title: mTEChi, adult, AireKO, cell198


title: mTEChi, adult, AireKO, cell199

status: Public on Mar 12 2025

type: SRA

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

library_source: transcriptomic single cell

data_processing:
Trimming reads to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Trimming low-quality parts and adapter sequences by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using STAR (v2.7.3a, Dobin et al., STAR: ultrafast universal RNA-seq aligner, 2013) with a GTF file downloaded from http://www.ensembl.org (GRCm38.99)
Removing unmapped reads and reads mapped with low-quality scores (MAPQ < 5) by SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Removing duplicated reads using Picard Tools (v2.21.1, http://broadinstitute.github.io/picard/)
Counting mapped reads on each gene using htseq-count (v0.11.2, Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, 2015) using a --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
GeTMM (Gene length corrected trimmed mean of M-values) normalization by edgeR package in R programming language (Robinson et al., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010) and gene length data obtained from EMBL-EBI, as described by Smid et al. (Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons, 2018)
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw read counts for each gene by each Sample
Supplementary files format and content: comma-separated values file includes GeTMM normalized values for each gene by each Sample

molecule: total RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
Mouse thymus was enzymatically digested and CD45+ cells were depleted using mouse CD45 MicroBeads and a LS Column (Miltenyi Biotec). After staining with an antibody cocktail, mTEChi (DAPI-CD45-EpCAM+Ly51-MHCII-high), mTEClo (DAPI-CD45-EpCAM+Ly51-MHCII-low), and cTEC (DAPI-CD45-EpCAM+Ly51+) were sorted by FACSAria into a 96well plate containing 1uL of lysis buffer (0.3% NP40; Thermo Scientific, 1U/uL RNasinPlus; Promega in 1x Lysis Buffer, Takara)
scRNA-seq libraries were prepared by a RamDA-seq method (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018). Specifically, RNA was denatured by incubating at 70C for 90sec, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 5min. Then cDNA was synthesized in 3uL of 1xRT Buffer containing RT Enzyme Mix (0.15uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (2.7uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 0.5uL of 10x NEB buffer2 (NEB), 0.125uL of dNTP mix (10mM each nt, NEB), 0.15uL of Klenow Fragment (3'→5' exo-, NEB), 0.4uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 0.825uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (Beckman Coulter) and applied for Tn5 tagmentation in a 5uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). After dissociating Tn5 protein by adding SDS (0.04% in final), tagmented DNA was amplified by 17 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.0 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

