title: WT_Suc_rep2


title: Unstim 58-A022686-L004

status: Public on Mar 12 2025

type: SRA

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

description:
Library name: 1436-A022686_1_S17_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

value: Extracellular vesicles (EVs)

tag: cell type

value: BM-MSCs

tag: disease

value: Unstimulated


title: mTEClo, adult, WT, cell285

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

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.

value: thymus

value: epitherial cells

value: mTEClo

tag: strain

tag: genotype

value: WT

tag: age

tag: Sex

value: male

tag: exp. batch


title: Unstim 60-A022688-L002

description:
Library name: 1436-A022688_1_S10_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell39


title: WT_Suc_rep1

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

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

tag: treatment

value: sucrose


title: Unstim 58-A022686-L003

description:
Library name: 1436-A022686_1_S17_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell34


title: mTEClo, adult, WT, cell284


title: Unstim 58-A022686-L002

description:
Library name: 1436-A022686_1_S17_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell283


title: WT_Glu_rep2

value: glucose


title: mTEClo, adult, WT, cell282


title: Unstim 58-A022686-L001

description:
Library name: 1436-A022686_1_S17_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: WT_Glu_rep3


title: WT_Glu_rep1


title: mTEClo, adult, WT, cell30


title: mTEClo, adult, WT, cell32


title: Unstim 57-A022685_L004

description:
Library name: 1436-A022685_1_S65_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell281


title: mTEClo, adult, WT, cell33


title: Rpd3_2SA_Suc_rep3


title: mTEClo, adult, WT, cell29


title: Rpd3_2SA_Suc_rep2


title: Unstim 57-A022685_L003

description:
Library name: 1436-A022685_1_S65_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Rpd3_2SA_Suc_rep1


title: Unstim 57-A022685_L002

description:
Library name: 1436-A022685_1_S65_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell279


title: mTEClo, adult, WT, cell28


title: mTEClo, adult, WT, cell280


title: mTEClo, adult, WT, cell27


title: mTEClo, adult, WT, cell278


title: Rpd3_2SA_Glu_rep3


title: mTEClo, adult, WT, cell26


title: 11072701-A022684-L004

description:
Library name: 1436-A022684_1_S69_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: Unstim 57-A022685_L001

description:
Library name: 1436-A022685_1_S65_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell277


title: mTEClo, adult, WT, cell31


title: mTEClo, adult, WT, cell276


title: mTEClo, adult, WT, cell25


title: Rpd3_2SA_Glu_rep1


title: GAW24

type: genomic

city: San Francisco

first: Stephanie

middle: L.

last: Gaw

state: CA

address: 513 Parnassus Avenue, Health Sciences East 1622

department: Obstetrics, Gynecology and Reproductive Sciences

country: USA

institute: University of California, San Francisco

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina IScan Reader using standard recommended Illumina scanner setting

data_processing: R (version 4.2.1) and minfi package (version 1.44.0)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: placental malaria associated FGR

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human placenta samples using Qiagen DNeasy Kit according to standard instructions

value: placenta

tag: study site

value: Uganda

tag: fetal growth restriction (fgr) status

value: FGR

tag: placental malaria (pm) status

value: PM

tag: study group

value: PM-FGR


title: GAW23


title: mTEClo, adult, WT, cell275


title: mTEClo, adult, WT, cell274


title: 11072701-A022684-L001

description:
Library name: 1436-A022684_1_S69_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: mTEClo, adult, WT, cell22


title: 11071803-A022683-L004

description:
Library name: 1436-A022683_1_S76_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs


title: GAW22


title: mTEClo, adult, WT, cell23


title: mTEClo, adult, WT, cell273


title: mTEClo, adult, WT, cell21


title: mTEClo, adult, WT, cell272


title: GAW21


title: 11071803-A022683-L003

description:
Library name: 1436-A022683_1_S76_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell20


title: 11071803-A022683-L002

description:
Library name: 1436-A022683_1_S76_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell271


title: GAW20


title: Rpd3_2SA_Glu_rep2


title: 11072701-A022684-L003

description:
Library name: 1436-A022684_1_S69_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell270


title: mTEClo, adult, WT, cell19


title: 11071803-A022683-L001

description:
Library name: 1436-A022683_1_S76_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW19


title: mTEClo, adult, WT, cell18


title: 11072701-A022684-L002

description:
Library name: 1436-A022684_1_S69_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell24


title: 11062107-A022682-L004

description:
Library name: 1436-A022682_1_S73_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW18


title: mTEClo, adult, WT, cell269


title: mTEClo, adult, WT, cell17


title: mTEClo, adult, WT, cell268


title: GAW17


title: mTEClo, adult, WT, cell16


title: 11062107-A022682-L002

description:
Library name: 1436-A022682_1_S73_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW16

source_name: non-malarial FGR

value: US

value: No PM


title: mTEClo, adult, WT, cell267

value: thymus

value: epitherial cells


title: mTEClo, adult, WT, cell15

value: mTEClo

value: WT


title: 11062107-A022682-L001

description:
Library name: 1436-A022682_1_S73_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW15


title: mTEClo, adult, WT, cell266

value: male


title: mTEClo, adult, WT, cell14


title: GAW14


title: mTEClo, adult, WT, cell265


title: SAT108-A022681-L004

description:
Library name: 1436-A022681_1_S9_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Healthy Control


title: mTEClo, adult, WT, cell13


title: SAT108-A022681-L003

description:
Library name: 1436-A022681_1_S9_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW13


title: mTEClo, adult, WT, cell264


title: mTEClo, adult, WT, cell263


title: mTEClo, adult, WT, cell12


title: SAT108-A022681-L002

description:
Library name: 1436-A022681_1_S9_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW12


title: SAT108-A022681-L001

description:
Library name: 1436-A022681_1_S9_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell11


title: mTEClo, adult, WT, cell262


title: GAW11


title: 11062107-A022682-L003

description:
Library name: 1436-A022682_1_S73_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell261


title: mTEClo, adult, WT, cell10


title: mTEClo, adult, WT, cell9


title: GAW10


title: SH96-A022680-L003

description:
Library name: 1436-A022680_1_S2_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW09


title: mTEClo, adult, WT, cell8


title: SH96-A022680-L002

description:
Library name: 1436-A022680_1_S2_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell259


title: GAW08

source_name: healthy controls from Uganda

value: No FGR

value: Ctrl-PM-FGR


title: mTEClo, adult, WT, cell7


title: mTEClo, adult, WT, cell258


title: CO99-A022679-L004

description:
Library name: 1436-A022679_1_S18_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW07

value: placenta


title: GAW06

value: Uganda


title: mTEClo, adult, WT, cell257


title: mTEClo, adult, WT, cell5


title: mTEClo, adult, WT, cell4


title: GAW05


title: mTEClo, adult, WT, cell256


title: CO99-A022679-L002

description:
Library name: 1436-A022679_1_S18_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell255


title: CO99-A022679-L003

description:
Library name: 1436-A022679_1_S18_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell3


title: SH96-A022680-L004

description:
Library name: 1436-A022680_1_S2_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: CO99-A022679-L001

description:
Library name: 1436-A022679_1_S18_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell260


title: GAW03

source_name: healthy controls from the US

value: Ctrl-FGR


title: mTEClo, adult, WT, cell254


title: mTEClo, adult, WT, cell253


title: mTEClo, adult, WT, cell2


title: 11063035-A022678-L004

description:
Library name: 1436-A022678_1_S70_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: GAW04


title: SH96-A022680-L001

description:
Library name: 1436-A022680_1_S2_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: 11063035-A022678-L003

description:
Library name: 1436-A022678_1_S70_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW01


title: mTEClo, adult, WT, cell252


title: mTEClo, adult, WT, cell6


title: 11063035-A022678-L002

description:
Library name: 1436-A022678_1_S70_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: GAW02


title: mTEClo, adult, WT, cell1


title: mTEClo, adult, WT, cell251


title: Genomic_DNA_from_surgery_LGG_P670_145

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software was used for primary data acqusition. Raw data was imported into R (version 4.4.1 and further processed using R/Bioconductor package minfi (1.50). The raw pre-processing (Illumina method) was used for data normalization.
MPT_tabIntensity_PBADY.csv: unmetylated and methylated signals
MPT_tabProcessed_PBADY.csv: processed data
processed value definition: normalized (Illumina pre-processing) Average Beta

source_name: Tissue from Human Low Grade Glioma tumor (LGG)

extract_protocol: Genomic DNA were isolated using the AllPrep DNA/RNA Micro Kit (Qiagen, Cat. No. / ID: 80284) on a QIAcube® QIAGEN automat according to the protocol.

