title: Lung_young_Bleo_miRNA_SK1.1.12

description:
miRNA_READS_727.txt
727_1

tag: age

value: young

tag: treatment

value: Bleo

value: Male

tag: strain

value: Lung


title: M82-HS-0h ChIP-seq_H3K27ac Rep2

status: Public on Jan 05 2023

type: SRA

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

description: Bio rep 2

library_source: genomic

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam   -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using anti-H3K27me1 (Millipore, 07-448), anti-H3K9ac (Millipore, 07-352), anti-H3K14ac (Millipore, 07-353), anti-H3K18ac (Millipore, 07-354), anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 07-473) and anti-polymerase II (Abcam, ab26721) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. Two independently biological replicates were generated for each time point of heat stress. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

treatment_protocol: 4 weeks old plants were treated at 45°C 0h, 1h and 6h in the climatic chamber (aralab).

tag: cultivar

value: cv. M82 (Tomato cultivar M82)

tag: genotype

value: WT

tag: tissue

value: Leaf

value: Heat stress 0h


title: Exp1 Macrophage TB40/E 48hpi

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

library_source: transcriptomic

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
The fastq files, include in the header, the barcodes and the quality of the barcodes coming from the other read, and the cell name.
It is first the quality of the batch barcode, the cell barcode and the read UMI, and then the barcodes in the same order, all separated by -
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per cell, and a TOC  cell name, plate name, plate coordinate, cell barcode, plate barcode, etc.

molecule: total RNA

organism: Homo sapiens

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 48hpi

growth_protocol: Primary human CD14+ monocytes were maintained in X-vivo-15 media (Lonza) supplemented with 2.25mM L-glutamine. PMA-induced monocyte-derived macrophages were grown in RPMI supplemented with 10% FBS, 1%pen-strep and 1% glutamine.

extract_protocol:
Single cells were sorted into lysis buffer in 384 well plates and RT was carried out with oligo dT primers.
Single cell 3' RNA seq

treatment_protocol: Cells were infected with HCMV strain TB40E with an SV40-GFP tag

tag: cell type

tag: infection

value: HCMV-GFP

tag: time

tag: population

value: total

tag: experiment


title: Δnac cytidine 2 (RNA-seq)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Transcripts Per kilobase Megabase of library size (TPM) were calculated using DEseq2.0
Assembly: NC_000913.2
Supplementary files format and content: comma-delimited text files include TPM values for each Sample.

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: E. coli K-12 MG1655 nac and ntrC mutant cells were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: nitrogen source

value: cytidine

value: delta nac

tag: phase

value: mid-log phase

tag: medium

value: W2 minimal media


title: M82-HS-6h ChIP-seq_H3K18ac Rep2

description: Bio rep 2

value: Heat stress 6h


title: Δnac cytidine 1 (RNA-seq)


title: Lung_young_Bleo_miRNA_SK1.1.38

city: Biberach

first: Sergio

last: Picart-Armada

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
miRNA_READS_727.txt
727_7

data_processing:
Illumina reads were converted to the industry standard FASTQ format and aligned to the mouse reference genome from Ensembl 70 using the STAR v2.5.2a aligner on default settings. For increased alignment accuracy, the STAR genome index was generated to include splice junction annotations with the options ‘—sjdbGTFfile’ and ‘—sjdbOverhang 49’.
The quality of the RNA-Seq samples was verified with FASTQC 0.11.2 and RNASeQC version 1.1.8. The featureCounts tool of the subRead package v1.5.0 was used to quantify the per-gene read counts with the “-s 2” parameter.
Cufflinks v2.2.1  was used to calculate the FPKM values with the following parameters “--max-bundle-frags 1000000000 --max-bundle-length 5000000 --library-type fr-firststrand --no-effective-length-correction --compatible-hits-norm --max-frag-multihits 1”.
The matrix of read counts and were imported into R and per-sample read count normalization factors were calculated using trimmed mean of M-values (TMM) and subsequently normalized using the Bioconductor LIMMA-Voom analysis R package for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM_685.txt: counts for mRNAs. miRNA_READS_727.txt: counts for microRNAs

organism: Mus musculus

source_name: Lung

extract_protocol:
Lung tissue was perfused twice with 10ml 1x PBS (Sigma, city, country) through the right side of the heart entering the pulmonary vasculature. Subsequently, lung was removed from the chest cavity, each lobe was separated and thereafter immediately flash frozen in liquid nitrogen. Lungs were then stored at -80°C until homogenized in 2ml Eppendorf tubes (Eppendorf, Hamburg, Germany) using a TissueLyser LT (Qiagen, Hilden, Germany). Samples remained frozen throughout the entire procedure. Lung powder was generated for next generation sequencing (NGS; 20mg tissue).
Total RNA was isolated using the Qiazol procedure according to manufacturer´s protocol (Qiagen, Hilden, Germany). A total of 20mg tissue was used for RNA isolation. Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Male mice were randomized before the study. Mice were instilled intratracheally (i.t.) under 3-4% isoflurane anesthesia once on day 0. Bleomycin administration was performed in a hanging position with a Vasofix-Braunüle 22G (B.Braun, Melsungen, Germany). Mice were instilled using 0.7 and 0.63 mg/kg of bleomycin sulphate (Merck, Darmstadt, Germany) in saline solution for the young and old mice, respectively. Control mice received saline solution only. Mice were analyzed 21 days after bleomycin administration.

tag: day

tag: animal id

tag: Sex


title: Exp1 Macrophage TB40/E 24hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 24hpi


title: NC2 [miRNA-seq]

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

country: China

institute: CAS

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
Cutadapt was used to trim the adapters for short reads.
miRDeep2 was used for the prediction of new miRNAs and the quantification of miRNAs.
Based on CPM standardized miRNAs, the DE miRNAs were calculated and screened by R software edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: microglial cells

growth_protocol: BV2 microglial cells were cultured in Dulbecco’s modified Eagle medium high glucose media containing 10% fetal bovine serum.

extract_protocol:
Total RNA in the BV2 cells was isolated using TRIzol reagent. The quality and quantity of the RNA was assessed using a NanoDrop ND-1000.
We constructed the small RNA library using the  NEB Multiplex Small RNA Library Prep Set for Illumina.
The sequencing libraries of samples were denatured with 0.1 M NaOH to produce single-stranded DNA and sequenced by an Illumina NextSeq 500 sequencer.

treatment_protocol: Half the cells of this subline provided the negative control group (Ad-NC). The other half were then infected with adenovirus for 48 hours to give the experimental group (Ad-shGCH1).

value: negative control


title: Exp1 Macrophage TB40/E 12hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 12hpi


title: NC1 [miRNA-seq]


title: M82-HS-0h ChIP-seq_H3K18ac Rep2

description: Bio rep 2


title: Δnac glutamine 1 (RNA-seq)

value: glutamine


title: M82-HS-1h ChIP-seq_H3K18ac Rep2

description: Bio rep 2

value: Heat stress 1h


title: T3 [miRNA-seq]


title: Exp1 Macrophage TB40/E 5hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 5hpi


title: M82-HS-6h ChIP-seq_H3K9ac Rep2

description: Bio rep 2


title: Δnac ammonia 1 (RNA-seq)

value: ammonia

value: M9 minimal media


title: M82-HS-1h ChIP-seq_H3K9ac Rep2

description: Bio rep 2


title: Exp1 Macrophage Mock 5hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages mock-infected 5hpi

value: mock-infected


title: Δnac ammonia 2 (RNA-seq)


title: Exp1 Macrophage Mock 144hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages mock-infected 144hpi


title: T2 [miRNA-seq]


title: T1 [miRNA-seq]


title: Pseudomonas protegens CHA0, DkaiC, rep. 2

status: Public on Jan 04 2023

city: Neuchâtel

first: Diego

last: Gonzalez

address: Rue Emile-Argand

country: Switzerland

institute: Laboratory of Microbiology, University of Neuchâtel

data_processing:
fastp (v. 0.20.0) / trimming and adaptor removal
bowtie2 (v. 2.3.4.3)  / mapping
featureCounts (v. 2.0.0) / counts

organism: Pseudomonas protegens CHA0

source_name: bacteria

extract_protocol:
Trizol / RNeasy mini-kit column (Qiagen)
Novogene bacterial total RNA library for RNA-sequencing

value: bacteria

value: DkaiC

value: LB broth


title: M82-HS-0h ChIP-seq_H3K9ac Rep2

description: Bio rep 2

value: cv. M82 (Tomato cultivar M82)

value: WT

value: Leaf

value: Heat stress 0h


title: Pseudomonas protegens CHA0, wild-type, rep. 3

value: wild-type


title: Pseudomonas protegens CHA0, DkaiC, rep. 1


title: 12mpf_Sox10CreUbiswitch_ear

city: Los Angeles

first: Tuo

last: Shi

state: California

address: 1425 San Pablo St BCC 403

country: USA

institute: University of Southern California

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles
Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 (14dpf) or cellranger-arc count v2.0.0 (12mpf)
Downstream analysis was performed in R and Python
Assembly: danRer11
Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library
Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries, including the two libraries here and other published data

organism: Danio rerio

source_name: inner ear

extract_protocol:
For 14 dpf animals, heads from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals, utricle, saccule, and lagena were extracted from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish after brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min, followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS) and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Cells were pelleted (376 × g, 5 min, 4 °C) and resuspended in suspension media (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/mL streptomycin (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)) twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence-activated cell sorted (FACS) to isolate live cells that excluded the nuclear stain DAPI
10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 (14 dpf) or Single Cell Multiome ATAC + Gene Expression kit (12 mpf)

value: inner ear

tag: sample type

value: nuclear RNA

value: mixed

value: Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry

tag: age

value: 12 mpf


title: Δnac glutamine 2 (RNA-seq)

tag: strain

value: glutamine

value: delta nac

value: mid-log phase

value: W2 minimal media


title: Pseudomonas protegens CHA0, wild-type, rep. 1

value: bacteria

tag: treatment


title: Ramazzottius varieornatus storage cells biol rep 5

city: Tsuruoka

first: Kazuharu

last: Arakawa

state: Yamagata

address: Nihonkoku 403-1, Daihoji

country: Japan

institute: Institute for Advanced Biosciences, Keio University

description:
Storage-Rv5
Storage cells are dissected.