tag: tissue

value: thymus

tag: cell type

value: epitherial cells

value: mTEChi

tag: strain

tag: genotype

value: AireKO

tag: age

tag: Sex

value: male

tag: exp. batch


title: mTEChi, adult, AireKO, cell197


title: mTEChi, adult, AireKO, cell194


title: mTEChi, adult, AireKO, cell195


title: mTEChi, adult, WT, cell161

value: WT


title: mTEChi, adult, AireKO, cell193


title: mTEChi, adult, WT, cell162


title: mTEChi, adult, AireKO, cell192


title: mTEChi, adult, WT, cell159


title: mTEChi, adult, WT, cell160


title: mTEChi, adult, WT, cell157


title: mTEChi, adult, WT, cell158


title: mTEChi, adult, AireKO, cell190


title: mTEChi, adult, WT, cell168


title: mTEChi, adult, AireKO, cell191


title: mTEChi, adult, WT, cell156


title: mTEChi, adult, WT, cell155


title: mTEChi, adult, AireKO, cell188


title: mTEChi, adult, AireKO, cell189


title: mTEChi, adult, WT, cell154


title: mTEChi, adult, WT, cell166


title: mTEChi, adult, AireKO, cell187


title: mTEChi, adult, WT, cell153


title: mTEChi, adult, WT, cell152


title: mTEChi, adult, AireKO, cell186


title: mTEChi, adult, AireKO, cell184


title: mTEChi, adult, AireKO, cell196


title: mTEChi, adult, AireKO, cell179


title: mTEChi, adult, WT, cell146


title: mTEChi, adult, WT, cell151


title: mTEChi, adult, AireKO, cell183


title: mTEChi, adult, AireKO, cell178


title: mTEChi, adult, WT, cell149


title: mTEChi, adult, AireKO, cell182


title: mTEChi, adult, WT, cell150


title: mTEChi, adult, WT, cell143


title: mTEChi, adult, AireKO, cell181


title: mTEChi, adult, WT, cell147


title: mTEChi, adult, AireKO, cell180


title: mTEChi, adult, AireKO, cell175


title: mTEChi, adult, AireKO, cell176


title: mTEChi, adult, AireKO, cell174


title: mTEChi, adult, WT, cell145


title: mTEChi, adult, AireKO, cell177


title: mTEChi, adult, WT, cell144


title: mTEChi, adult, WT, cell139


title: mTEChi, adult, WT, cell142


title: mTEChi, adult, WT, cell141


title: mTEChi, adult, WT, cell137


title: mTEChi, adult, WT, cell148


title: mTEChi, adult, WT, cell140


title: mTEChi, adult, WT, cell138


title: mTEChi, adult, AireKO, cell185


title: mTEChi, adult, AireKO, cell172


title: mTEChi, adult, AireKO, cell173


title: mTEChi, adult, AireKO, cell170


title: mTEChi, adult, AireKO, cell171


title: mTEChi, adult, AireKO, cell168


title: mTEChi, adult, WT, cell136


title: mTEChi, adult, AireKO, cell169


title: mTEChi, adult, WT, cell135


title: mTEChi, adult, WT, cell134


title: mTEChi, adult, AireKO, cell167


title: mTEChi, adult, AireKO, cell166


title: mTEChi, adult, WT, cell133


title: mTEChi, adult, WT, cell131


title: mTEChi, adult, WT, cell130


title: mTEChi, adult, WT, cell132


title: mTEChi, adult, AireKO, cell163


title: mTEChi, adult, AireKO, cell164


title: mTEChi, adult, AireKO, cell165


title: mTEChi, adult, AireKO, cell162


title: mTEChi, adult, WT, cell128


title: mTEChi, adult, WT, cell129


title: mTEChi, adult, AireKO, cell161


title: mTEChi, adult, WT, cell127


title: mTEChi, adult, AireKO, cell160


title: mTEChi, adult, WT, cell126


title: mTEChi, adult, AireKO, cell159


title: mTEChi, adult, AireKO, cell158


title: mTEChi, adult, WT, cell125


title: mTEChi, adult, WT, cell123


title: mTEChi, adult, AireKO, cell156


title: mTEChi, adult, AireKO, cell157


title: mTEChi, adult, WT, cell122


title: mTEChi, adult, WT, cell121


title: mTEChi, adult, AireKO, cell154


title: mTEChi, adult, AireKO, cell153


title: mTEChi, adult, WT, cell120


title: mTEChi, adult, WT, cell119


title: mTEChi, adult, AireKO, cell152


title: mTEChi, adult, AireKO, cell151


title: mTEChi, adult, WT, cell117


title: mTEChi, adult, AireKO, cell150


title: mTEChi, adult, WT, cell116


title: mTEChi, adult, WT, cell115


title: mTEChi, adult, AireKO, cell149


title: mTEChi, adult, AireKO, cell148


title: mTEChi, adult, WT, cell114


title: mTEChi, adult, AireKO, cell147


title: mTEChi, adult, WT, cell113


title: mTEChi, adult, AireKO, cell146


title: mTEChi, adult, WT, cell112


title: mTEChi, adult, WT, cell124


title: mTEChi, adult, AireKO, cell144


title: mTEChi, adult, AireKO, cell145


title: mTEChi, adult, WT, cell110


title: mTEChi, adult, AireKO, cell143


title: mTEChi, adult, AireKO, cell155


title: mTEChi, adult, WT, cell109


title: mTEChi, adult, WT, cell108


title: mTEChi, adult, AireKO, cell141


title: mTEChi, adult, AireKO, cell142


title: mTEChi, adult, WT, cell118


title: mTEChi, adult, WT, cell104


title: mTEChi, adult, WT, cell102


title: mTEChi, adult, WT, cell106


title: mTEChi, adult, AireKO, cell139


title: mTEChi, adult, WT, cell99


title: mTEChi, adult, WT, cell105


title: mTEChi, adult, AireKO, cell138


title: mTEChi, adult, AireKO, cell136


title: mTEChi, adult, AireKO, cell135


title: mTEChi, adult, WT, cell103


title: mTEChi, adult, WT, cell97


title: mTEChi, adult, AireKO, cell134


title: mTEChi, adult, WT, cell96


title: mTEChi, adult, WT, cell101


title: mTEChi, adult, AireKO, cell129


title: mTEChi, adult, WT, cell100


title: mTEChi, adult, WT, cell111


title: mTEChi, adult, AireKO, cell133


title: mTEChi, adult, AireKO, cell132


title: mTEChi, adult, WT, cell98


title: mTEChi, adult, AireKO, cell130


title: mTEChi, adult, WT, cell107


title: mTEChi, adult, AireKO, cell126


title: mTEChi, adult, WT, cell95


title: mTEChi, adult, AireKO, cell137


title: mTEChi, adult, AireKO, cell140


title: mTEChi, adult, AireKO, cell128


title: mTEChi, adult, WT, cell94


title: mTEChi, adult, AireKO, cell122


title: mTEChi, adult, WT, cell93


title: mTEChi, adult, WT, cell92


title: mTEChi, adult, AireKO, cell124


title: mTEChi, adult, AireKO, cell125


title: mTEChi, adult, AireKO, cell131


title: mTEChi, adult, WT, cell88


title: mTEChi, adult, WT, cell86


title: mTEChi, adult, AireKO, cell120


title: mTEChi, adult, AireKO, cell127


title: mTEChi, adult, AireKO, cell119


title: mTEChi, adult, AireKO, cell123


title: mTEChi, adult, WT, cell90


title: mTEChi, adult, WT, cell85


title: mTEChi, adult, AireKO, cell118


title: mTEChi, adult, WT, cell89


title: mTEChi, adult, WT, cell91


title: mTEChi, adult, WT, cell83


title: mTEChi, adult, WT, cell87


title: mTEChi, adult, WT, cell84


title: mTEChi, adult, AireKO, cell117


title: mTEChi, adult, AireKO, cell116


title: mTEChi, adult, WT, cell82


title: mTEChi, adult, AireKO, cell115


title: mTEChi, adult, AireKO, cell114


title: mTEChi, adult, WT, cell80


title: mTEChi, adult, AireKO, cell121


title: mTEChi, adult, AireKO, cell113


title: mTEChi, adult, WT, cell79


title: mTEChi, adult, AireKO, cell112


title: mTEChi, adult, WT, cell78


title: mTEChi, adult, AireKO, cell111


title: mTEChi, adult, WT, cell77


title: mTEChi, adult, AireKO, cell110


title: mTEChi, adult, WT, cell76


title: mTEChi, adult, AireKO, cell109


title: mTEChi, adult, WT, cell75


title: mTEChi, adult, WT, cell74


title: mTEChi, adult, AireKO, cell107


title: mTEChi, adult, AireKO, cell108


title: mTEChi, adult, AireKO, cell105


title: mTEChi, adult, WT, cell71


title: mTEChi, adult, AireKO, cell104


title: mTEChi, adult, WT, cell70


title: mTEChi, adult, AireKO, cell106


title: mTEChi, adult, WT, cell69


title: mTEChi, adult, AireKO, cell102


title: mTEChi, adult, WT, cell81


title: mTEChi, adult, WT, cell67


title: mTEChi, adult, WT, cell68


title: mTEChi, adult, AireKO, cell101


title: mTEChi, adult, AireKO, cell100


title: mTEChi, adult, WT, cell66


title: mTEChi, adult, AireKO, cell99


title: mTEChi, adult, WT, cell65


title: mTEChi, adult, AireKO, cell98


title: mTEChi, adult, AireKO, cell97


title: mTEChi, adult, WT, cell64


title: mTEChi, adult, WT, cell63


title: mTEChi, adult, AireKO, cell96


title: mTEChi, adult, WT, cell62


title: mTEChi, adult, WT, cell61


title: mTEChi, adult, AireKO, cell95


title: mTEChi, adult, AireKO, cell94


title: mTEChi, adult, WT, cell60


title: mTEChi, adult, WT, cell59


title: mTEChi, adult, AireKO, cell92


title: mTEChi, adult, AireKO, cell91


title: mTEChi, adult, WT, cell58


title: mTEChi, adult, WT, cell57


title: mTEChi, adult, AireKO, cell93


title: mTEChi, adult, AireKO, cell90


title: mTEChi, adult, WT, cell56


title: mTEChi, adult, WT, cell73


title: mTEChi, adult, AireKO, cell88


title: mTEChi, adult, AireKO, cell89


title: mTEChi, adult, WT, cell55


title: mTEChi, adult, WT, cell53


title: mTEChi, adult, AireKO, cell87


title: mTEChi, adult, WT, cell54


title: mTEChi, adult, AireKO, cell86


title: mTEChi, adult, WT, cell52


title: mTEChi, adult, WT, cell72


title: mTEChi, adult, AireKO, cell103


title: mTEChi, adult, WT, cell51


title: mTEChi, adult, AireKO, cell85


title: mTEChi, adult, WT, cell50


title: mTEChi, adult, AireKO, cell84


title: mTEChi, adult, WT, cell49


title: mTEChi, adult, AireKO, cell83


title: mTEChi, adult, AireKO, cell82


title: mTEChi, adult, WT, cell48


title: mTEChi, adult, AireKO, cell81


title: mTEChi, adult, WT, cell47


title: mTEChi, adult, AireKO, cell80


title: mTEChi, adult, WT, cell46


title: mTEChi, adult, AireKO, cell79


title: mTEChi, adult, WT, cell45


title: mTEChi, adult, WT, cell44


title: mTEChi, adult, AireKO, cell77


title: mTEChi, adult, AireKO, cell78


title: mTEChi, adult, AireKO, cell76


title: mTEChi, adult, WT, cell43


title: mTEChi, adult, WT, cell41


title: mTEChi, adult, AireKO, cell74


title: mTEChi, adult, WT, cell40


title: mTEChi, adult, WT, cell42


title: mTEChi, adult, AireKO, cell73


title: mTEChi, adult, WT, cell38


title: mTEChi, adult, AireKO, cell72


title: mTEChi, adult, AireKO, cell71


title: mTEChi, adult, AireKO, cell70


title: mTEChi, adult, WT, cell36


title: mTEChi, adult, WT, cell35


title: mTEChi, adult, WT, cell37


title: mTEChi, adult, AireKO, cell69


title: mTEChi, adult, AireKO, cell68


title: mTEChi, adult, AireKO, cell67


title: mTEChi, adult, AireKO, cell66


title: mTEChi, adult, WT, cell32


title: mTEChi, adult, AireKO, cell65


title: mTEChi, adult, WT, cell31


title: mTEChi, adult, AireKO, cell63


title: mTEChi, adult, WT, cell29


title: mTEChi, adult, AireKO, cell62


title: mTEChi, adult, AireKO, cell61


title: mTEChi, adult, AireKO, cell75


title: mTEChi, adult, AireKO, cell64


title: mTEChi, adult, WT, cell39


title: mTEChi, adult, AireKO, cell60


title: mTEChi, adult, AireKO, cell59


title: mTEChi, adult, AireKO, cell58


title: mTEChi, adult, WT, cell27


title: mTEChi, adult, AireKO, cell57


title: mTEChi, adult, AireKO, cell56


title: mTEChi, adult, WT, cell25


title: mTEChi, adult, WT, cell23


title: mTEChi, adult, WT, cell26


title: mTEChi, adult, WT, cell22


title: mTEChi, adult, WT, cell34


title: mTEChi, adult, WT, cell24


title: mTEChi, adult, AireKO, cell55


title: mTEChi, adult, WT, cell33


title: mTEChi, adult, AireKO, cell53


title: mTEChi, adult, WT, cell20


title: mTEChi, adult, WT, cell30


title: mTEChi, adult, AireKO, cell52


title: mTEChi, adult, WT, cell18


title: mTEChi, adult, WT, cell28


title: mTEChi, adult, AireKO, cell51


title: mTEChi, adult, WT, cell17


title: mTEChi, adult, AireKO, cell50


title: mTEChi, adult, AireKO, cell49


title: mTEChi, adult, WT, cell15


title: mTEChi, adult, AireKO, cell48


title: mTEChi, adult, WT, cell14


title: mTEChi, adult, WT, cell13


title: mTEChi, adult, AireKO, cell47


title: mTEChi, adult, WT, cell21


title: mTEChi, adult, WT, cell10


title: mTEChi, adult, WT, cell9


title: mTEChi, adult, AireKO, cell43


title: mTEChi, adult, WT, cell11


title: mTEChi, adult, AireKO, cell45


title: mTEChi, adult, WT, cell12


title: mTEChi, adult, AireKO, cell54


title: mTEChi, adult, AireKO, cell44


title: mTEChi, adult, AireKO, cell42


title: mTEChi, adult, WT, cell7


title: mTEChi, adult, WT, cell8


title: mTEChi, adult, AireKO, cell41


title: mTEChi, adult, WT, cell19


title: mTEChi, adult, WT, cell6


title: mTEChi, adult, WT, cell5


title: mTEChi, adult, WT, cell16


title: mTEChi, adult, AireKO, cell39


title: mTEChi, adult, AireKO, cell38


title: mTEChi, adult, AireKO, cell37


title: mTEChi, adult, AireKO, cell36


title: mTEChi, adult, WT, cell4


title: mTEChi, adult, WT, cell2


title: mTEChi, adult, AireKO, cell35


title: mTEChi, adult, WT, cell1


title: mTEChi, neonate, WT, cell171

value: unknown


title: mTEChi, adult, AireKO, cell33


title: mTEChi, adult, AireKO, cell34


title: mTEChi, adult, AireKO, cell46


title: mTEChi, neonate, WT, cell170


title: mTEChi, neonate, WT, cell169


title: mTEChi, neonate, WT, cell168


title: mTEChi, adult, AireKO, cell30


title: mTEChi, adult, AireKO, cell32


title: mTEChi, adult, AireKO, cell40


title: mTEChi, adult, AireKO, cell31


title: mTEChi, neonate, WT, cell166


title: mTEChi, neonate, WT, cell165


title: mTEChi, neonate, WT, cell167


title: mTEChi, adult, AireKO, cell27


title: mTEChi, adult, AireKO, cell28


title: mTEChi, neonate, WT, cell164


title: Ht_IAMP_KO_3

city: Guangzhou

first: Tailai

last: Du

state: Guangdong

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

country: China

institute: Sun Yat-sen University

library_source: transcriptomic

data_processing:
For RNA-seq data analysis, the sequencing data was filtered with cutadapt. The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using HISAT2. Expression level of genes was calculated by  StringTie, respectively. The raw counts were then analyzed using DESeq2.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: csv;raw counts

source_name: Heart

growth_protocol: Adult mouse cardiac fibroblasts were isolated by enzymatic disassociation repeatedly. All isolated cells were plated on collagen-coated platesfor 3 hours. Non-adherent cells were discarded. Adherent cells were  cultured in DMEM high glucose medium (Gibco) supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNAs were isolated using Trizol Reagent from adult mouse cardiac fibroblasts and mouse heart samples.
RNA libraries were prepared for sequencing using standard BGIseq/MGIseq protocols

treatment_protocol: Adult mouse cardiac fibroblasts treated with IAMP siRNA for 24h and then stimulated with IL-17 for another 24h

value: Heart

value: KO


title: mTEChi, neonate, WT, cell162


title: Ht_IAMP_KO_4


title: Ht_IAMP_KO_1


title: mTEChi, adult, AireKO, cell26


title: mTEChi, adult, WT, cell3


title: mTEChi, neonate, WT, cell161


title: Ht_IAMP_Het_4

value: Het


title: mTEChi, adult, AireKO, cell24


title: Ht_IAMP_KO_2


title: mTEChi, adult, AireKO, cell23


title: Ht_IAMP_Het_2


title: mTEChi, adult, AireKO, cell29


title: Ht_IAMP_Het_1


title: Ht_IAMP_Het_3


title: mTEChi, adult, AireKO, cell21


title: AF_si-IAMP-2_TGF_3

description:
Library name: Sample 9
CFsi1055TGF3.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz

source_name: Adult fibroblast

extract_protocol:
Total RNAs were isolated using Trizol Reagent from adult mouse heart fibroblasts and mouse heart samples.
RNA libraries were prepared for sequencing using standard BGIseq/MGIseq protocols

value: Adult fibroblast

tag: treatment

value: si-IAMP-2+TGF-β treatment


title: AF_si-IAMP-2_TGF_2

description:
Library name: Sample 8
CFsi1055TGF2.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: mTEChi, adult, AireKO, cell22


title: mTEChi, neonate, WT, cell158


title: AF_si-IAMP-2_TGF_1

description:
Library name: Sample 7
CFsi1055TGF1.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: mTEChi, adult, AireKO, cell25


title: mTEChi, adult, AireKO, cell20


title: AF_si-IAMP-1_TGF_3

description:
Library name: Sample 6
CFsi1259TGF3.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz

value: si-IAMP-1+TGF-β treatment


title: mTEChi, neonate, WT, cell163


title: mTEChi, neonate, WT, cell157


title: mTEChi, neonate, WT, cell160


title: AF_si-IAMP-1_TGF_2

description:
Library name: Sample 5
CFsi1259TGF2.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: mTEChi, adult, AireKO, cell19


title: AF_si-IAMP-1_TGF_1

description:
Library name: Sample 4
CFsi1259TGF1.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: mTEChi, neonate, WT, cell156


title: mTEChi, adult, AireKO, cell18


title: AF_si-NC_TGF_3

description:
Library name: Sample 3
CFsiNCTGF3.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz

value: si-NC+TGF-β treatment


title: mTEChi, neonate, WT, cell155


title: AF_si-NC_TGF_2

description:
Library name: Sample 2
CFsiNCTGF2.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: AF_si-NC_TGF_1

description:
Library name: Sample 1
CFsiNCTGF1.gtf
AF_si-IAMP_TGF-β_RNA_raw_counts.csv.gz


title: AF_si-IAMP-2_IL17_3

source_name: Adult mouse cardiac fibroblast

value: Adult mouse cardiac fibroblast

value: si-IAMP-2+IL17 treatment


title: mTEChi, adult, AireKO, cell17


title: mTEChi, neonate, WT, cell154


title: AF_si-IAMP-2_IL17_2


title: mTEChi, neonate, WT, cell159


title: mTEChi, adult, AireKO, cell16


title: AF_si-IAMP-2_IL17_1


title: AF_si-IAMP-1_IL17_3

value: si-IAMP-1+IL17 treatment


title: mTEChi, neonate, WT, cell153

value: thymus


title: mTEChi, adult, AireKO, cell15

value: epitherial cells


title: mTEChi, adult, AireKO, cell14

value: mTEChi


title: AF_si-IAMP-1_IL17_1


title: AF_si-IAMP-1_IL17_2


title: AF_si-NC_IL17_3

value: si-NC+IL17 treatment


title: mTEChi, neonate, WT, cell152


title: AF_si-NC_IL17_2


title: mTEChi, adult, AireKO, cell13

value: AireKO

value: male


title: mTEChi, neonate, WT, cell151

value: WT

value: unknown


title: AF_si-NC_IL17_1


title: AF_si-IAMP-2_2


title: AF_si-IAMP-2_3


title: mTEChi, adult, AireKO, cell12


title: mTEChi, neonate, WT, cell150


title: mTEChi, neonate, WT, cell149


title: AF_si-IAMP-1_3


title: mTEChi, adult, AireKO, cell11


title: AF_si-IAMP-1_2


title: mTEChi, adult, AireKO, cell10


title: mTEChi, neonate, WT, cell148


title: mTEChi, neonate, WT, cell147


title: AF_si-NC_3

value: si-NC


title: mTEChi, adult, AireKO, cell9


title: AF_si-NC_2


title: mTEChi, neonate, WT, cell146


title: AF_si-NC_1


title: mTEChi, adult, AireKO, cell8


title: mTEChi, neonate, WT, cell145


title: mTEChi, adult, AireKO, cell7


title: mTEChi, adult, AireKO, cell6


title: mTEChi, neonate, WT, cell144


title: F2

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

description: Library name: Sample8

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Sus_scrofa_GCF_000003025.6.gtf
Supplementary files format and content: xls files include raw counts for each Sample

organism: Sus scrofa

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Heart

value: Doxorubicin+Formononetin


title: F1

description: Library name: Sample7


title: D3

description: Library name: Sample6

value: Doxorubicin


title: AF_si-IAMP-2_1


title: D2

description: Library name: Sample5


title: C3

description: Library name: Sample3

value: Vehicle


title: D1

description: Library name: Sample4


title: mTEChi, neonate, WT, cell142


title: mTEChi, adult, AireKO, cell5


title: C2

description: Library name: Sample2


title: mTEChi, neonate, WT, cell143


title: mTEChi, adult, AireKO, cell4


title: mTEChi, adult, AireKO, cell3


title: C1

description: Library name: Sample1


title: mTEChi, neonate, WT, cell140


title: AF_si-IAMP-1_1


title: Neuron, wt, ChIPseq, Control, rep1

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Library name: 19ChIPseq_Cont_rep1d6

library_source: genomic

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using TrimGalore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Assembly: mm10
Supplementary files format and content: BIGWIG (wiggle type files using the program wigToBigWig)

molecule: genomic DNA

source_name: mESC-derived motor neuron

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Jaura and Yeh et al., Nat. Commun, 2022) with some modifications.