value: low grade glioma

tag: batch

value: F

value: M

value: U

tag: purity

tag: subtype

value: codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Subtotal

tag: ntfsstatus


title: mTEClo, neonate, WT, cell123

tag: tissue

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, adult, WT, cell250

tag: cell type

value: male


title: Genomic_DNA_from_surgery_LGG_P670_144

value: Tissue from Human Low Grade Glioma tumor (LGG)

tag: disease


title: mTEClo, neonate, WT, cell122

tag: strain


title: 11063035-A022678-L001

description:
Library name: 1436-A022678_1_S70_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs


title: mTEClo, adult, WT, cell249

tag: genotype


title: 11063075-A022677-L004

description:
Library name: 1436-A022677_1_S38_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell121

tag: age


title: 11063075-A022677-L003

description:
Library name: 1436-A022677_1_S38_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell248

tag: Sex


title: Genomic_DNA_from_surgery_LGG_P670_143

value: low grade glioma

value: F

value: Biopsy


title: Genomic_DNA_from_surgery_LGG_P670_141

value: M

value: codel


title: mTEClo, neonate, WT, cell120

tag: exp. batch


title: mTEClo, adult, WT, cell247


title: Genomic_DNA_from_surgery_LGG_P670_140

value: U

value: control brain tissues

value: control tissue, hemispheric cortex

value: Total


title: mTEClo, adult, WT, cell246

value: thymus

value: epitherial cells

value: mTEClo


title: 11063075-A022677-L001

description:
Library name: 1436-A022677_1_S38_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell119

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_139

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Subtotal


title: mTEClo, neonate, WT, cell124


title: Genomic_DNA_from_surgery_LGG_P670_138

value: low grade glioma

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: mTEClo, adult, WT, cell245

value: male


title: mTEClo, neonate, WT, cell117


title: 11063084-A022676-L003

description:
Library name: 1436-A022676_1_S49_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, adult, WT, cell244


title: Genomic_DNA_from_surgery_LGG_P670_137

value: M

value: m

value: U


title: 11063084-A022676-L002

description:
Library name: 1436-A022676_1_S49_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell116

value: thymus

value: epitherial cells

value: mTEClo


title: mTEClo, adult, WT, cell243

value: WT


title: mTEClo, neonate, WT, cell115

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_134

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: diffuse glioma, IDH mutant

value: Partial


title: 11063084-A022676-L001

description:
Library name: 1436-A022676_1_S49_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_132

value: low grade glioma

value: non-codel

value: Subtotal


title: mTEClo, adult, WT, cell242

value: male


title: Genomic_DNA_from_surgery_LGG_P670_131

value: u

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: 11073327-A022675-L004

description:
Library name: 1436-A022675_1_S33_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, adult, WT, cell241

value: thymus


title: mTEClo, neonate, WT, cell113

value: epitherial cells


title: 11073327-A022675-L003

description:
Library name: 1436-A022675_1_S33_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: 11063075-A022677-L002

description:
Library name: 1436-A022677_1_S38_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_130

value: M

value: m

value: U


title: mTEClo, adult, WT, cell240

value: mTEClo

value: WT


title: 11073327-A022675-L002

description:
Library name: 1436-A022675_1_S33_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell112

value: unknown


title: mTEClo, adult, WT, cell239


title: mTEClo, neonate, WT, cell111


title: 11063084-A022676-L004

description:
Library name: 1436-A022676_1_S49_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell118


title: 11073327-A022675-L001

description:
Library name: 1436-A022675_1_S33_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_129

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: mTEClo, adult, WT, cell238

value: male


title: Genomic_DNA_from_surgery_LGG_P670_128

value: Subtotal


title: mTEClo, neonate, WT, cell110


title: CF71-A022674-L004

description:
Library name: 1436-A022674_1_S37_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, adult, WT, cell237

value: thymus

value: epitherial cells


title: mTEClo, neonate, WT, cell109


title: Genomic_DNA_from_surgery_LGG_P670_127

value: M

value: U

value: non-codel

value: medulloblastoma Group 3


title: CF71-A022674-L003

description:
Library name: 1436-A022674_1_S37_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell236

value: mTEClo

value: WT


title: Genomic_DNA_from_surgery_LGG_P670_126

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: mTEClo, neonate, WT, cell114

value: unknown


title: CF71-A022674-L002

description:
Library name: 1436-A022674_1_S37_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell235

value: male


title: mTEClo, neonate, WT, cell108


title: Genomic_DNA_from_surgery_LGG_P670_124

value: F

value: u

value: diffuse glioma, IDH mutant

value: Subtotal


title: Genomic_DNA_from_surgery_LGG_P670_123


title: CF71-A022674-L001

description:
Library name: 1436-A022674_1_S37_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, adult, WT, cell234

value: thymus

value: epitherial cells


title: mTEClo, neonate, WT, cell107


title: mTEClo, neonate, WT, cell105


title: Unstim 5-A022673-L003

description:
Library name: 1436-A022673_1_S61_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: Genomic_DNA_from_surgery_LGG_P670_122

value: U

value: non-codel

value: Partial


title: mTEClo, adult, WT, cell232

value: mTEClo

value: WT


title: mTEClo, neonate, WT, cell106

value: unknown


title: Unstim 5-A022673-L004

description:
Library name: 1436-A022673_1_S61_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell233

value: male


title: mTEClo, adult, WT, cell231


title: mTEClo, neonate, WT, cell104


title: Genomic_DNA_from_surgery_LGG_P670_121

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: M

value: codel

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: Genomic_DNA_from_surgery_LGG_P670_117

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: Unstim 5-A022673-L001

description:
Library name: 1436-A022673_1_S61_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Unstimulated


title: Genomic_DNA_from_surgery_LGG_P670_120

value: U


title: Unstim 4-A022672-L004

description:
Library name: 1436-A022672_1_S22_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell229

value: thymus

value: epitherial cells

value: mTEClo


title: Unstim 5-A022673-L002

description:
Library name: 1436-A022673_1_S61_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell103

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_115

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: medulloblastoma Group 3


title: mTEClo, neonate, WT, cell101


title: Unstim 4-A022672-L003

description:
Library name: 1436-A022672_1_S22_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell228

value: male


title: Unstim 4-A022672-L002

description:
Library name: 1436-A022672_1_S22_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell100


title: Genomic_DNA_from_surgery_LGG_P670_114

value: F

value: M

value: non-codel


title: mTEClo, adult, WT, cell227


title: Unstim 4-A022672-L001

description:
Library name: 1436-A022672_1_S22_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell99


title: mTEClo, adult, WT, cell226


title: Genomic_DNA_from_surgery_LGG_P670_113

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Total


title: mTEClo, neonate, WT, cell98


title: Unstim 3-A022671-L004

description:
Library name: 1436-A022671_1_S60_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Unstimulated


title: mTEClo, adult, WT, cell230

value: thymus

value: epitherial cells


title: mTEClo, adult, WT, cell225

value: mTEClo

value: WT


title: Unstim 3-A022671-L003

description:
Library name: 1436-A022671_1_S60_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell224


title: mTEClo, neonate, WT, cell102

value: unknown


title: mTEClo, neonate, WT, cell96


title: Genomic_DNA_from_surgery_LGG_P670_111

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: m

value: U

value: control brain tissues

value: control tissue, hemispheric cortex

value: Subtotal


title: Unstim 3-A022671-L002

description:
Library name: 1436-A022671_1_S60_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_108