data_processing:
Adaptor sequences were removed, and the reads were de-multiplexed using the bcl2fastq v. 2 software (Illumina).
Gene expression values were quantified using Kallisto v. 0.46.1 with the options: --bias -b 100 -t 31 --single -l 350 -s 50 (Bray et al., 2016).
Assembly: Amino acid and coding sequences and annotation for R. varieornatus and H. exemplaris were downloaded from www.ensembl.tardigrades.org (Yoshida et al., 2017).
Supplementary files format and content: *.abundance.tsv: Output of Kallisto 0.46.1; Tab-delimited text files.

organism: Ramazzottius varieornatus

source_name: storage cells

growth_protocol: Tardigrades were maintained using the methods previously described (Horikawa et al., 2008). Briefly, individuals were placed on 2% Bacto agar (Difco) gels prepared with Volvic water and fed with Chlorella vulgaris (Chlorella Industry). Temperature was kept at 22˚C for Ramazzottius varieornatus, and 18˚C for Hypsibius exemplaris.

extract_protocol:
Specimens were thoroughly washed with Milli-Q water on a sterile nylon mesh (Millipore), and were placed in a low-binding PCR tube. For active individuals, pipette tips were used to homogenize the animals and lysed with the TRIzol reagent (Life Technologies). Total RNA was extracted using a Direct-zol RNA kit (Zymo Research), and the quality was validated with High Sensitivity RNA ScreenTape on TapeStation 2200 (Agilent Technologies). For storage cells, collected storage cells were directly put into the lysis buffer of SMART-Seq v.4 kit (Clontech).
The mRNA was amplified with the SMART-Seq v.4, and Illumina libraries were prepared with the KAPA HyperPlus Kit (KAPA Biosystems). The library was quantified using the Qubit Fluorometer (Life Technologies), and size distribution was validated with TapeStation D1000 ScreenTape (Agilent Technologies). The library was size-selected for 200 bp by manually cutting out an agarose gel and was purified with a NucleoSpin Gel and PCR Clean-up kit (Clontech).

treatment_protocol: Storage cells were obtained by dissecting tardigrades in 0.1X PBS under a stereo microscope with sterile knife and quickly aspirating cells that are released.

value: storage cells


title: 14dpf_Sox10CreUbiswitch_ear

description: 10x Genomics

tag: genotype

value: 14 dpf


title: Ramazzottius varieornatus storage cells biol rep 2

description:
Storage-Rv2
Storage cells are dissected.

tag: tissue


title: Ramazzottius varieornatus storage cells biol rep 4

description:
Storage-Rv4
Storage cells are dissected.


title: Pseudomonas protegens CHA0, DkaiC, rep. 3

tag: cell type

value: DkaiC

value: LB broth


title: Ramazzottius varieornatus storage cells biol rep 3

description:
Storage-Rv3
Storage cells are dissected.


title: Ramazzottius varieornatus active biol rep 2

description:
Ramazzottius-Chlorella48h-2
Active control

source_name: whole body

value: whole body


title: Ramazzottius varieornatus storage cells biol rep 1

description:
Storage-Rv1
Storage cells are dissected.


title: hNECs, rep2

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

data_processing:
The adapter sequence and low-quality reads were removed using trimmomatic (v0.38).
Trimmed reads were mapped to reference genome hg38 using Kallisto (v0.46.2).
The count matrix data from Kallisto was loaded into R software (v4.2.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq RNA Library Prep Kit following manufacturer's protocols.

tag: cell line

value: iPSC derived NECs


title: hNCCs, rep1

value: iPSC derived NCCs


title: hNCCs, rep2


title: Ramazzottius varieornatus active biol rep 3

description:
Ramazzottius-Chlorella48h-3
Active control


title: hNECs, rep1


title: Ramazzottius varieornatus active biol rep 1

description:
Ramazzottius-Chlorella48h-1
Active control


title: hiPSCs, rep2

value: iPSCs


title: hiPSCs, rep1


title: Pseudomonas protegens CHA0, wild-type, rep. 2

tag: time

value: wild-type


title: Hypsibius exemplaris storage cells biol rep 3

description:
Storage-He3
Storage cells are dissected.

organism: Hypsibius exemplaris


title: Hypsibius exemplaris storage cells biol rep 2

description:
Storage-He2
Storage cells are dissected.


title: Hypsibius exemplaris storage cells biol rep 1

description:
Storage-He1
Storage cells are dissected.


title: Hypsibius exemplaris storage cells biol rep 4

description:
Storage-He4
Storage cells are dissected.


title: Hypsibius exemplaris storage cells biol rep 5

description:
Storage-He5
Storage cells are dissected.


title: Hypsibius exemplaris active biol rep 3

description:
Hypsibius-Chlorella48h-3
Active control


title: Healthy Controls, 06445

type: RNA

city: Philadelphia

first: Thomas H.

last: Leung

state: PA

address: 421 Curie Blvd.

department: Dermatology

institute: University of Pennsylvania

hyb_protocol: 6 ug of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Clariom D GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. RMA

label: biotin

source_name: Dermis

label_protocol: 10 ng of RNA was given to the University of Pennsylvania Genomic Analysis Core for downstream processing. Biotinylation were performed using GeneChip WT Pico reagent kit (Thermo Fisher Scientific).

growth_protocol: Skin samples were collected by 4mm punch biopsy and were instantly put in 10% formalin in room temperature.

extract_protocol: RNA was isolated from dermis using AllPrep DNA/RNA FFPE kit (Qiagen).

treatment_protocol: Formalin fixation of the skin samples were performed for 24 hours and standard protocol for tissue processing was performed for paraffin emdedding. 10 uM parafiin emebedded tissue sections were mounted on slides and were used for laser capture microdissection to isolate the dermis.

value: Dermis

tag: disease state

value: Healthy Control


title: Healthy Controls, 04124


title: Healthy Controls, 41846


title: Healthy Controls, 49128


title: Healthy Controls, 02726


title: Healthy Controls, 50795


title: Pseudomonas putida KT2442, mid stationary phase, DkaiC, rep. 2

organism: Pseudomonas putida


title: Pseudomonas putida KT2442, mid stationary phase, DkaiC, rep. 1


title: Other Sweet Syndrome, 11696

value: other Sweet Syndrome Patient


title: Pseudomonas putida KT2442, mid stationary phase, wild-type, rep. 2


title: Healthy Controls, 01247


title: Pseudomonas putida KT2442, mid stationary phase, wild-type, rep. 1


title: Healthy Controls, 00561


title: Healthy Controls, 01997


title: Healthy Controls, 19203


title: Hypsibius exemplaris active biol rep 2

description:
Hypsibius-Chlorella48h-2
Active control


title: Other Sweet Syndrome, 10237


title: H3 Ifnar1 KO + C. parvum 48h

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

data_processing:
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Rmats  v3.2.5 with parameters  -analysis U -t paired -a 8.
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
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Mus musculus

extract_protocol:
Intestinal epithelium in conditional Ifnar1 ko and wt mice following Cryptosporidium parvum Infection were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 platform

value: intestinal epithelium

value: ilium tissues

tag: genotype/variation

value: KO

value: C. parvum oocysts


title: Refractory Sweet syndrome, 51846

value: Refractory Sweet Syndrome Patient (Index patient)


title: Healthy Controls, 59292


title: H2 Ifnar1 KO + C. parvum 48h


title: Healthy Controls, 07871


title: Hypsibius exemplaris active biol rep 1

description:
Hypsibius-Chlorella48h-1
Active control


title: Healthy Controls, 52752


title: Pseudomonas putida KT2440, late stationary phase, DkaiC, rep. 1

organism: Pseudomonas putida KT2440

value: bacteria


title: Healthy Controls, 05253


title: Other Sweet Syndrome, 06289


title: Other Sweet Syndrome, 04687


title: Other Sweet Syndrome, 18585


title: Other Sweet Syndrome, 09541


title: H1 Ifnar1 KO + C. parvum 48h


title: Refractory Sweet syndrome, 48321


title: Pseudomonas putida KT2440, late stationary phase, wild-type, rep. 3


title: G3 Ifnar1 KO

value: PBS


title: Refractory Sweet syndrome,17287


title: Pseudomonas putida KT2440, late stationary phase, wild-type, rep. 1


title: Pseudomonas putida KT2440, late stationary phase, wild-type, rep. 2


title: G2 Ifnar1 KO


title: G1 Ifnar1 KO


title: Pseudomonas putida KT2440, early stationary phase, DkaiC, rep. 2

value: DkaiC


title: Pseudomonas putida KT2440, early stationary phase, DkaiC, rep. 3

value: LB broth


title: Pseudomonas putida KT2440, early stationary phase, wild-type, rep. 3


title: F1 Ifnar1 WT + C. parvum 48h

value: WT


title: Pseudomonas putida KT2440, early stationary phase, wild-type, rep. 2


title: Pseudomonas putida KT2440, early stationary phase, DkaiC, rep. 1


title: E2 Ifnar1 WT


title: Pseudomonas putida KT2440, early stationary phase, wild-type, rep. 1


title: E1 Ifnar1 WT


title: F3 Ifnar1 WT + C. parvum 48h


title: D3 Ifnar1 KO + C. parvum 48h


title: F2 Ifnar1 WT + C. parvum 48h


title: Pseudomonas putida KT2440, late stationary phase, DkaiC, rep. 2


title: Low sperm motility_11 [Low11_lncRNA]

