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


title: mTEClo, adult, AireKO, cell118

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: mTEClo

tag: strain

tag: genotype

value: AireKO

tag: age

tag: Sex

value: male

tag: exp. batch


title: mTEClo, adult, WT, cell223, G400

value: WT


title: C57BL/6N mice, miR-29ab1-/-5

city: China

first: Yu qi

last: Wang

address: 17 Haidian District, Beijing

country: China

institute: China agricultural univercity

library_source: transcriptomic

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

tag: cell line

value: no

tag: treatment

value: DSS


title: C57BL/6N mice, WT7


title: mTEClo, adult, WT, cell224, G400


title: mTEClo, adult, AireKO, cell124


title: IgG2a_biol_rep1

city: Bad Nauheim

first: Lei

last: Gu

state: Hessen

address: Parkstraße 1

department: Epigenetics

country: Germany

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: IgG2a antibody i.p injection


title: mTEClo, adult, AireKO, cell117


title: MCF-7, BisphenolB, ChIP

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

description: Library name: BisphenolB

library_source: genomic

data_processing:
ChIP-seq reads were filtered out of low quality reads and adapter sequences using fastp with default options.
Multi-mapped and duplicates reads were removed using samtools-1.17 and ENCODE blacklist regions were removed from the bam files.
Peaks were calling using callpeak command of MACS2 v2.2.8 from the bam files.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were cultured, treated as required, and cross-linked with 1% formaldehyde for 10 minutes at room temperature. To quench the cross-linking, 1X glycine was added for 5 minutes. The cells were then washed with PBS, scraped in PBS containing Halt cocktail, and pelleted by centrifugation at 3,000 × g for 5 minutes. The pellet was resuspended in membrane extraction buffer with inhibitors, vortexed briefly, and incubated on ice for 10 minutes. Nuclei were isolated by centrifugation at 9,000 × g for 3 minutes, resuspended in MNase digestion buffer, and digested with 2 μL of diluted MNase (1:10) per 4 × 10⁶ cells at 37°C for 15 minutes. The reaction was stopped, and the nuclei were pelleted, resuspended in IP dilution buffer, and sonicated (three 20-second pulses). The lysate was centrifuged at 9,000 × g for 5 minutes, and the supernatant containing chromatin was collected. Chromatin was then diluted in IP dilution buffer and incubated overnight at 4°C with antibodies (e.g., anti-RNA Pol II or target-specific antibodies). The following day, protein A/G magnetic beads were added and incubated for 2 hours. The beads were washed three times with wash buffer 1 and once with wash buffer 2. Chromatin was eluted with IP elution buffer for 30 minutes at 65°C and treated with NaCl and proteinase K for 1.5 hours at 65°C to reverse cross-linking. Finally, DNA was purified using a DNA cleanup column and eluted in elution buffer for use in downstream applications.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols. Post ampilfication libraries were cleanup using AMPure XP Beads from Beckman Coulter. Libraries were validated using the Agilent Tapestation 4200 instrument.

value: Human breast adenocarcinoma cell line

value: Bisphenol B


title: mTEClo, adult, WT, cell222, G400


title: C57BL/6N mice, WT6


title: MCF-7, Estradiol, ChIP

description: Library name: Estradiol

value: Estradiol


title: mTEClo, adult, WT, cell221, G400


title: mTEClo, adult, AireKO, cell115


title: MCF-7, Flutamide, ChIP

description: Library name: Flutamide

value: Flutamide


title: mTEClo, adult, WT, cell220, G400


title: C57BL/6N mice, miR-29ab1-/-4


title: mTEClo, adult, WT, cell219, G400


title: MCF-7, 5a_DTT, ChIP

description: Library name: 5a_DTT


title: C57BL/6N mice, miR-29ab1-/-3


title: mTEClo, adult, AireKO, cell113


title: IgG2a_biol_rep2


title: mTEClo, adult, AireKO, cell119


title: HEK293T, shControl, rep3

city: Hangzhou

first: Jiuhong

state: Zhejiang

address: No. 1369, West Wenyi Road

institute: Zhejiang university

description:
Library name: NT_rep3_nuc
Column name in 03.all_sample.PDUI.tsv.gz: NT rep3 nuc

data_processing:
PDUI matrix was generated from DaPars2
Assembly: hg38
Supplementary files format and content: space-delimited text files includes PDUI index for all samples

extract_protocol:
Nuclear RNA were isolated according to the manufacturer's instructions (Vazyme, E101).Total RNA was extracted using the Ultrapure RNA Kit(CWbio, CW0581S). according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) and checked using RNase free agarose gel electrophoresis.
mRNA was enriched by Oligo(dT) beads. Then, the enriched mRNA was fragmented using a fragmentation buffer and reversely transcribed into cDNA by NEBNext Ultra RNA Library Prep Kit for Illumina.


title: mTEClo, adult, AireKO, cell112


title: C57BL/6N mice, miR-29ab1-/-2


title: mTEClo, adult, WT, cell218, G400


title: HEK293T, shControl, rep1

description:
Library name: NT_rep1_nuc
Column name in 03.all_sample.PDUI.tsv.gz: NT rep1 nuc


title: HEK293T, shControl, rep2

description:
Library name: NT_rep2_nuc
Column name in 03.all_sample.PDUI.tsv.gz: NT rep2 nuc


title: mTEClo, adult, AireKO, cell111


title: mTEClo, adult, WT, cell216


title: C57BL/6N mice, miR-29ab1-/-1


title: mTEClo, adult, AireKO, cell110


title: C57BL/6N mice, WT4


title: HEK293T, shZNF384,rep2

description:
Library name: ZNF384_rep2
Column name in 03.all_sample.PDUI.tsv.gz: ZNF384 rep2

value: ZNF384 knockdown


title: mTEClo, adult, AireKO, cell116

value: thymus


title: mTEClo, adult, AireKO, cell109

value: epitherial cells


title: C57BL/6N mice, WT3


title: mTEClo, adult, WT, cell215

value: mTEClo


title: C57BL/6N mice, WT5


title: mTEClo, adult, AireKO, cell114

value: AireKO


title: HEK293T, shZNF384,rep1

description:
Library name: ZNF384_rep1
Column name in 03.all_sample.PDUI.tsv.gz: ZNF384 rep1


title: mTEClo, adult, WT, cell214

value: male


title: C57BL/6N mice, WT2

value: WT


title: mTEClo, adult, AireKO, cell108


title: HEK293T, shU2AF2, rep2

description:
Library name: U2AF2_rep2
Column name in 03.all_sample.PDUI.tsv.gz: U2AF2 rep2

value: U2AF2 knockdown


title: mTEClo, adult, WT, cell213


title: mTEClo, adult, AireKO, cell107


title: C57BL/6N mice, WT1

value: small intestinal cryptes

value: no


title: HEK293T, shU2AF2, rep1

description:
Library name: U2AF2_rep1
Column name in 03.all_sample.PDUI.tsv.gz: U2AF2 rep1


title: mTEClo, adult, AireKO, cell106


title: mTEClo, adult, WT, cell212


title: mTEClo, adult, WT, cell217


title: Brain,DENV,5dpi,rep3

city: Chongqing

first: Jintao

last: Li

address: No.30 Gaotanyan Street

institute: Army Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 10%;   Cell Gene Number < 10000;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: brain

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: brain

value: female

value: 4-6 weeks old

value: IFNAR knockout

value: DENV infected (i.n.), 5dpi


title: mTEClo, adult, AireKO, cell105


title: HEK293T, shSF3B4, rep2

description:
Library name: SF3B4_rep3
Column name in 03.all_sample.PDUI.tsv.gz: SF3B4 rep3

value: SF3B4 knockdown


title: HEK293T, shSF3B4, rep1

description:
Library name: SF3B4_rep2
Column name in 03.all_sample.PDUI.tsv.gz: SF3B4 rep2


title: Brain,DENV,3dpi,rep3

value: DENV infected (i.n.), 3dpi


title: mTEClo, adult, WT, cell210


title: mTEClo, adult, AireKO, cell103


title: HEK293T, shPCBP2, rep1

description:
Library name: PCBP2_rep1
Column name in 03.all_sample.PDUI.tsv.gz: PCBP2 rep1

value: PCBP2 knockdown


title: Brain,DENV,5dpi,rep1


title: Brain,DENV,3dpi,rep2


title: mTEClo, adult, AireKO, cell102

value: thymus


title: mTEClo, adult, WT, cell207

value: epitherial cells


title: HEK293T, shPABPN1, rep2

description:
Library name: PABPN1_rep2
Column name in 03.all_sample.PDUI.tsv.gz: PABPN1 rep2

value: PABPN1 knockdown


title: mTEClo, adult, AireKO, cell101

value: mTEClo

value: AireKO


title: Brain,DENV,3dpi,rep1


title: mTEClo, adult, WT, cell206

value: WT

value: male


title: HEK293T, shPABPN1, rep1

description:
Library name: PABPN1_rep1
Column name in 03.all_sample.PDUI.tsv.gz: PABPN1 rep1


title: Brain,mock,rep3

value: mock


title: HEK293T, shHDAC1, rep2

description:
Library name: HDAC1_rep2
Column name in 03.all_sample.PDUI.tsv.gz: HDAC1 rep2

value: HDAC1 knockdown


title: mTEClo, adult, AireKO, cell100


title: mTEClo, adult, WT, cell205


title: mTEClo, adult, AireKO, cell99


title: HEK293T, shHDAC1, rep1

description:
Library name: HDAC1_rep1
Column name in 03.all_sample.PDUI.tsv.gz: HDAC1 rep1


title: mTEClo, adult, WT, cell211


title: Brain,mock,rep2

value: brain


title: Brain,DENV,5dpi,rep2

value: female


title: mTEClo, adult, AireKO, cell104


title: HEK293T, shPCBP2, rep2

description:
Library name: PCBP2_rep2
Column name in 03.all_sample.PDUI.tsv.gz: PCBP2 rep2


title: mTEClo, adult, WT, cell209


title: Brain,mock,rep1

value: 4-6 weeks old


title: mTEClo, adult, WT, cell208


title: mTEClo, adult, WT, cell204


title: mTEClo, adult, WT, cell203


title: U87MG sphere Abe treat rep2

city: Taipei

first: Tsung-Han

last: Hsieh

address: XinYi dist.,WuXing Street, No.250.

