL 4

description: Library name: dyW_DL_35707


title: wild-type 5

description: Library name: WT_CTRL_27545


title: dyW/dyW 3

description: Library name: dyW_CTRL_19966


title: AAV9-Spc/CBh-DL 3

description: Library name: WT_DL_33398


title: dyW/dyW 4

description: Library name: dyW_CTRL_37896


title: ATAC-seq_NPC-day7_rep2

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

description: ATAC-seq library

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings
Filtered and trimmed reads were aligned to mm10 genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates as above. The 5′ ends of the reads were offset by +4 bases for reads on the Watson strand, and by −5 bases for the reads on the Crick strand, to reflect the exact location of Tn5 insertion. For visualization, a 20 bp fragment was centered on each Tn5 insertion site and its coverage was calculated at single-base resolution in the whole genome using bedtools genomeCoverageBed. Coverage data was normalized to sequence depth, scaled to 10e7 and  converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: Read density in bigwig format

source_name: mESC (46C)

growth_protocol: 46C cells were maintained in GMEM supplemented with 10% Serum and LIF.

extract_protocol:
ATAC-seq library (detailed protocol: PMID: 24097267)
ATAC-seq library prep using 50000 cells using protocol in Buenrostro et al., 2013 (PMID: 24097267)

treatment_protocol: For differentiation, three million 46C Cells were seeded 24 hours (h) prior to differentiation on 0.1% gelatine coated T75 Corning flasks in the maintenance medium. On Day-0, one flask of ESCs were harvested and rest of the cells were supplied with differentiation media ((1:1DMEM/F12: Neuro basal medium (GIBCO, #31330-032 and 21103-049 respectively) supplemented with 0.5x B27 (Invitrogen, #17504044), 0.5x N2 (Invitrogen, #17502048), L-Glutamine and 50mM 2--mercaptoethanol (GIBCO, #31350010)). Cells were then cultured for 7 days with daily media changes after day-2 NPC differentiation was monitored visually through expression of the Sox1-GFP reporter.

value: mESC (46C)

tag: time

value: 30 minutes

value: NPC differentiation Day-7


title: AAV9-Spc/CBh-DL 1

description: Library name: WT_DL_35708


title: wild-type 1

description: Library name: WT_CTRL_35674


title: ATAC-seq_NPC-day7_rep1

description: ATAC-seq library


title: ATAC-seq_mESC_rep2

description: ATAC-seq library

value: NPC differentiation Day-0


title: epi_D18.5-3

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

description:
Library name: epi_D18.5-3
e18_5_barcodes.tsv.gz
e18_5_features.tsv.gz
e18_5_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing,gene counting and aggregation were made using the Cell Ranger software v7.0.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoid

extract_protocol:
The organoids were dissociated into single cells using the STEMdiff Cardiomyocyte Dissociation Kit (Stemcell Technologies, #05025). The cell suspension was then loaded into Chromium microfluidic chips for single-cell RNA sequencing.
The cell suspension was processed with 3’ (v2 or v3, depending on the project) chemistry and barcoded using a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed using the Chromium Single Cell 3’ v2 (v2 or v3, depending on the project) reagent kit (10X Genomics), following the manufacturer’s instructions.

value: organoid


title: wild-type 2

description: Library name: WT_CTRL_39297


title: epi_D9.5-2

description:
Library name: epi_D9.5-2
e9_5_barcodes.tsv.gz
e9_5_features.tsv.gz
e9_5_matrix.mtx.gz


title: control_4wpi sample 3

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

description:
Library name: 24.0164
sci-RNA-seq3

data_processing:
Data were demultiplexed, barcode processing, gene counting, and aggregation according to the BBI pipeline available at https://github.com/bbi-lab/bbi-sci
Assembly: GRCm39
Supplementary files format and content: Monocle3 RDS matrix files

molecule: nuclear RNA

source_name: whole brain

extract_protocol:
Mice were euthanized with CO2, and whole brains removed. Brains were split down the midline, snap frozen in liquid nitrogen, and stored at -80C until snRNAseq protocol was initiated. snRNAseq was performed as a fee-for-service by the Brotman Baty Advanced Technology Lab (BAT-Lab) at the University of Washington.
Libraries were constructed as described for sci-RNA-seq3 in Martin et al, DOI: 10.1038/s41596-022-00752-0

value: whole brain

value: control


title: wild-type 4

description: Library name: WT_CTRL_27542


title: rNLS_4wpi sample 5

description:
Library name: 24.0169
sci-RNA-seq3

value: rNLS


title: Esophageal cells, K5:Smo - 5 days post tamoxifen administration - All living cells

city: Anderlecht

first: Louison

last: Descampe

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: Sample 2
All living cells from thoracic segment of the esophagus have been sorted based on EpCam expression

data_processing:
Data were demuliplexed using cellranger demux with Illumina bcl2fastq to generate FASTQs for R1 and R2 paired-end as well as the sample index.
Cell Ranger version 9.0.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome
Assembly: mm10
Supplementary files format and content: H5 binary format. Feature Barcode Matrix of single cell sequencing in hierarchical data format

source_name: Thoracic esophagus

extract_protocol:
Tissues were digested and sorted in 1ml PBS 0.04% BSA. Samples were loaded on a chromium chip and processed using the Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) following manufacturer’s recommendations.
Multiplexed libraries were obtained following manufacturer’s recommendations of Chromium Single Cell 3’ Reagent kits v4 (10x Genomics) and loaded on a Novaseq 6000 (Illumina). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Thoracic esophagus


title: wild-type 3

description: Library name: WT_CTRL_19967


title: PMA-induced THP-1 cells-2

city: Yantai

first: qingling

last: jiang

address: No. 346, Guanhai Road, Laishan District

institute: Binzhou Medical University

description:
Library name: SAMPLE8_PMA2
SAMPLE8_PMA2

data_processing:
Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained. Cuffdiff or edgeR was used for differential expression analysis.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: grch38
Supplementary files format and content: FPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood

value: mononuclear cells

value: PMA-induced


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis Isotype cont biol rep 3

city: Cincinnati

first: Mengchi

last: Jiao

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: K6_S53

data_processing:
Raw RNA-seq reads were processed using the nf-core/rnaseq pipeline (v3.17.0) executed via Nextflow (v23.04.1) and Singularity (v3.7.0).
Reads were aligned to the mouse reference genome GRCm39 (Ensembl release 109) using STAR (v2.7.10a).
Transcript-level quantification was performed with Salmon (v1.10.1) in selective alignment mode.
Gene-level counts were generated via tximport using the provided GTF annotation (Ensembl GRCm39.109).
Output gene count matrices were exported by the pipeline and used for downstream analysis in R.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

extract_protocol:
The cells were pelleted and resuspended in 700 μL of QIAzol lysis buffer. For homogenization, lysate was passed through a Qiashredder column (Qiagen, cat. 79656). The homogenized lysate was frozen at -80 °C for less than 1 week prior to RNA isolation. RNA was isolated using a MiRNeasy micro kit (Qiagen, cat. 217084) according to manufacturers’ instructions, with the optional DNase step and a minor modification. Specifically, 30 mL of ethanol specified in the instructions was substituted with 45 mL of isopropanol (added to buffer RWT).
Eluted RNA was shipped to Novogene (California) for quality control analysis, library preparation, and sequencing. A SMART-seq V4 Ultra Low input RNA kit (Takara Bio) was used to generate non-directional libraries from total RNA. Paired-end base-pair libraries were generated for all samples using a NovaSeq 6000 system. Samples were sequenced at a depth of 40 million reads per sample.