city: Beijing

first: yu

last: zhang

state: China

address: Yuan Mingyuan west road

institute: China Agricultural University

description:
long RNA library from Yorkshire boars seminal plasma-derived extracellular vesicles
raw_circRNA_count.txt

data_processing:
library strategy: lncRNA-seq
Sequence reads were trimmed for adaptor sequence/low-quality sequence by using cutadapt and fastQC software in miRNA-seq analysis and lncRNA-seq analysis.
Using Bowtie software, Trimmed sequence reads were sequence-aligned with Silva database, GtRNAdb database, Rfam database and Repbase database respectively, and ncRNAs such as ribosomal RNA (rRNA), transport RNA (tRNA), intranuclear small RNA (snRNA), nucleoli small RNA (snoRNA) and repeats were filtered to obtain unannotated reads containing miRNA. miRNAs were identified by using the miRDeep2 software.
CircRNA was identified using CIRI2 and find_circ software, and the results obtained by two methods were intersected as the final result.
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include raw count values for identified miRNA from each Sample
Supplementary files format and content: tab-delimited text files include raw count values for identified circRNA from each Sample

organism: Sus scrofa

source_name: Extracellular vesicles

extract_protocol:
For small RNA libraries, a total amount of 1 ng-500 ng RNA per sample was used as input material for RNA sample preparations; For long RNA libraries, a total amount of 250 pg-10 ng RNA per sample was used as input material for RNA sample preparations.
RNA libraries for miRNA-seq were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) according to the manufacturer’s instructions and index codes were added to attribute sequences to each sample; RNA libraries for lncRNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For each boar, 60 ml of semen plasma was centrifuged at 10000 g for 30 minutes at 4 temperature to remove cellular debris and smaller pieces of undissolved seminal gel. Then the supernatant was taken to a clean centrifugal tube and centrifuged at 12000 g for 1 hour. The third step, the supernatant was taken to a clean tube, and centrifuged at 120,000 g for 1.5 hour at 4 temperature. Subsequently, the sediments were re-suspended with 1XPBS and then repeated the previous step. Finally, the pellet was re-suspended in 2 ml PBS and filtered using 220 nm filters.

value: Extracellular vesicles of seminal plasma

tag: breed

value: Yorkshire boars

value: Extracellular vesicles

tag: phenotype

value: low sperm motility

value: For long RNA library, a total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: male


title: Low sperm motility_12 [Low12_lncRNA]


title: D2 Ifnar1 KO + C. parvum 48h


title: Low sperm motility_10 [Low10_lncRNA]


title: Pseudomonas putida KT2440, late stationary phase, DkaiC, rep. 3


title: D1 Ifnar1 KO + C. parvum 48h


title: E3 Ifnar1 WT


title: Low sperm motility_8 [Low8_lncRNA]


title: Low sperm motility_9 [Low9_lncRNA]


title: B3 Ifnar1 WT + C. parvum 48h


title: C1 Ifnar1 KO


title: C2 Ifnar1 KO


title: C3 Ifnar1 KO


title: Low sperm motility_5 [Low5_lncRNA]


title: B1 Ifnar1 WT + C. parvum 48h


title: Low sperm motility_7 [Low7_lncRNA]


title: Low sperm motility_4 [Low4_lncRNA]


title: Low sperm motility_6 [Low6_lncRNA]


title: B2 Ifnar1 WT + C. parvum 48h


title: A2 Ifnar1 WT


title: Low sperm motility_2 [Low2_lncRNA]


title: A3 Ifnar1 WT


title: A1 Ifnar1 WT


title: High sperm motility_12 [High12_lncRNA]

value: high sperm motility


title: Low sperm motility_1 [Low1_lncRNA]


title: Keratinocytes rep4

city: Guangzhou

first: Yi

last: Jin

address: Department of Toxicology, School of Public Health, Southern Medical University, Shatai Road, Baiyun, Guangzhou, China

institute: Southern Medical University

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: HaCaT

growth_protocol: HaCaT were cultured in Dulbecco’s modified Eagle medium supplemented with 12% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Non-treatment

value: HaCaT


title: High sperm motility_11 [High11_lncRNA]


title: Keratinocytes rep3


title: High sperm motility_10 [High10_lncRNA]


title: Keratinocytes rep1


title: High sperm motility_8 [High8_lncRNA]


title: High sperm motility_7 [High7_lncRNA]


title: HSV-320_Day37

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

description: RNAseq data from PBMC extracted from individual HSV-320

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: titre.txt includes titre and demographics information. 'serology' column provides serostatus group association for each sample.

source_name: PBMC

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturerâs instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.

tag: individual

value: PBMC

tag: day after vaccination


title: HSV-320_Day30


title: High sperm motility_6 [High6_lncRNA]


title: Low sperm motility_3 [Low3_lncRNA]


title: HSV-320_Day7


title: HSV-320_Day1


title: HSV-320_Day0


title: High sperm motility_4 [High4_lncRNA]


title: HSV-318_Day37

description: RNAseq data from PBMC extracted from individual HSV-318


title: High sperm motility_5 [High5_lncRNA]


title: High sperm motility_2 [High2_lncRNA]


title: High sperm motility_3 [High3_lncRNA]


title: HSV-318_Day30


title: Low sperm motility_12 [Low12_miRNA]

description:
small RNA library from Yorkshire boars seminal plasma-derived extracellular vesicles
raw_miRNA_count.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence by using cutadapt and fastQC software in miRNA-seq analysis and lncRNA-seq analysis.
Using Bowtie software, Trimmed sequence reads were sequence-aligned with Silva database, GtRNAdb database, Rfam database and Repbase database respectively, and ncRNAs such as ribosomal RNA (rRNA), transport RNA (tRNA), intranuclear small RNA (snRNA), nucleoli small RNA (snoRNA) and repeats were filtered to obtain unannotated reads containing miRNA. miRNAs were identified by using the miRDeep2 software.
CircRNA was identified using CIRI2 and find_circ software, and the results obtained by two methods were intersected as the final result.
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include raw count values for identified miRNA from each Sample
Supplementary files format and content: tab-delimited text files include raw count values for identified circRNA from each Sample

value: For small RNA libraries, a total amount of 1ng-500ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) according to the manufacturer’s instructions and index codes were added to attribute sequences to each sample.


title: Low sperm motility_11 [Low11_miRNA]


title: HSV-318_Day7


title: HSV-318_Day0


title: Keratinocytes rep2


title: High sperm motility_9 [High9_lncRNA]


title: Low sperm motility_10 [Low10_miRNA]


title: Low sperm motility_9 [Low9_miRNA]


title: Low sperm motility_8 [Low8_miRNA]


title: Low sperm motility_7 [Low7_miRNA]


title: HSV-317_Day37

description: RNAseq data from PBMC extracted from individual HSV-317


title: HSV-317_Day7


title: HSV-317_Day1


title: High sperm motility_1 [High1_lncRNA]


title: HSV-317_Day0


title: HSV-316_Day187

description: RNAseq data from PBMC extracted from individual HSV-316


title: Low sperm motility_5 [Low5_miRNA]


title: Low sperm motility_4 [Low4_miRNA]


title: Low sperm motility_6 [Low6_miRNA]


title: HSV-316_Day37


title: Low sperm motility_3 [Low3_miRNA]


title: HSV-316_Day1


title: High sperm motility_11 [High11_miRNA]


title: High sperm motility_10 [High10_miRNA]


title: High sperm motility_12 [High12_miRNA]


title: HSV-316_Day180


title: HSV-316_Day0


title: High sperm motility_8 [High8_miRNA]


title: HSV-316_Day7


title: HSV-314_Day180

description: RNAseq data from PBMC extracted from individual HSV-314


title: HSV-314_Day37


title: HSV-316_Day30


title: HSV-314_Day30


title: High sperm motility_9 [High9_miRNA]


title: HSV-314_Day7


title: HSV-314_Day1


title: High sperm motility_5 [High5_miRNA]


title: HSV-314_Day0


title: High sperm motility_3 [High3_miRNA]


title: High sperm motility_2 [High2_miRNA]


title: High sperm motility_4 [High4_miRNA]


title: HSV-313_Day187

description: RNAseq data from PBMC extracted from individual HSV-313


title: Low sperm motility_2 [Low2_miRNA]


title: HSV-313_Day180


title: HSV-314_Day187


title: Low sperm motility_1 [Low1_miRNA]


title: HSV-313_Day30


title: HSV-313_Day37


title: MCc_S1_L001_R1_001

city: Lausanne

first: Ludovic

last: Telley

address: Department of Biomedical Sciences University of Lausanne Rue du Bugnon 9

institute: UNIL

data_processing:
Alignment of sequenced reads to the mouse genome (GRCm38) and filtered gene–barcode matrices were realized by running Cell Ranger Single-Cell Software Suite v5.0.1 (10X Genomics).
The cell ranger count function was used to generate filtered gene/cell expression UMI corrected matrices by selecting probable nuclei and removing empty lipid droplets.
Command line use for cell ranger  /opt/cellranger-5.0.1/cellranger count --id=MAc --transcriptome=/refgenome/refdata-gex-mm10-2020-A --libraries=library.csv --expect-cells=2000 --include-introns --localcores=20 --localmem=32
Assembly: GRCm38
Supplementary files format and content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes and all cells after QC. The  values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contain the gene name that is quantified.    singlecell_metadata.tsv: is a table containing metadata information for each cells analyse in the paper in tab-separated.   src.src  R script to reproduce analysis  source.src R source script containing useful functions  all_umap.Rds Secondary processed file use in the script  habenula.integrated.Rds Secondary processed file use in the script containing external dataset use in this analysis.