country: Taiwan

institute: Taipei Medical University

description: Library name: sample 4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw count for every gene and every sample

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA), according to the manufacturer's instructions
poly-A mRNA-seq: RNA libraries were prepared for sequencing using TruSeq Stranded mRNA protocols

tag: medium

value: DMEM/F12, supplemented with 20 ng/ml EGF, 20 ng/ml bFGF, N2 supplement, and a B27 supplement at a final concentration of 2%

tag: time

value: Abemaciclib treatment


title: mTEClo, adult, AireKO, cell97


title: mTEClo, adult, WT, cell202


title: U87MG sphere Abe treat rep1

description: Library name: sample 3


title: mTEClo, adult, AireKO, cell96


title: N1En_del-E47KO-ETP-2

city: Kyoto

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Institute for Life and Medical Sciences, Kyoto University

data_processing:
Illumina bcl2fastq software used for basecalling (NovaSeq 6000).
The sequencing reads were mapped to the mm9 reference genome using STAR.
Tags mapped to unique DNA sequences were analyzed using HOMER.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Fetal thymus

extract_protocol:
RNA was harvested using RNeasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepaered using SMART-seq HT PLUS kit following manufacturer's protocols.

value: Fetal thymus

value: sorted primary cells

tag: cell

value: CD4-CD8-Lin-(CD3, TCRgd, CD19, B220, CD11b, Gr1, Ter119, Dx5, CD11c)CD44+CD25-Kithigh


title: U87MG sphere untreated rep2

description: Library name: sample 2

value: untreat


title: mTEClo, adult, WT, cell201

value: thymus

value: epitherial cells


title: N1En_del-ETP-2


title: mTEClo, adult, AireKO, cell95

value: mTEClo


title: U87MG sphere untreated rep1

description: Library name: sample 1


title: mTEClo, adult, WT, cell200


title: N1En_del-ETP-1


title: mTEClo, adult, AireKO, cell94

value: AireKO


title: QM59-Tumor-RNAseq

city: Hongkong

first: Yu

middle: university of

last: Liu

address: 10 Mui Fong Street

department: Faculty of Dentistry

country: Hong Kong

institute: The university of hongkong

description: Library name: QM59-Tumor

data_processing:
RNA data pre-processing followed the mRNA analysis pipeline from the National Cancer Institute. Raw fastq files underwent quality control with ‘FastQC’. Bases failing quality control were trimmed using ‘Trimmomatic’. Fastq files were aligned to the hg38 genome using ‘STAR’ to generate BAM files. Post-alignment quality control was performed using ‘CollectRNASeqMetrics’. Missing values were imputed using the impute.knn package, with imputation on the genes present in at least 50% of samples.
Assembly: hg38
Supplementary files format and content: csv files include raw counts for each sample

source_name: oral cavity

extract_protocol:
Tumor RNA was extracted from fresh frozen tumor tissue using Trizol. The tissue block was ground with liquid nitrogen, and 50-100 mg was transferred to a 2.0 mL centrifuge tube containing 1 mL of Trizol. Chloroform (1/5 volume) was added, and the mixture was shaken vigorously, incubated at room temperature for 2-3 minutes, and centrifuged at 12,000 rpm at 4°C for 10-15 minutes. The upper aqueous phase was transferred to a new tube, mixed with an equal volume of isopropanol, and incubated at room temperature for 10 minutes. After centrifugation at 12,000 rpm at 4°C for 10 minutes, the supernatant was discarded, and the RNA pellet was washed with 75% ethanol prepared with DEPC water. The pellet was air-dried, dissolved in RNase-free water (DEPC water), and stored at -80°C.
Total RNA was used to generate sequencing libraries using the NEB Next Ultra RNA Library Prep Kit for Illumina (Catalog #: E7530L). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed with divalent cations under elevated temperatures. First-strand cDNA synthesis was conducted using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H). Second-strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Overhangs were converted to blunt ends, and NEB Next Adaptor with a hairpin loop structure was ligated to the adenylated 3’ ends of DNA fragments. Library fragments were purified to select 370-420 bp cDNA fragments using the AMPure XP system. USER Enzyme was used for size selection, followed by PCR with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. PCR products were purified, and library quality was assessed using the Agilent 5400 system and quantified by QPCR (1.5 nM).

value: oral cavity

value: Lymph node metastasis


title: mTEClo, adult, WT, cell199

value: WT

value: male


title: E47KO-ETP-2


title: QM25-Tumor-RNAseq

description: Library name: QM25-Tumor


title: E47KO-ETP-1


title: mTEClo, adult, AireKO, cell98


title: mTEClo, adult, AireKO, cell92


title: QM21-Tumor-RNAseq

description: Library name: QM21-Tumor


title: QM20-Tumor-RNAseq

description: Library name: QM20-Tumor


title: mTEClo, adult, WT, cell196


title: B6-ETP-1

value: Wild type


title: mTEClo, adult, WT, cell198


title: B6-ETP-2


title: N1En_del-E47KO-ETP-1


title: mTEClo, adult, AireKO, cell93


title: mTEClo, adult, AireKO, cell91


title: mTEClo, adult, AireKO, cell90


title: E2A/HEB-dKO_NICD-ETP-2


title: mTEClo, adult, WT, cell195


title: QM14-Tumor-RNAseq

description: Library name: QM14-Tumor


title: mTEClo, adult, AireKO, cell89


title: QM19-Tumor-RNAseq

description: Library name: QM19-Tumor


title: mTEClo, adult, WT, cell197


title: mTEClo, adult, WT, cell194


title: E2A/HEB-dKO_NICD-ETP-1


title: E2A/HEB-dKO-ETP-2


title: QM13-Tumor-RNAseq

description: Library name: QM13-Tumor


title: mTEClo, adult, AireKO, cell87


title: QM11-Tumor-RNAseq

description: Library name: QM11-Tumor


title: E2A/HEB-dKO-ETP-1


title: mTEClo, adult, WT, cell192


title: mTEClo, adult, WT, cell193


title: QM15-Tumor-RNAseq

description: Library name: QM15-Tumor


title: mTEClo, adult, WT, cell191


title: Cont-ETP-2

value: Control


title: mTEClo, adult, AireKO, cell85


title: mTEClo, adult, WT, cell190


title: QM63-Tumor-RNAseq

description: Library name: QM63-Tumor

value: Non-metastasis


title: mTEClo, adult, WT, cell189


title: mTEClo, adult, AireKO, cell84


title: mTEClo, adult, AireKO, cell83


title: ATAC-E2A/HEB-dKO_NICD-ETP-2

data_processing:
Illumina bcl2fastq software used for basecalling (NovaSeq 6000).
The sequencing reads were trimmed using Skewer.
Trimmed reads were mapped to the mm9 reference genome using Bowtie2 (version 1.2.7).
Tags mapped to unique DNA sequences were analyzed using HOMER.
Assembly: mm9
Supplementary files format and content: Tab-delimited files containing peak positions for each ATAC-seq experiment.

extract_protocol:
ATAC-seq was performed as described previously (Corces et al. 2017).
ATAC-seq libraries were prepared as described previously (Corces et al. 2017). Cells were lysed, then treated with Tn5 transposase (Nextera DNA Sample Preparation Kit). After the treatment, the tagmentated DNA was cleaned up and purified with DNA Clean & Concentrator kit (Zymo Research). The purified DNA were amplified with determined cycles of PCR based on the amplification curve, then were size-selected using SPRI beads.


title: QM61-Tumor-RNAseq

description: Library name: QM61-Tumor


title: mTEClo, adult, WT, cell188


title: ATAC-E2A/HEB-dKO_NICD-ETP-1


title: mTEClo, adult, AireKO, cell82


title: mTEClo, adult, AireKO, cell88


title: mTEClo, adult, AireKO, cell81


title: ATAC-E2A/HEB-dKO-ETP-2


title: QM46-Tumor-RNAseq

description: Library name: QM46-Tumor


title: ATAC-E2A/HEB-dKO-ETP-1


title: mTEClo, adult, WT, cell186


title: QM40-Tumor-RNAseq

description: Library name: QM40-Tumor


title: mTEClo, adult, WT, cell185


title: ATAC-N1En_del-E47KO-ETP-2


title: QM30-Tumor-RNAseq

description: Library name: QM30-Tumor


title: mTEClo, adult, WT, cell184


title: ATAC-N1En_del-E47KO-ETP-1


title: mTEClo, adult, AireKO, cell78


title: QM62-Tumor-RNAseq

description: Library name: QM62-Tumor


title: mTEClo, adult, AireKO, cell86


title: mTEClo, adult, WT, cell187


title: ATAC-N1En_del-ETP-2


title: mTEClo, adult, WT, cell183


title: QM17-Tumor-RNAseq

description: Library name: QM17-Tumor


title: QM12-Tumor-RNAseq

description: Library name: QM12-Tumor


title: mTEClo, adult, WT, cell182


title: ATAC-N1En_del-ETP-1


title: QM48-Tumor-RNAseq

description: Library name: QM48-Tumor


title: QM56-Tumor-RNAseq

description: Library name: QM56-Tumor


title: mTEClo, adult, AireKO, cell76


title: mTEClo, adult, WT, cell181


title: ATAC-E47KO-ETP-2


title: mTEClo, adult, AireKO, cell80


title: mTEClo, adult, AireKO, cell77


title: mTEClo, adult, AireKO, cell74


title: QM39-Tumor-RNAseq

description: Library name: QM39-Tumor


title: mTEClo, adult, AireKO, cell79


title: mTEClo, adult, AireKO, cell75


title: mTEClo, adult, WT, cell179


title: QM24-Tumor-RNAseq

description: Library name: QM24-Tumor


title: mTEClo, adult, AireKO, cell73


title: ATAC-B6-ETP-2


title: QM18-Tumor-RNAseq

description: Library name: QM18-Tumor


title: mTEClo, adult, WT, cell178


title: mTEClo, adult, AireKO, cell72


title: ATAC-B6-ETP-1


title: QM06-Tumor-RNAseq

description: Library name: QM06-Tumor


title: MC38 tumor rep2, scRNAseq

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

description: 10x Genomics

data_processing:
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from scRNA-seq collected from immune cells to the 10x mm10 mouse reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used.
Unique molecular identifier (UMI) counts were analyzed using the Seurat R package v.4.0.1(Hao et al., 2021). Cells with <20% of mitochondrial contamination and between 500 and 6000 genes expressed were retained for further analysis.
The top 3000 variable genes for each line were then used to integrate sample datasets with the SCT method (SCTransform, SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData functions). PCA was performed on the scaled integrated data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 30 principal components) and FindClusters function. UMAP plots were used to visualize variation in the data.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MC38 tumor

extract_protocol:
immune cells within MC38 tumors are directly FACS sorted upon disected from mice
single cell RNA-seq libraries were prepared with the Chromium NextGEM Single Cell 3′ GEM Library & Gel Bead Kit v.3.1 (10x Genomics) as per manufacture’s instruction.