extract_protocol:
Cells were lysed and chromatin pellets were isolated, and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against the protein of interest.
ChIP-seq libraries were prepared according to the standard Illumina protocols. Briefly, DNA was end-repaired and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 8 x 10^4 cells per mL on day 0.1 uM retinoic acid and 0.25 uM Sonic Hedgehog Agonist were added to the medium on day 2.5 uM gamma-secretase inhibitors were added on days 4 and 5.

value: mESC-derived motor neuron

value: wt

value: N/A (no antibody control)


title: Neuron, wt, ChIPseq, Control, rep2

description: Library name: 20ChIPseq_Cont_rep2d6

value: IgG antibody (Cell Signaling, Cat# 2729; lot# 11)


title: Neuron, KO, ChIPseq, RNAPol2s5p, rep2

description: Library name: 18ChIPseq_Pol2s5p_rep2d6KO

value: KO

value: RNA polymerase II (phosph S5) antibody (Abcam, ab5408; lot# 1015861-7)


title: mTEChi, adult, AireKO, cell2

value: thymus

value: epitherial cells

value: mTEChi


title: Neuron, KO, ChIPseq, RNAPol2s5p, rep1

description: Library name: 17ChIPseq_Pol2s5p_rep1d6KO


title: mTEChi, neonate, WT, cell139


title: Neuron, wt, ChIPseq, RNAPol2s5p, rep2

description: Library name: 16ChIPseq_Pol2s5p_rep2d6


title: mTEChi, adult, AireKO, cell1

value: AireKO

value: male


title: F3

description: Library name: Sample9

value: WT


title: mTEChi, neonate, WT, cell137

value: unknown


title: mTEChi, neonate, WT, cell141


title: mTEChi, adult, WT, cell537


title: Neuron, wt, ChIPseq, H3K27me3, rep2

description: Library name: 12ChIPseq_H3K27me3_rep2d6

value: H3K27me3 antibody (Abcam, ab6002; lot# 1035698-1)


title: mTEChi, neonate, WT, cell136


title: Neuron, wt, ChIPseq, H3K27me3, rep1

description: Library name: 11ChIPseq_H3K27me3_rep1d6


title: Neuron, wt, ChIPseq, RNAPol2s5p, rep1

description: Library name: 15ChIPseq_Pol2s5p_rep1d6


title: Neuron, wt, ChIPseq, H3K4me3, rep2

description: Library name: 10ChIPseq_H3K4me3_rep2d6

value: H3K4me3 antibody (Abcam, ab8580; lot# GR3362386-3)


title: Neuron, wt, ChIPseq, H3K4me3, rep1

description: Library name: 9ChIPseq_H3K4me3_rep1d6


title: Neuron, wt, ChIPseq, CTCF, rep2

description: Library name: 14ChIPseq_CTCF_rep2d6

value: CTCF antibody (Millipore, 07-729; lot# 3515588)


title: mTEChi, neonate, WT, cell135


title: Neuron, wt, ChIPseq, H3K4me1, rep2

description: Library name: 8ChIPseq_H3K4me1_rep2d6

value: H3K4me1 antibody (Abcam, ab8895; lot# GR3442591-2)


title: Neuron, wt, ChIPseq, H3K4me1, rep1

description: Library name: 7ChIPseq_H3K4me1_rep1d6

value: mESC-derived motor neuron


title: mTEChi, neonate, WT, cell134


title: mTEChi, adult, WT, cell535


title: Neuron, wt, ChIPseq, Brg1, rep2

description: Library name: 6ChIPseq_Brg1_rep2d6

value: wt

value: Brg1 antibody (Abcam, ab110641; lot# 1000647-1)


title: mTEChi, neonate, WT, cell133


title: mTEChi, adult, WT, cell534


title: Neuron, wt, ChIPseq, Brg1, rep1

description: Library name: 5ChIPseq_Brg1_rep1d6


title: Neuron, KO, ChIPseq, Brm, rep2

description: Library name: 4ChIPseq_Brm_rep2d6KO

value: Brm antibody (Bethyl, A301-015A; lot# 2)


title: Neuron, KO, ChIPseq, Brm, rep1

description: Library name: 3ChIPseq_Brm_rep1d6KO

value: KO


title: mTEChi, neonate, WT, cell138


title: mTEChi, adult, WT, cell532


title: mTEChi, neonate, WT, cell132


title: Neuron, wt, ChIPseq, Brm, rep2

description: Library name: 2ChIPseq_Brm_rep2d6


title: mTEChi, adult, WT, cell533


title: mTEChi, adult, WT, cell538


title: Neuron, wt, ChIPseq, CTCF, rep1

description: Library name: 13ChIPseq_CTCF_rep1d6


title: mTEChi, adult, WT, cell536


title: Neuron, wt, ChIPseq, Brm, rep1

description: Library name: 1ChIPseq_Brm_rep1d6


title: Neuron, KO, ChIPseq, CBP, rep2

description: Library name: 12ChIPseq_CBP_rep2d6KO


title: mTEChi, neonate, WT, cell131


title: Neuron, KO, ChIPseq, CBP, rep1

description: Library name: 11ChIPseq_CBP_rep1d6KO


title: mTEChi, adult, WT, cell530


title: Neuron, wt, ChIPseq, CBP, rep2

description: Library name: 10ChIPseq_CBP_rep2d6


title: mTEChi, adult, WT, cell531


title: Neuron, wt, ChIPseq, CBP, rep1

description: Library name: 9ChIPseq_CBP_rep1d6


title: mTEChi, neonate, WT, cell129


title: Neuron, KO, ChIPseq, H3K27ac, rep2

description: Library name: 8ChIPseq_H3K27ac_rep2d6KO


title: mTEChi, adult, WT, cell529


title: Neuron, KO, ChIPseq, H3K27ac, rep1

description: Library name: 7ChIPseq_H3K27ac_rep1d6KO


title: Neuron, wt, ChIPseq, H3K27ac, rep2

description: Library name: 6ChIPseq_H3K27ac_rep2d6


title: mTEChi, neonate, WT, cell128


title: mTEChi, adult, WT, cell528


title: mTEChi, adult, WT, cell527


title: mTEChi, neonate, WT, cell127


title: Neuron, KO, ChIPseq, CREST, rep1

description: Library name: 3ChIPseq_CREST_rep1d6KO


title: Neuron, wt, ChIPseq, CREST, rep2

description: Library name: 2ChIPseq_CREST_rep2d6


title: mTEChi, neonate, WT, cell126


title: Neuron, wt, ChIPseq, CREST, rep1

description: Library name: 1ChIPseq_CREST_rep1d6


title: mTEChi, neonate, WT, cell124


title: mTEChi, adult, WT, cell525


title: mTEChi, neonate, WT, cell125


title: mTEChi, adult, WT, cell526


title: mTEChi, neonate, WT, cell123


title: mTEChi, adult, WT, cell524


title: mTEChi, neonate, WT, cell130


title: mTEChi, adult, WT, cell523


title: mTEChi, neonate, WT, cell120


title: mTEChi, neonate, WT, cell122


title: mTEChi, adult, WT, cell519


title: mTEChi, adult, WT, cell522


title: mTEChi, adult, WT, cell520


title: mTEChi, adult, WT, cell521


title: mTEChi, neonate, WT, cell119


title: mTEChi, neonate, WT, cell118


title: mTEChi, neonate, WT, cell121


title: mTEChi, adult, WT, cell518


title: mTEChi, adult, WT, cell517


title: mTEChi, neonate, WT, cell116


title: mTEChi, neonate, WT, cell115


title: mTEChi, adult, WT, cell516


title: mTEChi, neonate, WT, cell117


title: Neuron, KO, ChIPseq, CREST, rep2

description: Library name: 4ChIPseq_CREST_rep2d6KO


title: mTEChi, adult, WT, cell515


title: mTEChi, neonate, WT, cell114


title: 24_Chow_hind_2_GEX

city: Neuherberg

first: Robert

middle: Michael

last: Gutgesell

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Center Munich

description:
Library name: Sample_23L010436
10x Genomics

data_processing:
Reads were mapped to the pre-built mm10 mouse reference (University of California Santa Cruz mm10 reference genome) using Cell Ranger ARC (v2.0.2, 10X Genomics; Pleasanton, CA, USA) with default parameters. Resulting cell-by-peak and cell-by-gene matrices (ATAC and gene expression assays, respectively) from the 24 samples which were integrated using Cellranger aggr (10X Genomics; Pleasanton, CA, USA).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: DVC

extract_protocol:
Nuclei were isolated using the 10X Genomics Chromium Nuclei Isolation Kit including RNase Inhibitor (10X Genomics; Pleasanton, CA, USA; #PN-1000494), and using the 10X Genomics protocol for Single Cell Multiome ATAC + Gene Expression (10X Genomics; Pleasanton, CA, USA; #CG000505 Rev A).
Libraries were using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E) according to the manufacturer’s instruction.

value: DVC

value: Chow-fed vehicle


title: 23_DIO_hind_2_GEX

description:
Library name: Sample_23L010435
10x Genomics

value: 12 wks DIO + vehicle


title: mTEChi, adult, WT, cell514

value: thymus

value: epitherial cells

value: mTEChi


title: 22_GIPag_hind_2_GEX

description:
Library name: Sample_23L010434
10x Genomics

value: 12 wks DIO + acyl-GIP


title: mTEChi, adult, WT, cell513

value: WT

value: male


title: 21_GIPant_hind_2_GEX

description:
Library name: Sample_23L010433
10x Genomics

value: 12 wks DIO + GIPR antagonist


title: 20_GLP1ag_hind_2_GEX

description:
Library name: Sample_23L010432
10x Genomics

value: 12 wks DIO + acyl-GLP-1


title: mTEChi, neonate, WT, cell112

value: unknown


title: 19_MAR709_hind_2_GEX

description:
Library name: Sample_23L010431
10x Genomics

value: 12 wks DIO + MAR709


title: mTEChi, adult, WT, cell512


title: 18_MAR709_hind_1_GEX

description:
Library name: Sample_23L010430
10x Genomics


title: mTEChi, adult, WT, cell511


title: mTEChi, neonate, WT, cell111


title: 17_GLP1ag_hind_1_GEX

description:
Library name: Sample_23L010429
10x Genomics


title: 16_GIPant_hind_2_GEX

description:
Library name: Sample_23L010428
10x Genomics


title: mTEChi, neonate, WT, cell110


title: 15_GIPag_hind_1_GEX

description:
Library name: Sample_23L010427
10x Genomics


title: mTEChi, adult, WT, cell510


title: 14_DIO_hind_1_GEX

description:
Library name: Sample_23L010426
10x Genomics


title: 12_Chow_hypo_2_GEX

description:
Library name: Sample_23L010424
10x Genomics

source_name: Hypothalamus

value: Hypothalamus


title: mTEChi, adult, WT, cell509


title: mTEChi, adult, WT, cell508


title: 11_DIO_hypo_2_GEX

description:
Library name: Sample_23L010423
10x Genomics


title: 10_GIPag_hypo_2_GEX

description:
Library name: Sample_23L010422
10x Genomics


title: mTEChi, neonate, WT, cell108


title: mTEChi, neonate, WT, cell107


title: 9_GIPant_hypo_2_GEX

description:
Library name: Sample_23L010421
10x Genomics


title: mTEChi, neonate, WT, cell113


title: 8_GLP1ag_hypo_2_GEX

description:
Library name: Sample_23L010420
10x Genomics


title: mTEChi, neonate, WT, cell106


title: mTEChi, adult, WT, cell507


title: 7_MAR709_hypo_2_GEX

description:
Library name: Sample_23L010419
10x Genomics


title: mTEChi, adult, WT, cell506


title: 6_MAR709_hypo_1_GEX

description:
Library name: Sample_23L010418
10x Genomics


title: mTEChi, neonate, WT, cell105


title: 5_GLP1ag_hypo_1_GEX

description:
Library name: Sample_23L010417
10x Genomics


title: mTEChi, adult, WT, cell505


title: mTEChi, neonate, WT, cell104


title: 4_GIPant_hypo_1_GEX

description:
Library name: Sample_23L010416
10x Genomics


title: mTEChi, neonate, WT, cell109


title: 3_GIPag_hypo_1_GEX

description:
Library name: Sample_23L010415
10x Genomics


title: mTEChi, neonate, WT, cell103


title: mTEChi, adult, WT, cell504


title: 2_DIO_hypo_1_GEX

description:
Library name: Sample_23L010414
10x Genomics


title: 1_Chow_hypo_1_GEX

description:
Library name: Sample_23L010413
10x Genomics


title: mTEChi, adult, WT, cell503


title: 13_Chow_hind_1_GEX

description:
Library name: Sample_23L010425
10x Genomics


title: mTEChi, neonate, WT, cell102


title: Mouse naïve CD4+ T cells, WT, rep3

city: Shanghai

first: Haixin

last: Li

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

institute: Tongji University

description: Library name: Sample6

data_processing:
Bowtie 2 (version 2.2.3) was used to map the data to the Mus Musculus (mm10) reference genome.
Assembly: Bowtie 2 (version 2.2.3) was used to map the data to the Mus Musculus (mm10) reference genome.
Supplementary files format and content: MACS2 (version 2.1.1) was used to identify binding sites with the parameter '-q 0.05 --nomodel --extsize 150 --keep-dup all --call-summits'.