source_name: KASH-GFP+ BNST LHb neurons

extract_protocol:
Nuclei preparation and FAC-sorting: Three virgin males, three virgin females and three mothers were sacrificed and brains were extracted in ice-cold oxygenated ACSF (containing (in mM): NaCl (124); NaHCO3 (26.2); glucose (11); KCl (2.5); CaCl2 (2.5); MgCl2 (1.3); and NaH2PO4 (1)). Each brain was then sectioned coronally at 1250 μm using a vibrating microtome (Campden Instruments). The lateral habenula was micro-dissected under a stereomicroscope, incubated for 5 min in 500 μl chilled 0.1X NP40 Lysis Buffer (Tris-HCL pH 7.4 10mM, NaCl 10mM, MgCL2 3mM, Tween-20 0.1%, NP40 0.1%, BSA 1%, DTT 1mM and RNase inhibitor), mechanically dissociated using a pellet pestle (15 goings and ongoings) and finally incubated on ice for 5 min. The suspension was then washed with 500 µL chilled wash buffer (Tris-HCL pH 7.4 10mM, NaCl 10mM, MgCL2 3mM, Tween-20 0.1%, BSA 1%, DTT 1mM, RNase inhibitor). Nuclei were then filtered through a 30-μm cell strainer, centrifuged (1000g, 10 minutes at 4°C) and resuspended in 500 µL of FACS buffer (Tris-HCL pH 7.4 10mM, NaCl 10mM, MgCL2 3mM, BSA 1%, DTT 1mM, RNase inhibitor). Positive GFP nuclei were sorted using a BD FACS Aria II flow cytometer (BD Biosciences) and collected in ice-cold FACS buffer.
After sorting, nuclei were counted and immediately processed according to the 10X Chromium protocol. Briefly, an appropriate volume of each cell suspension containing 1000 cells from the three different conditions was combined with 10X Chromium reagent mix and samples were loaded into three separate lanes. Nuclei capture, lysis, mRNA reverse transcription, cDNA amplification and libraries were performed following 10X Genomics Chromium dual indexing Single Cell 3' V3.1 reagent kit instructions. Libraries were then multiplexed and sequenced according manufacture recommendations with paired-end reads using a HiSeq4000 platform (Illumina) with an expected depth of 250’000 reads per single nuclei. All the sequencing experiments were performed within the Genomics Core Facility of the University of Lausanne.

value: KASH-GFP+ BNST LHb neurons

value: female

tag: experimental group

value: virgin females


title: MAc_S1_L001_R1_001

tag: Sex

value: mothers


title: HSV-313_Day7


title: Day 60, Clone18

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.1.1)
Cells and genes filtering, dimension reduction: Scanpy (version 1.7.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol: 10X Chromium Single Cell 3' polyA v2 Chemistry

value: CD8 T cell

value: Spleen

value: 7-10 weeks old


title: HSV-313_Day0


title: Day 34, Clone17

description: 10x Genomics


title: HSV-313_Day1


title: High sperm motility_6 [High6_miRNA]

tag: sample type

value: Extracellular vesicles of seminal plasma


title: HSV-312_Day187

description: RNAseq data from PBMC extracted from individual HSV-312


title: HSV-312_Day180


title: High sperm motility_1 [High1_miRNA]

value: Yorkshire boars


title: HSV-318_Day1


title: HSV-312_Day30


title: Day 3, Clone13

description: 10x Genomics

tag: age


title: HSV-312_Day1


title: Division 1, Clone 13

description: 10x Genomics

tag: strain


title: Day 60, Armstrong

description: 10x Genomics


title: HSV-312_Day7


title: MBc_S1_L001_R1_001

value: virgin males


title: Day 22, Armstrong

description: 10x Genomics


title: HSV-311_Day180

description: RNAseq data from PBMC extracted from individual HSV-311


title: HSV-311_Day187


title: Day 22, Clone16

description: 10x Genomics


title: High sperm motility_7 [High7_miRNA]

value: Extracellular vesicles

tag: treatment


title: Day 5, Armstrong

description: 10x Genomics


title: Day 3, Armstrong

description: 10x Genomics


title: HSV-311_Day0


title: HSV-311_Day7


title: HSV-312_Day0


title: HSV-311_Day30


title: Naïve state

description: 10x Genomics


title: HSV-309_Day187

description: RNAseq data from PBMC extracted from individual HSV-309


title: Day 8, Clone15

description: 10x Genomics


title: HSV-312_Day37


title: HSV-309_Day37


title: brain lateral ventricular GFAP expressing cells, Knockout biol rep 4

city: Fukuoka

first: kunimasa

last: Ohta

address: Department of Stem Cell Biology, Faculty of Arts and Science , Kyushu University. 744, Motooka, Nishi-ku,

department: Stem Cell Biology

institute: Kyushu University

description: 100-cell input

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastP tool (parameter for cutoff- minimum readlength:25, phred quality :25, front read trimming: 13, tail read trimming: 1)
Trimmed sequence reads were mapped to GRCm39 (dowloaded from ENSMBL database) using HISAT2 (parameters-  default)
Read count extraction and normalization were performed using HISAT2:StringTie (2.2): Ballgown method in reference guidance mood according to Pertea et al., 2016, Nature Protocol
Assembly: GRCm39
Supplementary files format and content: GTF  files include RPKM and TPM values for each Sample computed from the stringtie_merged GTF file.

source_name: Brain Lateral ventricle

extract_protocol:
RNA-extraction was performed accordint to Hayashi et al., 2018,Nature Communication
RNA-libraries for RNA-seq were prepered using Nextera XT DNA sample Prep kit (Illumina Inc) following manufacturers protocol

value: Brain Lateral ventricle

value: GFAP positive

tag: genotype

value: Knockout (TSK-KO-GFAP-GFP)


title: brain lateral ventricular GFAP expressing cells, Knockout biol rep 3

description: 100-cell input

tag: tissue


title: Day 8, Armstrong

description: 10x Genomics

tag: cell type


title: HSV-309_Day7


title: brain lateral ventricular GFAP expressing cells, Knockout biol rep 1

description: 100-cell input


title: HSV-309_Day1


title: HSV-309_Day30


title: Day 7, Armstrong

description: 10x Genomics


title: Day 6, Armstrong

description: 10x Genomics


title: brain lateral ventricular GFAP expressing cells, Knockout biol rep 2

description: 100-cell input


title: HSV-309_Day0


title: brain lateral ventricular GFAP expressing cells, Wildtype biol rep 3

description: 100-cell input

value: Wildtype (GFAP-GFP)


title: HSV-308_Day180

description: RNAseq data from PBMC extracted from individual HSV-308

value: PBMC


title: HSV-308_Day187


title: brain lateral ventricular GFAP expressing cells, Wildtype biol rep 4

description: 100-cell input


title: Division 1, Armstrong

description: 10x Genomics


title: HSV-311_Day1


title: Day 5, Clone14

description: 10x Genomics


title: brain lateral ventricular GFAP expressing cells, Wildtype biol rep 1

description: 100-cell input


title: SKY-4; islets from chow fed NOD.SCID mouse

city: Chicago

first: Alexander

last: Chervonsky

state: IL

department: Pathology

institute: University of Chicago

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated values files

source_name: Pancreatic Islets of Langerhans

extract_protocol:
Mice were killed by cervical dislocation and the pancreata were perfused with 5 mL of collagenase P solution [0.5 mg/ml, (Roche) in HBSS (Gibco) supplemented with 0.1 M HEPES, 1 mM MgCl2, 5 mM D- glucose, 1.25 mM CaCl2, and 0.02% BSA] via the common bile duct. Perfused pancreata were then dissected away from the surrounding tissue and incubated for 10 minutes at 37°C. Digestion was halted by washing the tissue twice with supplemented HBSS. The tissue was then applied to a Histopaque-1119 (Sigma) gradient, and the interface was collected, washed in supplemented HBSS, and then placed in Click’s medium with 5% FBS. Islets were handpicked using an inverted microscope. Handpicked islets were dissociated by incubation in Trypsin-EDTA (Gibco) at 37° C for 2 minutes followed by washing in Click’s media containing 10% FBS. Single cell suspensions from each mouse were sequenced individually.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, islet single cell suspensions 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: Pancreatic Islets of Langerhans

value: 10 weeks old

tag: diet

value: Chow


title: HSV-308_Day37


title: SKY-5; islets from chow fed NOD.SCID mouse

description: 10x Genomics

value: 9 weeks old


title: HSV-308_Day7


title: scRNAseq 10X, Myometrium, E. coli, Rep 8, index4D

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

description: 10x Genomics

data_processing:
Data was demultiplexed using the Cell Ranger software v4.0.0
Sequencing data were processed using Cell Ranger version 4.0.0 (10x Genomics). The “cellranger counts” was also used to align the scRNA-seq reads by using the STAR aligner to produce the bam files necessary for demultiplexing the individual of origin based on genotype information using demuxlet and a custom vcf file. The genotype data were downloaded from ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz, the strains C57BL_6NJ and BALB_cJ were extracted, and a new synthetic vcf file was generated consisting of all the genetic variants where these two strains diverge, and containing a maternal genotype column identical to the C57BL_6NJ strain and a fetal genotype column with a “0/1” heterozygote genotype. Ambient RNA contamination and doublets were removed using SoupX version 1.5.2 and DoubletFinder 2.0.3. Additionally, any cell with < 200 genes or > 20,000 genes detected, or that had > 10% mitochondrial reads, was excluded. All count data matrices were then normalized and combined using the Seurat package in R (Seurat version 4.0.3). The first 100 principal components were obtained, and the different libraries were integrated and harmonized using the Harmony package in R version 1.0.0. The top 30 harmony components were then processed to embed and visualize the cells in a two-dimensional map via the Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) algorithm. A resolution of 0.5 was used to cluster the single cells.
Assembly: mm10
Supplementary files format and content: Cellranger filtered gene expression counts and barcodes in h5 format

source_name: Myometrium

growth_protocol: Mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and bred in the animal care facility at the C.S. Mott Center for Human Growth and Development, Wayne State University (Detroit, MI, USA). Mice were under a circadian cycle of light:dark = 12:12 h. Eight- to twelve-week-old C57BL/6 female mice were bred with BALB/cByJ male mice, and females were examined daily between 0800 and 0900 to check for the presence of a vaginal plug, which was considered as 0.5 days post coitum (dpc). Upon observation of a vaginal plug, females were removed from mating cages and housed separately, and their weights were monitored daily. At 12.5 dpc, a weight gain of ≥2g was considered confirmation ofpregnancy. All procedures and experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at Wayne State University under Protocol nos. 18-03-0584 and 21-04-3506.