value: MC38 tumor

value: immune cells

value: day 21


title: mTEClo, adult, WT, cell176


title: mTEClo, adult, WT, cell177


title: QM50-Tumor-RNAseq

description: Library name: QM50-Tumor


title: mTEClo, adult, AireKO, cell71


title: MC38 tumor rep1, scRNAseq

description: 10x Genomics


title: mTEClo, adult, AireKO, cell70


title: mTEClo, adult, WT, cell175


title: QM41-Tumor-RNAseq

description: Library name: QM41-Tumor


title: Treatment3 rep3 [saline-3]

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned with the Cutadapt package (v3.4). Reads <60 pbs were excluded from RNA-seq analysis.
Illumina Casava1.7 software used for basecalling.
The genome of Mus musculus (version GRC38, mm10) from the database of Ensembl was used as the reference sequences for RNA-seq analysis
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis. PCA analysis (for detecting outlier samples) and volcano plot analysis based on all identified genes in each analysis were performed with the R-package (v4.1.3). The gene expression levels were analyzed by a DESeq2-based R pipeline.
Genes from the RNA-seq analysis were filtered for fold change of ± 2 and Benjamini-Hochberg’s false discovery rate (FDR) at <5% and analyzed based on experimental evidence. Interactions networks were visualized using the STRING database with minimum required interaction score of high confidence (0.700). Networks were imported into Cytoscape 3.9.1
Assembly: Mus musculus (version GRC38, mm10)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

growth_protocol: Animals were tracked until the humane end point which was a 25% weight-loss cut-off or the inability to ambulate, ingest, hydrate, or defecate, and yeasts were grown in Sabouraud dextrose broth (pH 5.6; BD Difco) for 24 h at 30°C in an orbital shaker at 150 rpm

extract_protocol:
Mice were euthanized via CO2 inhalation at 7 days post-infection. Brains were harvested and flash-frozen in a dry ice and methylbutane slurry mix before infection sites were cut using a brain matrix. RNA extraction was done using the Zymo Quick-mRNA kit followed by an in-column DNase treatment. Isolated RNA was eluted in nuclease-free water and stored at -80
The RNA library prep was prepared using the Illumina RNA-Seq libraries Poly A kit with a normalized input of 250 ng per sample.  The RNA library prep was prepared using the Illumina Stranded mRNA Prep kit with a normalized input of 250 ng per sample. Libraries were checked for quality and quantified using the 4200 TapeStation

treatment_protocol: Animals were anesthetized with 1-2% isoflurane and ropivacaine (2 mg/kg) was  injected to the incision sites. And then 10**4 cryptococci cells were expelled in 1 ul to the different stereotaxic coordinates for the striatum

value: brain

tag: location

value: University of Florida, FL

tag: tissue type

value: 6-8 weeks

value: Treatment3; with the saline


title: ATAC-E47KO-ETP-1

value: Fetal thymus

value: sorted primary cells

value: CD4-CD8-Lin-(CD3, TCRgd, CD19, B220, CD11b, Gr1, Ter119, Dx5, CD11c)CD44+CD25-Kithigh


title: mTEClo, adult, WT, cell174

value: thymus

value: epitherial cells

value: mTEClo


title: QM43-Tumor-RNAseq

description: Library name: QM43-Tumor

value: oral cavity


title: mTEClo, adult, WT, cell180

value: WT

value: male


title: mTEClo, adult, AireKO, cell68

value: AireKO


title: mTEClo, adult, WT, cell173


title: Treatment3 rep1 [saline-1]


title: QM27-Tumor-RNAseq

description: Library name: QM27-Tumor

value: Non-metastasis


title: mTEClo, adult, AireKO, cell67


title: mTEClo, adult, WT, cell172


title: QM08-Tumor-RNAseq

description: Library name: QM08-Tumor


title: mTEClo, adult, AireKO, cell66


title: Control rep3 [naive-3]

value: Control


title: mTEClo, adult, WT, cell171


title: Control rep2 [naive-2]


title: mTEClo, adult, AireKO, cell64


title: QM42-Tumor-RNAseq

description: Library name: QM42-Tumor


title: mTEClo, adult, AireKO, cell65


title: QM33-Tumor-RNAseq

description: Library name: QM33-Tumor


title: mTEClo, adult, WT, cell170


title: mTEClo, adult, WT, cell169


title: mTEClo, adult, AireKO, cell69


title: Control rep1 [naive-1]


title: mTEClo, adult, AireKO, cell63


title: Treatment2 rep2 [H99-2]

value: Treatment2; with the wild-type fungus C. neoformans


title: QM10-Tumor-RNAseq

description: Library name: QM10-Tumor


title: mTEClo, adult, WT, cell168


title: Cont-ETP-1


title: Treatment2 rep3 [H99-3]

value: brain


title: mTEClo, adult, AireKO, cell62


title: mTEClo, adult, WT, cell167


title: QM09-Tumor-RNAseq

description: Library name: QM09-Tumor


title: QM26-Tumor-RNAseq

description: Library name: QM26-Tumor


title: mTEClo, adult, AireKO, cell61


title: mTEClo, adult, WT, cell166


title: HSMM myofiber sheet, condition No4-3

city: Shinjuku-ku

first: Kanae

last: Otsutomo

state: Tokyo

address: 8-1 Kawada-cho

department: Institute of Advanced Biomedical Engineering and Science

institute: Tokyo Women's Medical　University

description: Library name: Exp035_No4_D3

data_processing:
Libraries were sequenced using the Illumina NovaSeq 6000 platform with a paired-end sequencing pipeline.
The quality of raw reads was assessed using FastQC (version 0.11.7), and low-quality bases under 20 bases and adapter sequences were removed using Trimmomatic (version 0.38) with following parameters: ILLUMINACLIP:path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
The cleaned reads were aligned to the reference genome (GRCh38.107) using the RNA-seq aligner HISAT2 (version 2.1.0).
The read counts were quantified with featureCounts (version 1.6.3).
Assembly: GRCh38.107
Supplementary files format and content: text file for FPMK file
Supplementary files format and content: text file for TPM file
Supplementary files format and content: text file for raw count file

source_name: Skeletal muscle

growth_protocol: Human skeletal muscle myoblasts (#CC-2580, Lonza, passages 1–2) were seeded at a density of 6×104 cells/cm² onto a thermoresponsive substrate (UpCell culture dish, CellSeed, Inc.; seeding area: 15 × 15 mm²) and cultured in muscle cell growth medium (SkGM-2, #CC-3245, Lonza) until reaching confluence.

extract_protocol:
Myofiber sheets were incubated in an enzymatic digestion solution containing 2% v/v dispase (#354235, Corning) and 15 mg/mL collagenase type II (#LS0041174, Worthington-Biochem) for 3-5 min to detach cells from the gel. The cell suspension was immediately centrifuged to collect the detached cells. RNA was then isolated using the RNeasy Plus Mini Kit (#74104, Qiagen) according to the manufacturer’s protocol.
Poly(A) RNA preparation was conducted using Poly(A) mRNA magnetic isolation module (New england Biolabs, Ipswich, MA, USA) following the manufacturer's protocol. Library construction was conducted using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following the manufacturer's protocol.

treatment_protocol: A fibrin gel containing Cultrex Basement Membrane Extract (#3432-005-01, R&D Systems) was prepared on the cell reached confluence. The differentiation medium [DMEM/Ham’s F12 (#048-29785, supplemented with 2% horse serum (#26050-070, Thermo-Fisher), 1% penicillin-streptomycin, and 20 μg/mL aprotinin (#A1153, Merck-Millipore)] was then added to the culture dish. After two days, the culture dish was incubated at 20 °C for 30 min to release the cell layer from the culture substrate. The detached sheet-shaped cell assembly, adhered to the fibrin gel, was inverted and transferred to 6-well plates. The sheets were further cultured in differentiation medium with medium changes every three days. Catalase (from bovine liver, #039-12901, Fujifilm Wako) was supplemented in the "No.3" medium at 80 mg/L. Seven days after initiating differentiation, EPS was applied to the myofiber sheets using two carbon electrodes (C-Dish; IonOptix) and an electrical pulse generator (IonOptix). The electrical pulse parameters were set at 10 V, 1 Hz. No1; no-EPS applied No2; EPS was applied for 1 h, followed by 3 h of incubation without stimulation. This cycle was repeated for 3 days. No3 &4; Continuous EPS was applied for 3 days. Catalase was added to the media in "No3" condition.