treatment_protocol: Naïve OTI (1x105 cells, unless otherwise indicated) CD8 T cells were prepared in buffer containing gentamicin (100 μg/mL) and injected retro-orbitally. Myocarditis was induced via intraperitoneal administration of αCTLA-4 (BioXCell, clone: 9D9, Cat. BE0164, 200μg) and αPD-1 (Leinco, clone: RPM1-14, cat. P362, 200μg).

value: Heart

value: Immune cells, exclude T cells

value: Ova DTG

value: OTI + Isotype


title: epi_D9.5-1

description:
Library name: epi_D9.5-1
e9_5_barcodes.tsv.gz
e9_5_features.tsv.gz
e9_5_matrix.mtx.gz


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis Isotype cont biol rep 2

description: Library name: K5_S52


title: ATAC-seq_mESC_rep1

description: ATAC-seq library


title: THP-1 cells-2

description:
Library name: SAMPLE5_Normal2
SAMPLE5_Normal2


title: epi_D18.5-4

description:
Library name: epi_D18.5-4
e18_5_barcodes.tsv.gz
e18_5_features.tsv.gz
e18_5_matrix.mtx.gz


title: THP-1 cells-1

description:
Library name: SAMPLE4_Normal1
SAMPLE4_Normal1


title: ATRA-induced THP-1 cells-2

description:
Library name: SAMPLE2_ATRA2
SAMPLE2_ATRA2

value: ATRA-induced


title: rNLS_4wpi sample 4

description:
Library name: 24.0168
sci-RNA-seq3


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis ICI biol rep 1

description: Library name: K1_S48

value: OTI + ICI


title: epi_D18.5-2

description:
Library name: epi_D18.5-2
e18_5_barcodes.tsv.gz
e18_5_features.tsv.gz
e18_5_matrix.mtx.gz


title: control_4wpi sample 5

description:
Library name: 24.0167
sci-RNA-seq3


title: control_4wpi sample 4

description:
Library name: 24.0166
sci-RNA-seq3


title: C-KIT-MOUSE-3

city: Beijing

first: yu

middle: peng

last: Li

address: Dong Dan San Tiao 5 Beijing , China

institute: Peking Union Medical College

description:
Library name: C-KIT-MOUSE-3
C-KIT-MOUSE-3

data_processing:
The raw FASTQ format data were filtered and trimmed using Trimmomatic, and mapped to the complete mouse reference genome using STAR. The read counts aligned to genes were calculated using featureCounts, followed by the analysis of differentially expressed genes using the DESeq2R package. Enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed using the clusterProfiler package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample ...

source_name: testes

extract_protocol:
Cells sorted and purified by flow cytometry were subjected to total RNA extraction, followed by quantification using a NanoDrop 2000.
The Illumina RNA-Seq protocol was used to construct standard RNA-Seq libraries. The libraries were then sequenced on the Illumina NovaSeq platform, generating paired-end reads with a length of 150 bp.

value: testes

value: germ cell

value: WT


title: C-KIT-MOUSE-2

description:
Library name: C-KIT-MOUSE-2
C-KIT-MOUSE-2


title: C-KIT-MOUSE-1

description:
Library name: C-KIT-MOUSE-1
C-KIT-MOUSE-1


title: epi_D18.5-1

description:
Library name: epi_D18.5-1
e18_5_barcodes.tsv.gz
e18_5_features.tsv.gz
e18_5_matrix.mtx.gz

value: organoid


title: Esophageal cells, normal esophageal mucosa - All living cells

description:
Library name: Sample 1
All living cells from the esophageal biopsie have been sorted based on EpCam expression

data_processing:
Data were demuliplexed using cellranger demux with Illumina bcl2fastq to generate FASTQs for R1 and R2 paired-end as well as the sample index.
Cell Ranger version 7.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on GRCh38 reference genome
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 binary format. Feature Barcode Matrix of single cell sequencing in hierarchical data format

source_name: Esophageal mucosa

extract_protocol:
Biopsies were digested and sorted in 1ml PBS 0.04% BSA. Samples were loaded on a chromium chip and processed using the Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) following manufacturer’s recommendations.
Multiplexed libraries were obtained following manufacturer’s recommendations of Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) and loaded on a Novaseq 6000 (Illumina). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Esophageal mucosa


title: Esophageal cells, WT - All living cells

description:
Library name: Sample 1
All living cells from thoracic segment of the esophagus have been sorted based on EpCam expression


title: rNLS_4wpi sample 3

description:
Library name: 24.0165
sci-RNA-seq3

value: whole brain


title: control_4wpi sample 2

description:
Library name: 24.0163
sci-RNA-seq3

value: control


title: epi_D7.5-2

description:
Library name: epi_D7.5-2
e7_5_barcodes.tsv.gz
e7_5_features.tsv.gz
e7_5_matrix.mtx.gz


title: PMA-induced THP-1 cells-3

description:
Library name: SAMPLE9_PMA3
SAMPLE9_PMA3


title: rNLS_4wpi sample 1

description:
Library name: 24.016
sci-RNA-seq3

value: rNLS


title: CellLine_OvCAR3_rep2

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description: Library name: OvCAR3_2

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium) using STAR (v2.7.9a)
Counting of the reads was performed with rsem using the ensembl annotation GRCh37.87
Assembly: hg19
Supplementary files format and content: tab-delimited text file of rsem expected counts

growth_protocol: Isolated mesothelial cells and fibroblasts were cultured in DMEM:F12 Glutamax medium, supplemented either with 20% FBS for the mesothelial cells or 10% FBS for the fibroblasts, and 1% pen/strep until use. Mesothelial cells and fibroblasts were previously characterized using different markers, such as calretinin, α smooth muscle actin (αSMA) and/or fibroblast activation protein (FAP). Adipocytes were cast immediately in a collagen I based gel (ThermoFisher, Cat. A1048301) following the protocol previously described and kept in M199 medium (Gibco, Cat. 22350029) supplemented with 10% FBS and 1% pen/strep until further use.CD14+ monocytes were positively selected using CD14 MicroBeads (Milteny Biotec, Cat. 130-050-201) and LS columns (Milteny Biotec, Cat. 130-042-401) following the manufacturer protocol. AOCS1 and OvCAR3 cell lines were maintained in RPMI 1640 (Gibco, Cat. 21875034) supplemented with 10% fetal bovine serum (FBS, Gibco, Cat. ), 1% L-glutamine (Sigma, G7513-100ML) and 1% penicillin/streptomycin (pen/strep)(Sigma, Cat. P4333). G164 cell line was maintained in DMEM:F12 medium (Gibco, Cat. 31331093) with the addition of 4% human serum (Sigma, Cat. H4522) and 1% pen/strep. For the pentaculture model, adipocyte gels were anchored to the bottom of the well of a 96-well plate using a layer of activated collagen. 40,000 human primary fibroblasts were plated on the adipocyte gels, followed after 2 hours by 200,000 mesothelial cells per gel. After 24 hours, 40,000 malignant cells and 400,000 CD14+ monocytes per gel were added to the model. After 24 hours, gels were scooped out and placed in G164 culture medium in a 24-well plate, 3 gels per well.

extract_protocol:
RNA isolation was performed using RNeasy microkit (Qiagen, Cat. 74004) according to manufacturer’s instructions.
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using ribosomal depletion.

