title: RNA09_CHD8B_neuron_brep3

first: Alba

last: Corman

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Each sample was prepared with three independently differentiated biological replicates and analyzed with the DEseq2 package in RStudio
Assembly: hg19
Supplementary files format and content: Bulk RNA-seq, raw counts (.txt file)

growth_protocol: HUES66 human embryonic stem cells (hESCs) were were cultured on LDEV-free Geltrex-coated plates in mTeSR media (STEMCELL 85850). Media was supplemented with 10 uM Y-27632 Rho-kinase inhibitor for 24 hours after passaging and then removed.

extract_protocol:
Total RNA, Quick-RNA Mini kit (Zymo)
cDNA. RNA was extracted using the Quick-RNA Mini kit (Zymo)  and prepared for 3’ digital gene expression (DGE) RNA-sequencing with unique molecular identifiers. Sequencing was performed using 37 bp paired-end reads on a NextSeq (Illumina).

treatment_protocol: Differentiation of HUES66 cells into induced neurons (iNs) was performed as in Lu et al., (2019) FASEB, PMID: 30698461. Briefly, Doxycycline (2 μg/ml) was applied for induction of NEUROG2/1 overexpression at day 0 of neuron differentiation. Puromycin (1 μg/ml) was applied from day 1 to day 4 for selection. On days 1 to 3, a blended media of mTeSR and neuron media (Neurobasal (ThermoFisher 21103049) supplemented with 1x B27 (ThermoFisher 17504044) was used to gently transition the induced neurons. Media was changed daily as follows: Day 1: 75% mTeSR and 25% neuron media; Day 2: 50% mTeSR and 50% neuron media; Day 3: 25% mTeSR and 75% neuron media. On day 4, puromycin was removed by the exchange of the day 3 culture medium to 100% neuron media. Mouse glia cells were added on day 5. On day 7, Ara-C (1 μM, Sigma-Aldrich, C1768) was added to control the growth of glia. From day 5 onward, 25% of medium was replaced every 2-3 days to maintain the iN culture.

value: Neuron

value: KO

value: Ngn, Day9


title: Drosophila_F0-Rich_F1-Rich_F2-Poor_3

status: Public on Jul 12 2023

type: RNA

city: Aarhus C

first: Mads

middle: Fristrup

last: Schou

address: Nu Munkegade 114

department: Biology

country: Denmark

institute: Aarhus University

description:
Field collected lab stock
Gene expression data from Drosophila developed at poor or rich medium

hyb_protocol: Fifteen micrograms of cDNA were fragmented and loaded onto the Affymetrix probe array cartridge. Incubation, washing and staining procedures were performed in the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Affymetrix Scanner 3000 7G)

data_processing: The raw data was GC-RMA normalized and further analysed using several different approaches in R

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061

growth_protocol: Flies developed on poor or rich food  in F0, F1 or F2

treatment_protocol: Frozen directly

tag: Sex

value: male

tag: group


title: LUAD_03_PT

type: SRA

city: Kaohsiung City

first: Ying-Ming

last: Tsai

address: No.100, Shih-Chuan 1st Road, Sanmin Dist.

country: Taiwan

institute: Kaohsiung Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The criteria for differentially expressed:mRNA by NGS analysis were fold change > 2 and fragments per kilobase million (FPKM) > 0.3.
Assembly: hg38
Supplementary files format and content: CSV files include normalized abundance measurements for each Sample

organism: Homo sapiens

source_name: Lung organoid

extract_protocol:
The lung organoid specimens were extracted, rapidly frozen, and their RNA was collected using Trizol reagent. Subsequently, the Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was employed with 1 µg of total RNA to create sequencing libraries. Lastly, the RNA libraries were readied for sequencing following standard Illumina procedures.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: disease

value: Lung adenocarcinoma

tag: tissue

value: Lung organoid

tag: type

value: Tumor

tag: age

tag: gender

value: M

tag: Stage


title: LUAD_03_NT

value: Normal


title: LUAD_05_PT_Peripheral

value: F


title: EORTC_26101_2023_058

type: genomic

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Normalized Average Beta (BMIQ method)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: diffuse glioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions


title: Drosophila_F0-Rich_F1-Rich_F2-Poor_2

extract_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061


title: RNA08_CHD8B_neuron_brep2

city: New York

country: USA

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Drosophila_F0-Rich_F1-Rich_F2-Poor_1