value: Skeletal muscle

value: myoblast

value: myotube differentiation

tag: batch


title: Treatment2 rep1 [H99-1]

value: University of Florida, FL

value: 6-8 weeks


title: Treatment3 rep2 [saline-2]

value: Treatment3; with the saline


title: Treatment1 rep3 [cap59-3]

value: Treatment1; with the mutant fungus C. neoformans


title: mTEClo, adult, AireKO, cell60

value: thymus

value: epitherial cells


title: mTEClo, adult, WT, cell165

value: mTEClo


title: HSMM myofiber sheet, condition No3-3

description: Library name: Exp035_No3_D3

value: WT


title: mTEClo, adult, AireKO, cell59

value: male


title: HSMM myofiber sheet, condition No2-3

description: Library name: Exp035_No2_D3


title: Treatment1 rep2 [cap59-2]


title: mTEClo, adult, WT, cell164


title: Treatment1 rep1 [cap59-1]


title: mTEClo, adult, WT, cell163


title: mTEClo, adult, AireKO, cell58

value: AireKO


title: HSMM myofiber sheet, condition No1-3

description: Library name: Exp035_No1_D3


title: mTEClo, adult, AireKO, cell57


title: M

city: Chengdu

first: Feng

middle: Zhong

last: Xue

state: Sichuan

address: No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He Street

institute: Sichuan University

description:
Mild infection
10x Genomics

data_processing:
The Cell Ranger software pipeline (V 3.1.0) Provided by 10x Genomics was used to demultiplex cellular barcodes, map to the mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Blood

extract_protocol:
Blood samples were collected 8 hours after CLP surgery, PBMCs were isolated by density gradient centrifugation (1.080-1.085g/l). According to 10x Genomics® Cell Preparation Guide protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
RNA libraries were prepared with Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: Blood

value: PBMC

value: caecal ligation plus puncture (CLP, 22G, 0.25cm)


title: sh

description:
Sham
10x Genomics

value: sham-operated


title: HSMM myofiber sheet, condition No4-2

description: Library name: Exp034_No4_D3

value: Skeletal muscle


title: C

description:
Critical infection (sepsis)
10x Genomics

value: caecal ligation plus puncture (CLP, 18G, 0.85cm)


title: mTEClo, adult, AireKO, cell56


title: HSMM myofiber sheet, condition No3-2

description: Library name: Exp034_No3_D3

value: myoblast

value: myotube differentiation


title: mTEClo, adult, AireKO, cell55


title: mTEClo, adult, WT, cell160


title: HSMM myofiber sheet, condition No2-2

description: Library name: Exp034_No2_D3


title: mTEClo, adult, AireKO, cell54


title: HSMM myofiber sheet, condition No1-2

description: Library name: Exp034_No1_D3


title: mTEClo, adult, AireKO, cell53


title: C_BM_3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each sample

source_name: Bone Marrow

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).And RNA was harvested using Trizol reagent.IIIumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 3. ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using stanard IIIumina protocols.Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: Bone Marrow

value: Wild type

tag: replicate


title: mTEClo, adult, WT, cell159


title: HSMM myofiber sheet, condition No4-1

description: Library name: Exp033_No4_D3


title: mTEClo, adult, WT, cell158


title: C_BM_1


title: mTEClo, adult, AireKO, cell52


title: HSMM myofiber sheet, condition No3-1

description: Library name: Exp033_No3_D3


title: mTEClo, adult, WT, cell157


title: mTEClo, adult, WT, cell156


title: mTEClo, adult, AireKO, cell50


title: mTEClo, adult, WT, cell161


title: mTEClo, adult, WT, cell162


title: HSMM myofiber sheet, condition No2-1

description: Library name: Exp033_No2_D3


title: C_SPN_2

source_name: Spleen

value: Spleen


title: HSMM myofiber sheet, condition No1-1

description: Library name: Exp033_No1_D3


title: mTEClo, adult, WT, cell155

value: thymus


title: mTEClo, adult, AireKO, cell48

value: epitherial cells


title: mTEClo, adult, AireKO, cell49

value: mTEClo


title: C_LN_3

source_name: Lymph Nodes

value: Lymph Nodes


title: C_BM_2


title: RNA_RMGV_USP8i_6h

city: Chuo-ku

first: Hideaki

last: Ogiwara

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

description: Library name: RNA_RMGV_USP8i_6h

data_processing:
FeatureCounts version 2.0.6 was used to count mapped reads for GSEA 4.3.2.
The expression dataset was analyzed using the Molecular Signatures Database (MSigDB).
GSEA identified significant gene sets at the top or bottom of the ranked gene sets that were differentially expressed between the compared gene sets.
The present study used the MSigDB hallmark gene sets.
Gene sets with an FDR (False Discovery Rate) q value < 0.25 and a Normal p-value < 0.05 were considered to be enriched significantly.
Assembly: hg38
Supplementary files format and content: Raw sequencing data were trimmed using fastp version 0.12.4 and mapped to the hg38 genome using HISAT2 version 2.2.1.
Supplementary files format and content: BigWig files were generated using the bamCoverage command from deepTools version 3.5.1, with parameters --normalizeUsing CPM --binSize 10 --smoothLength 30, and then visualized by the Integrative Genomics Viewer (IGV) version 2.13.2.

source_name: Ovarian Clear Cell Carcinoma

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

treatment_protocol: 5 × 10^5 cells were plated into 6-well plates, incubated for 24 h, and treated without or with 2μM DUB-IN-2 for 6 h. The cells were then washed with PBS, and RNA was isolated using the RNeasy Mini Kit (Qiagen).

value: Ovarian Clear Cell Carcinoma

value: RMG-V

value: USP8i for 6 h


title: RNA_RMGV_NT

description: Library name: RNA_RMGV_NT

value: NT


title: C_LN_2


title: RNA_RMGI_USP8i_6h

description: Library name: RNA_RMGI_USP8i_6h

value: RMG-I


title: mTEClo, adult, WT, cell154

value: WT

value: male


title: mTEClo, adult, WT, cell152


title: mTEClo, adult, AireKO, cell47

value: AireKO


title: C_SPN_1


title: RNA_RMGI_NT

description: Library name: RNA_RMGI_NT


title: mTEClo, adult, WT, cell151


title: mTEClo, adult, AireKO, cell51


title: C_PBMC_3

source_name: PBMC

value: PBMC


title: mTEClo, adult, AireKO, cell45


title: C_LN_1


title: ADRCs, Female no. 07, scRNAseq

city: Odense M

first: Charlotte Harken

middle: Harken

last: Jensen

address: Campusvej 55

department: Clinical Biochemistry/Clinical Research

country: Denmark

institute: Odense University Hospital/University of Southern Denmark

description:
Library name: LY2_F7
10x Genomics

data_processing:
Single-cell count-matrices were generated using CellRanger (version  2.1.1 or 3.1.0). First, raw data was demultiplexed using CellRanger mkfastq. Reads were aligned and counted by CellRanger count using the GRCh38 reference genome
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous adipose tissue

extract_protocol:
ADRCs were isolated from human lipoaspirates using an automated processing Celution® 800/IV device (Lorem Cytori Therapeutics).To enable single-cell RNA sequencing (scRNA-seq), at least 1e+6 ADRCs from each of 14 subjects (7 males and 7 females) were methanol-fixed and stored at -80°C. Briefly, the cells were resuspended in 500 µl PBS with 1% BSA and 1 U/µl RNAsin PLUS RNase Inhibitor (Promega) and incubated on ice for 5 min to ensure the integrity of the RNA in the cells. The cells were passed through a 40 µm Flowmi® Cell strainer (VWR) to create a single-cell suspension. The cells were centrifuged at 400g for 3 min at 4°C, and washed in 1 ml RNase-free PBS and subsequently centrifuged at 400g for 3 min at 4°C, before the cell pellet was resuspended in 200 µl RNase-free PBS and 800 µl ice-cold methanol gently added dropwise to the cells. The cells were fixed for 30 min at -20°C and subsequently stored at -80°C until use.
Following rehydration, 8,000 cells were loaded onto the 10x Genomics Chromium controller (10X Genomics). Libraries were prepared according to the instructions of the manufacturer using the 10x Genomics Single-Cell 3’ v2 or v3, Chromium Single Cell B Chip Kit, 48 runs (10X Genomics) and sequenced on an Illumina NovaSeq 6000 System (10X Genomics).