extract_protocol:
Dams were euthanized on 17.5 dpc and the reproductive tissues (uterus, decidua, and cervix) were collected. Tissues collected for the preparation of single-cell suspensions were placed in sterile 1X PBS. Immediately following the collection of the cervix, the tissue was mechanically dissociated and enzymatically digested using Collagenase A (160 mg/mL) (Sigma Aldrich, St. Louis, MO, USA) and incubated at 37ºC. Then, the dissociated cells were pelleted by centrifugation at 16,000 x g for 10 min at 20ºC and resuspended with 0.05% trypsin-EDTA (Thermo Fisher Scientific, Waltham, MA) prior to a second round of mincing and incubation in 0.05% trypsin-EDTA at 37ºC. The enzymatic reaction was stopped by the addition of FBS (Fetal Bovine Serum, Thermo Fisher). Cells were then filtered using a 70µm cell strainer (Miltenyi Biotec, San Diego, CA, USA) and pelleted by centrifugation at 300 x g for 10 min. Erythrocytes were removed using ACK Lysing Buffer (Life Technologies, Grand Island, NY, USA). Finally, the cells were resuspended in 0.04% Bovine Serum Albumin (BSA) (Sigma Aldrich) diluted in 1X PBS and filtered through a 30µm cell strainer (Miltenyi Biotec). The cell concentration and viability were determined using an automatic cell counter (Cellometer Auto 2000, Nexcelom Bioscience, Lawrence, MA, USA).  and the Dead Cell Removal Kit (Miltenyi Biotec) was used to remove dead cells to obtain a cell viability of ≥80%. Immediately following tissue collection, the uterus and decidua were dissociated to prepare single-cell suspensions. The tissues were mechanically dissociated and enzymatically digested by incubating at 37ºC using enzymes from the Umbilical Cord Dissociation Kit (Miltenyi Biotec). A second round of mechanical dissociation was performed using the gentleMACS Dissociator (Miltenyi Biotec), and dissociated cells were rinsed with 1X PBS (Thermo Fisher Scientific), NY, USA) prior to filtration using a 100µm cell strainer (Miltenyi Biotec). Filtered cells were pelleted by centrifugation at 300 x g for 5 min, erythrocytes were eliminated using ACK Lysing Buffer (Life Technologies), and the cells were rinsed in 0.04% BSA (Sigma Aldrich) and 0.5 mM EDTA (Sigma Aldrich) diluted in 1X PBS. Finally, the cells were filtered using a 30µm cell strainer (Miltenyi Biotec), and the Dead Cell Removal Kit was used to remove dead cells to obtain a cell viability of ≥80%.
Generation of gel beads-in-emulsion (GEMs) and preparation of library constructs was performed on viable single-cell suspensions using the 10x Genomics Chromium Single Cell 3’ Gene Expression Version 3.1 Kit (10x Genomics, Pleasanton, CA, USA), according to the manufacturer’s instructions. Briefly, viable single cells were encapsulated in partitioning oil together with a single Gel Bead with barcoded oligonucleotides within the Chromium Controller. Reverse transcription of mRNA into complementary (c)DNA was performed using the Veriti 96-well Thermal Cycler (Thermo Fisher Scientific, Wilmington, DE, USA). Dynabeads MyOne SILANE (10x Genomics) and the SPRIselect Reagent (Beckman Coulter, Indianapolis, IN, USA) were used to purify resulting cDNA, which was optimized by enzymatic fragmentation, end-repair, and A-tailing. Next, adaptors and sample index were incorporated by ligation. The sample index PCR product was then amplified using the Veriti 96-well Thermal Cycler and double-sided size selection was performed using the SPRIselect Reagent kit. Following the formation of cDNA and final library construct, the Agilent Bioanalyzer High Sensitivity DNA Chip (Agilent Technologies, Wilmington, DE, USA) was used determine sample integrity and concentration.

treatment_protocol: Dams that underwent cervical measurement were maintained on the heating pad under anesthesia as described above. The ultrasound transducer was fixed and mobilized with a mechanical holder and was slowly moved toward the abdomen to localize the amniotic sacs. The syringe with E. coli suspension (10 CFU/25µL) was stabilized by a mechanical holder (VisualSonics). Ultrasound-guided intra-amniotic inoculation with E. coli was performed in each amniotic sac using a 30G needle (BD PrecisionGlide needle; Becton Dickinson, Franklin Lakes, NJ, USA). Controls were injected with 25 μL of sterile 1X PBS. After the ultrasound injection, the dams were placed under a heat lamp for recovery (defined as when the mouse resumed normal activities such as walking and responding), which typically occurred 10 - 20 min after removal from anesthesia. After recovery, mice were video monitored to observe pregnancy outcomes.

value: Heterogeneous

value: Myometrium

value: Maternal:C57BL/6, Fetal:C57BL/6 x BALB/cByJ

value: Maternal:8-12w, Fetal:17.5 dpc

tag: agent

value: E. coli


title: brain lateral ventricular GFAP expressing cells, Wildtype biol rep 2

description: 100-cell input


title: HSV-308_Day1


title: SKY-1; islets from chow fed NOD.SCID mouse

description: 10x Genomics


title: HSV-309_Day180


title: HSV-308_Day0


title: HSV-307_Day37

description: RNAseq data from PBMC extracted from individual HSV-307


title: scRNAseq 10X, Myometrium, Control, Rep 7, index4A

description: 10x Genomics

value: Control


title: HSV-307_Day30


title: FUN-2r; islets from 20% HC fed NOD.SCID mouse

description: 10x Genomics

value: 7 weeks old


title: FUN-1r; islets from chow fed NOD.SCID mouse

description: 10x Genomics

value: 8 weeks old


title: HSV-307_Day7


title: scRNAseq 10X, Myometrium, E. coli, Rep 6, index3D

description: 10x Genomics


title: scRNAseq 10X, Myometrium, Control, Rep 5, index3C

description: 10x Genomics


title: HSV-307_Day1


title: HSV-307_Day0


title: MAT-2; islets from 20% HC fed NOD mice

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated values files and matrix files

extract_protocol:
Mice were killed by cervical dislocation and the pancreata were perfused with 5 mL of collagenase P solution [0.5 mg/ml, (Roche) in HBSS (Gibco) supplemented with 0.1 M HEPES, 1 mM MgCl2, 5 mM D- glucose, 1.25 mM CaCl2, and 0.02% BSA] via the common bile duct. Perfused pancreata were then dissected away from the surrounding tissue and incubated for 10 minutes at 37°C. Digestion was halted by washing the tissue twice with supplemented HBSS. The tissue was then applied to a Histopaque-1119 (Sigma) gradient, and the interface was collected, washed in supplemented HBSS, and then placed in Click’s medium with 5% FBS. Islets were handpicked using an inverted microscope. Handpicked islets were dissociated by incubation in Trypsin-EDTA (Gibco) at 37° C for 2 minutes followed by washing in Click’s media containing 10% FBS. Single cells from 3 mice per group were then pooled.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, islet single cell suspensions 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: NOD/ShiLtJ

value: WT NOD

value: 15 Weeks old


title: scRNAseq 10X, Myometrium, E. coli, Rep 4, index2F

description: 10x Genomics


title: HSV-305_Day187

description: RNAseq data from PBMC extracted from individual HSV-305


title: HSV-308_Day30


title: MAT-1; islets from 16% HC+ 4% gluten fed NOD mice

description: 10x Genomics

value: 16% HC + 4% gluten


title: scRNAseq 10X, Myometrium, Control, Rep 3, index2C

description: 10x Genomics


title: HSV-305_Day37

value: PBMC


title: HSV-305_Day30


title: HSV-305_Day0


title: HSV-305_Day1


title: HSV-305_Day7


title: scRNAseq 10X, Myometrium, E. coli, Rep 2, index1H

description: 10x Genomics


title: Mouse_intestine_protein

city: New Haven

first: Yang

last: Liu

state: CT

address: 300 George St., Room 8300C 8th floor

institute: Yale University

library_source: other

data_processing:
ST pipeline
Assembly: mm10, hg38.p12
Supplementary files format and content: *.tsv: Expression matrices.

molecule: protein

source_name: intestine

extract_protocol: Nextera XT DNA library Preparation Kit.