source_name: Peripheral lymphoid organs

growth_protocol: Male mice aged 8-12 weeks were utilized in experiments

extract_protocol:
After being resuspended in nuclear lysis buffer, the DNA pellets were collected and treated with the TruePrepTM DNA Library Prep Kit V2 (Vazyme, TD501) following the manufacturer's instructions.
PCR was used to amplify the transposed DNA fragments using primers with different Barcodes.

treatment_protocol: Naïve CD4+ T cells were purified using the EasySep Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL Technologies) following the provided instructions.

value: Peripheral lymphoid organs

value: T cell


title: mTEChi, adult, WT, cell502


title: mTEChi, adult, WT, cell501


title: Mouse naïve CD4+ T cells, WT, rep1

description: Library name: Sample4


title: Mouse naïve CD4+ T cells, Nat10 KO, rep3

description: Library name: Sample3

value: Nat10 KO


title: Mouse naïve CD4+ T cells, Nat10 KO, rep2

description: Library name: Sample2


title: Mouse naïve CD4+ T cells, Nat10 KO, rep1

description: Library name: Sample1


title: mTEChi, neonate, WT, cell100


title: No developmental exposure to PM2.5, no OVA challene rep 7 (WGMS)

city: Ultimo

first: Razia

last: Zakarya

state: NSW

address: 15 Broadway

department: SoLS

country: Australia

institute: UTS

description:
Library name: Sham_7
178 bp PE

data_processing:
Trim Galore (Babraham Institute), DRAGEN Methylation Pipeline (v3.10) in single pass mode
Assembly: GRCm38
Supplementary files format and content: tab delimited text file containing %5mC (CG context) for each sample at all (100CpG) probes overlapping genes (as per ENCODE annotation)

source_name: Lung (RML)

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Hilden, Germany)
NEBNext Enzymatic Methyl-seq  spiked with non-methylated lambda DNA

value: Lung (RML)

value: Balb/c

value: developmental saline & PBS


title: Mouse naïve CD4+ T cells, WT, rep2

description: Library name: Sample5


title: mTEChi, adult, WT, cell499

value: thymus


title: mTEChi, neonate, WT, cell99

value: epitherial cells


title: mTEChi, neonate, WT, cell98

value: mTEChi


title: No developmental exposure to PM2.5, no OVA challene rep 6 (WGMS)

description:
Library name: Sham_6
177 bp PE


title: No developmental exposure to PM2.5, no OVA challene rep 5 (WGMS)

description:
Library name: Sham_5
176 bp PE


title: No developmental exposure to PM2.5, no OVA challene rep 4 (WGMS)

description:
Library name: Sham_4
175 bp PE


title: mTEChi, adult, WT, cell498


title: mTEChi, neonate, WT, cell97


title: No developmental exposure to PM2.5, no OVA challene rep 2 (WGMS)

description:
Library name: Sham_2
173 bp PE


title: No developmental exposure to PM2.5, no OVA challene rep 3 (WGMS)

description:
Library name: Sham_3
174 bp PE


title: mTEChi, adult, WT, cell497


title: No developmental exposure to PM2.5, no OVA challene rep 1 (WGMS)

description:
Library name: Sham_1
172 bp PE


title: No developmental exposure to PM2.5 w/ OVA challenge rep 7 (WGMS)

description:
Library name: Sham-OVA_8
171 bp PE

value: developmental saline & OVA


title: mTEChi, neonate, WT, cell101

value: WT


title: No developmental exposure to PM2.5 w/ OVA challenge rep 6 (WGMS)

description:
Library name: Sham-OVA_7
170 bp PE


title: mTEChi, adult, WT, cell496

value: male


title: mTEChi, neonate, WT, cell95


title: No developmental exposure to PM2.5 w/ OVA challenge rep 5 (WGMS)

description:
Library name: Sham-OVA_6
169 bp PE


title: No developmental exposure to PM2.5 w/ OVA challenge rep 4 (WGMS)

description:
Library name: Sham-OVA_5
168 bp PE


title: mTEChi, adult, WT, cell495


title: mTEChi, adult, WT, cell494


title: No developmental exposure to PM2.5 w/ OVA challenge rep 2 (WGMS)

description:
Library name: Sham-OVA_2
166 bp PE


title: mTEChi, adult, WT, cell500


title: No developmental exposure to PM2.5 w/ OVA challenge rep 1 (WGMS)

description:
Library name: Sham-OVA_1
165 bp PE


title: mTEChi, neonate, WT, cell93


title: mTEChi, adult, WT, cell493


title: Developmental exposure to PM2.5, no OVA rep 7 (WGMS)

description:
Library name: PM_7
164 bp PE

value: developmental PM2.5 & PBS


title: mTEChi, neonate, WT, cell92


title: Developmental exposure to PM2.5, no OVA rep 5 (WGMS)

description:
Library name: PM_5
162 bp PE


title: Developmental exposure to PM2.5, no OVA rep 4 (WGMS)

description:
Library name: PM_4
161 bp PE


title: mTEChi, neonate, WT, cell91


title: mTEChi, adult, WT, cell491


title: Developmental exposure to PM2.5, no OVA rep 3 (WGMS)

description:
Library name: PM_3
160 bp PE


title: mTEChi, neonate, WT, cell96


title: Developmental exposure to PM2.5, no OVA rep 2 (WGMS)

description:
Library name: PM_2
159 bp PE


title: mTEChi, neonate, WT, cell90


title: mTEChi, adult, WT, cell490


title: mTEChi, neonate, WT, cell89


title: Developmental exposure to PM2.5, no OVA rep 1 (WGMS)

description:
Library name: PM_1
158 bp PE


title: Developmental exposure to PM2.5 w/ OVA challenge rep 8 (WGMS)

description:
Library name: PM-OVA_Rel2
157 bp PE

value: developmental PM2.5 & OVA


title: mTEChi, neonate, WT, cell94

value: unknown


title: No developmental exposure to PM2.5 w/ OVA challenge rep 3 (WGMS)

description:
Library name: Sham-OVA_3
167 bp PE


title: mTEChi, adult, WT, cell489


title: mTEChi, neonate, WT, cell88


title: Developmental exposure to PM2.5 w/ OVA challenge rep 5 (WGMS)

description:
Library name: PM-OVA_6
154 bp PE


title: mTEChi, adult, WT, cell488


title: mTEChi, neonate, WT, cell87


title: Developmental exposure to PM2.5 w/ OVA challenge rep 4 (WGMS)

description:
Library name: PM-OVA_5
153 bp PE


title: mTEChi, neonate, WT, cell86


title: mTEChi, adult, WT, cell487


title: Developmental exposure to PM2.5 w/ OVA challenge rep 3 (WGMS)

description:
Library name: PM-OVA_4
152 bp PE


title: mTEChi, adult, WT, cell492


title: Developmental exposure to PM2.5 w/ OVA challenge rep 2 (WGMS)

description:
Library name: PM-OVA_2
151 bp PE


title: Developmental exposure to PM2.5, no OVA rep 6 (WGMS)

description:
Library name: PM_6
163 bp PE


title: mTEChi, neonate, WT, cell85


title: No developmental exposure to PM2.5 w/ OVA challenge rep 5

description: Library name: SHAM-OVA_6_RNA

data_processing:
bcl2fastq2
Assembly: mm10
Supplementary files format and content: tab delimited text file containing RPKM counts for each sample

molecule: polyA RNA

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Hilden, Germany)
Illumina Stranded mRNA library prep as per manufacturers instructions


title: mTEChi, adult, WT, cell485


title: No developmental exposure to PM2.5 w/ OVA challenge rep 4

description: Library name: SHAM-OVA_5_RNA


title: No developmental exposure to PM2.5 w/ OVA challenge rep 3

description: Library name: SHAM-OVA_4_RNA


title: mTEChi, neonate, WT, cell84


title: mTEChi, neonate, WT, cell83


title: No developmental exposure to PM2.5 w/ OVA challenge rep 2

description: Library name: SHAM-OVA_3_RNA


title: mTEChi, adult, WT, cell484


title: No developmental exposure to PM2.5 w/ OVA challenge rep 1

description: Library name: SHAM-OVA_1_RNA


title: Developmental exposure to PM2.5 w/ OVA challenge rep 6 (WGMS)

description:
Library name: PM-OVA_7
155 bp PE


title: mTEChi, adult, WT, cell483


title: No developmental exposure to PM2.5, no OVA challene rep 7

description: Library name: SHAM_7_RNA


title: mTEChi, neonate, WT, cell82


title: No developmental exposure to PM2.5, no OVA challene rep 5

description: Library name: SHAM_5_RNA


title: mTEChi, neonate, WT, cell81


title: No developmental exposure to PM2.5, no OVA challene rep 4

description: Library name: SHAM_4_RNA


title: mTEChi, adult, WT, cell481


title: mTEChi, adult, WT, cell486


title: mTEChi, neonate, WT, cell80


title: mTEChi, adult, WT, cell480


title: No developmental exposure to PM2.5, no OVA challene rep 6

description: Library name: SHAM_6_RNA


title: Developmental exposure to PM2.5 w/ OVA challenge rep 1 (WGMS)

description:
Library name: PM-OVA_1
150 bp PE


title: No developmental exposure to PM2.5, no OVA challene rep 1

description: Library name: SHAM_1_RNA


title: mTEChi, neonate, WT, cell79


title: Developmental exposure to PM2.5 w/ OVA challenge rep 4

description: Library name: PM-OVA_Rel1_RNA


title: mTEChi, adult, WT, cell479


title: No developmental exposure to PM2.5, no OVA challene rep 2

description: Library name: SHAM_2_RNA


title: Developmental exposure to PM2.5 w/ OVA challenge rep 2

description: Library name: PM-OVA_5_RNA


title: Developmental exposure to PM2.5 w/ OVA challenge rep 3

description: Library name: PM-OVA_6_RNA


title: Developmental exposure to PM2.5 w/ OVA challenge rep 1

description: Library name: PM-OVA_4_RNA


title: Developmental exposure to PM2.5, no OVA rep 7

description: Library name: PM_7_RNA


title: mTEChi, adult, WT, cell482


title: mTEChi, neonate, WT, cell76


title: mTEChi, adult, WT, cell477


title: Developmental exposure to PM2.5, no OVA rep 6

description: Library name: PM_6_RNA


title: mTEChi, adult, WT, cell478


title: Developmental exposure to PM2.5, no OVA rep 5

description: Library name: PM_5_RNA


title: No developmental exposure to PM2.5, no OVA challene rep 3

description: Library name: SHAM_3_RNA


title: mTEChi, neonate, WT, cell75


title: Developmental exposure to PM2.5, no OVA rep 4

description: Library name: PM_4_RNA


title: mTEChi, adult, WT, cell476


title: Developmental exposure to PM2.5, no OVA rep 3

description: Library name: PM_3_RNA


title: mTEChi, neonate, WT, cell74


title: Developmental exposure to PM2.5, no OVA rep 1

description: Library name: PM_1_RNA


title: mTEChi, neonate, WT, cell78


title: Developmental exposure to PM2.5, no OVA rep 2

description: Library name: PM_2_RNA


title: Baz2b-homo-3 mouse liver,ATAC

city: shanghai

first: shi-qing

last: cai

address: number 320 yueyang road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