value: subcutaneous adipose tissue

value: adipose derived regenerative cells/stromal vascular fraction

value: cells rehydrated in SSC-buffer

value: Female

tag: bmi


title: mTEClo, adult, WT, cell153

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

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


title: C_SPN_3

value: Spleen

value: Wild type


title: mTEClo, adult, AireKO, cell46

tag: cell type

value: epitherial cells

value: mTEClo


title: mTEClo, adult, WT, cell149

tag: strain


title: mTEClo, adult, AireKO, cell44

tag: genotype


title: C_PBMC_2


title: ADRCs, Female no. 06, scRNAseq

description:
Library name: LY2_F6
10x Genomics

tag: age


title: C_PBMC_1


title: mTEClo, adult, AireKO, cell43

tag: Sex


title: mTEClo, adult, WT, cell150

tag: exp. batch


title: ADRCs, Female no. 05, sample 2, scRNAseq

description:
Library name: LY2_F5_S2
10x Genomics


title: S_BM_3

value: Bone Marrow

value: sham-operated


title: mTEClo, adult, AireKO, cell42


title: mTEClo, adult, WT, cell147


title: S_BM_2


title: mTEClo, adult, WT, cell148


title: ADRCs, Female no. 05, sample 1, scRNAseq

description:
Library name: LY2_F5_S1
10x Genomics

value: cells rehydrated in PBS


title: mTEClo, adult, AireKO, cell41


title: mTEClo, adult, WT, cell146


title: S_BM_1


title: ADRCs, Female no. 04, scRNAseq

description:
Library name: LY2_F4
10x Genomics


title: mTEClo, adult, AireKO, cell40


title: mTEClo, adult, WT, cell145


title: S_SPN_3


title: ADRCs, Female no. 03, scRNAseq

description:
Library name: LY2_F3
10x Genomics


title: mTEClo, adult, AireKO, cell39


title: ADRCs, Female no. 02, sample 2, scRNAseq

description:
Library name: LY2_F2_S2
10x Genomics


title: S_SPN_2


title: mTEClo, adult, AireKO, cell38


title: mTEClo, adult, WT, cell143


title: mTEClo, adult, WT, cell144


title: ADRCs, Female no. 02, sample 1, scRNAseq

description:
Library name: LY2_F2_S1
10x Genomics


title: mTEClo, adult, AireKO, cell37


title: S_LN_3

value: Lymph Nodes


title: mTEClo, adult, AireKO, cell36


title: mTEClo, adult, WT, cell141

value: WT


title: ADRCs, Female no. 01, sample 1, scRNAseq

description:
Library name: LY2_F1_S1
10x Genomics


title: ADRCs, Female no. 01, sample 2, scRNAseq

description:
Library name: LY2_F1_S2
10x Genomics


title: S_LN_1


title: S_PBMC_3


title: ADRCs, Male no. 06, scRNAseq

description:
Library name: ED2_M6
10x Genomics

value: Male


title: mTEClo, adult, AireKO, cell34

value: AireKO

value: male


title: S_PBMC_2

value: PBMC


title: mTEClo, adult, WT, cell139


title: mTEClo, adult, AireKO, cell33


title: mTEClo, adult, WT, cell138


title: ADRCs, Male no. 05, scRNAseq

description:
Library name: ED2_M5
10x Genomics

value: subcutaneous adipose tissue

value: adipose derived regenerative cells/stromal vascular fraction


title: S_PBMC_1


title: mTEClo, adult, AireKO, cell32


title: ADRCs, Male no. 04, scRNAseq

description:
Library name: ED2_M4
10x Genomics


title: mTEClo, adult, WT, cell137


title: M_BM_3


title: mTEClo, adult, WT, cell136


title: M_BM_2


title: mTEClo, adult, WT, cell142


title: ADRCs, Male no. 03, scRNAseq

description:
Library name: ED2_M3
10x Genomics


title: mTEClo, adult, AireKO, cell30


title: ADRCs, Male no. 02, scRNAseq

description:
Library name: ED2_M2
10x Genomics


title: mTEClo, adult, AireKO, cell29


title: mTEClo, adult, WT, cell135


title: mTEClo, adult, WT, cell134


title: ADRCs, Male no. 01, scRNAseq

description:
Library name: ED2_M1
10x Genomics

value: cells rehydrated in SSC-buffer


title: mTEClo, adult, AireKO, cell35

value: thymus


title: mTEClo, adult, WT, cell140


title: ADRCs, Male no. 07, scRNAseq

description:
Library name: ED2_M7
10x Genomics


title: M_SPN_3

value: Spleen


title: M_BM_1

value: Wild type


title: mTEClo, adult, AireKO, cell28

value: epitherial cells


title: mTEClo, adult, WT, cell133

value: mTEClo


title: Ishikawa cells, snrpb kd, rep3

city: jinan

first: David

address: 44 Wenhua Xi Road,Jinan

institute: Shandong University

description:
knockdown
si-snrpb-3

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using TopHat software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software
Assembly: genome hg19
Supplementary files format and content: tab-delimited text file includes counts for each sample

source_name: endometrial cancer

extract_protocol:
RNA was harvested using Trizol agent.
RNA library were prepared for sequencing using standard Illumina protocols

value: endometrial cancer

tag: cell line

value: Ishikawa

value: endometrial cancer cells

value: snrpb knockdown

value: transient transfection


title: Ishikawa cells, snrpb kd, rep2

description:
knockdown
si-snrpb-2

tag: treatment


title: M_SPN_2


title: mTEClo, adult, AireKO, cell27


title: M_SPN_1


title: mTEClo, adult, WT, cell132

value: WT


title: Ishikawa cells, snrpb kd, rep1

description:
knockdown
si-snrpb-1


title: mTEClo, adult, AireKO, cell31

value: AireKO


title: S_SPN_1

value: sham-operated


title: M_LN_3

value: Lymph Nodes


title: Ishikawa cells, negative control, rep3

description:
control
si-nc-3

value: negattive control


title: mTEClo, adult, WT, cell130

value: male


title: Ishikawa cells, negative control, rep2

description:
control
si-nc-2


title: M_LN_2


title: mTEClo, adult, WT, cell129


title: mTEClo, adult, WT, cell128


title: Ishikawa cells, negative control, rep1

description:
control
si-nc-1


title: mTEClo, adult, AireKO, cell23


title: mTEClo, adult, AireKO, cell22


title: M_PBMC_3

value: PBMC


title: R-47-5

city: Sichuan

first: Jia

middle: yan

last: Huang

address: No.37 Guoxue Lane, Wuhou District

department: Ultrasound

institute: West China hospital

data_processing:
CLC Genomics Workbench v11.0.1
Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: Hg38
Supplementary files format and content: raw counts for all samples
Supplementary files format and content: FPKM value for all samples

source_name: liver cancer cell

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: liver cancer cell

value: human hepatocellular carcinoma cells

value: The samples were exposed to a water bath at 47℃ for 15 minutes and subsequently incubated in a standard cell incubator for 24 hours.


title: M_PBMC_2

value: Wild type


title: mTEClo, adult, WT, cell127

city: Tsurumi-ku, Yokohama

first: Hideyuki

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS

source_name: thymus

value: thymus

value: epitherial cells

value: mTEClo


title: mTEClo, adult, AireKO, cell21


title: mTEClo, adult, WT, cell126


title: mTEClo, adult, AireKO, cell26


title: mTEClo, adult, AireKO, cell20


title: R-47-3


title: R-47-4


title: M_PBMC_1


title: mTEClo, adult, WT, cell131


title: mTEClo, adult, AireKO, cell25


title: R-47-2


title: mTEClo, adult, WT, cell125


title: mTEClo, adult, AireKO, cell24


title: mTEClo, adult, WT, cell124


title: mTEClo, adult, AireKO, cell18


title: mTEClo, adult, WT, cell123


title: R-47-1


title: Sham_Lung_1

source_name: lung

value: lung


title: Sham_Lung_2


title: M_LN_1


title: R-37-5

value: The samples were exposed to a water bath at 37℃ for 15 minutes and subsequently incubated in a standard cell incubator for 24 hours.


title: Sham_Liver_3

source_name: Liver

value: Liver


title: mTEClo, adult, AireKO, cell16


title: mTEClo, adult, WT, cell121

value: WT


title: R-37-4


title: mTEClo, adult, WT, cell122


title: mTEClo, adult, AireKO, cell15

value: AireKO


title: Sham_Lung_3

value: sham-operated


title: mTEClo, adult, AireKO, cell19


title: mTEClo, adult, WT, cell120


title: R-37-3


title: R-37-2


title: Sham_Liver_1


title: mTEClo, adult, AireKO, cell14


title: Sham_Kidney_3

source_name: Kidney

value: Kidney


title: R-37-1


title: mTEClo, adult, AireKO, cell13


title: mTEClo, adult, WT, cell119


title: Sham_Kidney_2


title: NFS1-5

value: NFS1 knockdown


title: mTEClo, adult, WT, cell118

value: male


title: mTEClo, adult, AireKO, cell12


title: mTEClo, adult, AireKO, cell11


title: mTEClo, adult, AireKO, cell17


title: Sham_Kidney_1


title: NFS1-4


title: mTEClo, adult, WT, cell116


title: mTEClo, adult, WT, cell117


title: M_Lung_3


title: mTEClo, adult, AireKO, cell10


title: NFS1-3


title: mTEClo, adult, WT, cell115


title: M_lung_2


title: Sham_Liver_2


title: mTEClo, adult, AireKO, cell9


title: M_lung_1


title: mTEClo, adult, WT, cell114


title: NFS1-1


title: mTEClo, adult, AireKO, cell8


title: NFS1-2


title: M_Liver_3


title: mTEClo, adult, AireKO, cell7


title: mTEClo, adult, WT, cell113


title: M_Liver_2


title: NC-4


title: mTEClo, adult, WT, cell111


title: mTEClo, adult, AireKO, cell5


title: mTEClo, adult, WT, cell112


title: NC-3


title: M_liver_1


title: mTEClo, adult, AireKO, cell6


title: M_Kidney_3


title: mTEClo, adult, WT, cell109


title: M_Kidney_2


title: mTEClo, adult, AireKO, cell4


title: NC-2


title: NC-1


title: mTEClo, adult, AireKO, cell3


title: mTEClo, adult, WT, cell108


title: M_Kidney_1


title: mTEClo, adult, AireKO, cell2


title: RNA_RMGV_siUSP8_96h

treatment_protocol: 5 × 10^5 cells cultured in 6-well plates were transfected with siRNAs (50 nM) using Lipofectamine RNAiMAX (Thermo Fisher Scientific; 13778150) for 48 h. Next, 5 × 10^5 cells were trypsinized, reseeded in 6-well plates, and transfected repeatedly for 48 h with siRNAs (50 nM) using Lipofectamine RNAiMAX. The cells were then washed with PBS, and RNA was isolated using the RNeasy Mini Kit (Qiagen).

value: Ovarian Clear Cell Carcinoma

value: RMG-V

value: siUSP8 for 96 h


title: mTEClo, adult, WT, cell107


title: NC-5

value: liver cancer cell

value: human hepatocellular carcinoma cells

value: The samples were exposed to a water bath at 47℃ for 15 minutes and subsequently incubated in a standard cell incubator for 24 hours.


title: C_lung_3

value: Wild type


title: mTEClo, adult, WT, cell106

value: thymus

value: epitherial cells

value: mTEClo


title: RNA_RMGV_siNT_96h

value: siNT for 96 h


title: mTEClo, adult, AireKO, cell1


title: C_lung_1

value: lung


title: RNA_RMGI_siUSP8_96h

value: RMG-I


title: C_Liver_3

value: Liver


title: mTEClo, adult, WT, cell104

value: WT


title: C_Liver_2


title: mTEClo, adult, WT, cell103


title: RNA_OVTOKO_siUSP8_96h

value: OVTOKO


title: mTEClo, adult, WT, cell355

value: male


title: RNA_RMGI_siNT_96h

value: Ovarian Clear Cell Carcinoma


title: mTEClo, adult, WT, cell354


title: C_Liver_1


title: mTEClo, adult, WT, cell110


title: C_Kidney_3

value: Kidney


title: RNA_OVTOKO_siNT_96h


title: RNA_ES2_siUSP8_96h

value: siUSP8 for 96 h


title: mTEClo, adult, WT, cell353


title: mTEClo, adult, WT, cell101


title: mTEClo, adult, WT, cell102


title: C_Kidney_2


title: mTEClo, adult, WT, cell352


title: mTEClo, adult, WT, cell100


title: RNA_ES2_siNT_96h


title: mTEClo, adult, WT, cell357


title: C_Kidney_1


title: mTEClo, adult, WT, cell105


title: mTEClo, adult, WT, cell351


title: mTEClo, adult, WT, cell99


title: mTEClo, adult, WT, cell350


title: Human Granulosa Cells, Young, Rep 3 [miRNA-Seq]

city: Lone Tree

first: Ye

last: Yuan

state: Colorado

address: 10290 RidgeGate Circle

department: Research

institute: Colorado Center for Reproductive Medicine

data_processing:
Data were analyzed using the CLC Genomics Workbench software, version 21 (www.qiagenbioinformatics.com). Trimming of raw sequencing reads was based on quality score (Q‐score >30), ambiguous nucleotides (maximum two nucleotides allowed), read length (≥15 nucleotides), and removal of adapter sequences.
Small-RNA reads were annotated against human precursor and mature miRNAs listed in the mirBase database (release 22) using the Quantify miRNA tools with default software parameters applied.
Normalization of raw expression data was performed using the trimmed mean of M-values (TMM) normalization method and presented as transcripts per million (TPM) for genes.
Normalization of raw expression data was performed using the trimmed mean of M-values (TMM) normalization method and presented as TMM-adjusted counts per million (CPM) for miRNAs. A miRNA with a CPM ≥ 1 in at least 2 replicates was considered expressed.
The CLC Genomics Workbench Differential Expression tool was used for the expression analysis comparison of the two groups (Young v. Aged). Differential expression of miRNA was defined as a fold change ≥ 1.5, p-value ≤ 0.05, and false discovery rate (FDR) ≤ 0.25.
Assembly: mirBase database (release 22)
Supplementary files format and content: Comma delimited file (CSV) that includes raw counts and normalized counts (CPM = Counts per million) for each sample. It also includes fold change, p-value, and false discovery rate
Supplementary files format and content: Comma delimited file (CSV) that includes filtered list of differentially expressed (DE) miRNA with FC >1.5, p-value < 0.05, and FDR <0.25.