title: RNA07_CHD8B_neuron_brep1


title: LUAD_02_PT


title: EORTC_26101_2023_056


title: LUAD_02_NT


title: RNA05_CHD8A_neuron_brep2


title: RNA06_CHD8A_neuron_brep3


title: Drosophila_F0-Rich_F1-Rich_F2-Rich_3


title: LUAD_01_PT


title: Drosophila_F0-Rich_F1-Rich_F2-Rich_2


title: RNA04_CHD8A_neuron_brep1


title: Drosophila_F0-Rich_F1-Rich_F2-Rich_1


title: EORTC_26101_2023_054


title: LUAD_01_NT


title: EORTC_26101_2023_053

value: female


title: RNA03_H66_neuron_brep3

value: WT


title: Drosophila_F0-Rich_F1-Poor_3


title: EORTC_26101_2023_051


title: EORTC_26101_2023_052


title: Drosophila_F0-Rich_F1-Poor_2


title: EORTC_26101_2023_057


title: Drosophila_F0-Rich_F1-Poor_1


title: EORTC_26101_2023_050


title: EORTC_26101_2023_055


title: RNA01_H66_neuron_brep1


title: H66_neuron_brep2

library_source: genomic

data_processing:
We used bowtie to align reads to the genome (hg19) and allowed for up to 1 mismatch. We removed duplicates (Picard MarkDuplicates) and mitochondrial reads (bowtie). All samples were downsampled to the same number of aligned reads per sample (14M). Peak detection was performed using MACS2 software with parameters “--nomodel --shift -100 --extsize 200”. After peak detection, we combined biological replicates using bedtools merge. Unique peaks to each CHD8+/- cell line were identified using bedtools subtract. Peak-to-gene assignment was done using the bedtools closest function with parameter “-t first”.
Assembly: hg19
Supplementary files format and content: Bulk ATAC-seq, filtered and assigned peaks using bedtools (.bed files). Peak files are in UCSC broadPeak format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand, read count within peaks, -log10(1-posterior probability), -log10(qvalue).

extract_protocol:
Genomic DNA. We performed ATAC-seq as previously described (Buenrostro et al.(2013) Nat Methods, PMID: 24097267) with an optimized lysis buffer to lower mitochondrial contamination (Rickner et al. (2019) J Vis Exp, PMID: 30958473).Briefly, cell membranes were lysed in RSB (10mM Tris-HCL pH 7.4, 3mM MgCl2, 10mM NaCl) with 0.1% Tween-20 freshly added. After pipetting up and down, nuclei were isolated by centrifugation at 500 rcf for 10 minutes at 4C. After discarding the supernatant, nuclei were resuspended in Tagmentation DNA (TD) Buffer with 2.5 ul Nextera enzyme (Illumina) and incubated at 37C for 30 minutes.
After purification on a MinElute column (Qiagen), the purified, tagmented DNA was PCR amplified using Q5 enzyme (NEB) and barcoded primers for 10 cycles (with an initial 72C, 5 minute step for Nextera end filling). The PCR product was purified via a 1.5X SPRI cleanup (Agencourt) and checked for a characteristic nucleosome banding pattern using a TapeStation (Agilent). Samples were sequenced with paired-end 37bp reads on a NextSeq (Illumina). All 3 samples (WT, CHD8-A, CHD8-B) were processed with 2 biological replicates that were separated cultured, tagmented and analyzed.


title: Drosophila_F0-Rich_F1-Rich_2


title: Donor Id: Hu0235; Eye: OS; Tissue: Scl (Hu235OSSclera)

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

library_source: transcriptomic single cell

data_processing:
reads were aligned to the human genome GRCh38 with transcriptome version 101 using cellranger (version 4.0.0) count function
Assembly: GRCh38
Supplementary files format and content: comma-separated values files and matrix files

molecule: polyA RNA

source_name: Sclera

extract_protocol:
Frozen ocular tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with DAPI. and single nuclei were collectedusing a flow cytometer. The sorted nuclei were pelleted, resuspended in PBS solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single nucleus RNA sequecning (10X Genomics)

value: Sclera

tag: eye

value: OS

tag: individual


title: Donor Id: Hu0222; Eye: OD; Tissue: Scl (Hu222ODScl)

value: OD


title: Donor Id: Hu13; Eye: OD; Tissue: Scl (Pt13Scl)


title: H66_neuron_brep1


title: EORTC_26101_2023_049


title: Donor Id: Hu13; Eye: OD; Tissue: RPE/Cho (Pt13Cho)

source_name: Retinal Pigment Epithelium/Choroid

value: Retinal Pigment Epithelium/Choroid


title: Drosophila_F0-Rich_F1-Rich_1


title: Drosophila_F0-Rich_F1-Rich_3


title: EORTC_26101_2023_048


title: Donor Id: Hu0235; Eye: OS; Tissue: RPE/Cho (Hu235OSpRPE)

value: Retinal Pigment Epithelium/Choroid, peripheral retina


title: Drosophila_F0-Rich_3


title: CHD8B_neuron_brep2

value: Neuron


title: EORTC_26101_2023_047


title: CHD8B_neuron_brep1

value: KO


title: Donor Id: Hu0235; Eye: OS; Tissue: RPE/Cho (Hu235OSmRPE)

value: Retinal Pigment Epithelium/Choroid, macula


title: RNA02_H66_neuron_brep2

value: Ngn, Day9


title: Cisplatin_4

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Raw sequencing data was processed using 10x Genomics Cell Ranger v3.1
Assembly: Referecne created from Ensembl Rattus_norvegicus.Rnor_6.0.101
Supplementary files format and content: Cell Ranger raw feature barcode matrix

organism: Rattus norvegicus

source_name: frozen postmortem brain

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols

value: frozen postmortem brain

value: male

tag: developmental stage

value: Adult

tag: strain

value: Sprague Dawley Rat

value: Cisplatin


title: Drosophila_F0-Rich_2


title: EORTC_26101_2023_046


title: Donor Id: Hu0220; Eye: OS; Tissue: RPE/Cho (Hu220OSpRPE)