value: M

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: mTEClo, adult, WT, cell223

value: male


title: mTEClo, neonate, WT, cell95

value: thymus


title: mTEClo, adult, WT, cell222

value: epitherial cells


title: Genomic_DNA_from_surgery_LGG_P670_116

value: F

value: codel

value: medulloblastoma Group 3


title: Unstim 3-A022671-L001

description:
Library name: 1436-A022671_1_S60_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Unstimulated


title: Genomic_DNA_from_surgery_LGG_P670_107

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: U

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: mTEClo, adult, WT, cell221

value: mTEClo

value: WT


title: Genomic_DNA_from_surgery_LGG_P670_106

value: M

value: diffuse glioma, IDH mutant

value: Total


title: Unstim 2-A022670-L004

description:
Library name: 1436-A022670_1_S11_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell93

value: thymus

value: unknown


title: Unstim 2-A022670-L003

description:
Library name: 1436-A022670_1_S11_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_105

value: non-codel

value: Partial


title: mTEClo, adult, WT, cell220

value: epitherial cells

value: male


title: mTEClo, neonate, WT, cell92


title: Genomic_DNA_from_surgery_LGG_P670_112

value: codel

value: Subtotal


title: Unstim 2-A022670-L002

description:
Library name: 1436-A022670_1_S11_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Unstimulated


title: mTEClo, adult, WT, cell219


title: mTEClo, neonate, WT, cell97


title: mTEClo, neonate, WT, cell91


title: Unstim 2-A022670-L001

description:
Library name: 1436-A022670_1_S11_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, adult, WT, cell218


title: Genomic_DNA_from_surgery_LGG_P670_102

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: U

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: Genomic_DNA_from_surgery_LGG_P670_101

value: M

value: diffuse glioma, IDH mutant

value: Biopsy


title: AireKO, mTEClo, H3K27me3, rep2

library_source: genomic

data_processing:
Low-quality parts and adapter sequences were trimmed from the short reads by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
mapping to the mm10 and hg38 genome using bowtie2 with -X 1000 (v2.3.5, Langmead & Salzberg, Fast gapped-read alignment with Bowtie 2, 2012)
Removing reads with low mapping quality (MAPQ<30), improperly paired reads, and duplicated reads using SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Counting these quality-filtered reads (RQC) for normalization
Computing the fractions of spike-in cells (FrSpike) from the input libraries based on RQC normalized by the effective genome size (mm10:2.49x10^9, hg38:2.86x10^9, derived from deepTools documents) for normalization
Peaks calling from the pooled cut&tag datasets using MACS2 with --broad --broad-cutoff 0.05 (v2.1.4, Zhang et al., Model-based analysis of ChIP-Seq (MACS), 2008)
Counting the number of reads overlapping the peaks (reads in peaks; RiP) using bedtools (v2.29.0, Quinlan et al., BEDTools: a flexible suite of utilities for comparing genomic features, 2010) for normalization
Cut&tag assay efficiency was computed from the RiP divided by RQC (Eff=RiP/RQC) of spike-ins for each sample for normalization
The absolute scaling factor (Sfabs) for each sample was calculated as Sfabs = 1/ (RQC (hg38+mm10) x (1- FrSpike)) x 1/Eff
The relative scaling factors (Sfrel) were calculated by normalizing Sfabs to the highest Sfabs among all samples (Sfrel = Sfabs (sample) / max (all Sfabs)).
The normalized bedgraph files were generated using bedtools by piling up the fragments while applying an option -scale Sfrel
Converting bedgraph into bigwig files using bdg2bw (https://gist.github.com/taoliu/2469050)
Assembly: mm10
Supplementary files format and content: bigWig files: read coverage across the whole genome (normalized by spike-ins)
Library strategy: cut&tag

extract_protocol:
Mouse thymus was enzymatically digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria. 10,000 cells were sorted into 100 uL of BAMBANKER (GC LYMPHOTEC) and kept frozen until library constructions.
Cut&tag libraries were constructed as previously reported by Kaya-Okur et al. (CUT&Tag for efficient epigenomic profiling of small samples and single cells, 2019) employing spike-ins for normalizations (Greulich et al., Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation, 2021). Specifically, cell capturing beads for a sample were prepared by incubating 5uL of streptavidin-conjugated magnetic beads (Dynabeads MyOne Streptavidin T1, Invitrogen) with 20ug/mL biotin-conjugated ConA (Sigma-Aldrich, C2272) and 20ug/ml biotin-conjugated WGA (Sigma-Aldrich, L5142) in 100uL of PBS at room temperature for 30min. Then the beads were washed and resuspended in 20uL of binding buffer (20mM HEPES PH7.5, 10mM KCl, 1mM CaCl2, and 1mM MnCl2). Frozen cells in BAMBANKER were thawed and washed with PBS after adding 10,000 293FT cells (Invitrogen) as spike-in. Cells were resuspended in 100uL of wash buffer (20mM HEPES PH7.5, 150mM NaCl, 0.5mM spermidine, and protease inhibitor cocktail; Roche cOmplete ULTRA EDTA-free) and incubated with 20uL of cell capturing beads for 30min. Cells were isolated using a magnetic separator (DynaMag2 Magnet, Invitrogen) and resuspended in 55uL of antibody solution (1:100 diluted anti-H3K27me3 CST#9733 in 20mM HEPES PH7.5, 150mM NaCl, 0.5mM spermidine, protease inhibitor cocktail, 0.05% digitonin; WAKO water-soluble digitonin, 2mM EDTA, and 0.1% BSA). 5uL of the cell suspension was used for preparing the input library as described later and 50uL was incubated overnight at 4C with agitation using a rotary mixer (NISSINRIKA NRC-20D, Tokyo Japan). After the overnight incubation, cells were washed with Dig-wash buffer (0.05% digitonin, 20mM HEPES PH7.5, 150mM NaCl, 0.5mM spermidine, and protease inhibitor cocktail) and incubated in the secondary antibody buffer (1:100 diluted anti-rabbit IgG; ROCKLAND 611-201-122 in Dig-wash buffer) at 4C for 1hr with agitation. After the incubation, cells were washed 3 times with Dig-wash buffer and incubated in 100uL of 8ug/mL in-house pAG-Tn5 in Dig-300 buffer (20mM HEPES PH7.5, 300mM NaCl, 0.5mM spermidine, 0.01% digitonin, and protease inhibitor cocktail) at room temperature for 1 hour with agitation. In-house pAG-Tn5, in which Protein A and Protein G IgG binding domains were fused to Tn5 transposase, was prepared by utilizing pTXB1-Tn5 employing regular methods in molecular biology following the previous reports (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. pTXB1-Tn5 was a gift from Rickard Sandberg. Addgene plasmid #60240; http://n2t.net/addgene:60240). Then, cells were washed 3 times with Dig-300 buffer, resuspended in 100uL of Tagmentation buffer (Dig-300 buffer containing 10mM MaCl2), and incubated at 37C for 1hr mixing at 600rpm (ThermoMixer, Eppendorf) for DNA Tagmentation. The reaction was stopped by adding EDTA, SDS, and DNase-free RNaseA to 15mM, 0.5%, and 0.05mg/mL respectively, and incubated at 37C for 15min mixing at 600rpm. Then, tagmented DNA was purified by proteinase K treatment (Proteinase K, recombinant, PCR Grade, Roche) followed by phenol-chloroform extraction. DNA was amplified using indexed primers and KAPA HiFi DNA Polymerase (Roche) to construct an NGS library. The libraries were purified using AMPure XP beads (x1.1 vol) and quantified by MultiNA (SHIMADZU). For preparing the input libraries, DNA was purified from 5uL of cell suspension by proteinase K treatment followed by phenol-chloroform extraction. DNA tagmentation was performed using an in-house 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. pTXB1-Tn5 was a gift from Rickard Sandberg. Addgene plasmid #60240; http://n2t.net/addgene:60240). Then, Tn5 was dissociated by adding SDS to 0.04% and DNA was amplified by PCR using indexed primers and KAPA HiFi DNA Polymerase. The libraries were purified and size-selected by using AMPure XP beads (x0.55 vol. to remove large fragments and then x1.0 vol. for omitting smaller fragments). Libraries were quantified by MultiNA and pooled for next-generation sequencing.