source_name: Granulosa Cells

extract_protocol:
Granulosa cells were thawed on ice and total RNA was isolated from granulosa cells from each patient (9 in each group) using the RNeasy® Plus Micro Kit (Qiagen, cat. no. 74034) according to manufacturer’s instructions. RNase-free DNase (Qiagen) was used to remove potential genomic DNA contamination during the optional DNase step of the manufacturer’s instructions.  RNA integrity and concentration were measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and a NanoDrop™ 2000 Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000), respectively.
Equal volumes (10ul) of isolated RNA from three patients were pooled to limit individual variation, which resulted in three pooled samples per group. For small-RNA libraries, they were prepared using a TruSeq Small RNA Library Prep Kit (Illumina RS-200) according to the manufacturer’s instructions. Library quantity and quality assessments were performed using a Qubit® DNA HS Assay Kit on a Qubit® 2.0 Fluorometer and an Agilent DNA High Sensitivity Kit in an Agilent 2100 Bioanalyzer, respectively. Library concentrations were calculated using quantitative PCR measures then pooled in equimolar ratios and sequenced in a NovaSeq6000 sequencing instrument (Illumina) as single end (50 bases) reads. FASTQ files were generated for each sample using the software bcl2fastq (Illumina) with FastQC tool version 0.11.9 assessing their quality.

value: Granulosa Cells

value: Young (< 32 y.o.)


title: mTEClo, adult, WT, cell356


title: Human Granulosa Cells, Young, Rep 2 [miRNA-Seq]


title: genomic_DNAmethylation_PM161_vc_R1

type: genomic

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

extract_protocol: DNA salt extraction & bisulfite conversion

value: Villi

tag: sentrix

value: F

tag: ga


title: mTEClo, adult, WT, cell98

last: Yoshida

value: thymus


title: genomic_DNAmethylation_PL284_vc

value: M


title: Human Granulosa Cells, Young, Rep 1 [miRNA-Seq]


title: mTEClo, adult, WT, cell97

value: epitherial cells

value: mTEClo


title: mTEClo, adult, WT, cell349


title: mTEClo, adult, WT, cell348


title: genomic_DNAmethylation_PL295_v


title: mTEClo, adult, WT, cell96


title: Human Granulosa Cells, Aged, Rep 3 [miRNA-Seq]


title: mTEClo, adult, WT, cell347


title: mTEClo, adult, WT, cell95


title: mTEClo, adult, WT, cell346


title: mTEClo, adult, WT, cell94


title: Human Granulosa Cells, Aged, Rep 2 [miRNA-Seq]


title: genomic_DNAmethylation_FT58_vc


title: genomic_DNAmethylation_PM77_vc_R4


title: Human Granulosa Cells, Young, Rep 3

data_processing:
Data were analyzed using the CLC Genomics Workbench software, version 21 (www.qiagenbioinformatics.com). Trimming of raw sequencing reads was based on quality score (Q‐score >30), ambiguous nucleotides (maximum two nucleotides allowed), read length (≥15 nucleotides), and removal of adapter sequences.
Reads were mapped to the human reference genome (GRCh38.p14) using the CLC Genomics Workbench RNA-seq Analysis with default software parameters applied.
Normalization of raw expression data was performed using the trimmed mean of M-values (TMM) normalization method and presented as transcripts per million (TPM) for genes.
The expression threshold was determined by the zFPKM method using the zFPKM R package v.1.16.0. Genes with zFPKM > −3 in the three replicates were considered as expressed.
The CLC Genomics Workbench Differential Expression tool was used for the expression analysis comparison of the two groups (Young v. Aged). Differential expression of mRNA was defined as a fold change ≥ 1.5, p-value ≤ 0.05, and false discovery rate (FDR) ≤ 0.25.
Assembly: Human reference genome (GRCh38.p14)
Supplementary files format and content: Comma delimited file (CSV) that includes raw counts and normalized counts (TPM = transcripts per million) for each sample. It also includes fold change, p-value, and false discovery rate
Supplementary files format and content: Comma delimited file (CSV) that includes filtered list of DEGs with FC >1.5, p-value < 0.05, and FDR <0.25.

extract_protocol:
Granulosa cells were thawed on ice and total RNA was isolated from granulosa cells from each patient (9 in each group) using the RNeasy® Plus Micro Kit (Qiagen, cat. no. 74034) according to manufacturer’s instructions. RNase-free DNase (Qiagen) was used to remove potential genomic DNA contamination during the optional DNase step of the manufacturer’s instructions.  RNA integrity and concentration were measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and a NanoDrop™ 2000 Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000), respectively.
Equal volumes (10ul) of isolated RNA from three patients were pooled to limit individual variation, which resulted in three pooled samples per group. For mRNA transcriptome profiling, RNA libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB E7530L) according to the manufacturer’s instructions. Library quantity and quality assessments were performed using a Qubit® DNA HS Assay Kit on a Qubit® 2.0 Fluorometer and an Agilent DNA High Sensitivity Kit in an Agilent 2100 Bioanalyzer, respectively. Library concentrations were calculated using quantitative PCR measures then pooled in equimolar ratios and sequenced in a NovaSeq6000 sequencing instrument (Illumina) as paired (150 bases) reads. FASTQ files were generated for each sample using the software bcl2fastq (Illumina) with FastQC tool version 0.11.9 assessing their quality.


title: mTEClo, adult, WT, cell345


title: genomic_DNAmethylation_FT54_vc


title: mTEClo, adult, WT, cell93


title: Human Granulosa Cells, Young, Rep 2


title: genomic_DNAmethylation_PL158_vc


title: mTEClo, adult, WT, cell92


title: mTEClo, adult, WT, cell344


title: Human Granulosa Cells, Young, Rep 1


title: mTEClo, adult, WT, cell343


title: mTEClo, adult, WT, cell91


title: genomic_DNAmethylation_FT101_vc


title: genomic_DNAmethylation_PL293_v_R1


title: mTEClo, adult, WT, cell90


title: Human Granulosa Cells, Aged, Rep 3


title: mTEClo, adult, WT, cell342


title: genomic_DNAmethylation_PL149_vc


title: genomic_DNAmethylation_PL148_vc


title: mTEClo, adult, WT, cell89


title: mTEClo, adult, WT, cell88


title: mTEClo, adult, WT, cell340


title: Human Granulosa Cells, Aged, Rep 1 [miRNA-Seq]


title: genomic_DNAmethylation_PL294_v


title: Human Granulosa Cells, Aged, Rep 1


title: mTEClo, adult, WT, cell339


title: M2-3

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet file include FPKM values for each Sample.

source_name: Peripheral blood

growth_protocol: THP-1  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) .

extract_protocol:
Total RNA from cell lines was extracted using TRIzol reagent (Invitrogen).1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Peripheral blood

value: Macrophages

value: monocytes

value: mtDNA induced M2 polarization


title: mTEClo, adult, WT, cell87

value: WT


title: genomic_DNAmethylation_FT89_vc


title: mTEClo, adult, WT, cell338

value: male


title: genomic_DNAmethylation_FT42_vc


title: mTEClo, adult, WT, cell337


title: mTEClo, adult, WT, cell85


title: genomic_DNAmethylation_FT98_vc


title: M2-1


title: mTEClo, adult, WT, cell86


title: mTEClo, adult, WT, cell336


title: M2-2


title: M0-3


title: Human Granulosa Cells, Aged, Rep 2


title: mTEClo, adult, WT, cell341


title: genomic_DNAmethylation_FT60_vc


title: mTEClo, adult, WT, cell83


title: genomic_DNAmethylation_PL289_v


title: mTEClo, adult, WT, cell84


title: mTEClo, adult, WT, cell334


title: M0-2


title: mTEClo, adult, WT, cell335


title: mTEClo, adult, WT, cell333


title: genomic_DNAmethylation_PL292_v


title: mTEClo, adult, WT, cell82


title: DMSO treated 2

city: 成都市

first: Di

last: Yan

state: 四川省

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Illumina Casava(1.7) software used for base calling
Sequenced reads wrer trimmed for adaptor sequence, and masked for low-quality sequence,then mapped to hg19 whole genome used HISAT2(2-2.1.0)
raw read counts  were calculated by using htseq-count(0.12.4), then differential expression gene analysis was performed using DESeq2(1.38.0)
Assembly: hg19
Supplementary files format and content: separate text files include raw gene counts for each sample

extract_protocol:
The RNA was isolated by an RNA Mini Kit.
The  library quality was analyzed by dsDNA HS Assay Kit for Qubit® ssDNA Assay Kit