value: cell line


title: PMA-induced THP-1 cells-1

description:
Library name: SAMPLE7_PMA1
SAMPLE7_PMA1

value: Peripheral blood

value: mononuclear cells


title: rNLS_4wpi sample 2

description:
Library name: 24.0162
sci-RNA-seq3


title: epi_D7.5-1

description:
Library name: epi_D7.5-1
e7_5_barcodes.tsv.gz
e7_5_features.tsv.gz
e7_5_matrix.mtx.gz


title: control_4wpi sample 1

description:
Library name: 24.0161
sci-RNA-seq3


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis ICI biol rep 3

description: Library name: K3_S50

value: Heart


title: IL1R2-MOUSE-2

description:
Library name: IL1R2-MOUSE-2
IL1R2-MOUSE-2


title: ATRA-induced THP-1 cells-3

description:
Library name: SAMPLE3_ATRA3
SAMPLE3_ATRA3


title: THP-1 cells-3

description:
Library name: SAMPLE6_Normal3
SAMPLE6_Normal3


title: IL1R2-MOUSE-1

description:
Library name: IL1R2-MOUSE-1
IL1R2-MOUSE-1


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis Isotype cont biol rep 1

description: Library name: K4_S51

value: Immune cells, exclude T cells


title: ATRA-induced THP-1 cells-1

description:
Library name: SAMPLE1_ATRA1
SAMPLE1_ATRA1


title: THY1-MOUSE-1

description:
Library name: THY1-MOUSE-1
THY1-MOUSE-1


title: Purified CD45+CD90.2- cardiac-infiltrating cells myocarditis ICI biol rep 2

description: Library name: K2_S49

value: Ova DTG


title: Esophageal cells,  esophageal columnar metaplasia mucosa - All living cells

description:
Library name: Sample 2
All living cells from the esophageal biopsie have been sorted based on EpCam expression


title: K5:Smo organoids treated with TGFb + BMP4 + ibuprofen - 3 days rep1

description:
Library name: Sample 5
so-mm90_LDE8-ARN-TB-ibu-160924-29_S51

data_processing:
Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Cell Ranger version 3.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample and genome annotations

source_name: esophageal epithelial cells

growth_protocol: Esophagi were dissected from K5:Smo mice (5 days after tamoxifen injection) and digested. The single cell suspension was resuspended in matrigel. KSFM medium was then added. Cells were maintained during 13 days in culture. Medium was changed every 2 days. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Organoids were harvested and collected in TRK lysis buffer. Total RNA was extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)

treatment_protocol: TGFb inhibitor = A8301, 500 nM; BMP4, 20 ng/ml; TGFb1, 1ng/ml; Ibuprofen, 500 uM. Treatment of 72h  and renewed every 24h.

value: esophageal epithelial cells

value: TGFb1 + BMP4 + ibuprofen


title: mesothelial_cells_donor54

description: Library name: mesothelial_54

value: primary cells


title: K5:Smo organoids treated with TGFb + BMP4 - 3 days rep2

description:
Library name: Sample 4
so-mm90_LDE6-ARN-TB-160924-52_S49

value: TGFb1 + BMP4


title: CellLine_AOCS1_rep2

description: Library name: AOCS_2


title: THY1-MOUSE-3

description:
Library name: THY1-MOUSE-3
THY1-MOUSE-3

value: testes

value: germ cell


title: THY1-MOUSE-2

description:
Library name: THY1-MOUSE-2
THY1-MOUSE-2

value: WT


title: fibroblasts_donor54

description: Library name: svf_54


title: K5:Smo organoids treated with TGFb inhibitor (CTRL) - 3 days rep1

description:
Library name: Sample 1
so-mm90_LDE2-ARN-Tinh-160924-25_S45

value: TGFb inhibitor


title: CellLine_OvCAR3_rep1

description: Library name: OvCAR3_1


title: IL1R2-MOUSE-3

description:
Library name: IL1R2-MOUSE-3
IL1R2-MOUSE-3


title: CellLine_G164_rep1

description: Library name: G164_1


title: Esophageal cells, EpcamHigh K5:Smo + ibuprofen - 12 weeks post tamoxifen administration rep2

description:
Library name: Sample 5
LDE5-LD65-12K5Smoibu.5 CPM

extract_protocol:
Tissues were digested, sorted in TRK lysis buffer and extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)

treatment_protocol: Ibuprofen 0.6g/l in the drinking bottle

value: Thoracic esophagus

value: ibuprofen 0.6g/l

tag: sorted cells

value: All living cells from thoracic segment of the esophagus have been sorted based on EpCam expression


title: K5:Smo organoids treated with TGFb + BMP4 + ibuprofen - 3 days rep2

description:
Library name: Sample 6
so-mm90_LDE9-ARN-TB-ibu-160924-65_S52


title: CellLine_AOCS1_rep1

description: Library name: AOCS_1

value: cell line


title: monocytes_donor54

description: Library name: monocytes_54


title: CellLine_G164_rep2

description: Library name: G164_2


title: Esophageal cells, EpcamHigh K5:Smo + ibuprofen - 12 weeks post tamoxifen administration rep1

description:
Library name: Sample 4
LDE4-LD65-11K5Smoibu.4 CPM


title: K5:Smo organoids treated with TGFb + BMP4 - 3 days rep1

description:
Library name: Sample 3
so-mm90_LDE5-ARN-TB-160924-28_S48


title: fibroblasts_donor60

description: Library name: svf_60


title: K5:Smo organoids treated with TGFb inhibitor (CTRL) - 3 days rep2

description:
Library name: Sample 2
so-mm90_LDE3-ARN-Tinh-160924-61_S46


title: fibroblasts_donor61

description: Library name: svf_61


title: hCOs, SOBP 14Gy, rep3

city: Groningen

first: Yuting

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: University Medical Center Groningen

description: Library name: SOBP_14Gy_3

data_processing:
Sequencing read alignement Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform
Trimmed sequence reads were mapped to GRCh38 using the Lexogen BlueBee Genomics Platform
Read count extraction and CPM normalization were performed using RStudio, DEG analysis was performed using the function "edgeR"
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Cortical organoids

extract_protocol:
RNA was isolated from hCOs 48 hours after irradiation using the RNeasy Lipid Tissue Mini Kit (Qiagen, 74804) following the manufacture’s instruction.
Libraries were generated using the Lexogen QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen, 015.96), with 200 ng of RNA used as input for each sample. All libraries were pooled in equimolar concentrations, and a 1.8 pM superpool with a 15% PhiX spike-in was sequenced on a NextSeq 500 using 75 bp single reads.