value: intestine

value: WT

value: No treatment


title: Mouse_kidney_protein

source_name: kidney

value: kidney


title: HSV-304_Day187

description: RNAseq data from PBMC extracted from individual HSV-304


title: Mouse_colon_protein

source_name: colon

value: colon


title: scRNAseq 10X, Myometrium, Control, Rep 1, index1E

description: 10x Genomics

value: Heterogeneous

value: Myometrium


title: HSV-304_Day30


title: Mouse_spleen_protein

source_name: spleen

value: spleen


title: HSV-304_Day37


title: scRNAseq 10X, Decidua, Control, Rep 7, index3H

description: 10x Genomics

source_name: Decidua

value: Decidua

value: Maternal:C57BL/6, Fetal:C57BL/6 x BALB/cByJ

value: Maternal:8-12w, Fetal:17.5 dpc


title: HSV-304_Day7


title: scRNAseq 10X, Decidua, E. coli, Rep 8, index4C

description: 10x Genomics

value: E. coli


title: Mouse_kidney_RNA


title: scRNAseq 10X, Decidua, E. coli, Rep 6, index3B

description: 10x Genomics


title: HSV-305_Day180


title: HSV-304_Day1


title: Mouse_intestine_RNA


title: HSV-304_Day0


title: HSV-302_Day187

description: RNAseq data from PBMC extracted from individual HSV-302


title: scRNAseq 10X, Decidua, Control, Rep 5, index3A

description: 10x Genomics

value: Control


title: Mouse_colon_RNA


title: HSV-302_Day37


title: HSV-302_Day180


title: scRNAseq 10X, Decidua, E. coli, Rep 4, index2E

description: 10x Genomics


title: HSV-302_Day30


title: HSV-304_Day180


title: Mouse_spleen_RNA


title: HSV-301_Day187

description: RNAseq data from PBMC extracted from individual HSV-301


title: HSV-302_Day1


title: scRNAseq 10X, Decidua, E. coli, Rep 2, index1G

description: 10x Genomics


title: scRNAseq 10X, Decidua, Control, Rep 3, index2B

description: 10x Genomics


title: HSV-302_Day7


title: scRNAseq 10X, Decidua, Control, Rep 1, index1D

description: 10x Genomics


title: HSV-301_Day30


title: HSV-301_Day37


title: HSV-301_Day180


title: HSV-301_Day7


title: scRNAseq 10X, Cervix, E. coli, Rep 8, index4B

description: 10x Genomics

source_name: Cervix

value: Cervix


title: HSV-301_Day1


title: HSV-301_Day0


title: ACCLysM_4_LPS

city: Charlottesville

first: Scott

last: Yeudall

state: Virginia

address: 1340 Jefferson Park Avenue, Pinn Hall 5036

department: Pharmacology

institute: University of Virginia

data_processing:
paired-end sequencing fastq files were mapped to the mm10 reference mouse genome using STAR, and reads across each gene tabulated with FeatureCounts. Differential expression and normalized counts-per-million were calculated using EdgeR 4.0.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts per million data are in file "ACCLysM_LPS_normalized_cpm.csv"

source_name: Bone marrow-derived macrophage

growth_protocol: Bone marrow was isoated from the hind limbs of 10-12 week old flox control or ACC1/ACC2 deficient mice and cultiured in RPMI1640 with 20% L929 conditioned media for 7 days to generate bone marrow-derived macrophages. On day 7, cells were trypsinized, counted, and ~1x10^7 cells were plated on petri dishes in RPMI1640 with 10% heat-inactivated FBS and allowed to adhere overnight.

extract_protocol:
Total RNA was extracted from BMDMs using the RNEasy Mini Kit (Qiagen) according to the manufacturer's  protocol. Total RNA was shipped to GeneWiz (South Plainfield, NJ) who performed the library preparation and sequencing
Libraries for RNA sequencing were prepared by GENEWIZ according to standard protocols using the NEBNext Ultra II RNA Library Prep Kit for Illumina, and 2x150bp paired-end sequenced on an Illumina HiSeq 4000 series instrument.

treatment_protocol: BMDMs were treated for 6 hours with either control medium (RPMI1640 with 10% heat-inactivated FBS) or medium with LPS (100ng/mL) for 6 hours. At the end of the experiment cells were washed 1x in PBS and lysed into RLT lysis buffer (Qiagen) prior to RNA isolation.

value: BMDM

value: ACCLysM (ACC1/ACC2 deficient)

value: LPS treatment


title: scRNAseq 10X, Cervix, E. coli, Rep 6, index2H

description: 10x Genomics


title: flox_3_LPS

value: flox control


title: ACCLysM_4_control

value: control treatment


title: flox_4_LPS


title: flox_4_control


title: scRNAseq 10X, Cervix, Control, Rep 7, index3G

description: 10x Genomics


title: HSV-220_Day37

description: RNAseq data from PBMC extracted from individual HSV-220

value: PBMC


title: HSV-317_Day30


title: HSV-220_Day30


title: flox_3_control


title: scRNAseq 10X, Cervix, Control, Rep 5, index2G

description: 10x Genomics


title: ACCLysM_3_LPS


title: HSV-220_Day7


title: HSV-220_Day0


title: HSV-302_Day0


title: scRNAseq 10X, Cervix, E. coli, Rep 4, index2D

description: 10x Genomics


title: HSV-218_Day37

description: RNAseq data from PBMC extracted from individual HSV-218


title: scRNAseq 10X, Cervix, Control, Rep 3, index2A

description: 10x Genomics


title: HSV-218_Day30


title: ACCLysM_3_control


title: HSV-218_Day7


title: HSV-218_Day1


title: scRNAseq 10X, Cervix, E. coli, Rep 2, index1F

description: 10x Genomics


title: HSV-218_Day0


title: flox_2_control


title: HSV-217_Day37

description: RNAseq data from PBMC extracted from individual HSV-217


title: scRNAseq 10X, Cervix, Control, Rep 1, index1C

description: 10x Genomics


title: HSV-217_Day30


title: HSV-217_Day1


title: ACCLysM_2_control


title: HSV-217_Day7


title: NMJs from α-LTx treated mouse, collected 168 hours after α-LTx injection, replicate 5

city: Povo (TN)

first: Fabio

last: Lauria

address: Via alla Cascata 56

country: Italy

institute: Institute of Biophysics (Italian National Research Council)

description:
RNA-seq from NMJs collected after 168 hours of α-LTx injection in mouse hind limb, replicate 5
168hours_rep5

data_processing:
One hundred bp paired-end reads were processed by removing Illumina Nextera adapters using Trimmomatic (v0.36). Processed reads were aligned to the mouse genome (GRCm38.p6) with STAR (v020201), using the Gencode M17 gene annotation, based on ENSEMBL release 92. Read duplicates were removed with Picard Tools MarkDuplicates (v2.18.9). All programs were used with default settings unless otherwise specified.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NMJs form soleus muscle, mouse hind limb

growth_protocol: Eight to ten week-old CD1 mice were employed for laser microdissection and transcriptional profiling, and for electrophysiological recordings. Wild type CD1 mice were obtained from breeding at the University of Padua. C57BL/6 mice expressing cytosolic GFP under the plp promoter (Mallon et al, 2002) were kindly provided by Dr. W.B. Macklin (Aurora, Colorado), with the help of Dr. T. Misgeld (Munchen, Germany). Mice expressing the Tomato protein specifically in ChAT (choline acetyltransferase)-positive neurons were obtained by crossing the C57BL/6 ChAT-Cre Knock-in mice line with C57BL/6 Rosa26Tomato mice (Jackson Laboratories). Mice were maintained under a 12-hour light/12-hour dark cycle, and kept under constant temperature. Water and food were available ad libitum, and mice were fed with regular chow. All procedures were performed under general anaesthesia (a cocktail of xilazine (48 mg/kg) and zoletil (16 mg/kg) via i.p. injections). Paralysis was restricted to one hind limb, and did not impair food or water intake.

extract_protocol:
After different time points (0, 4, 16, 72 and 168 h) treated mice (5 mice /group) were sacrificed by anaesthetic overdose followed by cervical dislocation, then soleus muscles were rapidly collected, and frozen in isopentane cooled with liquid nitrogen. Cryo-sections (7-10 µm thick) were transferred to UV-treated microscope glass slides. Microdissection was performed under direct microscopic visualization with PALM RoboMover automatic laser microdissector (Carl Zeiss, Oberkochen, Germany). One hundred NMJs/sample were collected by laser microdissection (LCM) within 30 min, to preserve RNA integrity, and pooled. Total RNA was isolated by incubation with 50 µl lysis buffer PKD (Qiagen) and 10 µl proteinase K (Promega) at 55°C o.n., with the sample upside down. The day after samples were centrifuged for 10 min at 10000 rpm, and RNA extracted with the automated system Maxwell 16 (Promega), using the Maxwell® 16 LEV RNA FFPE Purification Kit. RNA extraction was performed following manufacturer’s protocol starting from the DNase treatment step.
cDNA synthesis was obtained using the SMARTer Universal Low Input RNA kit (Clontech Laboratories), according to manufacturer’s instructions. Libraries for RNA-Seq were obtained using the Nextera XT kit (Illumina) according to manufacturer’s guidelines. RNA sequencing was performed with NextSeq 500 (Illumina), loading a maximum of 6 pooling libraries for each cartridge NextSeq High Output (300 cycles).

treatment_protocol: Upon isoflurane anaesthetization CD1 male mice of around 20 gr were locally injected with a-LTx in the hind limb (5 µg/kg in 15 µl physiological saline). Few minutes before muscle collection, a local injection of fluorescent α-BTx was performed to visualize the NMJs.