value: Hepatic stellate cell

value: DMSO


title: genomic_DNAmethylation_FT47_vc


title: M0-1


title: DMSO treated 1


title: mTEClo, adult, WT, cell80


title: mTEClo, adult, WT, cell332


title: genomic_DNAmethylation_FT40_vc


title: mTEClo, adult, WT, cell331


title: FEBJ treated 2

value: FEBJ


title: mTEClo, adult, WT, cell79


title: genomic_DNAmethylation_PL296_v


title: mTEClo, adult, WT, cell330


title: mTEClo, adult, WT, cell78


title: mTEClo, adult, WT, cell329


title: Cynaroside treated 2

value: Cynaroside


title: mTEClo, adult, WT, cell77


title: mTEClo, adult, WT, cell328


title: genomic_DNAmethylation_PL290_v


title: genomic_DNAmethylation_FT82_vc


title: Cynaroside treated 1


title: mTEClo, adult, WT, cell76


title: mTEClo, adult, WT, cell81


title: mTEClo, adult, WT, cell75


title: genomic_DNAmethylation_PM256


title: mTEClo, adult, WT, cell327


title: mTEClo, adult, WT, cell325


title: mTEClo, adult, WT, cell74


title: genomic_DNAmethylation_PM332_vc


title: EV Cell FTY Replicate-3

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

country: Canada

institute: Montreal Clinical Research Institute

data_processing:
FASTQC (Andrews, 2010) was run on raw fastq files for quality check
Reads were mapped to human genome GRCh38/hg38 using STAR (Dobin et al., 2013)
pairwise comparison was performed by using DEseq2 (Love et al., 2014)
Assembly: hg38
Supplementary files format and content: Read count tables

source_name: Breast; Mammary gland

growth_protocol: Minimum Essential Medium MEM 1x (Corning, MT10010CV) supplemented with 10% foetal bovine serum (FBS), 0.1 mM non-essential amino acids (Thermo Fisher, MT25025CI), 1 mM sodium pyruvate (Wisent, 600-110-EL), 100 U mL-1 penicillin, and 100 µg mL-1 streptomycin (Wisent, 450-202-EL).

extract_protocol:
Total RNA (TRIzol)
RNA was ribodepleted, and library preparation was carried out using the KAPA RNA HyperPrep Kit with RiboErase (HMR) from Roche

treatment_protocol: EV-isolation media was supplemented with either EV-inhibitor drugs or vehicle: 0.2% DMSO (Sigma-Aldrich, D8418-100ML),  or 10 µM GW4869 (Sigma-Aldrich, D1692-5MG), or 5 µM FTY720 (Sigma-Aldrich, SML0700-5MG).

value: Breast; Mammary gland

value: Epithelial cell

value: FTY

tag: group

value: EV cell


title: mTEClo, adult, WT, cell324

value: thymus


title: EV Cell FTY Replicate-2


title: mTEClo, adult, WT, cell326

value: epitherial cells


title: mTEClo, adult, WT, cell72

value: mTEClo


title: EV Cell GW Replicate-3

value: GW


title: FEBJ treated 1


title: mTEClo, adult, WT, cell73


title: genomic_DNAmethylation_PM344_vc

value: Villi

value: M


title: genomic_DNAmethylation_FT100_vc

value: F


title: mTEClo, adult, WT, cell323

value: WT


title: mTEClo, adult, WT, cell71

value: male


title: EV Cell GW Replicate-2


title: CD1 cells, Reprogramming, shMtfr1l, shOpa1, Day 9

city: Chapel Hill

first: Brian

last: Spurlock

state: NC

address: 111 Mason Farm Road

department: MHI

institute: UNC-CH

description:
Library name: MO biol rep 3
mtfr1lopa1_counts_s2.txt

data_processing:
Quality control was performed using FastQC.
Sequencing reads were mapped to MM10_UCSC using bbmap/38.41.
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Heart

growth_protocol: Cardiac fibroblasts were isolated into gelatin-coated plates with IMDM supplemented with 20% FBS and antibiotics replaced on Day 1 with DMEM supplemented with 20% Media 199, 10% FBS and antibiotics in humidified atmousphere at 5% CO2 and 37C

extract_protocol:
RNA was extracted using Trizol, separated into an aqueous layer using chloroform, precipitated with isopropanol, washed with 70% EtOH and dissolved in RNAse free water. 1ug of total RNA was used for library preparation.
Sequencing libraries were prepared by NovoGene.

treatment_protocol: Cardiac reprogramming was induced through retrovrial transduction of poly-cistronic Meft2c, Gata4 and Tbx5

value: Heart

value: Primary

value: Cardiac Fibroblasts, Induced Cardiomyocytes

value: shMtfr1l + shOpa3

value: MGT Cardiac Reprogramming


title: mTEClo, adult, WT, cell322


title: genomic_DNAmethylation_FT73_v


title: CD1 cells, Reprogramming, shMtfr1l, shOpa1, Day 8

description:
Library name: MO biol rep 2
mtfr1lopa1_counts_s2.txt

value: shMtfr1l + shOpa2


title: EV Cell GW Replicate-1

value: Breast; Mammary gland

value: Epithelial cell


title: mTEClo, adult, WT, cell70

value: thymus


title: CD1 cells, Reprogramming, shMtfr1l, shOpa1, Day 7

description:
Library name: MO biol rep 1
mtfr1lopa1_counts_s2.txt

value: shMtfr1l + shOpa1


title: mTEClo, adult, WT, cell321

value: epitherial cells

value: mTEClo


title: mTEClo, adult, WT, cell69


title: EV Cell DMSO Replicate-3

value: Untreated

value: EV cell


title: mTEClo, adult, WT, cell68


title: EV Cell DMSO Replicate-2


title: EV Cell FTY Replicate-1

value: FTY


title: CD1 cells, Reprogramming, shOpa1, Day 9

description:
Library name: O biol rep 3
mtfr1lopa1_counts_s2.txt


title: mTEClo, adult, WT, cell320

value: WT


title: mTEClo, adult, WT, cell67

value: male


title: EV Cell DMSO Replicate-1


title: CD1 cells, Reprogramming, shOpa1, Day 8

description:
Library name: O biol rep 2
mtfr1lopa1_counts_s2.txt

value: Heart


title: mTEClo, adult, WT, cell319


title: mTEClo, adult, WT, cell318


title: Whole Cell FTY Replicate-3

value: Whole cell


title: mTEClo, adult, WT, cell66


title: Whole Cell FTY Replicate-2


title: CD1 cells, Reprogramming, shOpa1, Day 7

description:
Library name: O biol rep 1
mtfr1lopa1_counts_s2.txt

value: Primary

value: Cardiac Fibroblasts, Induced Cardiomyocytes


title: CD1 cells, Reprogramming, shMtfr1l, Day 9

description:
Library name: M biol rep 3
mtfr1lopa1_counts_s2.txt

value: MGT Cardiac Reprogramming


title: mTEClo, adult, WT, cell317


title: mTEClo, adult, WT, cell316


title: Whole Cell FTY Replicate-1


title: mTEClo, adult, WT, cell64


title: CD1 cells, Reprogramming, shMtfr1l, Day 8

description:
Library name: M biol rep 2
mtfr1lopa1_counts_s2.txt


title: mTEClo, adult, WT, cell315


title: mTEClo, adult, WT, cell63


title: CD1 cells, Reprogramming, shMtfr1l, Day 7

description:
Library name: M biol rep 1
mtfr1lopa1_counts_s2.txt


title: Whole Cell GW Replicate-3

value: GW


title: mTEClo, adult, WT, cell314


title: mTEClo, adult, WT, cell313


title: Whole Cell GW Replicate-2

value: Breast; Mammary gland


title: mTEClo, adult, WT, cell62


title: CD1 cells, Reprogramming, shNT, Day 9

description:
Library name: NT biol rep 3
mtfr1lopa1_counts_s2.txt

value: shNT


title: mTEClo, adult, WT, cell312

value: thymus


title: CD1 cells, Reprogramming, shNT, Day 8

description:
Library name: NT biol rep 2
mtfr1lopa1_counts_s2.txt


title: Whole Cell GW Replicate-1

value: Epithelial cell


title: Whole Cell DMSO Replicate-3


title: mTEClo, adult, WT, cell60

value: epitherial cells


title: Whole Cell DMSO Replicate-2


title: mTEClo, adult, WT, cell311

value: mTEClo


title: mTEClo, adult, WT, cell59


title: mTEClo, adult, WT, cell65


title: CD1 cells, CF control, shNT, NA, Day 7

value: Cardiac Fibroblasts


title: mTEClo, adult, WT, cell310


title: mTEClo, adult, WT, cell58


title: CD1 cells, CF control, shMtfr1l, 50% KD, Day 7


title: mTEClo, adult, WT, cell309


title: SRSF2_IP_KO

city: Hangzhou City

first: Jingyu

last: Hou

state: Zhejiang Province

address: Zhejiang University Student Apartment

institute: Zhejiang University

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
Illumina sequencing reads were treated with fastp (version 0.23.2)  for adaptor removal and quality trimming.
The remaining reads were mapped to  human transcriptome using Hisat2 with default parameters.
SAMtools(version 1.9) were used to select high-quality alignments, remove PCR duplications, and extract the reads mapping of every nucleotide in the transcriptome
Peaks were calling using MACS2. RPKM was calculated using in-house scripts following the definition of RPKM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each RNA-Seq Sample

extract_protocol:
Total RNA was isolated from cell lines by Trizol(Invitrogen). polyA+ RNA was purified using Dynabeads Oligo(dT)25 (Invitrogen).
RNA fragments  were converted to cDNA. RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human embryonic kidney

value: YTHDF1 knockout

value: X-ray


title: mTEClo, adult, WT, cell57

value: WT

value: male


title: CD1 cells, Reprogramming, shNT, NA, Day 7

value: Heart


title: SRSF2_IP_WT


title: CD1 cells, Reprogramming, shMtfr1l, 85% KD, Day 7

value: Primary


title: mTEClo, adult, WT, cell56


title: mTEClo, adult, WT, cell61


title: CD1 cells, CF control, shNT, NA, Day 5


title: mTEClo, adult, WT, cell55


title: CD1 cells, Reprogramming, shNT, Day 7

description:
Library name: NT biol rep 1
mtfr1lopa1_counts_s2.txt

value: Cardiac Fibroblasts, Induced Cardiomyocytes


title: SRSF2_KD


title: mTEClo, adult, WT, cell307


title: mTEClo, adult, WT, cell54


title: mTEClo, adult, WT, cell306


title: CD1 cells, CF control, shMtfr1l, 85% KD, Day 5


title: mTEClo, adult, WT, cell304


title: Whole Cell DMSO Replicate-1

value: Untreated

value: Whole cell


title: YTHDF1_KO


title: mTEClo, adult, WT, cell52


title: 03-01-B-A022691-L003

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

description:
Library name: 1436-A022691_1_S7_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