data_processing:
pair-end sequencing reads were aligned to the mouse genome (GRCm38/mm10) by using the BWA aligner 47. Peak calling was performed using commands from MACS2 (version 1.4.2) with -q 0.05 48. The differential peaks between sample groups were identified by using DiffBind (version 3.15) in R 49 and annotated by using the annotatedPeaks.pl, a command from HOMER 50. BigWig files, ChIP-seq heatmap, and profile plots were generated using the bamCoverage command or the plotHeatmap command from deeptools (version 3.5.0) with –binSize 5 51. All ChIP-seq and ATAC-seq data were from three biological replicates.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
CHIP-seq: for liver tissue, frozen samples were chopped into small pieces, immediately incubated in freshly prepared disuccinimidyl glutarate solution (2 mM in PBS), and rotated for 30 min at room temperature; for cell lines, samples were collected from 10 cm cultured dishes using cell scrapers. Then samples were washed in PBS buffer twice, crosslinked by 1% formaldehyde (in PBS with proteinase-inhibitor cocktail), and fixed on a nutator shaker for 10 min at room temperature. Fixed samples were quenched with 0.125 M glycine and washed with cold PBS buffer with protease inhibitors three times. Ground the liver tissues with a dounce homogenizer on ice, passed the homogenized tissue suspension through a 70 μM cell strainer to remove the connective tissue, and then washed samples with cold PBS buffer with protease inhibitors three times. Samples were then lysed by ice-cold lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 1 mM PMSF and protease inhibitor cocktail) with 0.1% SDS. Lysates were digested using 0.5 μl micrococcal nuclease (MNase) (10011S, CST) in reaction buffer (50 mM Tris, 5mM CaCl2, pH 8.0) for 3 min at 37 °C, and then were stopped with 25 mM EDTA. About 10 μg of the digested chromatin was used for immunoprecipitation. ATAC-seq: Briefly, frozen liver samples were chopped into small pieces, and immediately incubated in homogenization buffer (10mM Tris, 0.25mM sucrose, 25mM KCl, 5mM MgCl2, 0.1 mM DTT, 1% BSA, 0.1% NP 40 with RNase inhibitor). Ground the liver tissue pieces with a dounce homogenizer on ice, passed the homogenized tissue suspension through a 70 μM and 40 μM cell strainer, washed once in cold Nuclei Wash Buffer (20% iodixanol in HB solution), and then resuspended samples in Blocking Buffer (10% BSA in PBS with RNase inhibitor). The segmentation reaction was performed using transposases (Vazyme, TD501) for 30 min at 37 °C. Segmented DNAs were purified and amplified using the TruePrepTM Index Kit (Vazyme, TD202).
The ChIP-seq and ATAC-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed on an Illumina NovaSeq 6000.

value: liver


title: Baz2b-homo-2 mouse liver,ATAC


title: mTEChi, neonate, WT, cell72


title: mTEChi, adult, WT, cell472


title: mTEChi, adult, WT, cell474


title: Baz2b-homo-1 mouse liver,ATAC


title: mTEChi, neonate, WT, cell71


title: wt-3 mouse liver,ATAC


title: Embryonic murine secondary palate at ages of E12.5 & E13.5 (Pax9-/- vs. WT)

city: Okayama

first: Ziyi

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Molecular Biology and Biochemistry

institute: Okayama University

description:
Library name: E12.5_E13.5_Pax9KO_WT-H1-WXG4BXM-A1
FFPE Spatial transcriptome sequencing

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v6.1.2 with default parameters.
Assembly: Mouse mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots a parquet format
Library strategy: Spatial Transcriptomics

source_name: Embryonic secondary palate

extract_protocol:
Following 10x Genomics’ Manufacturers’ Protocol for Visium HD Spatial Transcriptomics Assay.
Libraries were prepared according to Illumina Single cell RNA seq preparation procotol.

value: Embryonic secondary palate


title: mTEChi, neonate, WT, cell73


title: wt-2 mouse liver,ATAC


title: wt-1 mouse liver,ATAC


title: Empty-flag AML12 cell line,Flag, chip

tag: cell line

value: mouse hepatocyte


title: mTEChi, adult, WT, cell471


title: mTEChi, neonate, WT, cell77


title: BAZ2B-OE-flag AML12 cell line, Flag,chip


title: mTEChi, neonate, WT, cell70


title: mTEChi, adult, WT, cell470


title: mTEChi, adult, WT, cell475


title: mTEChi, neonate, WT, cell69


title: Baz2b-homo-2 mouse liver,H3K4me3/H3K27ac, Input


title: mTEChi, neonate, WT, cell68


title: mTEChi, adult, WT, cell469


title: Baz2b-homo-3 mouse liver,H3K4me3/H3K27ac, Input


title: mTEChi, adult, WT, cell473


title: mTEChi, adult, WT, cell468


title: wt-3 mouse liver,H3K4me3/H3K27ac, Input


title: mTEChi, neonate, WT, cell67


title: Baz2b-homo-1 mouse liver,H3K27ac, Input


title: wt-1 mouse liver,H3K27ac, Input


title: mTEChi, adult, WT, cell467


title: mTEChi, neonate, WT, cell66


title: wt-2 mouse liver,H3K4me3/H3K27ac, Input


title: Baz2b-homo-1 mouse liver,H3K4me3, Input


title: mTEChi, adult, WT, cell466


title: wt-1 mouse liver,H3K4me3, Input


title: Baz2b-homo-3 mouse liver,H3K27ac, chip


title: mTEChi, adult, WT, cell465


title: mTEChi, neonate, WT, cell65


title: mTEChi, neonate, WT, cell64


title: Baz2b-homo-2 mouse liver,H3K27ac, chip


title: mTEChi, adult, WT, cell464


title: wt-2 mouse liver,H3K27ac, chip


title: mTEChi, neonate, WT, cell63


title: wt-3 mouse liver,H3K27ac, chip


title: Baz2b-homo-1 mouse liver,H3K27ac, chip


title: mTEChi, adult, WT, cell463


title: wt-1 mouse liver,H3K27ac, chip


title: mTEChi, neonate, WT, cell62


title: mTEChi, neonate, WT, cell61


title: Baz2b-homo-1 mouse liver,H3K4me3, chip


title: Baz2b-homo-2 mouse liver,H3K4me3, chip


title: Baz2b-homo-3 mouse liver,H3K4me3, chip


title: wt-2 mouse liver,H3K4me3, chip


title: mTEChi, adult, WT, cell461


title: wt-3 mouse liver,H3K4me3, chip


title: mTEChi, neonate, WT, cell60


title: mTEChi, adult, WT, cell460


title: 3dpi_ZT16

city: Chicago

first: Pei

last: Zhu

state: IL

address: 420 E. Superior St

department: Biochemistry and Molecular Genetics

country: USA

institute: northwestern university

description: 10x Genomics

data_processing:
Demultiplexing and read counting using Cell Ranger (v1.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
10,000 cells from each condition were loaded into a Chromium Controller (10X Genomics) using a Chromium Next GEM Chip G (10X Genomics). These were processed to form single-cell gel beads in the emulsion (GEM) following the manufacturer’s instructions.
cDNA synthesis and library preparation were performed using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 and Single Index Kit T Set A (10X Genomics) according to the provided manual.

treatment_protocol: Mononucleated cells from the tibialis anterior (TA) muscles of both hindlimbs were collected at ZT4 and ZT16 on day 0, 1, and 3 after injury.

value: Skeletal muscle

value: skeletal muscle cells

value: wildtype

value: muscle cells collected from cardiotoxin-injured TA muscle at ZT16 on day 3 post-injury


title: mTEChi, neonate, WT, cell59


title: mTEChi, neonate, WT, cell58


title: wt-1 mouse liver,H3K4me3, chip


title: 3dpi_ZT4

description: 10x Genomics

value: muscle cells collected from cardiotoxin-injured TA muscle at ZT4 on day 3 post-injury


title: 1dpi_ZT16

description: 10x Genomics

value: muscle cells collected from cardiotoxin-injured TA muscle at ZT16 on day 1 post-injury


title: mTEChi, adult, WT, cell458

value: thymus

value: epitherial cells


title: 1dpi_ZT4

description: 10x Genomics

value: muscle cells collected from cardiotoxin-injured TA muscle at ZT4 on day 1 post-injury


title: mTEChi, adult, WT, cell457

value: mTEChi

value: WT


title: 0dpi_ZT16

description: 10x Genomics

value: muscle cells collected from uninjured TA muscle at ZT16


title: mTEChi, neonate, WT, cell55


title: mTEChi, adult, WT, cell462

value: male


title: 0dpi_ZT4

description: 10x Genomics

value: muscle cells collected from uninjured TA muscle at ZT4


title: NET30,Tumor,Insulinoma

city: Riga

first: Helvijs

last: Niedra

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study centre

data_processing:
Quality control of raw sequencing data was performed using FastQC (v0.11.9) and MultiQC (v1.12) software. Subsequently, the paired-end reads were trimmed with fastp software (v0.23.2) to keep reads with average base quality (Phred score) of at least 20 and a minimum read length of 75 base pairs. The read count and quality of trimmed reads were once more inspected by above-mentioned QC software. Afterward, the ribosomal RNA (rRNA) was removed using SortMeRNA (v2.1), followed by final quality and read count evaluation. Reads were further quasi-mapped and quantified with Salmon software (v1.9.0) against GENCODE (v38) Homo sapiens genome. R software (v4.2.2) was used to summarise gene-level counts with the tximeta package (v1.16.0). DGE analysis was performed using DESeq2 (v1.38.3).
Assembly: GENCODE v38 GRCh38
Supplementary files format and content: Salmnon output, each .tar compressed file contains raw transcript counts (quant.sf) and log files with mapping statistics
Supplementary files format and content: Libraries NET22, NET3, NET5, and 4NT have additional salmon output files as the libraries of these samples contained two barcodes and the resulting .fastq files were not combined prior to data pre-processing

organism: Homo sapiens

source_name: FFPE tumor adjacent pancreatic tissue

extract_protocol:
Total RNA for transcriptome sequencing was extracted from the FFPE samples using the RNeasy FFPE Kit (Qiagen, Germany) following the manufacturer’s instructions. The concentration of extracted RNA was measured with the Qubit RNA HS Kit (Thermo Fisher, USA) using the Qubit 2.0 Fluorometer.
Prior to sequencing a cDNA synthesis  followed by cDNA amplification was carried out using the REPLI-g WTA Single Cell Kit (Qiagen, Germany) and Poly A+ mRNA amplification protocol provided by the manufacturer. After the cDNA was generated it was enzymatically fragmented and whole transcriptome libraries were prepared using the MGIEasy PCR–Free DNA Library Prep Set (MGI, PRC). The paired-end library sequencing was carried out on the DNBSEQ-G400 platform (MGI, PRC) with the aim of a minimum of 20 million reads per sample with a 150 bp read length.

value: FFPE tumor adjacent pancreatic tissue

tag: tumor grade

value: F

tag: age at_surgery

tag: date of_surgery


title: NET28,Tumor,Insulinoma

value: M


title: mTEChi, neonate, WT, cell57

value: unknown


title: QSC_ZT16-3

data_processing:
Sequence reads were trimmed for adaptor sequences using the Trimmomatic (v0.33) tool
The trimmed reads were mapped to the mm10 Mus musculus reference genome using STAR aligner (v2.5.2).
The number of alignments mapped to each gene was counted using RSEM (v1.3.3), followed by passing to DESeq2 using the tximport package
Differentially expressed genes (DEGs) were identified through the results function in DESeq2 and corrected for multiple testing (an adjusted P-value was generated using the Benjamini-Hochberg correction).
Assembly: mm10
Supplementary files format and content: Isoform-level quantifications obtained from RSEM.

source_name: skeletal muscle stem cells

extract_protocol:
Total RNA was extracted from in vivo light-fixed Pax7-zsgreen+ SCs using the miRNeasy FFPE Kit, adhering to the supplied instructions with a crucial modification that the digestion of RNA by proteinase K was performed at 56°C for 1 hour.
cDNA libraries were constructed using the SMART-seq v4 Ultra Low Input RNA Kit from Takara Bio.

treatment_protocol: SCs were extracted from the hindlimb muscles of Pax7-zsgreen mice, both uninjured and following cardiotoxin-induced injury at ZT4 and ZT16, on day 1 and 3 post-injury.