tag: tretment

value: alpha-LTx injection in mouse hind limb

tag: time point

value: 168 hours

tag: replicate


title: HSV-217_Day0


title: ACCLysM_1_LPS


title: HSV-220_Day1


title: NMJs from α-LTx treated mouse, collected 168 hours after α-LTx injection, replicate 3

description:
RNA-seq from NMJs collected after 168 hours of α-LTx injection in mouse hind limb, replicate 3
168hours_rep3


title: HSV-216_Day7

description: RNAseq data from PBMC extracted from individual HSV-216


title: HSV-216_Day30


title: HSV-216_Day1


title: ACCLysM_1_control


title: HSV-216_Day0


title: NMJs from α-LTx treated mouse, collected 168 hours after α-LTx injection, replicate 4

description:
RNA-seq from NMJs collected after 168 hours of α-LTx injection in mouse hind limb, replicate 4
168hours_rep4


title: HSV-215_Day187

description: RNAseq data from PBMC extracted from individual HSV-215


title: NMJs from α-LTx treated mouse, collected 168 hours after α-LTx injection, replicate 2

description:
RNA-seq from NMJs collected after 168 hours of α-LTx injection in mouse hind limb, replicate 2
168hours_rep2


title: flox_2_LPS


title: flox_1_LPS


title: HSV-215_Day37


title: flox_1_control


title: Human_GBM_protein

source_name: brain

value: brain

value: WT

value: No treatment


title: HSV-215_Day7


title: ACCLysM_2_LPS


title: HSV-215_Day30


title: HSV-215_Day180


title: HSV-216_Day37


title: Human_thymus_protein

source_name: thymus

value: thymus


title: NMJs from α-LTx treated mouse, collected 72 hours after α-LTx injection, replicate 2

description:
RNA-seq from NMJs collected after 72 hours of α-LTx injection in mouse hind limb, replicate 2
72hours_rep2

value: 72 hours


title: HSV-215_Day1


title: Human_skin_protein

source_name: skin

value: skin


title: HSV-213_Day187

description: RNAseq data from PBMC extracted from individual HSV-213

source_name: PBMC


title: HSV-213_Day37


title: NMJs from α-LTx treated mouse, collected 72 hours after α-LTx injection, replicate 1

description:
RNA-seq from NMJs collected after 72 hours of α-LTx injection in mouse hind limb, replicate 1
72hours_rep1


title: HSV-215_Day0


title: NMJs from α-LTx treated mouse, collected 168 hours after α-LTx injection, replicate 1

description:
RNA-seq from NMJs collected after 168 hours of α-LTx injection in mouse hind limb, replicate 1
168hours_rep1


title: NMJs from α-LTx treated mouse, collected 16 hours after α-LTx injection, replicate 5

description:
RNA-seq from NMJs collected after 16 hours of α-LTx injection in mouse hind limb, replicate 5
16hours_rep5

value: 16 hours


title: NMJs from α-LTx treated mouse, collected 16 hours after α-LTx injection, replicate 4

description:
RNA-seq from NMJs collected after 16 hours of α-LTx injection in mouse hind limb, replicate 4
16hours_rep4


title: HSV-213_Day7


title: HSV-213_Day1


title: NMJs from α-LTx treated mouse, collected 16 hours after α-LTx injection, replicate 3

description:
RNA-seq from NMJs collected after 16 hours of α-LTx injection in mouse hind limb, replicate 3
16hours_rep3


title: HSV-213_Day30


title: Human_spleen_protein

value: spleen


title: HSV-213_Day0


title: HSV-212_Day187

description: RNAseq data from PBMC extracted from individual HSV-212


title: HSV-213_Day180


title: NMJs from α-LTx treated mouse, collected 16 hours after α-LTx injection, replicate 2

description:
RNA-seq from NMJs collected after 16 hours of α-LTx injection in mouse hind limb, replicate 2
16hours_rep2


title: Human_GBM_RNA


title: HSV-212_Day180


title: NMJs from α-LTx treated mouse, collected 16 hours after α-LTx injection, replicate 1

description:
RNA-seq from NMJs collected after 16 hours of α-LTx injection in mouse hind limb, replicate 1
16hours_rep1


title: Human_skin_RNA


title: HSV-212_Day30


title: HSV-212_Day7


title: NMJs from α-LTx treated mouse, collected 72 hours after α-LTx injection, replicate 3

description:
RNA-seq from NMJs collected after 72 hours of α-LTx injection in mouse hind limb, replicate 3
72hours_rep3


title: HSV-212_Day0


title: Human_spleen_RNA


title: NMJs from α-LTx treated mouse, collected 4 hours after α-LTx injection, replicate 5

description:
RNA-seq from NMJs collected after 4 hours of α-LTx injection in mouse hind limb, replicate 5
4hours_rep5

value: 4 hours


title: HSV-210_Day187

description: RNAseq data from PBMC extracted from individual HSV-210


title: Human_tonsil_RNA

source_name: tonsil

value: tonsil


title: HSV-212_Day1


title: HSV-210_Day180


title: HSV-210_Day37


title: NMJs from α-LTx treated mouse, collected 4 hours after α-LTx injection, replicate 3

description:
RNA-seq from NMJs collected after 4 hours of α-LTx injection in mouse hind limb, replicate 3
4hours_rep3


title: siUSP36-3

city: jinan

first: Wenhao

last: Zhang

address: Beiyuan Street 247

institute: The Second Hospital of Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: human  hg18
Supplementary files format and content: Excel files include FPKM value, readcount and difference significance analysis for each gene in all comparison combinations for each Sample.

growth_protocol: ECA109 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with an RNA Easy Fast Tissue/Cell Kit (TIANGEN, China; Cat: #DP451) following the manufacturer’s specififications. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The small interfering RNA (siRNA) against USP36 were transduced into ECA109 cells by LipofectamineTM RNAiMAX (Invitrogen, USA). The cells were collected after 48 h of culture for subsequent experimentation.

tag: cell line

value: esophageal squamous cell carcinoma (ESCC) cell line

value: USP36 depletion


title: HSV-210_Day7

tag: individual


title: HSV-210_Day30

tag: day after vaccination


title: siUSP36-2


title: HSV-210_Day1


title: NMJs from α-LTx treated mouse, collected 4 hours after α-LTx injection, replicate 2

description:
RNA-seq from NMJs collected after 4 hours of α-LTx injection in mouse hind limb, replicate 2
4hours_rep2


title: siUSP36-1


title: HSV-210_Day0


title: HSV-209_Day180

description: RNAseq data from PBMC extracted from individual HSV-209


title: siControl-3

value: siControl


title: Human_thymus_RNA


title: HSV-209_Day37


title: NMJs from α-LTx treated mouse, collected 4 hours after α-LTx injection, replicate 1

description:
RNA-seq from NMJs collected after 4 hours of α-LTx injection in mouse hind limb, replicate 1
4hours_rep1


title: NMJs from control mouse, replicate 4

description:
RNA-seq from NMJs collected from control mouse, replicate 4
ctrl_rep4

value: untreated


title: NMJs from control mouse, replicate 3

description:
RNA-seq from NMJs collected from control mouse, replicate 3
ctrl_rep3


title: HSV-212_Day37

value: PBMC


title: NMJs from α-LTx treated mouse, collected 4 hours after α-LTx injection, replicate 4

description:
RNA-seq from NMJs collected after 4 hours of α-LTx injection in mouse hind limb, replicate 4
4hours_rep4

value: alpha-LTx injection in mouse hind limb


title: HSV-209_Day7


title: HSV-209_Day1


title: NMJs from control mouse, replicate 2

description:
RNA-seq from NMJs collected from control mouse, replicate 2
ctrl_rep2


title: HSV-209_Day30


title: HSV-208_Day187

description: RNAseq data from PBMC extracted from individual HSV-208


title: siControl-2


title: siControl-1


title: NMJs from control mouse, replicate 1

description:
RNA-seq from NMJs collected from control mouse, replicate 1
ctrl_rep1


title: HSV-209_Day0


title: Adjacant non-tumor tissue-Ctrl_43

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned clean reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.lncRNA_transcripts.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: adjacent non-tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

value: adjacent non-tumor


title: HSV-208_Day180


title: Adjacant non-tumor tissue-Ctrl_42


title: HSV-208_Day30


title: HSV-209_Day187


title: Adjacant non-tumor tissue-Ctrl_40


title: HSV-208_Day1


title: HSV-208_Day0


title: Adjacant non-tumor tissue-Ctrl_36


title: HSV-207_Day180

description: RNAseq data from PBMC extracted from individual HSV-207


title: L27388: Cortex_neg_3

city: Dresden

first: Charlotte

last: Steenblock

state: Saxony

address: Fetscherstraße 74

department: Medizinische Klinik und Poliklinik III

institute: Universitätsklinikum Carl Gustav Carus

data_processing:
bcl2fastq: 2.19.1
alignment: alignment was done with GSNAP (2018-03-11) to the mm10 reference with support of Ensembl annotation version 87 (-d mm10 --gunzip -A sam -t 14 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-87.ss.mm10.iit)
gene counts: alignment files were processed with featureCounts v1.6.0 and the support of annotation from Ensembl version 87 (featureCounts -a EnsemblGene-87.mm10.TR.gtf -s 0 -Q 1 -T 8)
gene expression: deseq2 (v. 1.18.1) was used to test for differential gene expression: the comparison are Cortex_gfp vs Cortex_neg, Medulla_gfp vs Medulla_neg and Cortex_gfp vs Medulla_gfp
Genome_build: mm10
Supplementary_files_format_and_content: bfx1249.deg.CortexGFP_vs_CortexNegativ.tsv.gz is a tab separated file which is from the deseq output; the rows are  genes and the first columns show deseq values (e.g. log2 fold change, p-value and padj value) which is followed by the normalised counts of each sample, mean normalised counts of the condition and the information about the gene
Supplementary_files_format_and_content: bfx1249.deg.CortexGFP_vs_MedullaGFP.tsv.gz is a tab separated file which is from the deseq output; the rows are  genes and the first columns show deseq values (e.g. log2 fold change, p-value and padj value) which is followed by the normalised counts of each sample, mean normalised counts of the condition and the information about the gene
Supplementary_files_format_and_content: bfx1249.deg.MedullaGFP_vs_MedullaNegativ.tsv.gz is a tab separated file which is from the deseq output; the rows are  genes and the first columns show deseq values (e.g. log2 fold change, p-value and padj value) which is followed by the normalised counts of each sample, mean normalised counts of the condition and the information about the gene
Supplementary_files_format_and_content: bfx1249.gene_count.tsv.gz is a tab separated files which list the genes and their characteristics, followed by the counts of the samples

source_name: FACS-sorted Nestin-negative cells

extract_protocol:
Cells were sorted directly in RNA lysis buffer.
The RNA-seq library preparation was performed on the basis of Picelli et al. 2013  with some modifications. Into a PCR tube containing 2 µl of a 0.2% Triton-X 100 solution in nuclease free water and 4 U murine RNase Inhibitor (NEB), 180-300 cells were sorted using a BD FACS Aria III. The cells were frozen at -80°C to enhance the lysis effect. After thawing, the RNA in the cell lysate was denatured for 3 minutes at 72 °C in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer (C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, where N represents a random base and V any base beside thymidine) and 4 U RNase Inhibitor (NEB). The reverse transcription and addition of the template switch oligo was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, where rG stands for ribo-guanosine), 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase was inactivated at 70 °C for 15 min. The single stranded cDNA was subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 250 nM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 17 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration was determined with a Fragment Analyzer (Agilent). For library preparation 1 ng cDNA was tagmented using 0.5 µl Tagment DNA Enzyme and 1x Tagment DNA Buffer (Nextera DNA Library Prep Kit, Illumina), followed by an incubation step at 55 °C for 5 min. Next, Illumina indices were added during PCR (72°C 3min, 98°C 30sec, 12 cycles [98°C 10sec, 63°C 20sec, 72°C 1min], 72°C 5min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 700nM dual indexing primers. After PCR, libraries were purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer.