title: CHD8A_neuron_brep2


title: CHD8A_neuron_brep1


title: EORTC_26101_2023_045


title: Cisplatin_3

description: 10x Genomics


title: EORTC_26101_2023_044


title: Calu-3, biological replicate 2, sample 2, scRNAseq

first: Sam

last: Reffsin

address: 415 Curie Blvd

description: 10x Genomics

data_processing:
Base calling and preliminary quality scoring was done in real time on a NextSeq 500 with RTA 2.0. The sequencing runs were stored on the Illumina BaseSpace website.
We mapped single cell RNA-sequencing reads to transcripts and cells using the Cell Ranger pipeline v3.0.2 by 10x Genomics. We used mkfastq with default parameters to demulitplex raw base call files into library-specific FASTQ files. We alligned FASTQ files to the human genome (hg38) and extracted gene expression count matrices using cellranger counts based on Gencode v32 annotation, filtering and correcting for cell identifiers and unique molecular identifiers (UMIs) with default settings.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files; *barcodes.tsv contain cell labels; *matrix.mtx contain sparse gene expression matrices where rows are genes and columns are cell labels; *feaures.tsv contain gene labels

extract_protocol:
Calu-3 cells were trypsinized with TrypLE for 10 minutes at 37C and subsequently resuspended in PBS for library construction.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, Calu-3 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: lung adenocarcinoma


title: EORTC_26101_2023_043


title: Calu-3, biological replicate 2, sample 1, scRNAseq

description: 10x Genomics


title: Donor Id: Hu0218; Eye: OD; Tissue: RPE/Cho (Hu218ODMacularRPE)


title: Cisplatin_1

description: 10x Genomics


title: Donor Id: Hu0218; Eye: OS; Tissue: RPE/Cho (Hu218OSpRPE)


title: Cisplatin_2

description: 10x Genomics


title: EORTC_26101_2023_042


title: Calu-3, biological replicate 1, sample 2, scRNAseq

description: 10x Genomics


title: Donor Id: Hu0222; Eye: OD; Tissue: RPE/Cho (Hu222ODCho)


title: Calu-3, biological replicate 1, sample 1, scRNAseq

description: 10x Genomics


title: AFQ_AJ050_het_f_septum

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

data_processing:
Raw reads were aligned with STAR (v2.6.1a) against the GRCm38 reference and quantified using featureCounts (v1.6.3) with the Gencode vM12 annotation.
The technical quality of RNAseq data was assessed for the number of uniquely, multiple and unmapped reads.
Differential expression analysis was performed in R (v3.4.1) using DESeq2 (v1.18.1).
Assembly: GRCm38
Supplementary files format and content: feature counts output table per each sample
Supplementary files format and content: raw_counts.txt: all raw feature counts from all samples in one file

organism: Mus musculus

source_name: heart

growth_protocol: Mice were grown until the age of 8 month.

extract_protocol:
Total murine RNA was isolated from liquid nitrogen crashed and powdered heart tissue with TRIzol reagent (Invitrogen, USA).
stranded, reverse, paired-end, TruSeq stranded mRNA kit

treatment_protocol: No treatment.

value: heart

value: Prdm16_csp1/wt (het)

value: no

value: female


title: AFQ_AJ052_het_f_septum


title: Calu3_unsorted_Rep03

data_processing:
After sequencing, we aligned reads to the human genome (assembly 38; hg38) using kallisto and performed subsequent differential expression analysis using limma
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

extract_protocol:
RNA was harvested using the NucleoSpin totalRNA FFPE micro kit (Macherey-Nagel #740969.50).
To prepare sequencing libraries, we used the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). To index our samples, we used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S).
All sequencing was performed using an Illumina NextSeq 75 cycle high-output kit (Illumina 20024906) in a paired end format (38 cycles read 1 + 37 cycles read 2).

treatment_protocol: Calu-3 cells were co-stained for ACE2 protein and TIG1 mRNA and subsequently subjected to FACS on each signal. Low and high bins for each combination of signals were collected.

value: WT

tag: cell subtype

value: unsorted


title: Donor Id: Hu6; Eye: OS; Tissue: PPS (Pt6PeripapillarySclera)

source_name: Peripapillary Sclera

value: Peripapillary Sclera

value: OS


title: Drosophila_F0-Rich_1

tag: Sex


title: EORTC_26101_2023_040


title: Donor Id: Hu12; Eye: OS; Tissue: PPS (Pt12OSPPS)


title: EORTC_26101_2023_041


title: Calu3_unsorted_Rep02


title: EORTC_26101_2023_039


title: Donor Id: Hu0220; Eye: OS; Tissue: RPE/Cho (Hu220OSmRPE)


title: AFQ_AJ049_het_f_septum


title: Calu3_unsorted_Rep01


title: Donor Id: Hu11; Eye: OD; Tissue: PPS (Pt11PeripapillarySclera)

value: OD


title: AFQ_AJ053_het_f_septum


title: Donor Id: Hu8; Eye: OS; Tissue: PPS (Pt8PPS)


title: AFQ_AJ042_wt_f_septum

value: Prdm16_wt/wt (wt)


title: Donor Id: Hu6; Eye: OS; Tissue: ONH (Pt6ONH)

source_name: Optic Nerve Head

value: Optic Nerve Head


title: AFQ_AJ041_wt_f_septum


title: Donor Id: Hu11; Eye: OD; Tissue: ONH (Pt11ONH)


title: Calu3_ACE2highTIG1high_Rep03


title: Calu3_ACE2highTIG1high_Rep02


title: EORTC_26101_2023_036


title: AFQ_AJ040_wt_f_septum


title: Donor Id: Hu10; Eye: OD; Tissue: ONH (Pt10ONH)


title: AFQ_AJ048_het_f_septum


title: Calu3_ACE2highTIG1high_Rep01


title: Calu3_ACE2lowTIG1low_Rep03


title: AFQ_AJ039_wt_f_septum


title: Donor Id: Hu0235; Eye: OS; Tissue: ONH (Hu235OSONH)