value: thymus

value: MHCII-low epitherial cells

value: AireKO

tag: chip antibody


title: mTEClo, neonate, WT, cell90

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: Unstim 1-A022669-L004

description:
Library name: 1436-A022669_1_S39_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: mTEClo, neonate, WT, cell94


title: Genomic_DNA_from_surgery_LGG_P670_100

value: F

value: non-codel

value: medulloblastoma Group 3

value: Subtotal


title: Unstim 1-A022669-L003

description:
Library name: 1436-A022669_1_S39_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Unstimulated


title: Unstim 1-A022669-L002

description:
Library name: 1436-A022669_1_S39_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_099

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: AireKO, mTEChi, H3K27me3, rep2

value: thymus

value: MHCII-high epitherial cells

value: AireKO

value: male


title: Unstim 1-A022669-L001

description:
Library name: 1436-A022669_1_S39_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: AireKO, mTEChi, H3K27me3, rep1


title: Genomic_DNA_from_surgery_LGG_P670_097

value: diffuse glioma, IDH mutant


title: mTEClo, neonate, WT, cell86

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_104

value: non-codel

value: medulloblastoma Group 3

value: Subtotal


title: Genomic_DNA_from_surgery_LGG_P670_095

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: F


title: WT, mTEClo, H3K27me3, rep2

value: MHCII-low epitherial cells


title: mTEClo, neonate, WT, cell85


title: Genomic_DNA_from_surgery_LGG_P670_093

value: low grade glioma

value: M

value: U

value: codel


title: mTEClo, neonate, WT, cell84

value: thymus


title: 11082404-A022668-L003

description:
Library name: 1436-A022668_1_S1_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell89

value: epitherial cells

value: mTEClo


title: Genomic_DNA_from_surgery_LGG_P670_092

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: WT, mTEChi, H3K27me3, rep2

value: MHCII-high epitherial cells

value: WT

value: male


title: WT, mTEChi, H3K27me3, rep1


title: AireKO, mTEClo, H3K27me3, rep1

value: AireKO


title: mTEClo, neonate, WT, cell88

value: unknown


title: 11082404-A022668-L002

description:
Library name: 1436-A022668_1_S1_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_089

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: m

value: non-codel

value: Partial


title: 11082405-A022667-L004

description:
Library name: 1436-A022667_1_S29_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: mTEClo, neonate, WT, cell82

value: thymus


title: Genomic_DNA_from_surgery_LGG_P670_090

value: M

value: U

value: u

value: control brain tissues

value: control tissue, white matter (corpus callosum)

value: Biopsy

value: Subtotal


title: mTEClo, neonate, WT, cell83

value: epitherial cells

value: mTEClo

value: WT


title: AireKO, mTEClo, input, rep2

value: MHCII-low epitherial cells

value: AireKO

value: male


title: mTEClo, neonate, WT, cell81

value: unknown


title: mTEClo, neonate, WT, cell87


title: 11082405-A022667-L003

description:
Library name: 1436-A022667_1_S29_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_088

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: m

value: Glioblastoma, IDH-wildtype

value: glioblastoma, IDH-wildtype, mesenchymal type


title: AireKO, mTEClo, input, rep1

value: thymus


title: 11082404-A022668-L004

description:
Library name: 1436-A022668_1_S1_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: Genomic_DNA_from_surgery_LGG_P670_085

value: M

value: U

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: AireKO, mTEChi, input, rep2

value: MHCII-high epitherial cells

value: AireKO

value: male


title: WT, mTEClo, H3K27me3, rep1

value: MHCII-low epitherial cells

value: WT


title: mTEClo, neonate, WT, cell79

value: epitherial cells

value: mTEClo

value: unknown


title: 11082405-A022667-L001

description:
Library name: 1436-A022667_1_S29_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_084

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F


title: mTEClo, neonate, WT, cell78

value: thymus


title: 11082404-A022668-L001

description:
Library name: 1436-A022668_1_S1_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: 11091601-A022666-L004

description:
Library name: 1436-A022666_1_S48_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: AireKO, mTEChi, input, rep1


title: WT, mTEClo, input, rep2


title: Genomic_DNA_from_surgery_LGG_P670_082

value: M

value: U

value: codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Biopsy


title: 11091601-A022666-L003

description:
Library name: 1436-A022666_1_S48_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_080

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Total


title: Genomic_DNA_from_surgery_LGG_P670_078

value: m

value: Subtotal


title: mTEClo, neonate, WT, cell76

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: WT, mTEClo, input, rep1

value: thymus

value: MHCII-low epitherial cells

value: male


title: mTEClo, neonate, WT, cell77


title: 11091601-A022666-L002

description:
Library name: 1436-A022666_1_S48_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell75


title: mTEClo, neonate, WT, cell80


title: WT, mTEChi, input, rep2

value: MHCII-high epitherial cells


title: WT, mTEChi, input, rep1


title: mTEClo, neonate, WT, cell74


title: 11092002-A022665-L004

description:
Library name: 1436-A022665_1_S28_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_077

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type], high grade


title: 11091601-A022666-L001

description:
Library name: 1436-A022666_1_S48_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: 11082405-A022667-L002

description:
Library name: 1436-A022667_1_S29_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell73

value: epitherial cells


title: Genomic_DNA_from_surgery_LGG_P670_076

value: Glioblastoma, IDH-wildtype

value: glioblastoma, IDH-wildtype, mesenchymal type

value: Biopsy


title: 11092002-A022665-L003

description:
Library name: 1436-A022665_1_S28_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_075

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: mTEChi, AireKO, rep3 [Aire_22]

data_processing:
Sequence reads were trimmed to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Low-quality parts and adapter sequences were trimmed by fastp (v0.20.0)
Trimmed short reads were mapped to the mm10 genome using STAR (v2.7.3a) with a GTF file from EMBL-EBI (GRCm38.99)
Unmapped reads and reads mapped with low-quality scores (MAPQ < 5) were removed by SAMtools (v1.9)
Duplicated reads were filtered out using Picard Tools (v2.21.1)
Mapped reads on each gene were counted using htseq-count (v0.11.2) with --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Raw counts were normalized using edgeR package in R programming language
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for all samples
Supplementary files format and content: comma-separated values file includes edgeR normalized abundances for all samples

extract_protocol:
Mouse thymus was enzymatically  digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria directly into tubes containing TCL buffer (QIAGEN)
RNA-seq libraries were prepared by applying a RamDA-seq method for single-cell RNA-seq (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018) with some modifications. Specifically, RNA was isolated using RNAClean XP beads (x2.2 vol., Beckman Coulter) directly from the lysis buffer, and was eluted into 10 uL of water containing RNase inhibitor (4u/uL RNasinPlus RNase Inhibitor, Promega). The RNA was denatured by incubating at 65C for 5min, 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 15min. Then cDNA was synthesized in 30uL of 1xRT Buffer containing RT Enzyme Mix (1.5uL 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 (3.3uM, 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 5uL of 10x NEB buffer2 (NEB), 1.25uL of dNTP mix (10mM each nt, NEB), 1.5uL of Klenow Fragment (3'→5' exo-, NEB), 5uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 7.25uL 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 (x2 vol., Beckman Coulter) and quantified using Qubit (Qubit dsDNA HS Assay Kit, Invitrogen). Then ds-cDNA less than 1ng was applied for Tn5 tagmentation in a 25uL 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). DNA was purified using AMPure XP beads (x1.7 vol.) and amplified by 10~15 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.2 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: thymus

value: AireKO

value: male


title: mTEClo, neonate, WT, cell72

value: mTEClo

value: WT

value: unknown


title: 11092002-A022665-L002

description:
Library name: 1436-A022665_1_S28_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_074