value: Cortical organoids

value: Embryonic stem cells

value: Wildtype


title: hCOs, SOBP 14Gy, rep4

description: Library name: SOBP_14Gy_4


title: hCOs, SOBP 14Gy, rep1

description: Library name: SOBP_14Gy_1


title: Esophageal cells, EpcamHigh K5:Smo + ibuprofen - 12 weeks post tamoxifen administration rep3

description:
Library name: Sample 6
LDE6-LD65-14K5Smoibu.6 CPM


title: pentaculture_G164_donor61

description: Library name: penta_G164_61

value: primary cells and cell lines


title: pentaculture_AOCS1_donor61

description: Library name: penta_AOCS_61


title: Esophageal epithelial cells, EpcamHigh, K5:Smo untreated - 12 weeks post tamoxifen administration rep2

description:
Library name: Sample 2
LDE2-LD62-16K5Smo.2 CPM

value: untreated


title: pentaculture_OvCAR3_donor61

description: Library name: penta_OvCAR3_61


title: Esophageal epithelial cells, EpcamHigh, K5:Smo untreated - 12 weeks post tamoxifen administration rep3

description:
Library name: Sample 3
LDE3-LD62-17K5Smo.3 CPM


title: pentaculture_OvCAR3_donor60

description: Library name: penta_OvCAR3_60


title: hCOs, SOBP 14Gy, rep2

description: Library name: SOBP_14Gy_2


title: adjacent_tissue_donor61

description: Library name: adjacent_tissue_61


title: hCOs, Plateau 14Gy, rep4

description: Library name: Plateau_14Gy_4


title: Esophageal epithelial cells, EpcamHigh, K5:Smo untreated - 12 weeks post tamoxifen administration rep1

description:
Library name: Sample 1
LDE1-LD62-13K5Smo.1 CPM


title: pentaculture_AOCS1_donor60

description: Library name: penta_AOCS_60


title: adjacent_tissue_donor54

description: Library name: adjacent_tissue_54


title: pentaculture_G164_donor60

description: Library name: penta_G164_60


title: hCOs, Plateau 14Gy, rep1

description: Library name: Plateau_14Gy_1


title: hCOs, Plateau 14Gy, rep3

description: Library name: Plateau_14Gy_3


title: hCOs, Photon 14Gy, rep4

description: Library name: Photon_14Gy_4


title: hCOs, Plateau 14Gy, rep2

description: Library name: Plateau_14Gy_2


title: hCOs, SOBP 7Gy, rep4

description: Library name: SOBP_7Gy_4


title: hCOs, Photon 14Gy, rep2

description: Library name: Photon_14Gy_2


title: pentaculture_OvCAR3_donor54

description: Library name: penta_OvCAR3_54


title: hCOs, Photon 14Gy, rep1

description: Library name: Photon_14Gy_1


title: organoids treated with TGFb + BMP4 - 3 days rep2

description:
Library name: Sample 8
LDE14

data_processing:
Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Cell Ranger version 3.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Assembly: mm10
Supplementary files format and content: Excel file including raw counts for each sample and genome annotations

growth_protocol: Esophagi were dissected from wild-type mice and digested. The single cell suspension was resuspended in matrigel. KSFM medium was then added. Cells were maintained during 13 days in culture. Medium was changed every 2 days. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

treatment_protocol: TGFb inhibitor = A8301, 500 nM; BMP4, 20 ng/ml; TGFb1, 1ng/ml. Treatment of 72h  and renewed every 24h.

value: esophageal epithelial cells

value: wild-type


title: organoids treated with TGFb + BMP4 - 3 days rep1

description:
Library name: Sample 7
LDE4


title: organoids treated with TGFb - 3 days rep1

description:
Library name: Sample 5
LDE3


title: organoids treated with BMP4 + TGFb inhibitor (BMP4) - 3 days rep2

description:
Library name: Sample 4
LDE12

value: BMP4 + TGFb inhibitor


title: pentaculture_AOCS1_donor54

description: Library name: penta_AOCS_54


title: hCOs, SOBP 7Gy, rep3

description: Library name: SOBP_7Gy_3


title: hCOs, Photon 14Gy, rep3

description: Library name: Photon_14Gy_3


title: hCOs, SOBP 7Gy, rep2

description: Library name: SOBP_7Gy_2


title: organoids treated with BMP4 + TGFb inhibitor (BMP4) - 3 days rep1

description:
Library name: Sample 3
LDE2


title: hCOs, SOBP 7Gy, rep1

description: Library name: SOBP_7Gy_1


title: hCOs, Plateau 7Gy, rep3

description: Library name: Plateau_7Gy_3


title: hCOs, Plateau 7Gy, rep2

description: Library name: Plateau_7Gy_2


title: hCOs, Photon 7Gy, rep4

description: Library name: Photon_7Gy_4


title: hBMSC-TERT4 cells, Ad 7 days + Ob 4 days

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description:
Library name: SingleCellRNA_7dAd_4dOb_BM
column label in processed files: TERT_7dAd_4dOb

data_processing:
Bulk RNA-seq reads were aligned to GRCh37 (hg19) genome using STAR (Dobin A, et al., Bioinformatics 29:15-21) and default settings. Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing all time points and including Replicate information in the model.
Raw base calls of 10x libraries were demultiplexed into fastq files and then aligned and quantified at the exon and intron level using zUMI (Parekh S, et al., Gigascience 7:giy059) and STAR (Dobin A, et al., Bioinformatics 29:15-21) with genome GRCh38. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411) to yield a gene count matrix for 29939 cells.
Raw base calls of Parse libraries were demultiplexed into fastq files, which contain sequencing information of several libraries. Spliting of reads according to  loading scheme of a WTmini and alignment to genome GRCh38 as well as quantification of gene counts were done using the Parse Trailmaker pipeline, with the libraries of interest being distributed in wells A7 to A9 (Ob-Ad-Ob-Ad-Ob-Ad-Ob-Ad) and A10 to A12 (Ad-Ob-Ad-Ob-Ad-Ob-Ad-Ob). Due to low recovery of sample Ad-Ob-Ad-Ob-Ad-Ob-Ad-Ob, we later only analyzed the Ob-Ad-Ob-Ad-Ob-Ad-Ob-Ad sample. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411).
Assembly: GRCh38 for scRNA-seq and snRNA-seq, GRCh37 for bulk RNA-seq
Supplementary files format and content: Counts_normalDiff_TERT.txt, tab delimited file with Homer derrived raw gene counts of bulk RNA-seq data for normal differentiation (derrived from Rauch A, et al., Nature Genetics 51:716-727).
Supplementary files format and content: Counts_Media_Change.txt, tab delimited file with Homer derrived raw gene counts of bulk RNA-seq data for cells with media change.
Supplementary files format and content: TERT_MSC.dgecounts.rds, TERT_7dOb.dgecounts.rds, TERT_7dAd.dgecounts.rds, TERT_7dOb_4dAd.dgecounts.rds, and TERT_7dAd_4dOb.dgecounts.rds, tab delimited files to retrieve zUMI derrived raw gene count matrices of the individual 10x scRNA-seq libraries.
Supplementary files format and content: Parse_transdiff.mtx, all_genes_parse.csv, and cell_metadata_parse.csv, tab delimited files to retrieve Parse trailmaker derrived raw gene count matrices of Parse snRNA-seq data.

source_name: immortalized human stromal cells from bone marrow

growth_protocol: hBMSC-TERT4 cells (Simonsen JL, et al. 2002. Nat Biotechnol. 20(6):592-6.) were seeded in tissue culture flasks and expanded in culture medium consisting of minimum essential medium (MEM, 32561-094, Invitrogen) supplemented with 10% fetal bovine serum (FBS, 16000044, Life Technologies) and 1% penicillin/streptomycin (P/S, 15140-130, Invitrogen). They were incubated at 37 °C with 5% CO2 and 95% humidity. The culture medium was changed three times a week, and the cells were either passaged or set out for differentiation when reaching 80-90% confluency.