title: Calu3_ACE2lowTIG1low_Rep02


title: Donor Id: Hu0220; Eye: OS; Tissue: ONH (Hu220OSONH)


title: AFQ_AJ038_wt_f_septum


title: EORTC_26101_2023_033


title: EORTC_26101_2023_035


title: EORTC_26101_2023_034


title: AFQ_AJ024_wt_m_septum


title: EORTC_26101_2023_038


title: EORTC_26101_2023_032


title: Donor Id: Hu0218; Eye: OS; Tissue: ONH (Hu218OSONH)


title: AFQ_AJ023_wt_m_septum


title: Calu3_ACE2lowTIG1low_Rep01


title: EORTC_26101_2023_037


title: Donor Id: Hu1059; Eye: OD; Tissue: ONH (Hu105916ODONHallnuc)


title: Calu3_ACE2highTIG1low_Rep03


title: EORTC_26101_2023_031


title: Donor Id: Hu0887; Eye: OS; Tissue: ONH (Hu088716OSONHallnuc)


title: AFQ_AJ022_wt_m_septum


title: EORTC_26101_2023_030


title: AFQ_AJ021_wt_m_septum


title: Calu3_ACE2highTIG1low_Rep01


title: EORTC_26101_2023_029


title: AFQ_AJ015_het_m_septum


title: Donor Id: Hu0564; Eye: OS; Tissue: ONH (Hu056416OSONHallnuc)


title: EORTC_26101_2023_028


title: EORTC_26101_2023_027


title: AFQ_AJ014_het_m_septum


title: Calu3_ACE2lowTIG1high_Rep02


title: Calu3_ACE2lowTIG1high_Rep03


title: AFQ_AJ013_het_m_septum


title: Calu3_ACE2lowTIG1high_Rep01


title: Donor Id: Hu0355; Eye: OS; Tissue: ONH (Hu035516OSONHallnuc)


title: EORTC_26101_2023_026


title: COVID_M5_T

city: Munich

first: Stefan

last: Engelhardt

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

data_processing:
paired-end run was performed using a NextSeqHigh
Most steps of this pipeline were performed using the Galaxy platform.
Reads were trimmed with Flexbar 3.5.0. and aligned to human reference genome (hg38) using HISAT 2.1.0. and for transcript assembly and quantification StringTie 2.1.1 was used.
Assembly: hg38
Supplementary files format and content: raw gene counts in txt.format

source_name: lung

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions.
low-input mRNA-Seq; Libraries were generated using  NEBNext® NEBNext Single Cell/Low Input RNA Library Prep Kit according to manufacturer's instructions.

value: lung

value: total lung


title: EORTC_26101_2023_025


title: Donor Id: Hu0326; Eye: OD; Tissue: ONH (Hu032616ODONHallnuc)


title: EORTC_26101_2023_024

value: male


title: Donor Id: Hu6; Eye: OS; Tissue: ON (Pt6ON)

source_name: Optic Nerve

value: Optic Nerve


title: NMP-3

description: Sample 61_T

data_processing:
paired-end run was performed using a NextSeqHigh
Most steps of this pipeline were performed using the Galaxy platform.
STAR 2.7.8a was used for alignment to mouse reference genome 10 (mm10). StringTie merge (v 2.1.1) was used to merge transcripts and DESeq2 1.32.027 was used for differentially expressed analysis.
Assembly: mm10
Supplementary files format and content: raw gene counts in txt.format

value: other leukocytes

value: no tretament


title: COVID_M4_T


title: Calu3_ACE2highTIG1low_Rep02

value: lung adenocarcinoma


title: AFQ_AJ011_het_m_septum

value: heart

value: Prdm16_csp1/wt (het)


title: EORTC_26101_2023_023

value: female


title: Donor Id: Hu0869; Eye: OD; Tissue: ONH (Hu086916ODONHallnuc)


title: NMP-2

description: Sample 60_T

value: WT


title: Donor Id: Hu14; Eye: OD; Tissue: ON (HuPt14ODON)


title: Donor Id: Hu14; Eye: OS; Tissue: ON (Pt14OSON)


title: COVID_L25_T


title: EORTC_26101_2023_022


title: Donor Id: Hu0563; Eye: OD; Tissue: ONH (Hu056316ODONHallnuc)


title: EORTC_26101_2023_021


title: AFQ_AJ012_het_m_septum

value: no


title: Donor Id: Hu0235; Eye: OD; Tissue: ON (Hu235ODON)


title: COVID_L24_T


title: EORTC_26101_2023_020


title: COVID_L23_T


title: IM 257

description: Sample 57_T

value: Interstitial macrophages


title: Donor Id: Hu0221; Eye: OS; Tissue: ON (Hu221OSON)

value: OS


title: NMP-1

description: Sample 59_T


title: IM 175-1

description: Sample 55_T


title: COVID_L22_T


title: EORTC_26101_2023_018


title: Donor Id: Hu0220; Eye: OS; Tissue: ON (Hu220OSON)


title: Donor Id: Hu0355; Eye: OS; Tissue: ON (Hu035516OSONallnuc)


title: EORTC_26101_2023_017


title: Donor Id: Hu0222; Eye: OS; Tissue: ON (Hu222OSON)