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: u

value: diffuse glioma, IDH mutant


title: mTEChi, AireKO, rep2 [Aire_21]

value: MHCII-high epitherial cells


title: 11092002-A022665-L001

description:
Library name: 1436-A022665_1_S28_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_067

value: F

value: codel

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Subtotal


title: mTEClo, neonate, WT, cell71

value: thymus

value: epitherial cells

value: mTEClo


title: mTEChi, AireKO, rep1 [Aire_20]

value: AireKO

value: male


title: mTEClo, neonate, WT, cell70

value: WT

value: unknown


title: 11101213-A022664-L004

description:
Library name: 1436-A022664_1_S53_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEChi, WT, rep7 [Aire_19]


title: mTEClo, neonate, WT, cell69


title: 11101213-A022664-L003

description:
Library name: 1436-A022664_1_S53_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_064

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: Genomic_DNA_from_surgery_LGG_P670_066

value: u

value: diffuse glioma, IDH mutant

value: Subtotal


title: mTEChi, AireKO, rep4 [Aire_23]

value: thymus

value: MHCII-high epitherial cells


title: 11101213-A022664-L002

description:
Library name: 1436-A022664_1_S53_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell68

value: epitherial cells

value: mTEClo


title: Genomic_DNA_from_surgery_LGG_P670_063

value: F

value: codel


title: mTEClo, neonate, WT, cell67

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_062

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: 11101213-A022664-L001

description:
Library name: 1436-A022664_1_S53_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_061

value: low grade glioma

value: M

value: U


title: mTEClo, neonate, WT, cell66


title: 11102704-A022663-L004

description:
Library name: 1436-A022663_1_S67_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, AireKO, rep2 [Aire_10]

value: MHCII-low epitherial cells

value: AireKO

value: male


title: 11102704-A022663-L003

description:
Library name: 1436-A022663_1_S67_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell65

value: thymus

value: epitherial cells


title: 11102704-A022663-L002

description:
Library name: 1436-A022663_1_S67_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, AireKO, rep1 [Aire_9]


title: Genomic_DNA_from_surgery_LGG_P670_060

value: diffuse glioma, IDH mutant

value: Subtotal


title: Genomic_DNA_from_surgery_LGG_P670_059

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: mTEChi, WT, rep6 [Aire_18]

value: MHCII-high epitherial cells

value: WT


title: 11102704-A022663-L001

description:
Library name: 1436-A022663_1_S67_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: mTEClo, neonate, WT, cell63

value: mTEClo

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_058

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: m


title: mTEClo, AireKO, rep4 [Aire_12]

value: MHCII-low epitherial cells


title: 11063056-A022662-L003

description:
Library name: 1436-A022662_1_S79_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Cystic Fibrosis


title: 11063056-A022662-L004

description:
Library name: 1436-A022662_1_S79_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: P19_S21 s+K+S+L

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
raw_delcourte.txt
resfinal_untreated_naives_vs_untreated_stress.txt
resfinal_untreated_stress_vs_treated_stress_KScL.txt

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes the raw counts for each sample.

source_name: PFC

extract_protocol:
PFCs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Libraries were prepared using Illumina’s TruSeq Stranded mRNA HT kit with 700 ng of total RNA.
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry

value: PFC

value: 10 weeks old

value: wild type

tag: treatment

value: stressed, Ketamine, Scopolamine, and light


title: P14_S18 ns+V

value: non-stressed and vehicle


title: P21_S22 s+K+S+L


title: Genomic_DNA_from_surgery_LGG_P670_056

value: F

value: M

value: U

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Partial


title: Genomic_DNA_from_surgery_LGG_P670_057

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: Subtotal


title: mTEClo, neonate, WT, cell60

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, neonate, WT, cell61


title: 11063056-A022662-L002

description:
Library name: 1436-A022662_1_S79_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: P2_S14 s

value: PFC

value: 10 weeks old

value: wild type

value: stressed


title: Genomic_DNA_from_surgery_LGG_P670_055

value: F

value: U

value: control brain tissues

value: control tissue, hemispheric cortex


title: 11063056-A022662-L001

description:
Library name: 1436-A022662_1_S79_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_053

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: P13_S17 ns+V

value: non-stressed and vehicle


title: mTEClo, neonate, WT, cell64

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: P1_S13 s

value: PFC

value: 10 weeks old

value: wild type

value: stressed


title: mTEClo, neonate, WT, cell58


title: mTEClo, neonate, WT, cell62


title: 11063066-A022661-L004

description:
Library name: 1436-A022661_1_S42_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_052

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: non-codel

value: Partial


title: mTEClo, neonate, WT, cell57

value: thymus


title: Genomic_DNA_from_surgery_LGG_P670_051

value: F

value: U

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: Neuron, wt, ChIPseq, H3K27ac, rep1

city: Mississauga

first: Ho Sung

last: Rhee

address: 3359 Mississauga Rd

department: Cell and Systems Biology

institute: University of Toronto

description: Library name: 5ChIPseq_H3K27ac_rep1d6

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

source_name: mESC-derived motor neuron

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

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

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

value: mESC-derived motor neuron


title: 11063066-A022661-L002

description:
Library name: 1436-A022661_1_S42_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Primary Hepatocyte, IL-1β recombinant protein treated, rep3

city: Cheongju

first: JeongSu

last: Park

address: 194-21 Osong-saeng-myung-1 Ro

department: College of Pharmacy

country: South Korea

institute: Chungbuk National University

description: Treatment 3

data_processing:
Read Alignment: Sequencing reads were aligned to the genome or transcriptome using Bowtie2.
Transcript Assembly and Abundance Estimation: Aligned reads were used to assemble transcripts and estimate their abundance.
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Data Visualization: For data mining and visualization, the results were processed in ExDEGA (Ebiogen Inc.), allowing comprehensive graphical representation of findings.
Assembly: mm10 (the Mouse Genome Assembly, GRCm38)
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, Treated Group/Control Group, Control Group, Treated Group, C2, C4, B3, B5, Entrez ID, Gene ID, Chromosome, Start, End, Width, Strand, p_id, Transcript ID, tss_id, bioType, Aliases, Description, and NCBI Search.

source_name: liver

extract_protocol:
RNA was extracted from liver tissues and cells using the Hybrid-R kit (Geneall, Cat. 305-101), according to the manufacturer’s instructions.
Murine primary hepatocyte RNA sequencing was performed with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) following the manufacturer's protocol. cDNA libraries were prepared with an oligo-dT primer for first-strand synthesis and a random primer for second-strand synthesis, then purified using magnetic beads. Final libraries were amplified to include adapter sequences and purified post-PCR. Sequencing was performed as single-end 75 bp reads on an Illumina NextSeq 550.  Reads were aligned with Bowtie2 to the genome or transcriptome. Transcripts were assembled, and differential expression was analyzed with EdgeR using TMM+CPM normalization. Gene classification utilized DAVID and Medline databases, with data visualization by ExDEGA (Ebiogen Inc.).

value: liver

value: Primary Hepatocyte

value: IL-1β recombinant protein


title: mTEClo, neonate, WT, cell56

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: Primary Hepatocyte, IL-1β recombinant protein treated, rep2

description: Treatment 2


title: Genomic_DNA_from_surgery_LGG_P670_050

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: codel


title: mTEClo, neonate, WT, cell55

value: thymus


title: Primary Hepatocyte, IL-1β recombinant protein treated, rep1

description: Treatment 1


title: Genomic_DNA_from_surgery_LGG_P670_049

value: F

value: U

value: non-codel


title: 11063066-A022661-L001

description:
Library name: 1436-A022661_1_S42_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell54


title: 11063058-A022660-L004

description:
Library name: 1436-A022660_1_S54_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_048

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: mTEClo, AireKO, rep3 [Aire_11]

value: MHCII-low epitherial cells

value: AireKO

value: male


title: mTEClo, neonate, WT, cell53

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, neonate, WT, cell59

value: thymus


title: Primary Hepatocyte, no treatment, rep2

description: Control 2

value: liver

value: Primary Hepatocyte


title: mTEClo, neonate, WT, cell52


title: 11063058-A022660-L002

description:
Library name: 1436-A022660_1_S54_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_047