value: skeletal muscle stem cells

value: uninjured muscle


title: mTEChi, adult, WT, cell455


title: NET29,Tumor,Insulinoma


title: QSC_ZT16-2


title: mTEChi, adult, WT, cell454


title: NET28,Non-tumor,Tumor adjacent pancreatic tissue


title: mTEChi, neonate, WT, cell53


title: mTEChi, adult, WT, cell459


title: QSC_ZT16-1


title: mTEChi, neonate, WT, cell54


title: NET4,Non-tumor,Tumor adjacent pancreatic tissue


title: NET61,Non-tumor,Tumor adjacent pancreatic tissue


title: mTEChi, adult, WT, cell452


title: mTEChi, neonate, WT, cell56


title: QSC_ZT4-3


title: mTEChi, neonate, WT, cell51


title: QSC_ZT4-2


title: mTEChi, adult, WT, cell456


title: mTEChi, neonate, WT, cell50


title: mTEChi, adult, WT, cell450


title: NET3,Non-tumor,Tumor adjacent pancreatic tissue, 4NT_79


title: mTEChi, neonate, WT, cell49


title: NET3,Non-tumor,Tumor adjacent pancreatic tissue, 4NT_80


title: mTEChi, adult, WT, cell449


title: QSC_ZT4-1


title: NET2,Non-tumor,Tumor adjacent pancreatic tissue


title: mTEChi, adult, WT, cell447


title: 3dpi_ASC_ZT16-2

value: 3 day post-carditoxin injury


title: mTEChi, adult, WT, cell448


title: NET9,Tumor,Non-functioning

source_name: FFPE tumor tissue

value: FFPE tumor tissue


title: mTEChi, adult, WT, cell453


title: NET1,Non-tumor,Tumor adjacent pancreatic tissue


title: mTEChi, neonate, WT, cell48


title: mTEChi, neonate, WT, cell47


title: 3dpi_ASC_ZT16-3


title: mTEChi, neonate, WT, cell52


title: mTEChi, neonate, WT, cell46


title: 3dpi_ASC_ZT16-1


title: mTEChi, adult, WT, cell445


title: NET8,Tumor,Non-functioning


title: NET6,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell44


title: mTEChi, neonate, WT, cell43


title: mTEChi, adult, WT, cell443


title: 3dpi_ASC_ZT4-3


title: mTEChi, adult, WT, cell446


title: mTEChi, neonate, WT, cell45


title: mTEChi, adult, WT, cell451


title: 3dpi_ASC_ZT4-2


title: mTEChi, adult, WT, cell444


title: NET5,Tumor,Non-functioning, NET5_13


title: 3dpi_ASC_ZT16-4


title: NET5,Tumor,Non-functioning, NET5_14


title: mTEChi, neonate, WT, cell42


title: 3dpi_ASC_ZT4-4


title: mTEChi, adult, WT, cell440


title: mTEChi, adult, WT, cell441


title: 1dpi_ASC_ZT16-4

value: 1 day post-carditoxin injury


title: 3dpi_ASC_ZT4-1


title: mTEChi, neonate, WT, cell39

value: thymus


title: mTEChi, adult, WT, cell442

value: epitherial cells


title: 1dpi_ASC_ZT16-3


title: NET4,Tumor,Non-functioning


title: NET3,Tumor,Non-functioning, NET3_77


title: mTEChi, neonate, WT, cell40


title: mTEChi, adult, WT, cell439


title: NET27,Tumor,Non-functioning


title: NET3,Tumor,Non-functioning, NET3_78


title: mTEChi, neonate, WT, cell38


title: 1dpi_ASC_ZT16-1


title: 1dpi_ASC_ZT16-2


title: mTEChi, neonate, WT, cell37


title: 1dpi_ASC_ZT4-4


title: mTEChi, adult, WT, cell437


title: NET16,Tumor,Non-functioning


title: NET18,Tumor,Non-functioning


title: mTEChi, adult, WT, cell436


title: 1dpi_ASC_ZT4-3


title: mTEChi, neonate, WT, cell36


title: NET15,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell41


title: mTEChi, neonate, WT, cell35


title: 1dpi_ASC_ZT4-2


title: mTEChi, adult, WT, cell435


title: NET12,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell34


title: 1dpi_ASC_ZT4-1


title: NET7,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell33


title: mTEChi, adult, WT, cell434


title: RA model with PBS treatment, 144h, scRNA-seq

first: Ming

last: Hao

address: Shuangqing Rd.

institute: Tsinghua Univ

description: 10X Genomics

data_processing:
Paired seq data was mapped to mouse transcriptome and quantified using Salmon
Assembly: mm10
Supplementary files format and content: The .sf  files are text files,  contenting Salmon quantified counts and abundance of each mouse gene.

source_name: knee joints

extract_protocol:
cells were sorted into lysis buffer composed of 0.2%(v/v) TritonX-100 and 2 U/ul Recombinant Rnase Inhibitor
Extracted RNA was reverse transcripted and amplified as SMART-Seq2 protocol
Purified cDNA library was fragmented and tagmented using Vazyme TruePrep DNA Library Prep Kit V2

value: knee joints

value: Cx3cr1-cre; Rosa26-tdTomato

value: healthy mice received a single intraperitoneal injection of K/BxN serum, and inter-knee injection of PBS, and knee joints were collected and lysised to single cell suspension 6 days after injection.


title: mTEChi, adult, WT, cell432

value: mTEChi

value: WT


title: RA model with ADSCs treatment, 144h, scRNA-seq

description: 10X Genomics

value: Cx3cr1-cre; Rosa26-tdTomato; CAG-EGFP

value: healthy mice received a single intraperitoneal injection of K/BxN serum, and inter-knee injection of ADSCs, and knee joints were collected and lysised to single cell suspension 6 days after injection.


title: mTEChi, adult, WT, cell433

value: male


title: ADSCs, recovered from mice knee, 168h, repeat3

value: adipose-derived mesenchymal stem cells

value: ADSCs were extracted, cultured in vito, and injected into mouse knees joints, and collected from knee joints 7 Days after injection


title: mTEChi, adult, WT, cell438


title: mTEChi, neonate, WT, cell31

value: unknown


title: mTEChi, neonate, WT, cell32


title: NET25,Tumor,Non-functioning

value: F


title: mTEChi, adult, WT, cell431


title: NET24,Tumor,Non-functioning

value: Sandostatin


title: mTEChi, neonate, WT, cell30


title: ADSCs, recovered from mice knee, 168h, repeat2


title: ADSCs, recovered from mice knee, 168h, repeat1


title: mTEChi, neonate, WT, cell29


title: NET23,Tumor,Non-functioning

value: FFPE tumor tissue


title: mTEChi, adult, WT, cell429


title: NET22,Tumor,Non-functioning, NET22_4

value: M


title: mTEChi, neonate, WT, cell28

value: thymus


title: ADSCs, recovered from mice knee, 96h, repeat6

value: ADSCs were extracted, cultured in vito, and injected into mouse knees joints, and collected from knee joints 2 Days after injection


title: mTEChi, neonate, WT, cell27

value: epitherial cells


title: NET22,Tumor,Non-functioning, NET22_3


title: ADSCs, recovered from mice knee, 96h, repeat5

value: knee joints

value: Cx3cr1-cre; Rosa26-tdTomato


title: mTEChi, adult, WT, cell428

value: mTEChi


title: mTEChi, neonate, WT, cell26

value: WT


title: NET21,Tumor,Non-functioning


title: NET26,Tumor,Non-functioning


title: mTEChi, adult, WT, cell427


title: NET20,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell25


title: ADSCs, recovered from mice knee, 96h, repeat4


title: mTEChi, neonate, WT, cell24


title: ADSCs, recovered from mice knee, 96h, repeat2


title: ADSCs, recovered from mice knee, 96h, repeat3


title: mTEChi, adult, WT, cell424


title: mTEChi, adult, WT, cell425


title: NET2,Tumor,Non-functioning


title: Developmental exposure to PM2.5 w/ OVA challenge rep 7 (WGMS)

description:
Library name: PM-OVA_Rel1
156 bp PE

value: Lung (RML)

value: Balb/c

value: developmental PM2.5 & OVA


title: NET19,Tumor,Non-functioning


title: mTEChi, adult, WT, cell430

value: male


title: mTEChi, adult, WT, cell423


title: ADSCs, recovered from mice knee, 96h, repeat1

value: adipose-derived mesenchymal stem cells

value: ADSCs were extracted, cultured in vito, and injected into mouse knees joints, and collected from knee joints 4 Days after injection


title: mTEChi, neonate, WT, cell22

value: unknown


title: mTEChi, neonate, WT, cell23


title: NET17,Tumor,Non-functioning


title: mTEChi, adult, WT, cell422


title: NET14,Tumor,Non-functioning


title: mTEChi, neonate, WT, cell21


title: ADSCs, recovered from mice knee, 48h, repeat6


title: ADSCs, recovered from mice knee, 48h, repeat5


title: mTEChi, adult, WT, cell421


title: mTEChi, neonate, WT, cell20


title: mTEChi, adult, WT, cell420


title: mTEChi, adult, WT, cell426


title: NET13,Tumor,Non-functioning

value: F


title: mTEChi, neonate, WT, cell19


title: ADSCs, recovered from mice knee, 48h, repeat4


title: mTEChi, adult, WT, cell419


title: NET11,Tumor,Non-functioning

value: FFPE tumor tissue


title: ADSCs, recovered from mice knee, 48h, repeat3


title: mTEChi, neonate, WT, cell18


title: mTEChi, adult, WT, cell418


title: mTEChi, neonate, WT, cell17


title: mTEChi, adult, WT, cell417


title: Sample 24: Bulk, Human, NUGC3, shIQGAP3-3

city: Singapore

first: Mitsuhiro

last: Shimura

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. [1] Li R, Li Y, Kristiansen K, Wang J. (2008). SOAP: short oligonucleotide alignment program. Bioinformatics. 24(5):713-4
Assembly: you can refer the genome information in Dr. tom.
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Human cancer cell

growth_protocol: Hs746T was cultured in DMEM (Dulbecco’s Modified Medium, Nacalai Tesque) supplemented with 10% FBS (Fetal bovine serum, biowest) and penicillin (100 IU/ml), and streptomycin (100 µg/ml) (Thermo Fisher Scientific) at 37oC in a humidified 5% CO2 incubator. The other GC cell lines were cultured similarly, except that RPMI-1640 (Nacalai Tesque) was used instead of DMEM.

extract_protocol:
Total RNA from AGS, NUGC3, Hs746T, and NUGC3 subcutaneous tumors were extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq using MGIEasy RNA Directional Library Prep Set（1000006385，made in MGI）following manufacturer’s protocols.

treatment_protocol: ON-TARGET plus SMARTpool siRNAs targeting human IQGAP3 (Horizon Discovery, L-009077-00-0005) and a non-targeting siRNA pool (Horizon Discovery, D001810-10-50) as the control siRNA were used for the siRNA knockdown experiments. At 24 hours after seeding 1.0 x 106 AGS and NUGC3 cells and 2.0 x 106 Hs746T cells onto a 10 cm dish, cells were transfected with 35 nM of siRNAs using jetPRIME (Polypus, 101000046) according to the manufacturer’s protocol. At 72 hours after the transfection, the medium was changed and then transfected in a similar manner as a 2nd siRNA knockdown. Cells were harvested 48 hours after the 2nd siRNA transfection. Total RNA from AGS, NUGC3, Hs746T, and NUGC3 subcutaneous tumors were extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA from AGS, NUGC3, Hs746T, and bulk tumors from NUGC3 shCtrl/shIQGAP3 (bulk RNA-sequence) were sent to Beijing Genomics Institute (BGI) for PCR amplification, transcriptome library preparation, sequencing, and analysis.

value: Human cancer cell

value: Human gastric cancer

value: shIQGAP3 knockdown

value: shIQGAP3 transfected stable cell


title: ADSCs, recovered from mice knee, 48h, repeat2

value: knee joints

value: ADSCs were extracted, cultured in vito, and injected into mouse knees joints, and collected from knee joints 2 Days after injection


title: ADSCs, recovered from mice knee, 0h, repeat3

value: Cx3cr1-cre; Rosa26-tdTomato

value: cultured alone in vito


title: mTEChi, adult, WT, cell416

source_name: thymus

value: thymus

value: epitherial cells

value: mTEChi

value: WT


title: mTEChi, neonate, WT, cell16


title: mTEChi, neonate, WT, cell15


title: Sample 23: Bulk, Human, NUGC3, shIQGAP3-2


title: mTEChi, adult, WT, cell415

value: male


title: ADSCs, recovered from mice knee, 0h, repeat2

value: adipose-derived mesenchymal stem cells


title: ADSCs, recovered from mice knee, 0h, repeat1


title: Sample 22: Bulk, Human, NUGC3, shIQGAP3-1


title: mTEChi, neonate, WT, cell13

value: unknown


title: MFs, co-cultured with ADSCs, repeat4

value: Macrophage

value: co-cultured with ADSCs for 96h


title: mTEChi, neonate, WT, cell12


title: Sample 20: Bulk, Human, NUGC3, shCtrl-2

value: Human cancer cell

value: shContorol transfected stable cell


title: mTEChi, adult, WT, cell413


title: NET10,Tumor,Non-functioning

value: FFPE tumor tissue

value: M


title: MFs, co-cultured with ADSCs, repeat3

value: knee joints


title: NET1,Tumor,Non-functioning


title: mTEChi, adult, WT, cell414


title: ADSCs, recovered from mice knee, 48h, repeat1

value: ADSCs were extracted, cultured in vito, and injected into mouse knees joints, and collected from knee joints 2 Days after injection