title: AM 257

description: Sample 54_T

value: Alveolar macropahges


title: COVID_M3_T


title: COVID_L15_T


title: EORTC_26101_2023_019


title: COVID_L13_T


title: EORTC_26101_2023_015


title: COVID_L14_T


title: EORTC_26101_2023_016


title: EnC 162-9

description: Sample 51_T

value: Endothelial cells


title: COVID_L9_T


title: EORTC_26101_2023_014


title: EORTC_26101_2023_013


title: IM 174-7

description: Sample 56_T


title: EORTC_26101_2023_012


title: COVID_L8_T


title: EnC 162-8

description: Sample 49_T


title: COVID_L16_T


title: COVID_L6_T


title: EnC 154-3

description: Sample 50_T


title: Control4_H_T


title: EpC 174-8

description: Sample 47_T

value: Epithelial cells


title: EpC 162-8

description: Sample 48_T

value: lung


title: EORTC_26101_2023_011


title: Control2_H_T

value: total lung


title: EORTC_26101_2023_010

value: male


title: EpC 26-1

description: Sample 46_T


title: Control1_H_T


title: DCs 257

description: Sample 45_T

value: Dendritic cells


title: PKO_IFN_rep3 [DX12]

city: West Haven

first: John

middle: David

last: MacMicking

state: CT

address: 850 West Campus Dr.

department: Microbial pathogenesis and immunobiology

institute: Yale University

description:
DX12
gene_counts.csv

data_processing:
The RNA-seq reads were mapped to human genome (hg38) with STAR version 2.8 using default parameters
SAMtools version 1.11 was used to convert SAM files, sort and index BAM files
The uniquely mapped reads were counted to GENCODE gene annotation using FeatureCounts
R package DESeq2 version 3.9 was used to determine differentially expressed genes
Assembly: hg38
Supplementary files format and content: CSV files including counts per gene for each sample

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy plus micro kit, based on the standard protocol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hepatocyte

value: IFN-γ


title: PKO_IFN_rep2 [DX11]

description:
DX11
gene_counts.csv


title: DCs 174-7

description: Sample 44_T

value: no tretament


title: AM 96

description: Sample 52_T


title: EORTC_26101_2023_009


title: EORTC_26101_2023_008


title: Control13_M_T


title: PKO_IFN_rep1 [DX10]

description:
DX10
gene_counts.csv


title: PKO_untreated_rep3 [DX9]

description:
DX9
gene_counts.csv

value: untreated


title: EORTC_26101_2023_007


title: DCs 175-1

description: Sample 43_T


title: EORTC_26101_2023_005


title: EORTC_26101_2023_006


title: Control10_M_T


title: Control7_M_T


title: Wild type 4

city: Boston

first: Christopher

last: Sudduth

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
Timmomatic v 0.36 was used to removed adapter sequences and nucleotides with poor quality. Trim reads were mapped to Mus musculus GRCm38 reference genome. Reads were normalized using DESeq2's median of ratios. Differential gene expression analysis was performed using DESeq2 and genes were identified that had adjusted p values < 0.05 after comparing for multiple comparisons using hthe Benjamini-Hochberg method.
Assembly: GRCm38
Supplementary files format and content: count

source_name: Brain

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions (
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Brain

value: Wild type


title: EORTC_26101_2023_004

value: female


title: PKO_untreated_rep2 [DX8]

description:
DX8
gene_counts.csv


title: PKO_untreated_rep1 [DX7]

description:
DX7
gene_counts.csv


title: Control14_M_T


title: Control5_M_T


title: Wild type 2


title: Control6_M_T


title: Wild type 3


title: WT_IFN_rep3 [DX6]

description:
DX6
gene_counts.csv

value: WT


title: EORTC_26101_2023_003


title: Wild type 1


title: WT_IFN_rep2 [DX5]

description:
DX5
gene_counts.csv


title: Control3_M_T


title: WT_IFN_rep1 [DX4]

description:
DX4
gene_counts.csv


title: Mutant 4

value: Map2k1 K57N


title: Control2_M_T


title: Mutant 3


title: Control1_M_T


title: WT_untreated_rep3 [DX3]

description:
DX3
gene_counts.csv


title: Mac_630

data_processing:
Single-end run (SE50) run was performed using a NextSeq500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: hg38
Supplementary files format and content: raw microRNA counts in txt.format

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input according to manufacturer's instructions.

value: macrophages


title: Mutant 1


title: WT_untreated_rep2 [DX2]

description:
DX2
gene_counts.csv


title: Mutant 2


title: WT_untreated_rep1 [DX1]

description:
DX1
gene_counts.csv


title: DRG scRNA-seq

city: Cincinnati

first: Temugin

last: Berta

state: OH

address: 231 Albert Sabin Way, MSB 3408

department: Anesthesiology

institute: University of Cincinnati

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: CellRanger output in Market Exchange Format (MEX)

source_name: Dorsal root ganglia

extract_protocol:
DRG tissues were dissected and pooled from three male CD-1 mice from the cervical (C1-C8), thoracic (T1-T13), and lumbar (L1-L6) segments. Single-cell susoension was obtained by incubation of tissues with papain in HBSS (60 U, cat# P3125, Millipore Sigma, St. Louis, MO) for 20 min at 37°C, then collagenase in HBSS (1 mg/ml, cat# C6885, Millipore Sigma) for another 20 min at 37°C. The tisseus were then triturated with 1 and 200 µl pipettes, passed through a 40-µm filter, and centrifuged through 15% bovine serum albumin (BSA) solution to remove cell doublets and debris. Single cells were resuspended in PBS-BSA 0.01% at a concentration of 1000 cells/µl .
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Dorsal root ganglia