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: M

value: U

value: non-codel


title: Genomic_DNA_from_surgery_LGG_P670_045

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Partial


title: Primary Hepatocyte, no treatment, rep1

description: Control 1


title: 11063058-A022660-L001

description:
Library name: 1436-A022660_1_S54_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell51

value: epitherial cells

value: mTEClo

value: WT


title: 11063066-A022661-L003

description:
Library name: 1436-A022661_1_S42_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_044

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type], high grade

value: Subtotal


title: Primary Hepatocyte, no treatment, rep3

description: Control 3

value: liver

value: Primary Hepatocyte


title: spleen6_mock

city: Lanzhou

first: Jingjing

last: Pei

address: No.1, Xujiaping, Chengguan District, Lanzhou, Gansu Province, P. R. China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (LVRI, CAAS)

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
The spleens were washed twice with the pre-cooled RPIM1640 (containing 0.04% BSA) and then subjected to scissors for mincing. Subsequently, the tissues were digested in enzymatic hydrolysate containing 3 mg/mL Collagenase I (Gibco, USA) at 37℃ for 1 h. After that, the cell suspensions were twice subjected to a 40μm filter and harvested by centrifugation under 300g for 5 minutes. Cells were then subjected to red blood cell lysis (MACS, Germany) at 4℃ for 10 minutes before enrichment. Finally, the cells were resuspended by 100μl RPIM1640, and cell viability and number were measured using LUNA-FL™ Counter (Logos Biosystems).
The single-cell libraries were generated using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10× Genomics) and Chip Kit according to the manufacturer’s protocol.

value: spleen


title: 11063054-A022659-L004

description:
Library name: 1436-A022659_1_S4_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell49

value: thymus

value: unknown


title: spleen5_mock

description: 10x Genomics


title: 11063054-A022659-L003

description:
Library name: 1436-A022659_1_S4_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_042

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: non-codel


title: spleen4_mock

description: 10x Genomics


title: Genomic_DNA_from_surgery_LGG_P670_043

value: F

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: 11063058-A022660-L003

description:
Library name: 1436-A022660_1_S54_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: spleen3_5000

description: 10x Genomics


title: mTEClo, neonate, WT, cell46

value: epitherial cells

value: mTEClo

value: WT


title: mTEClo, neonate, WT, cell48


title: Genomic_DNA_from_surgery_LGG_P670_039

value: Partial


title: mTEClo, neonate, WT, cell47

value: thymus


title: Genomic_DNA_from_surgery_LGG_P670_038

value: m

value: codel

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: spleen2_5000

description: 10x Genomics

value: spleen


title: 11063048-A022658-L004

description:
Library name: 1436-A022658_1_S40_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_037

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: Biopsy

value: Subtotal


title: mTEClo, neonate, WT, cell45

value: unknown


title: M_H_E_07

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.4.1106 and biomaRt V2.46.0
edgeR V3.38.4 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: Mouse GRCm38.84 mm10
Supplementary files format and content: tab-delimited text containing rawcounts for all Samples

source_name: Gastrocnemius Muscle Tissue

growth_protocol: Mice were maintained on chow 5015 diet with or without exposure to voluntary wheel running from 10 to 20 weeks of age

extract_protocol:
Gastrocs were collected, snap frozen in liquid nitrogen, and tissue homogenization was done using Trizol reagent. Total RNA was isolated using RNeasy Mini kit from Qiagen.
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: 14 Control and 14 HuR Skeletal Muscle Knockout mice (7 males and 7 females each) at 5 months of age were exposed to running wheels for 10 weeks, while 14 Control and 14 HuR Skeletal Muscle Knockout mice (7 males and 7 females each) at 5 months of age were exposed to locked wheels

value: Gastrocnemius Muscle Tissue

tag: group

value: HuR skeletal Muscle Knockout

value: Male

value: Exercise


title: spleen1_5000

description: 10x Genomics


title: 11063048-A022658-L003

description:
Library name: 1436-A022658_1_S40_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_036Bis

value: F

value: codel

value: diffuse glioma, IDH mutant


title: Genomic_DNA_from_surgery_LGG_P670_035

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: mTEClo, neonate, WT, cell44

value: thymus

value: epitherial cells

value: mTEClo

value: WT


title: 11063048-A022658-L002

description:
Library name: 1436-A022658_1_S40_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_H_E_06


title: mTEClo, neonate, WT, cell50

value: unknown


title: 11063054-A022659-L002

description:
Library name: 1436-A022659_1_S4_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_034

value: low grade glioma

value: M

value: U

value: Partial


title: M_H_E_04

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male

value: Exercise


title: mTEClo, neonate, WT, cell42


title: 11063054-A022659-L001

description:
Library name: 1436-A022659_1_S4_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: M_H_E_22


title: 11063036-A022657-L004

description:
Library name: 1436-A022657_1_S35_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell41


title: mTEClo, neonate, WT, cell40


title: Genomic_DNA_from_surgery_LGG_P670_033

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: F

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: Genomic_DNA_from_surgery_LGG_P670_031

value: low grade glioma


title: 11063036-A022657-L003

description:
Library name: 1436-A022657_1_S35_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_H_E_21


title: 11063036-A022657-L002

description:
Library name: 1436-A022657_1_S35_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_H_E_02


title: mTEClo, neonate, WT, cell39

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: M_H_E_01

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male


title: 11063036-A022657-L001

description:
Library name: 1436-A022657_1_S35_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs


title: Genomic_DNA_from_surgery_LGG_P670_029

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: M

value: U

value: Biopsy


title: mTEClo, neonate, WT, cell38


title: Unstim-A022656-L004

description:
Library name: 1436-A022656_1_S20_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: M_H_09

value: Baseline


title: Unstim-A022656-L003

description:
Library name: 1436-A022656_1_S20_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_027

value: low grade glioma

value: control brain tissues

value: control tissue, white matter (corpus callosum)

value: Subtotal


title: mTEClo, neonate, WT, cell37

value: thymus

value: epitherial cells

value: mTEClo

value: WT


title: M_H_08

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male


title: Genomic_DNA_from_surgery_LGG_P670_028

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: 11063048-A022658-L001

description:
Library name: 1436-A022658_1_S40_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Genomic_DNA_from_surgery_LGG_P670_030

value: low grade glioma

value: F

value: M

value: U

value: codel

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Biopsy


title: Genomic_DNA_from_surgery_LGG_P670_026

value: Subtotal


title: M_H_24

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Baseline


title: Unstim-A022656-L002

description:
Library name: 1436-A022656_1_S20_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: Genomic_DNA_from_surgery_LGG_P670_025

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: non-codel

value: control brain tissues

value: control tissue, hemispheric cortex

value: Partial


title: mTEClo, neonate, WT, cell36

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, neonate, WT, cell35


title: Genomic_DNA_from_surgery_LGG_P670_023

value: low grade glioma

value: M

value: U

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: SK105-A022655-L004

description:
Library name: 1436-A022655_1_S78_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Healthy Control


title: mTEClo, neonate, WT, cell34


title: M_H_12

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male

value: Baseline


title: Genomic_DNA_from_surgery_LGG_P670_022

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type], high grade

value: Subtotal


title: mTEClo, neonate, WT, cell33

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, neonate, WT, cell43


title: Genomic_DNA_from_surgery_LGG_P670_021

value: low grade glioma

value: F

value: M

value: U

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]


title: Genomic_DNA_from_surgery_LGG_P670_019

value: u


title: Genomic_DNA_from_surgery_LGG_P670_020

value: control brain tissues

value: control tissue, hemispheric cortex


title: mTEClo, neonate, WT, cell32


title: SA100-A022654-L004

description:
Library name: 1436-A022654_1_S34_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Healthy Control


title: M_H_11

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male

value: Baseline


title: M_C_E_28

value: Controls

value: Exercise


title: Genomic_DNA_from_surgery_LGG_P670_018

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: m

value: non-codel

value: Biopsy

value: Partial


title: mTEClo, neonate, WT, cell31

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: SK105-A022655-L001

description:
Library name: 1436-A022655_1_S78_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Healthy Control