title: mTEChi, neonate, WT, cell11


title: mTEChi, neonate, WT, cell10


title: Sample 19: Bulk, Human, NUGC3, shCtrl-1

value: Human gastric cancer


title: MFs, co-cultured with ADSCs, repeat1

value: Cx3cr1-cre; Rosa26-tdTomato


title: Sample 18: Hs746T, siIQGAP3-3

value: siIQGAP3 knockdown

value: siRNA-mediated knockdown of IQGAP3


title: mTEChi, adult, WT, cell410

value: thymus

value: epitherial cells

value: mTEChi


title: mTEChi, neonate, WT, cell14

value: WT


title: Sample 17: Hs746T, siIQGAP3-2


title: mTEChi, neonate, WT, cell9

value: unknown


title: Sample 16: Hs746T, siIQGAP3-1


title: mTEChi, adult, WT, cell409

value: male


title: mTEChi, neonate, WT, cell8


title: MFs, cultured alone, repeat3

value: Macrophage

value: cultured alone in vito for 96h


title: MFs, cultured alone, repeat4


title: mTEChi, adult, WT, cell408


title: Sample 15: Hs746T, siCtrl-3

value: Human cancer cell

value: non-target siRNA


title: Sample 21: Bulk, Human, NUGC3, shCtrl-3

value: shContorol transfected stable cell


title: mTEChi, neonate, WT, cell7


title: mTEChi, adult, WT, cell412


title: MFs, cultured alone, repeat2

value: knee joints


title: MFs, cultured alone, repeat1


title: mTEChi, neonate, WT, cell6


title: MFs, co-cultured with ADSCs, repeat2

value: co-cultured with ADSCs for 96h


title: mTEChi, adult, WT, cell406


title: Sample 14: Hs746T, siCtrl-2

value: Human gastric cancer


title: mTEChi, adult, WT, cell411


title: ADSCs, co-cultured with MFs, repeat3

value: adipose-derived mesenchymal stem cells

value: CAG-EGFP

value: co-cultured with Macrophages for 96h


title: Sample 11: NUGC3, siIQGAP3-2

value: siIQGAP3 knockdown

value: siRNA-mediated knockdown of IQGAP3


title: Sample 12: NUGC3, siIQGAP3-3


title: mTEChi, neonate, WT, cell5

value: thymus

value: epitherial cells

value: mTEChi


title: mTEChi, neonate, WT, cell3

value: WT

value: unknown


title: mTEChi, neonate, WT, cell4


title: ADSCs, co-cultured with MFs, repeat4


title: ADSCs, co-cultured with MFs, repeat2


title: Sample 10: NUGC3, siIQGAP3-1


title: mTEChi, adult, WT, cell402

value: male


title: Sample 9: NUGC3, siCtrl-3

value: Human cancer cell


title: ADSCs, co-cultured with MFs, repeat1


title: mTEChi, neonate, WT, cell2


title: mTEChi, neonate, WT, cell1


title: mTEChi, adult, WT, cell401


title: mTEChi, adult, WT, cell407


title: ADSCs, cultured alone, repeat2

value: cultured alone in vito for 96h


title: mTEChi, adult, WT, cell400


title: Sample 8: NUGC3, siCtrl-2

value: non-target siRNA


title: Sample 7: NUGC3, siCtrl-1


title: mTEClo, adult, WT, cell291, G400

value: mTEClo


title: mTEChi, adult, WT, cell405


title: mTEClo, adult, WT, cell290, G400


title: mTEChi, adult, WT, cell399


title: Sample 6: AGS, siIQGAP3-3

value: AGS


title: mTEChi, adult, WT, cell404


title: mTEChi, adult, WT, cell398


title: mTEClo, adult, WT, cell289, G400


title: Sample 5: AGS, siIQGAP3-2

value: Human gastric cancer


title: mTEChi, adult, WT, cell403


title: mTEClo, adult, WT, cell288, G400


title: 8w_Final_2_IEC [scRNA-seq]

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

data_processing:
inhouse pipeline
Sequences were mapped using cell ranger (v3.0.2) to the GRCm38 Mus musculus genome reference.
We used the unfiltered feature-barcode matrices and applied custom filter settings under Seurat package environment (v3.1.2).
Cells that were potentially disrupted or had an increased likelihood of being doublets (cells with less than 200 or more than 5000 reads mapping to genome, with more than 25% of mitochondrial reads or less than 10% of housekeeping reads), were removed.
We further normalized, find variable features, run PCA, and found clusters
We futher followed the seurat workflow (Normalization, scaling, find variable features, PCA, clustered)
We use in/house biomarkers for cell annotation (please see the list in the methods of the manuscript)
Assembly: GRCm38
Supplementary files format and content: value files and count matrix

source_name: Small Intestine

extract_protocol:
These IEC and LP cell fractions were immediately subjected to emulsion PCR using the 10x Chromium system and the 10x Chromium Single Cell gene expression V3 reagent kit according to the manufacturer’s instructions.
Eleven libraries were pooled and then sequenced on an Illumina NovaSeq6000 with 2x100bp on an S2 flow

treatment_protocol: 8-week-old male C57Bl6/J mice (n=60) were subjected to successive 8-week-long cycles consisting of (i) a microbiome depletion for 14 days via antibiotic treatment, (ii) immediate recolonization via fecal microbiota transfer and (iii) 6 weeks of an intermittent phase. Briefly, freshly collected fecal pellets of unrelated and untreated male C57Bl6/J mice of the same age (isochronic microbiome transfer, iMB) or 8 weeks of age (young microbiome transfer, yMB) were orally gavaged with suspension to restore the depleted microbiomes. 3 mice per group were selected at the end of the experiment and prepared for single cell procedure. We separated the tissue into lamina propria (LP)  and intestinal epithelium (IEC) and performed the single cell experiment seperately.

value: Small Intestine

value: Intestinal Epithelium

value: IEC


title: mTEChi, adult, WT, cell397

extract_protocol:
Mouse thymus was enzymatically digested and CD45+ cells were depleted using mouse CD45 MicroBeads and a LS Column (Miltenyi Biotec). After staining with an antibody cocktail, mTEChi (DAPI-CD45-EpCAM+Ly51-MHCII-high), mTEClo (DAPI-CD45-EpCAM+Ly51-MHCII-low), and cTEC (DAPI-CD45-EpCAM+Ly51+) were sorted by FACSAria into a 96well plate containing 1uL of lysis buffer (0.3% NP40; Thermo Scientific, 1U/uL RNasinPlus; Promega in 1x Lysis Buffer, Takara)
scRNA-seq libraries were prepared by a RamDA-seq method (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018). Specifically, RNA was denatured by incubating at 70C for 90sec, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 5min. Then cDNA was synthesized in 3uL of 1xRT Buffer containing RT Enzyme Mix (0.15uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (2.7uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 0.5uL of 10x NEB buffer2 (NEB), 0.125uL of dNTP mix (10mM each nt, NEB), 0.15uL of Klenow Fragment (3'→5' exo-, NEB), 0.4uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 0.825uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (Beckman Coulter) and applied for Tn5 tagmentation in a 5uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). After dissociating Tn5 protein by adding SDS (0.04% in final), tagmented DNA was amplified by 17 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.0 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.


title: 8w_Final_2_LP [scRNA-seq]

value: LP


title: Sample 4: AGS, siIQGAP3-1

value: siIQGAP3 knockdown

value: siRNA-mediated knockdown of IQGAP3


title: mTEClo, adult, WT, cell287, G400

value: thymus

value: epitherial cells


title: mTEChi, adult, WT, cell396

value: mTEChi

value: WT


title: Sample 3: AGS, siCtrl-3


title: ADSCs, cultured alone, repeat3

value: knee joints

value: adipose-derived mesenchymal stem cells

value: CAG-EGFP


title: mTEClo, adult, WT, cell286, G400

value: male


title: mTEChi, adult, WT, cell395


title: Sample 2: AGS, siCtrl-2

value: Human cancer cell

value: non-target siRNA


title: ADSCs, cultured alone, repeat1

value: cultured alone in vito for 96h


title: mTEChi, adult, WT, cell394


title: aging-MB_Final_10_IEC [scRNA-seq]

value: Small Intestine

value: aging-mb


title: Sample 1: AGS, siCtrl-1

value: AGS

value: Human gastric cancer


title: mTEClo, adult, WT, cell284, G400

value: mTEClo


title: mTEChi, adult, WT, cell393


title: aging-MB_Final_10_LP [scRNA-seq]

value: Intestinal Epithelium

value: LP


title: HA+L3  rep3

city: Ning bo

first: Jiangfang

last: Lian

address: No. 57 Xingning Road, Yinzhou District, Ningbo, Zhejiang Province, China

department: cardiology

institute: Lihuili Hospital Facilitated to Ningbo University, Ningbo University.

data_processing:
Raw sequencing reads were trimmed using Trimmomatic (version 0.36) to remove adapter sequences and low-quality bases.
The trimmed reads were aligned to the human reference genome (hg38) using HISAT2 (version 2.1.0)
Gene expression levels were quantified using featureCounts (version 1.6.2).
Differential gene expression analysis was performed using the DESeq2 (version 1.22.2) package in R.
Assembly: The human reference genome build hg38 was used for read alignment.
Supplementary files format and content: The processed data files include gene expression values (in FPKM and TPM units), raw counts, and differential expression analysis results (fold change, p-value, and adjusted p-value) in tabular format.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TransZol Up following the manual (TransGen, Beijing, China).
RNA-seq libraries were prepared using MGI's DNBSEQStr and-Specific Transcriptom Kit following the manufacturer's instructions. Briefly, poly(A)-tailed mRNA was purified and fragmented, followed by cDNA synthesis, end repair, adapter ligation, and PCR amplification. The quality and quantity of the libraries were assessed using a Qubit fluorometer and an Agilent Bioanalyzer.

treatment_protocol:
Equal amounts of pcDNA3-hERG and pcDNA3-hERG-A561V plasmids were transfected into HEK-293 cells using TransIT-2020 transfection reagent (Cat No. 5405, Mirus) to construct heterozygous hERG/A561V (hERG-WT, 1.25 μg + hERG-A561V, 1.25 μg) cell models
hERG/A561V HEK-293 cells were treated with 15 μM LUM or DMSO for 24 hours

value: HEK-293 cells

value: lumacaftor

tag: time

value: Day 2


title: mTEClo, adult, WT, cell283, G400

data_processing:
Trimming reads to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Trimming low-quality parts and adapter sequences by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using STAR (v2.7.3a, Dobin et al., STAR: ultrafast universal RNA-seq aligner, 2013) with a GTF file downloaded from http://www.ensembl.org (GRCm38.99)
Removing unmapped reads and reads mapped with low-quality scores (MAPQ < 5) by SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Removing duplicated reads using Picard Tools (v2.21.1, http://broadinstitute.github.io/picard/)
Counting mapped reads on each gene using htseq-count (v0.11.2, Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, 2015) using a --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
GeTMM (Gene length corrected trimmed mean of M-values) normalization by edgeR package in R programming language (Robinson et al., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010) and gene length data obtained from EMBL-EBI, as described by Smid et al. (Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons, 2018)
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw read counts for each gene by each Sample
Supplementary files format and content: comma-separated values file includes GeTMM normalized values for each gene by each Sample

value: thymus

value: epitherial cells

value: WT


title: mTEChi, adult, WT, cell392

value: mTEChi

value: male


title: 8w_Final_16_IEC [scRNA-seq]

value: IEC


title: mTEChi, adult, WT, cell391


title: HA+L2  rep2


title: 8w_Final_3_IEC [scRNA-seq]


title: 8w_Final_16_LP [scRNA-seq]


title: mTEChi, adult, WT, cell390


title: mTEClo, adult, WT, cell281, G400


title: mTEClo, adult, WT, cell282, G400


title: HA+L1  rep1


title: mTEChi, adult, WT, cell389


title: 8w_Final_3_LP [scRNA-seq]


title: HA2  rep2

value: DMSO


title: aging-MB_Final_36_IEC [scRNA-seq]

value: Small Intestine


title: aging-MB_Final_36_LP [scRNA-seq]

value: aging-mb


title: HA3  rep3


title: mTEClo, adult, WT, cell280, G400


title: mTEClo, adult, WT, cell279, G400


title: mTEClo, adult, WT, cell285, G400


title: Sample 13: Hs746T, siCtrl-1

value: Human cancer cell

value: non-target siRNA


title: mTEChi, adult, WT, cell388


title: HA1 rep1


title: aging-MB_Final_54_IEC [scRNA-seq]


title: mTEClo, adult, WT, cell278, G400

value: mTEClo


title: aging-MB_Final_54_LP [scRNA-seq]

value: Intestinal Epithelium


title: mTEChi, adult, WT, cell387


title: mTEClo, adult, WT, cell277, G400


title: control_Final_29

data_processing:
nf-core pipeline rnaseq
We used Tophat 2 and Bowtie 2 to align reads.
Reads were mapped to mouse genome (MGI assembly version 10) using Tophat program.
Expression counts were normalized by library size.
Normalized gene expression values of the transcripts were computed by HTSeq
Assembly: mm10
Supplementary files format and content: comma separated values of the raw reads for each samples
Supplementary files format and content: comma separated values concerning sample information

source_name: Colon

extract_protocol:
Total RNA was extracted from colon biopsies using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: 8-week-old male C57Bl6/J mice (n=60) were subjected to successive 8-week-long cycles consisting of (i) a microbiome depletion for 14 days via antibiotic treatment, (ii) immediate recolonization via fecal microbiota transfer and (iii) 6 weeks of an intermittent phase. Briefly, freshly collected fecal pellets of unrelated and untreated male C57Bl6/J mice of the same age (isochronic microbiome transfer, iMB) or 8 weeks of age (young microbiome transfer, yMB) were orally gavaged with suspension to restore the depleted microbiomes.