extract_protocol:
Bulk RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
For Parse snRNA-seq, cells have been trypsinized and spun down at 200 g cells. Supernatant was carefully removed without touching the upper layer. Cells were subjected to nuclei isolation following a protocol adjusted from Hauwaert et al. (STAR Protocols 2:100612). Briefly, cells were dounced 5 times in nuclei isolation buffer consisting of 250 mM Sucrose (84097, Sigma-Aldrich), 10 mM HEPES (22320022, Thermo Fisher Scientific), 1.5 mM MgCl2 (M2670, Sigma-Aldrich), 10 mM KCl (P9541, Sigma-Aldrich), 0.001% IGEPAL CA-630 (I8896, Sigma-Aldrich), 0.2 mM DL-Dithiothreitol (43819, Sigma-Aldrich) and 0.5 U/mL RNase inhibitor (40,000 U/mL, M0314L, Bionordika) in DEPC-treated water. Nuclei were passed through a 30 µm cell strainer, centrifugated at 200 g for 10 min at 4C and resuspended in nuclei resuspension buffer consisting of 1% BSA (A9418, Sigma-Aldrich) in PBS, 2 mM MgCl2 and 0.04 U/µL RNase inhibitor in PBS followed by a final transfer through a 30 µm cell strainer. Nuclei fixation was carried out according to manufacturer’s instructions (Parse Biosciences Evercode WT, version 2).
For 10x scRNA-seq, cells have been trypsinized and spun down at 200 g and washed twice in culture media. Cells were separated using a 40 µm mesh, washed 3 times in PBS with 0.04% non-acetylated BSA, and cell numbers were adjusted to 0.7 million cells per ml followed by a final transfer through a 40 µm mesh.
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.
scRNA-seq: Libraries were prepared according to manufactures instructions (10x Genomics). snRNA-seq: Libraries were prepared using a WTmini loading scheme according to manufactures instructions (Parse).

treatment_protocol: hBMSC-TERT4 cells were stimulated with osteogenic (MEM (32561-094, Invitrogen)  supplemented with 10% FBS, 1% P/S, 5mM ß-glycerophosphate (50020-100, Sigma-Aldrich), 10nM dexamethasone (D4902, Sigma-Aldrich), 50µg/mL 2-phosphate ascorbic acid (A4544, Sigma-Aldrich) and 10nM 1,25-vitamin D3 (D1530, Sigma-Aldrich)) or adipogenic (DMEM (41965062, Thermo Fisher Scientific) supplemented with 10% FBS, 1% P/S, 100nM dexamethasone, 3µg/mL insulin (I9278, Sigma-Aldrich), 1µM rosiglitazone (BRL, 71740, Cayman Chemicals) and 225µM 3-isobutyl-1-methylxanthine (IBMX, I5879-5G, Sigma-Aldrich)) media according to the time points indicated.

value: adipogenic diff 7 days + osteogenic diff 4 days

tag: time point

value: 7 + 4 days


title: organoids treated with TGFb inhibitor (CTRL) - 3 days rep2

description:
Library name: Sample 2
LDE11


title: hBMSC-TERT4 cells, Ob 7 days + Ad 4 days

description:
Library name: SingleCellRNA_7dOb_4dAd_BM
column label in processed files: TERT_7dOb_4dAd

value: immortalized human stromal cells from bone marrow

value: osteogenic diff 7 days + adipogenic diff 4 days


title: hCOs, Plateau 7Gy, rep1

description: Library name: Plateau_7Gy_1

tag: tissue


title: hCOs, Photon 7Gy, rep3

description: Library name: Photon_7Gy_3

tag: genotype


title: organoids treated with TGFb inhibitor (CTRL) - 3 days rep1

description:
Library name: Sample 1
LDE1

value: TGFb inhibitor


title: organoids treated with TGFb - 3 days rep2

description:
Library name: Sample 6
LDE13


title: hCOs, Plateau 7Gy, rep4

description: Library name: Plateau_7Gy_4


title: hCOs, Photon 7Gy, rep1

description: Library name: Photon_7Gy_1


title: hBMSC-TERT4 cells, Ad 7 days

description:
Library name: SingleCellRNA_7dAd_BM
column label in processed files: TERT_7dAd

value: adipogenic diff 7 days

value: 7 days


title: Sample 2 Esophageal cells, K5:Smo + ibuprofen - 12 weeks post tamoxifen administration - All living cells

description: Library name: Sample 2

data_processing:
Data were demuliplexed using cellranger demux with Illumina bcl2fastq to generate FASTQs for R1 and R2 paired-end as well as the sample index.
Cell Ranger version 3.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome
Assembly: mm10
Supplementary files format and content: H5 binary format. Feature Barcode Matrix of single cell sequencing in hierarchical data format

extract_protocol:
Tissues were digested and sorted in 1ml PBS 0.04% BSA. Samples were loaded on a chromium chip and processed using the Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) following manufacturer’s recommendations.
Multiplexed libraries were obtained following manufacturer’s recommendations of Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) and loaded on a Novaseq 6000 (Illumina). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Thoracic esophagus

value: ibuprofen, 0.6g/l

value: All living cells from thoracic segment of the esophagus have been sorted based on EpCam expression


title: Sample 1 Esophageal cells, K5:Smo untreated - 12 weeks post tamoxifen administration - All living cells

description: Library name: Sample 1


title: hCOs, Photon 7Gy, rep2

description: Library name: Photon_7Gy_2

value: Cortical organoids

value: Embryonic stem cells


title: hBMSC-TERT4 cells, Ob 4 days + Ad 4 days + Ob 4 days + Ad 4 days + Ob 4 days + Ad 4 days + Ob 4 days + Ad 4 days

description:
Library name: SingleCellRNA_MultipleSwitch_BM_Parse
column label in processed files: StartOb


title: hCOs, Control, rep3

description: Library name: Control_3

value: Wildtype


title: hCOs, Control, rep4

description: Library name: Control_4


title: hBMSC-TERT4 cells, day 0

description:
Library name: SingleCellRNA_Msc_BM
column label in processed files: TERT_MSC

value: undifferentiated

value: day 0


title: hCOs, Control, rep2

description: Library name: Control_2


title: L. johnsonii mono-colonized, male, rep4

city: Atlanta

first: Timothy

middle: R

last: Sampson

state: Georgia

address: 615 Michael St

institute: Emory University

description: Library name: 21173FL-01-38

data_processing:
Sequencing quality control was performed using FastQC (version 0.11.9) and reads were pseudoaligned to the mouse reference genome (GRCm39) using Kallisto (version 0.44.0)
Assembly: GRCm39
Supplementary files format and content: Kallisto abundance.h5 files

source_name: Brain

extract_protocol:
Brains were perfused with PBS then homogenized using a Wheaton dounce tissue grinder (with 0.114 ±0.025mm pestle clearance) in culture media comprised of HBBS with 1.5% HEPES, and 0.5% glucose. Cells were then transferred to a 35% isotonic percoll gradient solution and spun 20 minutes at 700 x g to remove the myelin layer. Transcription (Actinomycin D, Sigma #A1410) and translation (Anisomycin, Sigma #A9789) inhibitors were added to every solution throughout both procedures to prevent transcriptional changes that could impact downstream results. The remaining cells were washed several times in HBBS culture media before undergoing immunopanning. Cells were resuspended in 0.02% BSA in PBS and incubated at room temperature on a 10cm petri dish with anti-CD11b and secondary antibody already adhered to the dish (Thermo Scientific, 14-0112-82 and Jackson 112-005-167) for 10-15 minutes. After incubation the unadhered cells were washed away and remaining cells scraped off the plate directly into Trizol (Zymo Research R2050-1-200) and stored at -80 C until later use.
RNA was extracted from isolated brain myeloid cells using the Qiagen RNeasy Kit (#74106) according to the manufacturer’s guidelines. Bulk RNA-sequencing libraries were created for each sample using the Takara SMART-Seq mRNA HT LP kit (#634792) according to the manufacturer’s protocol and recommendations.