title: mTEClo, neonate, WT, cell29


title: M_C_E_05

value: Gastrocnemius Muscle Tissue

value: Male


title: SA100-A022654-L003

description:
Library name: 1436-A022654_1_S34_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_C_E_27

value: Controls

value: Exercise


title: SA100-A022654-L002

description:
Library name: 1436-A022654_1_S34_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_H_15

value: HuR skeletal Muscle Knockout

value: Baseline


title: mTEClo, neonate, WT, cell28


title: M_C_E_25


title: Genomic_DNA_from_surgery_LGG_P670_017

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: M

value: U

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: Unstim-A022656-L001

description:
Library name: 1436-A022656_1_S20_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: Unstimulated


title: M_C_E_26


title: mTEClo, neonate, WT, cell27

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEClo, neonate, WT, cell26


title: M_H_23

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Male


title: Genomic_DNA_from_surgery_LGG_P670_015

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: m


title: SA100-A022654-L001

description:
Library name: 1436-A022654_1_S34_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Healthy Control


title: 11063086-A022653-L004

description:
Library name: 1436-A022653_1_S77_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: SK105-A022655-L003

description:
Library name: 1436-A022655_1_S78_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell30


title: SK105-A022655-L002

description:
Library name: 1436-A022655_1_S78_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_C_E_13

value: Controls

value: Exercise


title: mTEClo, neonate, WT, cell24


title: Genomic_DNA_from_surgery_LGG_P670_012

value: M

value: U

value: non-codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Partial


title: Genomic_DNA_from_surgery_LGG_P670_014

value: Subtotal


title: M_C_31

value: Gastrocnemius Muscle Tissue

value: Baseline


title: 11063086-A022653-L002

description:
Library name: 1436-A022653_1_S77_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: 11063086-A022653-L003

description:
Library name: 1436-A022653_1_S77_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_C_E_10

value: Male


title: mTEClo, neonate, WT, cell25

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_011

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F


title: 11063086-A022653-L001

description:
Library name: 1436-A022653_1_S77_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell23


title: M_C_29

value: Controls


title: mTEClo, neonate, WT, cell22


title: 11063085-A022652-L004

description:
Library name: 1436-A022652_1_S63_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_C_20


title: M_C_19


title: 11063085-A022652-L003

description:
Library name: 1436-A022652_1_S63_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Genomic_DNA_from_surgery_LGG_P670_008

value: M

value: U

value: codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]


title: mTEClo, neonate, WT, cell21


title: mTEClo, neonate, WT, cell20


title: M_C_18

value: Gastrocnemius Muscle Tissue

value: Male

value: Baseline


title: 11063085-A022652-L002

description:
Library name: 1436-A022652_1_S63_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: Genomic_DNA_from_surgery_LGG_P670_004

value: non-codel

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: 11063085-A022652-L001

description:
Library name: 1436-A022652_1_S63_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: M_C_17


title: mTEClo, neonate, WT, cell19

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: Genomic_DNA_from_surgery_LGG_P670_010

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: M

value: m

value: medulloblastoma Group 3

value: Partial


title: M_C_16

value: Gastrocnemius Muscle Tissue

value: Controls

value: Male

value: Baseline


title: mTEClo, neonate, WT, cell18


title: Genomic_DNA_from_surgery_LGG_P670_003

value: U

value: codel

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Subtotal


title: mTEClo, neonate, WT, cell17

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: NPG 104-A022651-L004

description:
Library name: 1436-A022651_1_S14_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Healthy Control


title: Genomic_DNA_from_surgery_LGG_P670_002

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: F

value: non-codel


title: mTEClo, neonate, WT, cell16


title: NPG 104-A022651-L003

description:
Library name: 1436-A022651_1_S14_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: F_H_E_07

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Female

value: Exercise


title: Genomic_DNA_from_surgery_LGG_P670_009

value: M

value: U

value: diffuse glioma, IDH mutant

value: diffuse glioma, IDH-mutant and 1p19q retained [astroglial type]

value: Biopsy


title: Genomic_DNA_from_surgery_LGG_P670_001

value: codel

value: diffuse glioma, IDH-mutant and 1p19q co-deleted [oligodendroglial type]

value: Subtotal


title: F_H_E_03


title: mTEClo, neonate, WT, cell14

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: pnp-1 RNAi Rep4

city: La Jolla

first: Emily

last: Troemel

address: 9500 Gilman Dr, 4205 Bonner Hall

department: Cell and Developmental Biology

institute: UC San Diego

data_processing:
Reads were aligned to WS235 using Rsubreads in R studio
Reads were counted using Featurecounts in Galaxy
Differential gene expression analysis was performed using limma-voom filtering out undetected and lowly expressed genes (CPM < 1). An adjusted p-value of 0.05 and no fold-change cutoff was used to define differentially expressed genes.
Assembly: Wormbase Release WS235
Supplementary files format and content: Matrix table of normalized counts from lima-voom

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Ten C. elegans N2 at L4 stage (P0) were picked onto RNAi plates seeded with adah-1, pnp-1, or L4440 cultures in E. coli HT115 background and incubated at 20°C until their progeny (F1) became gravid adults, which were bleached to obtain synchronized L1 progeny. 1500 L1 progeny (F2) were plated on two 10cm RNAi plates seeded with the respective RNAi culture. These animals were incubated at 20°C for 56 hours, at which point animals were adults and collected for RNA extraction.

extract_protocol:
Total RNA was extracted using TriReagent(Sigma-Aldrich)and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
TruSeq stranded mRNA method followed by sequencing using run type SR75 on an Illumina HiSeq4000 sequencer (Illumina)

treatment_protocol: RNA interference was performed using the feeding method: overnight cultures of E. coliHT115were plated on NGM plates supplemented with 5 mM IPTG and 1 mM carbenicillin followed by incubation at room temperature for 3 - 4 days. Animals were transferred to these plates and incubated at 20°C.

value: Whole animal


title: F_H_E_22

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout


title: Genomic_DNA_from_surgery_LGG_P670_006

value: Tissue from Human Low Grade Glioma tumor (LGG)

value: low grade glioma

value: control brain tissues

value: control tissue, hemispheric cortex


title: SDA 109-A022650-L004

description:
Library name: 1436-A022650_1_S24_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Healthy Control


title: pnp-1 RNAi Rep2


title: mTEClo, neonate, WT, cell12


title: F_H_E_21

value: Female

value: Exercise


title: F_H_E_02


title: SDA 109-A022650-L002

description:
Library name: 1436-A022650_1_S24_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: pnp-1 RNAi Rep3


title: SDA 109-A022650-L003

description:
Library name: 1436-A022650_1_S24_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: NPG 104-A022651-L001

description:
Library name: 1436-A022651_1_S14_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: pnp-1 RNAi Rep1


title: F_H_E_08


title: mTEClo, neonate, WT, cell13

value: thymus


title: SDA 109-A022650-L001

description:
Library name: 1436-A022650_1_S24_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: NPG 104-A022651-L002

description:
Library name: 1436-A022651_1_S14_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: L4440 RNAi Rep4

value: L4440 empty vector RNAi


title: mTEClo, neonate, WT, cell10

value: epitherial cells

value: mTEClo


title: F_H_E_10


title: mTEClo, neonate, WT, cell15

value: WT

value: unknown


title: L4440 RNAi Rep3

value: Whole animal


title: F_H_34

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Baseline


title: mTEClo, neonate, WT, cell9


title: F_H_31


title: SG91-A022649-L003

description:
Library name: 1436-A022649_1_S6_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell8


title: SG91-A022649-L002

description:
Library name: 1436-A022649_1_S6_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: L4440 RNAi Rep1


title: L4440 RNAi Rep2


title: mTEClo, neonate, WT, cell7


title: SG91-A022649-L001

description:
Library name: 1436-A022649_1_S6_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: F_H_19


title: adah-1 RNAi Rep4

value: adah-1 RNAi


title: F_H_17


title: AAP97-A022647-L004

description:
Library name: 1436-A022647_1_S66_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell6