value: DRG cells

value: CD-1 mice (6-week old, males)

value: Naïve


title: hASMC_Recovered_168h

city: Aarhus

first: Juan Luis

last: Garcia-Rodriguez

address: Høegh-Guldbergs Gade 10

department: Biomedicine

data_processing:
Trim Galore phred > 20
STAR alignement
Subread used for Feature counts calling
CIRI2 algorithm for circRNA annotation
Assembly: hg19/GRCh37
Supplementary files format and content: Raw Feature counts with linear RNA
Supplementary files format and content: Raw counts and chromosomal- information of circRNAs

source_name: Human Aortic Smooth Muscle

extract_protocol:
Rneasy Plus Mini Kit (Qiagen)
SMARTer Stranded Total RNA-seq kit v3-Pico Input Mammalian (Takara)

value: Human Aortic Smooth Muscle

value: hASMC

value: Smooth Muscle cell

value: no FBS and Complete media after


title: Mac_520

value: lung


title: RNAseq_BMP2_rep3

city: La Jolla

first: Matthew

last: Wortham

state: CA

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

data_processing:
Single-end 50bp RNA-seq reads were mapped to the UCSC mouse genome (mm9) by STAR v. 2.4.0 (--outSAMstrandField intronMotif--outFilterMultimapNmax 1 --rethread 5), allowing for up to 10 mismatches (default by STAR)
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Expression levels of all genes were estimated by Cufflinks v2.2.1 (-p 6 -G $gtf_file --max-bundle-frags 1000000000) using only the reads with exact matches. Differential gene expression was performed using Cuffdiff (Cufflinks v2.2.1), with FDR < 0.05 considered significant.
In homer, function "makeUCSCfile" was used to generate bigWig files
Assembly: mm9
Supplementary files format and content: bigWig

source_name: pancreatic islets

growth_protocol: Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and  BMP2 were changed every 5th day

extract_protocol:
RNA was harvest using Rneasy Micro Kit (Qiagen) according to the manufacturer instructions.
RNA libraries were constructed from 35ng of isolated RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Islets were cultured in the absence or presence of 50ng/ml BMP2

value: pancreatic islets

value: male

value: 12 weeks

value: BMP2 10 d


title: RNAseq_BMP2_rep1


title: Mac_419


title: Mac_629


title: hASMC_Starvation_96h

value: no FBS


title: EORTC_26101_2023_002


title: EORTC_26101_2023_001


title: RNAseq_Ctrl_rep3

description: This sample submitted previously in GSE110690

value: Ctrl 10d


title: hASMC_24h

value: Complete media


title: RNA from liver from ST_YoungIso4

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Short-term young isochronic parabiosis
Young4

data_processing:
Reads were mapped with STAR (version 2.5.2b) (Dobin et al., 2013)
Reads were  counted via featureCounts (version 1.5) (Liao et al., 2014)
Data was passed through RLD transformation (Love et al., 2014)
Genes with |transformed normalized count| < 1 were filtered out
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: liver

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol:
RNA was isolated from mouse tissues using the Ambion RNAqueous Total RNA Isolation Kit (Invitrogen). ~25 mg of solid tissue was used as starting material. Concentration of RNA samples was determined using the Qubit RNA HS assay kit (Invitrogen). Total RNA isolated as described above was checked for quality using an Agilent 2100 Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis. Short-term parabiosis pairs were maintained for 1 month prior to euthanasia and tissue collection.

tag: mouse strain

value: C57BL/6 WT

value: liver

tag: age (years)

tag: mouseid


title: RNA from liver from ST_YoungIso3

description:
Short-term young isochronic parabiosis
Young3

tag: tissue


title: RNA from liver from ST_YoungIso5

description:
Short-term young isochronic parabiosis
Young5


title: Omikron_P2_MAN21_II

data_processing:
Single-end run (SE50) run was performed using a MiSeq or a NextSeq500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: hg38
Supplementary files format and content: raw microRNA counts in txt.format

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: hPCLS

value: infected with SARS-CoV-2 (MOI1) + Treatment with RCS-24


title: RNA from liver from ST_YoungIso2

description:
Short-term young isochronic parabiosis
Young2


title: RNAseq_Ctrl_rep2

tag: age


title: Caco2_Recovered_168h

source_name: Human Colon

value: Human Colon

value: Adenocarcinoma


title: Omikron_P2_MAN21_I

value: infected with SARS-CoV-2 (MOI1) + Treatment with RCS-23


title: RNA from liver from ST_YoungIso1

description:
Short-term young isochronic parabiosis
Young1


title: RNAseq_Ctrl_rep1


title: Omikron_P1_MAN21_III

value: infected with SARS-CoV-2 (MOI1) + Treatment with RCS-22


title: RNAseq_BMP2_rep2


title: hASMC_Starvation_120h

value: Human Aortic Smooth Muscle

value: hASMC

value: Smooth Muscle cell


title: inputDNA_BMP2_re2

data_processing:
Data was mapped to the UCSC mouse genome NCBI37/mm9 (July 2007).
Bowtie 2 was used to map data to the genome with the following settings: the seed length was set as 33 with a maximum number of 2 mismatches allowed in the seed region, and reads aligning to multiple locations were discarded. Duplicate reads were removed using samtools
In homer, function "makeUCSCfile" was used to generate bigWig file
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and BMP2 were

extract_protocol:
After sonication chromatin immunoprecipitation was performed using ChIP-IT High Sensitivit (Active Motif). Histone-DNA complexes were isolated with  the corresponding antibody.
Libraries were prepared using KAPA DNA Library Preparation Kits for Illumina.