treatment_protocol: Germ-free 3-4 month old DBA/2NTac mice were mono-colonized with either Bacteroides thetaiotaomicron, Clostridium celatum, Lactobacillus johnsonii, or Escherichia coli for 2 weeks.

value: Brain

value: CD11b+ brain myeloid cells

value: L. johnsonii mono-colonized

value: male

tag: bacterial strain

value: Lactobacillus johnsonii str. VPI 7960


title: hBMSC-TERT4 cells, Ob 7 days

description:
Library name: SingleCellRNA_7dOb_BM
column label in processed files: TERT_7dOb

value: immortalized human stromal cells from bone marrow

value: osteogenic diff 7 days


title: hBMSC-TERT4 cells, Ad 3 days + Ob 4 days + Ad 4 days, rep 2

description:
Library name: RNA_3dAd_4dOb_4dAd_BM_rep2
Counts_Media_Change.txt
column label in processed files: 3dAd_4dOb_4dAd_2

value: adipogenic diff 3 days + osteogenic diff 4 days + adipogenic diff 4 days


title: hCOs, Control, rep1

description: Library name: Control_1


title: L. johnsonii mono-colonized, male, rep3

description: Library name: 21173FL-01-37


title: pentaculture_G164_donor54

description: Library name: penta_G164_54

value: primary cells and cell lines


title: Purkinje cells P7 Kir biol rep7

city: Rotterdam

first: Catarina

last: Osorio

address: Westzeedijk 353

department: Neuroscience

institute: Erasmus Medical Center Rotterdam

description: Library name: I21-1029-03

data_processing:
For data analysis, Illumina adapter sequences and poly-A stretches were trimmed from the reads. The remaining sequences were mapped to the mouse reference sequence GRCm38 (mm10) using HISAT2 (version 2.1.0). From the alignments, the reads per gene were determined with the htseq-count program (version 0.11.2). Gene and transcript information was obtained from Ensembl (build 101) using ccds genes. Count data were then analyzed using R studio (version 0.99.484) according to the edgeR-limma package workflow. Briefly, Ensembl IDs were annotated to Entrez gene IDs, gene symbols, gene names, and chromosomes using the Mus.musculus package. Next, raw counts were transformed into counts per million (CPM) and log2-CPM, and genes with a CPM below 0.2 in at least three samples were filtered out. Normalization of gene expression distributions was performed using the Trimmed Mean of M-values method.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include Gene Counts values for each Sample.

source_name: cerebellum

growth_protocol: Purkinje cells collected from either P7 Pcp2+/+;Kir2.1 or P7 Pcp2cre/+;Kir2.1 mice

extract_protocol:
Sagittal slices of vermal cerebellar tissue were transferred into a recording chamber and maintained at 34C under continuous perfusion with equilibrated aCSF. For P7 Pcp2cre/+;Kir2.1 mice, Purkinje cells were selected based on their expression of Kir2.1-mCherry. Neurons were extracted into a glass pipette using negative pressure and 50 cells were sampled across the cerebellar cortex. For each genotype, eight biological samples were used for RNA sequencing. Cells were collected in a mild hypotonic lysis buffer composed of 0.2% Triton-X and 2U/µl of RNAse inhibitor. Isolated cells were kept on ice during the collection process or immediately stored at -80°C for RNA extraction.
For each biological sample, cDNA libraries were generated using the Smart-seq2 method. In brief, cells were lysed, and polyA+ RNA was reverse-transcribed using an oligo(dT) primer. Template switching by reverse transcriptase was achieved by using an LNA containing TSO oligo. The reverse transcribed cDNA was pre-amplified with primers for 18 cycles, followed by clean-up. Tagmentation was performed on 1 ng of the pre-amplified cDNA using Illumina Nextera DNA Flex kit. The tagmented library was extended with Illumina adaptor sequences by PCR for 12 cycles and purified. The resulting sequencing library was measured on Bioanalyzer and equimolar loaded onto a flowcell and sequenced according to the Illumina TruSeq v3 protocol on the Illumina HiSeq2500 platform with a single read 50 base-pairs and dual 9 base-pairs indices.

value: cerebellum

tag: Stage

value: Postnatal day 7

value: Purkinje cells


title: Purkinje cells P7 Kir biol rep8

description: Library name: I21-1044-03


title: hBMSC-TERT4 cells, Ad 3 days + Ob 4 days + Ad 4 days, rep 1

description:
Library name: RNA_3dAd_4dOb_4dAd_BM_rep1
Counts_Media_Change.txt
column label in processed files: 3dAd_4dOb_4dAd_1


title: Purkinje cells P7 Kir biol rep5

description: Library name: I21-1027-01


title: hBMSC-TERT4 cells, Ob 3 days + Ad 4 days + Ob 4 days, rep 2

description:
Library name: RNA_3dOb_4dAd_4dOb_BM_rep2
Counts_Media_Change.txt
column label in processed files: 3dOb_4dAd_4dOb_2

value: osteogenic diff 3 days + adipogenic diff 4 days + osteogenic diff 4 days


title: Purkinje cells P7 Kir biol rep4

description: Library name: I21-1044-02


title: C. celatum mono-colonized, male, rep3

description: Library name: 21173FL-01-32

value: C. celatum mono-colonized

value: Clostridium celatum str. VPI 8759-1


title: Purkinje cells P7 Kir biol rep3

description: Library name: I21-1029-02


title: hBMSC-TERT4 cells, Ob 3 days + Ad 4 days + Ob 4 days, rep 1

description:
Library name: RNA_3dOb_4dAd_4dOb_BM_rep1
Counts_Media_Change.txt
column label in processed files: 3dOb_4dAd_4dOb_1


title: Purkinje cells P7 Kir biol rep2

description: Library name: I21-1027-02


title: C. celatum mono-colonized, male, rep2

description: Library name: 21173FL-01-31


title: hBMSC-TERT4 cells, Ad 3 days + Ob 4 days, rep 2

description:
Library name: RNA_3dAd_4dOb_BM_rep2
Counts_Media_Change.txt
column label in processed files: 3dAd_4dOb_2

value: adipogenic diff 3 days + osteogenic diff 4 days

value: 3 + 4 days


title: Purkinje cells P7 control biol rep8

description: Library name: I21-1146-02


title: C. celatum mono-colonized, male, rep1

description: Library name: 21173FL-01-30

value: Brain


title: Purkinje cells P7 Kir biol rep1

description: Library name: I21-1044-01


title: Purkinje cells P7 control biol rep6

description: Library name: I21-1045-02


title: Purkinje cells P7 Kir biol rep6

description: Library name: I21-1029-01


title: hBMSC-TERT4 cells, Ad 3 days + Ob 4 days, rep 1

description:
Library name: RNA_3dAd_4dOb_BM_rep1
Counts_Media_Change.txt
column label in processed files: 3dAd_4dOb_1


title: Germ-free, male, rep3

description: Library name: 21173FL-01-29

value: CD11b+ brain myeloid cells

value: Germ-free


title: Purkinje cells P7 control biol rep5

description: Library name: I21-1015-03


title: hBMSC-TERT4 cells, Ob 3 days + Ad 4 days, rep 2

description:
Library name: RNA_3dOb_4dAd_BM_rep2
Counts_Media_Change.txt
column label in processed files: 3dOb_4dAd_2