title: mTEClo, neonate, WT, cell11


title: mTEClo, neonate, WT, cell5


title: F_H_14


title: adah-1 RNAi Rep2


title: AAP97-A022647-L003

description:
Library name: 1436-A022647_1_S66_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: AAP97-A022647-L002

description:
Library name: 1436-A022647_1_S66_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: adah-1 RNAi Rep1


title: AAP97-A022647-L001

description:
Library name: 1436-A022647_1_S66_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, WT, cell3


title: SG91-A022649-L004

description:
Library name: 1436-A022649_1_S6_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: F_H_30


title: mTEClo, neonate, WT, cell2


title: F_C_E_09

value: Controls


title: F_C_E_05


title: CF80-A022646-L004

description:
Library name: 1436-A022646_1_S44_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: Cystic Fibrosis


title: mTEClo, neonate, WT, cell1


title: F_C_E_28


title: CF80-A022646-L003

description:
Library name: 1436-A022646_1_S44_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs


title: mTEChi, neonate, EEDcKO, rep3 [EED_13]

value: MHCII-high epitherial cells

value: EEDcKO

value: pooled male and female


title: CF80-A022646-L002

description:
Library name: 1436-A022646_1_S44_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: adah-1 RNAi Rep3


title: F_C_E_27

value: Female

value: Exercise


title: CF80-A022646-L001

description:
Library name: 1436-A022646_1_S44_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Liver from PD7.5 neonate. SL (obese) replicate 4

type: RNA

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

country: Spain

institute: University of Barcelona

description: Gene expression data from liver from 7.5 day-old SL mice.

hyb_protocol: The hybridization was conducted at 45°C for 16-18 hours with rotary agitation (60-70 rpm). Hybridization volume was around 200 µL.

scan_protocol: Clariom S plates from Affymetrix were scanned using the GeneChip Scanner 3000 7G. Images were acquired with the Affymetrix GeneChip Command Console (AGCC) software to handle the image acquisition and data analysis process.

data_processing: Raw expression values were obtained directly from .CEL files and were processed using the RMA method in oligo R package to get normalized expression values (log2 scale) summarized at the gene level. A complete quality report was obtained using arrayQualityMetrics R package. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance.  P-values are adjusted to obtain strong control over the false discovery rate using the Benjamini and Hochberg method.

label: biotin

source_name: Liver from 7.5 day old neonates

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All samples were collected from euthanized animals (CO2) and rapidly snap-frozen at liquid nitrogen until RNA was extracted.

value: Liver

value: Postnatal day 7.5 (PD7.5)


title: F_C_E_26


title: mTEClo, neonate, WT, cell4

value: thymus

value: epitherial cells

value: mTEClo

value: WT

value: unknown


title: mTEChi, neonate, Ctrl, rep5 [EED_10]

value: Ctrl


title: F_H_13

value: Gastrocnemius Muscle Tissue

value: HuR skeletal Muscle Knockout

value: Baseline


title: CF79-A022645-L004

description:
Library name: 1436-A022645_1_S50_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs

value: Cystic Fibrosis


title: Liver from PD7.5 neonate. SL (obese) replicate 3


title: F_C_E_25

value: Controls


title: F_C_E_01

value: Female


title: Liver from PD7.5 neonate. SL (obese) replicate 2


title: mTEChi, neonate, Ctrl, rep4 [EED_9]

value: MHCII-high epitherial cells

value: male


title: CF79-A022645-L003

description:
Library name: 1436-A022645_1_S50_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Liver from PD7.5 neonate. Control replicate 4

description: Gene expression data from liver from 7.5 day-old Control mice.

value: Liver

value: Postnatal day 7.5 (PD7.5)


title: mTEChi, neonate, Ctrl, rep3 [EED_8]

value: thymus

value: female


title: F_C_33


title: CF79-A022645-L002

description:
Library name: 1436-A022645_1_S50_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, EEDcKO, rep2 [EED_5]

value: MHCII-low epitherial cells

value: EEDcKO

value: pooled male and female


title: mTEChi, neonate, EEDcKO, rep2 [EED_12]


title: CF79-A022645-L001

description:
Library name: 1436-A022645_1_S50_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: F_C_32

value: Gastrocnemius Muscle Tissue


title: Liver from PD7.5 neonate. Control replicate 3


title: Liver from PD7.5 neonate. Control replicate 2


title: Liver from PD7.5 neonate. Control replicate 1


title: F_C_20


title: Liver from PD7.5 neonate. SL (obese) replicate 1


title: CF-78-A022644-L004

description:
Library name: 1436-A022644_1_S41_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, EEDcKO, rep1 [EED_4]


title: CF-78-A022644-L003

description:
Library name: 1436-A022644_1_S41_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: CF-78-A022644-L002

description:
Library name: 1436-A022644_1_S41_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: mTEClo, neonate, Ctrl, rep2 [EED_2]

value: Ctrl


title: mTEClo, neonate, Ctrl, rep1 [EED_1]


title: CF24-A022643-L004

description:
Library name: 1436-A022643_1_S21_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, silent, 24h, biol rep 3

city: Kyoto

first: Masahiro

last: Kumeta

address: Yoshidakonoe

department: Graduate School of Biostudies

institute: Kyoto University

data_processing:
Trimming of noise signals (poly G), low-quality reads (~30 bases), and additional base at 76th position were performed by Cutadapt and Trimmomatic.
Mapping and identification of differentially expressed genes were performed using CLC Genomics Workbench 21.
Assembly: mm10
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: TPM values for each Sample

growth_protocol: C2C12 cells were maintained in DMEM supplimented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested usint RNeasy kit (Quiagen).
RNA libraries were prepared using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina, following manufacture's instruction.

treatment_protocol: A vibrational transducer attached on a laboratory scissor jack was inversely fixed to a small metal shelf. Diaphragm custom made with polyether ether ketone was atached to the transducer. Position of the head of the diaphragm was adjusted to attach to the culture medium to generate acoustic wave directly in the medium. Sound signal was output by a conventional MP3 player, adjusted by an amplifier, and input into the transducer.

tag: cell line

value: myoblast

value: silent, 24h


title: CF24-A022643-L002

description:
Library name: 1436-A022643_1_S21_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: BM-MSCs


title: mTEClo, neonate, Ctrl, rep3 [EED_3]


title: C2C12 cells, silent, 24h, biol rep 2


title: Aging5

city: kunming

first: Rui-ze

last: Niu

address: Chunrong West Road

institute: kunming medical university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence
Supplementary files format and content: Tab-separated values files and matrix files

organism: Tupaia belangeri

source_name: Hippocampus

extract_protocol:
The hippocampus was carefully dissected out from TS with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Hippocampus


title: F_C_15

value: Controls

value: Female

value: Baseline


title: Adult6

description: 10x Genomics


title: F_C_12


title: Adult5

description: 10x Genomics


title: Aging4

description: 10x Genomics


title: CF24-A022643-L003

description:
Library name: 1436-A022643_1_S21_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: Uns SRE-A022642-L004

description:
Library name: 1436-A022642_1_S71_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: ED14.5 embryo SL (obese) replicate 2

description: Gene expression data from embryos from SL mice.

source_name: Whole embryo at day 14.5

value: Whole embryo

value: Embryonic day 14.5 (ED14.5)


title: ED14.5 embryo Control replicate 2

description: Gene expression data from embryos from Control mice.


title: Infancy5

description: 10x Genomics


title: ED14.5 embryo Control replicate 1


title: ED14.5 embryo SL (obese) replicate 4


title: ED14.5 embryo Control replicate 3


title: ED14.5 embryo SL (obese) replicate 3


title: ED14.5 embryo Control replicate 4


title: C2C12 cells, silent, 24h, biol rep 1


title: CF24-A022643-L001

description:
Library name: 1436-A022643_1_S21_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

source_name: Extracellular vesicles (EVs)


title: Adult4

description: 10x Genomics


title: C2C12 cells, WN, 24h, biol rep 3


title: F_C_16


title: Uns SRE-A022642-L001

description:
Library name: 1436-A022642_1_S71_L001_R1_001.fastq.gz
VLP00436 Sample ID Key