value: pancreatic islets

value: male

value: BMP2 10d

tag: chip antibody

value: none (input)


title: Omikron_P1_MAN21_II

value: lung

value: infected with SARS-CoV-2 (MOI1) + Treatment with RCS-21


title: Caco2_24h

value: Complete media


title: Caco2_Starvation_96h

value: no FBS


title: inputDNA_Ctrl_rep2

description: This sample submitted previously in GSE110689

value: 12 weeks

value: Ctrl 10d


title: RNA from liver from ST_OldIso4

description:
Short-term old isochronic parabiosis
Iso4

value: C57BL/6 WT

value: liver


title: Omikron_P2_MAN21_III

value: hPCLS

value: infected with SARS-CoV-2 (MOI1) + Treatment with RCS-25


title: RNA from liver from ST_OldIso5

description:
Short-term old isochronic parabiosis
Iso5


title: Omikron_P2_MOI1_III

value: infected with SARS-CoV-2 (MOI1)


title: Omikron_P2_MOI1_II


title: C: SU-DHL-4 cells treated with PBS

city: Xi'an

first: Xiao

last: Yang

state: Shaanxi

address: 157#, Xiwu Road, Xincheng District

department: The Second Affiliated Hospital

country: China

institute: Xi'an Jiaotong University

description: SU-DHL-4 cells treated with PBS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: SU-DHL-4 cells

growth_protocol: SU-DHL-4 cells were maintained in RPMI-1640 Medium and supplemented with 10% FBS.

extract_protocol:
SU-DHL-4 cells were harvested and resuspended in Trizol reagent.Total RNA is exacted. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SU-DHL-4 cells were treated with PBS, 50 uM Bz-ATP or 50 uM A740003 for 48h respectively.

value: Diffuse large B-cell lymphoma (DLBCL)

value: treated with PBS


title: Omikron_P2_MOI1_I


title: B: SU-DHL-4 cells treated with 50uM BZ-ATP for 48hous

value: treated with 50uM BZ-ATP for 48hous


title: A: SU-DHL-4 cells treated with 50uM A740003 for 48hous

value: treated with 50uM A740003 for 48hous


title: H3K27me3_ChIPseq_BMP2_rep2

value: pancreatic islets

value: male

value: BMP2 10d

value: H3K27me3 (Cat#07-449 Milipore)


title: inputDNA_BMP2_rep1

value: none (input)


title: inputDNA_Ctrl_rep1


title: RNA from liver from ST_OldIso1

description:
Short-term old isochronic parabiosis
Iso1


title: Caco2_Starvation_120h

value: Human Colon

value: Adenocarcinoma

value: no FBS


title: RNA from liver from ST_OldIso2

description:
Short-term old isochronic parabiosis
Iso2

value: C57BL/6 WT


title: H3K27me3_ChIPseq_Ctrl_rep2

value: 12 weeks

value: Ctrl 10d


title: Omikron_P1_MOI1_III

value: lung

value: hPCLS


title: Omikron_P1_MOI1_II

value: infected with SARS-CoV-2 (MOI1)


title: VD10D7V

city: Shenzhen

first: Shumin

last: Liao

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

description:
FPKM_VDorganoids.txt
counts_VDorganoids.txt

data_processing:
fastp, HISAT2, HTSeq-count
Raw reads of fastq format were firstly processed using fastp sofetware and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: airway epithelial cells

growth_protocol: An 18-day air-liquid interface (ALI) culture in Pneumacult ALI Medium was undertaken to allow cellular differentiation into a pseudostratified mucociliary airway epithelium prior to performing infection experiments.

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
10nM or 100nM 1,25(OH)2D3 was added into the Pneumacult ALI Medium during different coure of ALI culture, including day 1 of differentiation (D1), day 7 of differentiation (D7), and 1 day before infection (B1).
On day 18 of ALI culture, the airway organoids were differentiated and were inoculated with influenza H1N1 virus at at MOI  of 0.01 for 2 hours. The infected and non-infected organoids were harvested at 48 hours after infection for total RNA extraction.

value: airway epithelial cells

value: 10nM VD treatment and H1N1 infection

tag: time

value: D7 (day 7 of differentiation)


title: H3K4me3_ChIPseq_BMP2_rep2

value: pancreatic islets

value: H3K4me3 (Cat#04-745 Milipore)


title: RNA from liver from ST_OldHet4

description:
Short-term old heterochronic parabiosis
Het4

value: liver


title: VD10D7C

value: 10nM VD treatment control


title: RNA from liver from ST_OldHet3

description:
Short-term old heterochronic parabiosis
Het3


title: H3K4me3_ChIPseq_Ctrl_rep2

value: male


title: VD10D1V

value: D1 (day 1 of differentiation)


title: Omikron_P2_uninfected_II

value: no treatment


title: RNA from liver from ST_OldIso3

description:
Short-term old isochronic parabiosis
Iso3


title: H3K27ac_ChIPseq_BMP2_rep2

value: BMP2 10d

value: H3K27ac (Cat#39133 Active Motif)


title: VD10D1C


title: H3K27ac_ChIPseq_Ctrl_rep2

value: 12 weeks


title: Omikron_P1_uninfected_III


title: H3K27me3_ChIPseq_BMP2_rep1

value: H3K27me3 (Cat#07-449 Milipore)


title: MCF7 con

city: chuncheon

first: okhwa

last: kim

country: South Korea

institute: kangwon national university

description: tag2b vector expressed MCF7 exosome

hyb_protocol: Biotin-labeled sample were hybridized for 16 h at 48°C on an Affymetrix miRNA 3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GCS 3000 canner (Affymetrix, Santa Clara, California, United States).