value: osteogenic diff 3 days + adipogenic diff 4 days


title: Purkinje cells P7 control biol rep4

description: Library name: I21-1146-01


title: Purkinje cells P7 control biol rep7

description: Library name: I21-1048-02


title: Germ-free, male, rep2

description: Library name: 21173FL-01-28

value: male


title: hBMSC-TERT4 cells, Ob 3 days + Ad 4 days, rep 1

description:
Library name: RNA_3dOb_4dAd_BM_rep1
Counts_Media_Change.txt
column label in processed files: 3dOb_4dAd_1

value: immortalized human stromal cells from bone marrow


title: Purkinje cells P7 control biol rep1

description: Library name: I21-1015-02


title: Germ-free, female, rep4

description: Library name: 21173FL-01-27

value: female


title: Purkinje cells P7 control biol rep2

description: Library name: I21-1045-01


title: hBMSC-TERT4 cells, Ad 7 days + Ob 4 days, rep 2

description:
Library name: RNA_7dAd_4dOb_BM_rep2
Counts_Media_Change.txt
column label in processed files: 7dAd_4dOb_2

value: adipogenic diff 7 days + osteogenic diff 4 days

value: 7 + 4 days


title: KO2

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description: Library name: KO2

data_processing:
For WT1 and WT2 all sequenced reads were processed whereas KO1 and KO2 reads were subset to 412M per replicate with seqtk command to have comparable number of reads between conditions.
Mapping was performed according to an iterative-based strategy as previously described {Imakaev, 2012, PubMed:22941365} to the reference genome mouse December 2011 (GRCm38/mm10).
TADbit filtering module was used to remove noninformative contacts and to create contact matrices. PCR duplicates were removed, and the Hi-C filters applied corresponded to potential nondigested fragments (extra-dangling ends), non-ligated fragments (dangling ends), self-circles, and random breaks.
Contact matrices next were normalized for sequencing depth and genomic biases using cooler balance {Abdennur, 2020, PubMed:31290943}.
Further analyses of Hi-C matrices were performed by cooltools {Open2C, 2024, PubMed:38709825} and in-house scripts at different genomic resolutions (i.e., genomic decay at 20 kb, cis-trans interaction rations at 500 kb, A and B chromatin compartment at 100 kb, TAD boundary at 40kb and loop analysis at 20 kb).
Assembly: GRCm38/mm10
Supplementary files format and content: mcool

source_name: Urothelial organoids

growth_protocol: Organoid suspensions were plated as 10 mL in Matrigel drops (12,500 cells/drop), maintained in CM for 5 days, and then cultured for 3 days in GF-depleted medium with 4-OH-TMX, to induce quiescence and Stag2 inactivation, respectively.

extract_protocol:
After crosslinking (1% (w/v) methanol-free formaldehyde 10 min RT 65 rpm), the reaction was quenched with 0.125 M glycine (5 min RT 65 rpm) followed by 30 min at 4 ºC. Organoid suspensions were collected on ice, centrifuged (3 min, 300 g at 4 ºC), washed with cold PBS, dissociated with 0.25% Trypsin-EDTA, and disaggregated for 3 min. Cells were centrifuged, washed, flash-frozen, and stored at -80 ºC. Cells were lysed overnight at 37 ºC 300 rpm and chromatin digested.
Biotinylated DNA from the Hi-C was selected using Dynabeads MyOne Streptavidin T1 beads from ThermoFisher Scientific. Hi-C libraries were prepared using the NEBnext End Repair Module, NEBNext dA-Tailing Module and NEBnext Quick Ligation Reaction Buffer(5X) from New England Biolabs, complemented with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) from New England Biolabs. 1µg of DNA was used as starting material. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected at 100-600bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent 4150 TapeStation system (D5000 ScreenTape).

value: Urothelial organoids


title: Germ-free, female, rep3

description: Library name: 21173FL-01-26


title: KO1

description: Library name: KO1


title: L. johnsonii mono-colonized, female, rep4

description: Library name: 21173FL-01-21

value: L. johnsonii mono-colonized

value: Lactobacillus johnsonii str. VPI 7960


title: hBMSC-TERT4 cells, Ob 7 days + Ad 4 days, rep 2

description:
Library name: RNA_7dOb_4dAd_BM_rep2
Counts_Media_Change.txt
column label in processed files: 7dOb_4dAd_2

value: osteogenic diff 7 days + adipogenic diff 4 days


title: NU1 cells, quiescent, CTCF, biol rep 2

description: Library name: CTCF_quiesc2

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
ChIP-Seq data were analyzed using the Rubioseq pipeline
reads were aligned to the reference genome (mm10) using BWA  and duplicates removed with Picard
Genomic regions were called using MACS2
Consensus peak sets per experimental condition were generated using the mergePeaks function of HOMER. For STAG1 and STAG2 ChIP-Seq, significant peaks were defined based on the following criteria: FDR < 0.05, fold enrichment vs. input > 10, and pileup > 30.
Assembly: mm10
Supplementary files format and content: narrow peaks and bigwigs

source_name: Spontaneously immortalized normal mouse urothelial cells

growth_protocol: NU1 cells were cultured in Cascade Biologics Epilife Medium (Gibco M-Epi-500-CA) supplemented with 15% chelated fetal bovine serum, 5 ng/ml EGF, 1 X insulin/transferrin, 2.24×10−11 M T3 (3,3’,5-Triiodo-L-thyronine), 225ug hydrocortisone, 5.3 ul cholera toxin, 0.3 mM CaCl₂, and 1 X penicillin/streptomycin (Gibco). NU1 cells were spontaneously immortalized through sequential passaging.

extract_protocol:
Cells (4 × 107) were harvested and chromatin was crosslinked, quenched, sonicated and bound to protein A/G agarose beads. The supernatant was divided into aliquots (550 μg/assay) and incubated with 25 μg of antibody (STAG1, STAG2, CTCF, non-related IgG) overnight at 4 ºC on a rotating platform. Beads were sequentially washed with low-salt wash buffer, high-salt wash buffer, LiCl wash buffer, and TE 1X. DNA was eluted (1% SDS, 0.1 M NaHCO3) and purified by phenol–chloroform extraction once cross-linking was reversed.
5ng of DNA per sample was used as provided by the user. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 450 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: To induce quiescence, NU1 cells were cultured in complete medium until confluence and then in complete medium supplemented with 1uM rosiglitazone (Merck) and 0.5uM erlotinib.

value: WT

value: Quiescence

tag: chip antibody

value: CTCF, Millipore, 07-729

tag: antibody amount

value: 25 ug


title: WT1

description: Library name: WT1


title: NU1 cells, quiescent, CTCF, biol rep 1

description: Library name: CTCF_quiesc1

value: Spontaneously immortalized normal mouse urothelial cells


title: hBMSC-TERT4 cells, Ob 7 days + Ad 4 days, rep 1

description:
Library name: RNA_7dOb_4dAd_BM_rep1
Counts_Media_Change.txt
column label in processed files: 7dOb_4dAd_1


title: Purkinje cells P7 control biol rep3

description: Library name: I21-1048-01

value: cerebellum

value: Postnatal day 7

value: Purkinje cells


title: NU1 cells, quiescent, STAG2, biol rep 2

description: Library name: SA2_quiesc2

value: STAG2, (Remeseiro et al. 2012)


title: NU1 cells, quiescent, STAG1, biol rep 2

description: Library name: SA1_quiesc2

value: STAG1, (Remeseiro et al. 2012)