value: Colon

value: Final

value: control


title: H33KD_8C_2

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were processed with Trim Galore (v0.6.4) to remove adaptor sequences and poor quality bases. Trimmed reads were then aligned to the to the mouse reference genome (mm10) using Bismark (v0.22.3). PCR duplicates were removed using Picard (v2.23.3).
Assembly: mm10
Supplementary files format and content: bw file for each sample

source_name: embryo

extract_protocol:
A total of 5-10 mouse 8-cell embryos were collected.
The WGBS libraries were prepared using a Post-bisulfite adapter tagging (PBAT) approach by Annoroad Gene Technology

value: embryo


title: H33KD_8C_1


title: mTEChi, adult, WT, cell386

value: thymus


title: control_Final_27


title: mTEChi, adult, WT, cell385

value: epitherial cells


title: mTEClo, adult, WT, cell276, G400

value: WT


title: mTEChi, adult, WT, cell384

value: mTEChi


title: mTEClo, adult, WT, cell275, G400

value: male


title: Mfn1KD_8C_1


title: mTEClo, adult, WT, cell274, G400


title: Mfn1KD_8C_2


title: 8w_Final_19


title: Con_8C_2


title: control_Final_11


title: mTEChi, adult, WT, cell382


title: Con_8C_1


title: mTEClo, adult, WT, cell273, G400


title: mTEClo, adult, WT, cell272, G400


title: 8w_Final_18


title: mTEChi, adult, WT, cell381


title: MfnKD3_8C

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file includes FPKM values for each samples

extract_protocol:
5-10 early embryos per group were collected in tubes with lysis component and ribonuclease inhibitor.
we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2KB. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip GX Touch and Step OnePlus Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.


title: aging-MB_Final_37

value: aging-MB


title: mTEClo, adult, WT, cell271, G400


title: mTEChi, adult, WT, cell380


title: MfnKD2_8C


title: control_Final_58


title: MfnKD1_8C


title: mTEClo, adult, WT, cell270, G400


title: control_Final_15


title: mTEClo, adult, WT, cell269, G400


title: mTEChi, adult, WT, cell378


title: 8w_Final_5


title: mTEClo, adult, WT, cell268, G400


title: aging-MB_Final_9


title: mTEChi, adult, WT, cell377


title: control_Final_59


title: H33KD2_8C


title: mTEChi, adult, WT, cell376


title: H33KD1_8C


title: mTEClo, adult, WT, cell266, G400


title: 8w_Final_17


title: mTEChi, adult, WT, cell375


title: Con3_8C


title: mTEClo, adult, WT, cell265, G400


title: aging-MB_Final_55


title: mTEChi, adult, WT, cell374


title: mTEChi, adult, WT, cell379


title: Con2_8C


title: mTEClo, adult, WT, cell264, G400


title: mTEChi, adult, WT, cell373


title: Con1_8C


title: 8w_Final_16


title: mTEChi, adult, WT, cell372


title: Pol_MfnKD_8C_2

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig file for each sample

extract_protocol:
A total of 100-200 early embryos were used in each ChIP-seq experiment
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.


title: mTEClo, adult, WT, cell267, G400


title: aging-MB_Final_54


title: mTEChi, adult, WT, cell371


title: H33KD3_8C


title: mTEClo, adult, WT, cell262, G400


title: mTEClo, adult, WT, cell261, G400


title: control_Final_60


title: mTEClo, adult, WT, cell263, G400


title: mTEClo, adult, WT, cell260, G400


title: mTEClo, adult, AireKO, cell154

value: AireKO


title: mTEClo, adult, WT, cell259, G400


title: mTEChi, adult, WT, cell370


title: aging-MB_Final_36


title: Pol_MfnKD_8C_1


title: mTEClo, adult, AireKO, cell153


title: control_Final_12


title: mTEClo, adult, WT, cell258, G400


title: mTEChi, adult, WT, cell383


title: control_Final_26


title: Pol_Con_8C_1


title: mTEClo, adult, AireKO, cell152


title: Pol_Con_8C_2


title: mTEClo, adult, WT, cell257, G400


title: 8w_Final_2


title: mTEClo, adult, AireKO, cell151


title: H3K27ac_MfnKD_8C_2


title: mTEClo, adult, WT, cell256, G400


title: mTEClo, adult, WT, cell255, G400


title: H3K27ac_MfnKD_8C_1


title: aging-MB_Final_10


title: Pol_H33KD_8C_2


title: 8w_Final_3


title: control_Final_14


title: mTEClo, adult, AireKO, cell149


title: Pol_H33KD_8C_1


title: mTEClo, adult, WT, cell254, G400


title: H3K27ac_H33KD_8C_2


title: H3K27ac_H33KD_8C_1


title: control_Final_30


title: mTEClo, adult, AireKO, cell148


title: mTEClo, adult, WT, cell253, G400


title: mTEClo, adult, WT, cell252, G400


title: 8w-mb_w40_50


title: mTEClo, adult, AireKO, cell147


title: mTEClo, adult, AireKO, cell146


title: H3K27ac_Con_8C_2


title: 8w-mb_w40_49


title: mTEClo, adult, WT, cell251, G400


title: H3K27ac_Con_8C_1


title: mTEClo, adult, WT, cell250, G400


title: H33_MfnKD_8C_2


title: 8w-mb_w40_48


title: mTEClo, adult, AireKO, cell145


title: mTEClo, adult, AireKO, cell150


title: H33_MfnKD_8C_1


title: mTEClo, adult, AireKO, cell144


title: 8w-mb_w40_47


title: mTEClo, adult, WT, cell249, G400


title: 8w-mb_w40_46


title: mTEClo, adult, AireKO, cell143


title: mTEClo, adult, WT, cell248, G400


title: H33_Con_8C_2


title: mTEClo, adult, AireKO, cell142


title: aging-mb_Final_52


title: mTEClo, adult, WT, cell247, G400


title: mTEClo, adult, AireKO, cell141


title: BRQ+PD-1_biol_rep6

city: Bad Nauheim

first: Lei

last: Gu

state: Hessen

address: Parkstraße 1

department: Epigenetics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were trimmed for adapter sequence/low-quality sequences using Trim Galore v0.6.7 (--stringency 4, --length 35, --quality 25)
The quality of filtered reads was inspected using FastQC v0.11.8 and MultiQC v1.11
Trimmed reads were then mapped to GRCm39/mm39 reference genome using hisat2 v2.2.1 (--dta)
Reads aligned to each gene were counted and normalized using StringTie v2.2.1 (default parameters)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM value for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample

source_name: D4M tumor

extract_protocol:
Tumor tissue was isolated by lysis buffer and extracted RNA with RNeasy mini kit from Qiagen (Cat#74104). RNA quality (RIN > 9) was confirmed using the TapeStation 4200 system (Agilent Technologies).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD ( Sacramento, CA)

value: D4M tumor

value: C57BL/6 WT

value: BRQ and anti-PD1 antibody i.p injection


title: H33_Con_8C_1


title: mTEClo, adult, WT, cell246, G400

first: Hideyuki

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS


title: ctrl_w40_44

value: ctrl


title: ctrl_w40_45


title: mTEClo, adult, AireKO, cell140

value: mTEClo


title: ctrl_w40_43

value: Intestinal Epithelium


title: mTEClo, adult, AireKO, cell139


title: mTEClo, adult, WT, cell245, G400


title: mTEClo, adult, WT, cell244, G400


title: ctrl_w40_42

value: Colon


title: BRQ+PD-1_biol_rep4


title: BRQ+PD-1_biol_rep3


title: BRQ+PD-1_biol_rep5


title: ctrl_w40_41


title: mTEClo, adult, AireKO, cell138


title: mTEClo, adult, WT, cell243, G400


title: mTEClo, adult, AireKO, cell137


title: mTEClo, adult, WT, cell242, G400


title: aging-mb_w40_25

value: aging-mb


title: BRQ+PD-1_biol_rep2


title: mTEClo, adult, WT, cell241, G400


title: aging-mb_w40_24


title: mTEClo, adult, AireKO, cell136


title: mTEClo, adult, AireKO, cell135


title: BRQ+IgG2a_biol_rep6

value: BRQ and IgG2a antibody i.p injection


title: aging-mb_w40_23


title: mTEClo, adult, WT, cell240, G400


title: BRQ+IgG2a_biol_rep5


title: mTEClo, adult, WT, cell239, G400


title: mTEClo, adult, AireKO, cell133


title: BRQ+IgG2a_biol_rep4


title: mTEClo, adult, AireKO, cell132


title: BRQ+IgG2a_biol_rep3


title: mTEClo, adult, WT, cell238, G400


title: mTEClo, adult, WT, cell237, G400


title: Acot12-/- UUO day7 3

city: Seoul

first: Ee Hyun

last: Kim

state: State...

address: 52 Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha University

data_processing:
The data were  normalized based on Quantile normalization method using EdgeR within R.
Assembly: mm10
Supplementary files format and content: CSV files inculde FPKM values for each sample

source_name: kidney cortex

extract_protocol:
RNA was extracted with Trizol reagent. RNA quality was assessed by Agilent 2100 bioanalyzer.
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit.

value: kidney cortex


title: Acot12-/- UUO day7 2


title: mTEClo, adult, AireKO, cell131

city: Tsurumi-ku, Yokohama

last: Yoshida

value: thymus


title: BRQ+IgG2a_biol_rep2


title: mTEClo, adult, WT, cell236, G400

value: epitherial cells


title: Acot12-/- UUO day7 1


title: BRQ+IgG2a_biol_rep1


title: BRQ+PD-1_biol_rep1


title: mTEClo, adult, WT, cell235, G400

value: WT


title: mTEClo, adult, AireKO, cell129


title: Acot12-/- CL day7 3


title: PD-1_biol_rep6

value: anti-PD1 antibody i.p injection


title: mTEClo, adult, AireKO, cell128

value: male


title: PD-1_biol_rep5


title: Acot12-/- CL day7 2


title: mTEClo, adult, WT, cell234, G400


title: mTEClo, adult, AireKO, cell134


title: mTEClo, adult, AireKO, cell127


title: PD-1_biol_rep4


title: aging-mb_w40_22


title: mTEClo, adult, WT, cell232, G400


title: Acot12-/- CL day7 1


title: WT UUO day7 3

value: Wildtype


title: mTEClo, adult, WT, cell233, G400


title: PD-1_biol_rep3


title: PD-1_biol_rep2


title: mTEClo, adult, WT, cell231, G400


title: WT UUO day7 2


title: WT UUO day7 1


title: mTEClo, adult, AireKO, cell125

value: AireKO


title: mTEClo, adult, WT, cell230, G400


title: mTEClo, adult, AireKO, cell126


title: mTEClo, adult, AireKO, cell130


title: mTEClo, adult, WT, cell229, G400


title: PD-1_biol_rep1

value: D4M tumor


title: WT CL day7 3


title: mTEClo, adult, AireKO, cell123


title: IgG2a_biol_rep6

value: C57BL/6 WT

value: IgG2a antibody i.p injection


title: mTEClo, adult, WT, cell228, G400


title: mTEClo, adult, AireKO, cell122


title: mTEClo, adult, WT, cell227, G400


title: IgG2a_biol_rep5


title: WT CL day7 1


title: WT CL day7 2


title: mTEClo, adult, AireKO, cell121


title: IgG2a_biol_rep4


title: mTEClo, adult, WT, cell226, G400


title: mTEClo, adult, AireKO, cell120


title: IgG2a_biol_rep3


title: mTEClo, adult, WT, cell225, G400


title: C57BL/6N mice, miR-29ab1-/-7

city: China

first: Yu qi

address: 17 Haidian District, Beijing

institute: China agricultural univercity

data_processing:
Reads were mapped to reference genome with Hisat2
Differential expression analysis was conducted using DESeq2 R
Assembly: UCSCmm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: small intestinal cryptes

extract_protocol:
RNA was harvested using TRIzol method.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

value: small intestinal cryptes

value: no

value: DSS