data_processing:
Raw read counts were imported into R to perform differential expression analyses with the R package DESeq2 11. Variance stabilization transformation was used to prepare data for analyses. Significance analyses of microarrays (SAM) was ran using one class analysis approach to identify miRNAs over-represented in EVs derived from control hMSCs based on the normalized data using Variance stabilization transformation. The delta value was set to 7 (the best delta parameter value selected by the software with the lowest False Discovery Rate (FDR]) using 1000 permutations, FDR cut-off was 0 (%).
Assembly: OP-00037
Supplementary files format and content: The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data.
Supplementary files format and content: Data file  include compiled for all groups Raw data, QC Raw, QC summary, CMP and Median

source_name: Extracellular vesicles (EVs)

growth_protocol: The hMSCs have been previously characterized according to criteria from the International Society for Cell and Gene Therapy - cultured in MEM/EBSS medium supplemented with 1% penicillin/streptomycin and 20% fetal bovine serum in standard tissue culture incubators. hMSCs were utilized at passages 3-5

extract_protocol:
EVs obtained either from hMSCs exposed to serum-free medium or experimental samples. Evs were prepared in accordance with recent recommendations from the International Society for Extracellular Vesicles (ISEV). EV-derived miRNAs were prepared from the conditioned medium and BALF samples using the exoRNeasy Serum/Plasma Maxi/Maxi Midi Kit (Qiagen, Germantown, MD, USA), according to manufacturer’s instructions.
microRNA sequence was outsource to HTG and performed according to manufacture's protocols. A total of 35 ul (35 ng/µl) of eRNA (EV preparation-derived RNA) was used for miRNA sequencing performed using the HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA, as per manufacturer’s instructions as published). The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data. Raw read counts were imported into R to perform differential expression analyses with the R package DESeq2. The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data.

treatment_protocol: hMSCs were seeded into 6-well plates (Corning, 2 x 105 cells/well, 2 wells/BALF sample or control) in cell culture conditions outlined above and incubated overnight. The next day, cells were washed twice with PBS and synchronized for 24 hours in serum-free medium. After synchronization, the serum-free medium was replaced with 1 ml of serum-free medium containing either individual ARDS or individual HV (healthy vlunteer) BALF samples at a 20% (v/v) concentration. Control hMSCs were exposed to serum-free medium only. After 5 hours incubation at 37°C in a standard tissue culture incubator, cell culture medium was removed, cells were washed once with PBS, and 2 ml serum-free medium added per well. After 48 hours incubation (37°C), the conditioned medium was collected, passed through a 0.8 μm syringe filter, and processed for EV preparation, NTA, and miRNA assessments, as described below.

value: Extracellular vesicles (EVs)

value: BM-MSCs

tag: disease

value: ARDS


title: 03-01-B-A022691-L002

description:
Library name: 1436-A022691_1_S7_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell53

value: thymus


title: mTEClo, adult, WT, cell303

value: epitherial cells


title: m6A_IP


title: mTEClo, adult, WT, cell305

value: mTEClo


title: mTEClo, adult, WT, cell51


title: 03-01-B-A022691-L001

description:
Library name: 1436-A022691_1_S7_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: mTEClo, adult, WT, cell302


title: mTEClo, adult, WT, cell308


title: mTEClo, adult, WT, cell50


title: m6A_Input

value: Human embryonic kidney


title: DF1_IP

molecule: nuclear RNA


title: Unstim 62-A022690-L004

description:
Library name: 1436-A022690_1_S57_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell301


title: Unstim 62-A022690-L003

description:
Library name: 1436-A022690_1_S57_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Calu-3_DMSO_inf_c

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

data_processing:
Basecalling was performed with RTAVersion v3.4.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a.
Assembly: GRCh38
Supplementary files format and content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

growth_protocol: Calu-3 cells, derived from lung adenocarcinoma, were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10 % fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin. All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy Mini kit (QIAGEN, Hilden, Germany).
TruSeq Stranded mRNA Library Prep Kit
Oligo-dT beads capture polyA tails

treatment_protocol: SARS-CoV-2 isolate (SARS-CoV-2/Hu/DP/Kng/19-027), kindly provided by the Kanagawa Prefectural Institute of Public Health, was propagated in VeroE6/TMPRSS2 cells, which was used as the virus stock after clarification of cell debris. Calu-3  cells were pre-treated with 10 μM CaNDY or 0.1% DMSO for 24 h, infected with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.01, and maintained in the presence of 10 μM CaNDY or 0.1% DMSO.

value: Lung cancer cell line

value: SARS-CoV-2 infection

value: DMSO


title: mTEClo, adult, WT, cell49

value: WT

value: male


title: Unstim 62-A022690-L002

description:
Library name: 1436-A022690_1_S57_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Calu-3_DMSO_inf_b


title: mTEClo, adult, WT, cell299


title: SRSF2_CTL

value: shTRC

value: X-ray


title: mTEClo, adult, WT, cell298


title: mTEClo, adult, WT, cell45


title: mTEClo, adult, WT, cell46


title: Calu-3_CND10_inf_c

value: CaNDY


title: Unstim 62-A022690-L001

description:
Library name: 1436-A022690_1_S57_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Unstim 61-A022689-L003

description:
Library name: 1436-A022689_1_S72_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell47


title: Unstim 61-A022689-L004

description:
Library name: 1436-A022689_1_S72_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell44


title: mTEClo, adult, WT, cell296


title: Unstim 61-A022689-L002

description:
Library name: 1436-A022689_1_S72_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell43


title: HMEC_NC

city: Shanghai

first: Shuxun

last: Liu

address: Xiangyin Rd.800

department: Immunology

institute: Naval Medical University

description: gRNAs sequencing with endothelial cells without significant CD59 changes

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw   data) by base calling and these short reads are recorded in FASTQ format, which contains sequence   information and corresponding sequencing quality information.
Raw data (raw reads) of fastq format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Trimmed sequence reads were mapped to original sgRNA library.
Reads count of each sgRNA were normalized by MAGeCK with median-normalized.
Assembly: gRNA pooled library in lentiCRISPRv2(Addgene, #1000000048)
Supplementary files format and content: Excel spreadsheet file include normalized reads count for each sample

source_name: HMEC-1 cell line

extract_protocol:
Genomic DNA was extracted from sorted cells using DNAzol reagent and inserted gRNAs were amplified by PCR, and then the bands at 250bp were cut and extracted for gRNA sequencing.
Sequencing libraries were generated using Illumina TruSeq DNA PCR-Free Library Preparation Kit (Illumina, USA) following manufacturer’s recommendations.
Crispr screen

treatment_protocol: Endothelial cells transfected with crispr/cas9-gRNA library were selected by puromycin, and the  surviving cells were culture into several wells and respectively transfected with a mix of SARS-CoV-2 protein plasmids, SARS-CoV-2 N protein plasmid or control plasmid, in the presence of regular culture or high glucose condition. Endothelial cells with significant CD59 changes and those cells with no significant CD59 changes were pooled respectively as experimental (HMEC_E) and control (HMEC_NC) groups as compared to control group .

value: HMEC-1 cell line

value: Dermal endothelium


title: Calu-3_CND10_inf_a


title: mTEClo, adult, WT, cell300


title: Unstim 61-A022689-L001

description:
Library name: 1436-A022689_1_S72_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs


title: mTEClo, adult, WT, cell295

value: thymus


title: mTEClo, adult, WT, cell48

value: epitherial cells


title: mTEClo, adult, WT, cell293

value: mTEClo


title: HMEC_E

description: gRNAs sequencing with endothelial cells with significant CD59 changes


title: Unstim 60-A022688-L004

description:
Library name: 1436-A022688_1_S10_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: Calu-3_DMSO_inf_a


title: mTEClo, adult, WT, cell41


title: Caco-2_DMSO_3

growth_protocol: Caco-2 cells, derived from Colon adenocarcinoma, were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10 % fetal bovine serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 1% NEAA (Nacalai Tesque, Kyoto, Japan). Cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HeLa cells using Trizol and Direct-zol RNA mini-prep kit (Zymo research, CA, USA).
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Caco-2 cells were treated with 0.1% DMSO or 10 μM CaNDY for 18 h.

value: cancer cell line

tag: derived tissue

value: Colon adenocarcinoma


title: mTEClo, adult, WT, cell42


title: mTEClo, adult, WT, cell292


title: Calu-3_CND10_inf_b

value: Lung cancer cell line

value: SARS-CoV-2 infection


title: mTEClo, adult, WT, cell297

value: WT


title: Caco-2_DMSO_2

value: DMSO


title: Caco-2_DMSO_1


title: Unstim 60-A022688-L001

description:
Library name: 1436-A022688_1_S10_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell291

value: male


title: mTEClo, adult, WT, cell40


title: Caco-2_CND_3


title: mTEClo, adult, WT, cell290


title: Unstim 59-A022687-L004

description:
Library name: 1436-A022687_1_S19_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell294


title: mTEClo, adult, WT, cell289


title: Caco-2_CND_2


title: mTEClo, adult, WT, cell37


title: Unstim 59-A022687-L003

description:
Library name: 1436-A022687_1_S19_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell288


title: Caco-2_CND_1


title: Unstim 60-A022688-L003

description:
Library name: 1436-A022688_1_S10_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell38


title: Unstim 59-A022687-L002

description:
Library name: 1436-A022687_1_S19_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell35


title: Unstim 59-A022687-L001

description:
Library name: 1436-A022687_1_S19_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell36


title: WT_Suc_rep3

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: sacCer3
Supplementary files format and content: GeneCounts

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD or sucrose until mid-log phase

extract_protocol:
RNA Extraction by Acid Phenol Method
Libraries were prepared using the HTP KAPA kit

value: saccharomyces cerevisiae

value: sucrose


title: mTEClo, adult, WT, cell287

state: Kanagawa


title: mTEClo, adult, WT, cell286