title: NU1 cells, quiescent, STAG2, biol rep 1

description: Library name: SA2_quiesc1


title: L. johnsonii mono-colonized, male, rep2

description: Library name: 21173FL-01-19

value: Brain

value: CD11b+ brain myeloid cells

value: male


title: hBMSC-TERT4 cells, Ad 14 days, rep 3

description:
Library name: RNA_14dAd_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 14dAd_3

value: immortalized human stromal cells from bone marrow

value: adipogenic diff 14 days

value: 14 days


title: WT2

description: Library name: WT2

value: Urothelial organoids


title: L. johnsonii mono-colonized, male, rep1

description: Library name: 21173FL-01-18

value: L. johnsonii mono-colonized

value: Lactobacillus johnsonii str. VPI 7960


title: hBMSC-TERT4 cells, Ad 14 days, rep 2

description:
Library name: RNA_14dAd_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 14dAd_2


title: NU1 cells, input

description: Library name: input

value: WT

value: IgG, Millipore, 12-370


title: hBMSC-TERT4 cells, Ad 7 days + Ob 4 days, rep 1

description:
Library name: RNA_7dAd_4dOb_BM_rep1
Counts_Media_Change.txt
column label in processed files: 7dAd_4dOb_1

value: adipogenic diff 7 days + osteogenic diff 4 days

value: 7 + 4 days


title: Germ-free, female, rep2

description: Library name: 21173FL-01-17

value: Germ-free

value: female


title: NU1 cells, quiescent, STAG1, biol rep 1

description: Library name: SA1_quiesc1

value: Spontaneously immortalized normal mouse urothelial cells

value: Quiescence

value: 25 ug


title: NU1 cells, proliferating, CTCF, biol rep 2

description: Library name: CTCF_prol2

value: Proliferation

value: CTCF, Millipore, 07-729


title: hBMSC-TERT4 cells, Ob 14 days, rep 3

description:
Library name: RNA_14dOb_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 14dOb_3

value: immortalized human stromal cells from bone marrow

value: osteogenic diff 14 days


title: Germ-free, female, rep1

description: Library name: 21173FL-01-16

value: Brain

value: CD11b+ brain myeloid cells


title: NU1 cells, proliferating, STAG2, biol rep 1

description: Library name: SA2_prol1

value: STAG2, (Remeseiro et al. 2012)


title: Germ-free, male, rep1

description: Library name: 21173FL-01-15

value: male


title: NU1 cells, proliferating, STAG2, biol rep 2

description: Library name: SA2_prol2

value: WT


title: NU1 cells, proliferating, STAG1, biol rep 2

description: Library name: SA1_prol2

value: STAG1, (Remeseiro et al. 2012)


title: hBMSC-TERT4 cells, Ob 14 days, rep 2

description:
Library name: RNA_14dOb_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 14dOb_2

value: 14 days


title: NU1 cells, proliferating, CTCF, biol rep 1

description: Library name: CTCF_prol1


title: B. thetaiotaomicron mono-colonized, male, rep3

description: Library name: 21173FL-01-12

value: B. thetaiotaomicron mono-colonized

value: Bacteroides thetaiotaomicron str. VPI 5482


title: hBMSC-TERT4 cells, Ob 14 days, rep 1

description:
Library name: RNA_14dOb_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 14dOb_1


title: NU1 cells, proliferating, STAG1, biol rep 1

description: Library name: SA1_prol1


title: hBMSC-TERT4 cells, Ad 14 days, rep 1

description:
Library name: RNA_14dAd_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 14dAd_1

value: adipogenic diff 14 days


title: B. thetaiotaomicron mono-colonized, male, rep2

description: Library name: 21173FL-01-11


title: hBMSC-TERT4 cells, Ad 7 days, rep 2

description:
Library name: RNA_7dAd_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 7dAd_2

value: adipogenic diff 7 days

value: 7 days


title: NU1 cells, quiescent (differentiation day 7), shNT, experiment 9

description: Library name: Exp9_d7_shNT

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Analyses were performed using Nextpresso RNA-seq pipeline.
Raw files were aligned to mm10 reference genome using Bowtie and TopHat aligners.
Raw counts were generated using htseq
Differential expression analysis was performed using DEseq2.
Assembly: mm10
Supplementary files format and content: text file

extract_protocol:
RNA was extracted using ReliaPrepTM RNA Cell Miniprep System Kit (Promega, TM370).
1 µg of total RNA samples, containing ERCC ExFold RNA Spike-In Mixes (Ambion 4456739), was used as provided by the user. Average sample RNA Integrity Numbers was 9.7 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: Spontaneously immortalized normal mouse urothelial cells

value: quiescence (differentiation day 7)

tag: batch


title: NU1 cells, quiescent (differentiation day 7), shNT, experiment 5

description: Library name: Exp5_d7_shNT

tag: cell type


title: E. coli mono-colonized, female, rep3

description: Library name: 21173FL-01-09

tag: treatment

value: E. coli mono-colonized

value: female

value: Escherichia coli str. K12 MC4100


title: B. thetaiotaomicron mono-colonized, male, rep1

description: Library name: 21173FL-01-10

value: Brain


title: hBMSC-TERT4 cells, Ad 7 days, rep 3

description:
Library name: RNA_7dAd_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 7dAd_3

value: immortalized human stromal cells from bone marrow


title: C. celatum mono-colonized, male, rep4

description: Library name: 21173FL-01-33

value: CD11b+ brain myeloid cells

value: C. celatum mono-colonized

value: Clostridium celatum str. VPI 8759-1


title: NU1 cells, proliferating, sh4, experiment 5

description: Library name: Exp5_prol_sh4

value: proliferation


title: NU1 cells, proliferating, shNT, experiment 5

description: Library name: Exp5_prol_shNT

value: WT


title: NU1 cells, proliferating, sh4, experiment 9

description: Library name: Exp9_prol_sh4


title: NU1 cells, quiescent (differentiation day 7), sh4, experiment 9

description: Library name: Exp9_d7_sh4


title: hBMSC-TERT4 cells, Ad 7 days, rep 1

description:
Library name: RNA_7dAd_BM_rep1
Counts_normalDiff_TERT.txt
column label in processed files: 7dAd_1


title: L. johnsonii mono-colonized, female, rep3

description: Library name: 21173FL-01-20

value: L. johnsonii mono-colonized

value: Lactobacillus johnsonii str. VPI 7960


title: E. coli mono-colonized, female, rep2

description: Library name: 21173FL-01-08


title: NU1 cells, quiescent (differentiation day 7), sh4, experiment 7

description: Library name: Exp7_d7_sh4


title: NU1 cells, quiescent (differentiation day 7), sh4, experiment 5

description: Library name: Exp5_d7_sh4


title: hBMSC-TERT4 cells, Ob 7 days, rep 3

description:
Library name: RNA_7dOb_BM_rep3
Counts_normalDiff_TERT.txt
column label in processed files: 7dOb_3

value: osteogenic diff 7 days


title: NU1 cells, proliferating, shNT, experiment 9

description: Library name: Exp9_prol_shNT


title: NU1 cells, quiescent (differentiation day 7), shNT, experiment 7

description: Library name: Exp7_d7_shNT


title: E. coli mono-colonized, female, rep1

description: Library name: 21173FL-01-07


title: NU1 cells, proliferating, sh4, experiment 7

description: Library name: Exp7_prol_sh4


title: hBMSC-TERT4 cells, Ob 7 days, rep 2

description:
Library name: RNA_7dOb_BM_rep2
Counts_normalDiff_TERT.txt
column label in processed files: 7dOb_2


title: NU1 cells, proliferating, shNT, experiment 7

description: Library name: Exp7_prol_shNT