treatment_protocol: Adrenals from 6 male Nestin-GFP mice perfused with PBS were excised and placed in petri dishes with ice-cold PBS. Fat tissue surrounding the adrenals was carefully removed and the adrenal cortex was thoroughly isolated from the medulla. Cortical and medullary tissues, respectively, were pooled in 3 groups (2 mice per group), pelleted (350 x g, 5 min), and digested for 20 min at 37oC while shaking (1.8 mg/ml collagenase, 10 mg/ml BSA, 0.18 mg/ml DNAse in PBS; all from Sigma-Aldrich). The digestion was stopped by washing twice in PBS and red blood cell lysis was performed using ACK Lysis buffer (Thermo Fisher Scientific). After washing in PBS the cells were suspended in 250 µl PBS containing 2% FCS and propidium iodide (BioLegend). The flow sorting was performed on a FACSAriaII flow cytometer (BD Biosciences) using FACSDiva Software

value: Nes-GFP

value: ~2,5 months

value: Adrenal cortex


title: Human_tonsil_protein

value: WT

value: No treatment


title: L27389: Cortex_gfp_3

source_name: FACS-sorted Nestin-positive cells


title: L27390: Medulla_neg_2

value: ~3.5 months

value: Adrenal medulla


title: Adjacant non-tumor tissue-Ctrl_35


title: HSV-207_Day187


title: HSV-207_Day37


title: HSV-207_Day30


title: Bladder cancer tumor tissue-BC_43

source_name: bladder cancer tissue

value: bladder cancer


title: L27386: Medulla_neg_1


title: HSV-207_Day7


title: Bladder cancer tumor tissue-BC_42


title: HSV-207_Day1


title: L27391: Medulla_gfp_3


title: HSV-207_Day0


title: L27387: Medulla_gfp_2


title: Bladder cancer tumor tissue-BC_40


title: L27385: Cortex_gfp_2


title: HSV-208_Day7


title: HSV-205_Day180

description: RNAseq data from PBMC extracted from individual HSV-205


title: Bladder cancer tumor tissue-BC_36


title: HSV-208_Day37


title: HSV-205_Day37


title: L27384: Cortex_neg_2


title: HSV-205_Day30


title: HSV-205_Day7


title: L27383: Medulla_gfp_1


title: HSV-205_Day1


title: Bladder cancer tumor tissue-BC_35


title: HSV-204_Day187

description: RNAseq data from PBMC extracted from individual HSV-204


title: HSV-204_Day180


title: Alginate HLO - TGFB treated

city: Ann Arbor

first: Joseph

last: Decker

address: 1011 N University Avenue

department: Cariology, Restorative Sciences, and Endodontics

institute: University of Michigan

data_processing:
CellRanger read mapping from fastq files
Genome_build: hg19
Supplementary_files_format_and_content: CellRanger output folders

source_name: lung-like tissue

growth_protocol: H1 human embryonic stem cell (hESC) line (NIH registry #0043) was obtained from the WiCell Research Institute and was used to derive all HLOs for these experiments. H1 hESC cells were approved by the University of Michigan Human Pluripotent Stem Cell Research Oversight Committee. hESCs were maintained as previously described in Spence et al. Nature, 2011. HLOs were derived as previously described in Dye et al. Elife, 2019 and placed in ratios of 100% Matrigel or 1-2% alginate. Roughly 50 foregut spheroids were suspended in Matrigel or alginate and placed in a 50µL droplet. The alginate formed by placing a 5µL 2% CaCl2 droplet on the bottom of the well and then dropping the spheroids suspended in 45µL of alginate (1-2%, with varying ratios of Matrigel).

extract_protocol: As previously described in Miller et al. Dev. Cell, 2020

treatment_protocol: 100ng/mL TGFB was added to HLO media for 1 (initial study) week or 4 weeks (fibrosis model) with media changed every 3 days. Treatments were performed on organoids at 55 days.

value: H1 ESC-derived lung

value: 100ng/mL TGFB

tag: gel

value: 1:7 Matrigel:2% alginate


title: HSV-205_Day0


title: Alginate HLO - control


title: HSV-204_Day30


title: HSV-204_Day37


title: HSV-204_Day1


title: URB1_iCLIP_rep1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Raw read quality was evaluated by FastQC (v0.11.9). Deep sequencing datasets were mapped with Bowtie2 (Bowtie2 v2.3.5, parameters: -q --sensitive -a -p 8 --no-mixed --reorder --no-unal) and aligned to 45SrRNA sequence in human reference genome, then we removed reads introduced by PCR duplicates via a custom script. We got the read-coverage on 45SrRNA using genomeCoverageBed (genomeCoverageBed v2.29.0, parameters: -split), and calculated the fraction of reads overlapping each position in 45S rDNA.
Genome_build: 45SrRNA reference sequence for human samples
Supplementary_files_format_and_content: bedgraph files for RNA sequencing

source_name: HeLa cells

growth_protocol: HeLa cells with Flag-tag knock-in at the N-terminal of URB1 were maintained in DMEM, which was supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
HeLa cells expressing Flag-tagged URB1 were UV-crosslinked, resuspended in lysis buffer and sonicated for 20 s x 6 times on 25% duty. Supernatants were incubated with anti-Flag antibodies (Shanghai Genomics) or control IgG-conjugated beads for 2h at 4°C. Beads with protein-RNA complexes were treated with 5 Kunz U/ml of micrococcal nuclease in the presence of 5 μg yeast tRNAs for 5 min at 37°C, followed by dephosphorylation of RNA 3’ ′ ends with PNK. Then pre-adenylated linker L3 (3′ modification with biotin) was linked to 3′ end of RNA using T4 RNA ligase 1 at 16°C overnight. The 5′ end of RNA was labeled with [γ- 32P] ATP using PNK. Protein-RNA complexes were eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min, resolved on 4%–12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposed to a Fuji film at −80°C. Bands corresponding to specific protein-RNA complexes were excised and then digested with proteinase K. RNAs were purified and cDNAs were made using Superscript III (Invitrogen) with Rclip primers. cDNAs were separated on 6% denaturing urea polyacrylamide gel, then three bands at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low) were excised, purified and circularized by Circligase II (Epicenter). Single-stranded cDNAs were hybridized with Cut-Oligo and then digested by BamH I. Linearized cDNAs were PCR amplified and purified. The obtained iCLIP libraries were subjected to high throughput deep sequencing.
Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries, which were subjected to Illumina HiSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

value: HeLa

tag: type

value: HeLa cells expressing Flag-tagged URB1

tag: antibody

value: anti-Flag

tag: barcode sequence

value: NNNGCCGNN


title: L27382: Cortex_gfp_1

tag: strain

tag: age


title: HSV-204_Day7

value: PBMC


title: sarcoma sample 10

city: Linhai

first: BINXIANG

last: CHU

address: XINMEN street

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: mRNA_Expression_Summary.xlsx files include RPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tumor tissue

tag: gender

value: Male

tag: genotype

tag: grade

value: iii


title: HSV-203_Day187

description: RNAseq data from PBMC extracted from individual HSV-203

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: titre.txt includes titre and demographics information. 'serology' column provides serostatus group association for each sample.

tag: cell type


title: sarcoma sample 11

tag: tissue

value: i


title: HSV-203_Day180


title: sarcoma sample 12

value: WT


title: HSV-204_Day0


title: HSV-203_Day30


title: sarcoma sample 9


title: HSV-203_Day7


title: control 5637 cells-1

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
We aligned clean reads of samples to the reference genome using HISAT2 package.
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: human urothelial cell

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5637 cells were transfete with LNPPS plasmid or its control plasmid to construct LNPPS-overexpressing 5637 cells or control 5637 cells

tag: genotype/variation

value: control


title: HSV-203_Day1

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturerâs instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.


title: control 5637 cells-3


title: control 5637 cells-2


title: L27381: Cortex_neg_1

value: Nes-GFP

value: ~3.5 months

value: Adrenal cortex


title: HSV-203_Day0


title: HSV-202_Day187

description: RNAseq data from PBMC extracted from individual HSV-202


title: sarcoma sample 7

value: Female


title: LNPPS overexpressing 5637 cells-3

source_name: bladder cancer cells

value: LNPPS-overexpressing


title: LNPPS overexpressing 5637 cells-2


title: HSV-203_Day37


title: sarcoma sample 4


title: HSV-202_Day7