data_processing: Affymetrix GeneChip Command Console software (version 4.0, Affymetrix) was used to get raw data and then RMA normalization method was taken. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MCF7 exosome

label_protocol: Exosomal RNA were tailed with Poly A. FlashTag Biotin HSR labeled RNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA (FlashTag™ Biotin RNA Labeling Kit For miRNA Arrays, Affymetrix).

growth_protocol: MCF7 were cultured in RPMI supplemented with 10% fetal bovine serum (Gibco-BRL), 100 units/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: Exosomal RNA was extracted using TriZol according to the manufacturer's instructions.

treatment_protocol: MCF7 and MCF7-KRasV12 cultured to confluency were incubated with serum-free RPMI for 24 h. The CM was collected and filtered through a 0.22 μm PVDF filter. Exosomes were purified from CM using ultracentrifugation.

tag: cell line

value: MCF7 exosome


title: MCF7 KrasV12

description: KRasV12 expressed MCF7 exosome

source_name: MCF7Kras exosome

tag: cell type

value: KrasV12 expressed MCF7 exosome


title: RNA from liver from ST_OldHet5

description:
Short-term old heterochronic parabiosis
Het5

value: C57BL/6 WT


title: RNA from liver from OldHetRec3

description:
Old heterochronic recovery
liver63


title: RNA from liver from ST_OldHet1

description:
Short-term old heterochronic parabiosis
Het1


title: Omikron_P2_uninfected_I

value: lung

value: hPCLS


title: RNA from liver from OldHetRec2

description:
Old heterochronic recovery
liver62


title: H3K27me3_ChIPseq_Ctrl_rep1

value: Ctrl 10d


title: Omikron_P1_uninfected_II


title: Omikron_P1_uninfected_I


title: Omikron_P1_MOI1_I

value: infected with SARS-CoV-2 (MOI1)


title: RNA from liver from OldHetRec1

description:
Old heterochronic recovery
liver61


title: VD10B1C

value: airway epithelial cells

value: B1 (1 day before infection)


title: VD100D7V

value: 100nM VD treatment and H1N1 infection

value: D7 (day 7 of differentiation)


title: H3K4me3_ChIPseq_BMP2_rep1

value: pancreatic islets

value: male

value: H3K4me3 (Cat#04-745 Milipore)


title: RNA from liver from ST_OldHet2

description:
Short-term old heterochronic parabiosis
Het2

value: liver


title: COVID_L25

value: total lung


title: H3K4me3_ChIPseq_Ctrl_rep1

value: 12 weeks


title: RNA from liver from OldHet3

description:
Old heterochronic parabiosis
liver53


title: VD100D1V

value: D1 (day 1 of differentiation)


title: RNA from liver from OldHet2

description:
Old heterochronic parabiosis
liver52


title: COVID_L24


title: H3K27ac_ChIPseq_BMP2_rep1

value: BMP2 10d

value: H3K27ac (Cat#39133 Active Motif)


title: VD10B1V

value: 10nM VD treatment and H1N1 infection


title: COVID_L23

value: lung


title: VD100D1C

value: 100nM VD treatment control


title: H3K27ac_ChIPseq_Ctrl_rep1

value: Ctrl 10d


title: RNA from liver from OldHet1

description:
Old heterochronic parabiosis
liver51

value: C57BL/6 WT


title: COVID_L22


title: RNA from liver from OldIsoRec3

description:
Old isochronic recovery
liver43


title: VD100B1V

value: airway epithelial cells

value: B1 (1 day before infection)


title: VD100B1C


title: VD100D7C

value: D7 (day 7 of differentiation)


title: NDV

value: 0nM VD treatment and H1N1 infection


title: M5a_right-ear_treatment_10min

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

description: Maus 5 - 10 min

data_processing:
We performed the pre-processing step according to our pipeline miRMaster 2.0 with standard parameter settings (https://doi.org/10.1093/nar/gkab268). Detection filtering was processed for at least in one ear type (left-ear_treatment, right-ear_treatment, left-ear_control and right-ear_control) 100% of the samples needed to be expressed.
Assembly: mm10
Supplementary files format and content: miRNA_expression_raw.tsv: Tab-separated file of raw feature counts per sample.

source_name: ear skin

extract_protocol:
The ears were immersed in RNAlater for 12 hours at 4°C and subsequently frozen at -80°C. RNA was isolated using miRNeasy Mini kit (Qiagen, Hilden, Germany) after manufacturers recommendations. RNA quantity and quality was determined using Nanodrop (ThermoFisher Scientific, Waltham, MA, USA) and Bioanalyzer RNA Nano Chip Kit (Agilent Technologies, Santa Clara, CA, USA). Mean RNA Integrity Number (RIN) of the samples was 8.2 ± 0.9.
SmallRNA sequencing libraries were prepared using MGIEasy Small RNA Library Prep Kit on the high-throughput MGI SP-960 sample prep system (MGI Tech, Shenzhen, China). According to the manufacturer's protocols, the 3’- and 5’-adapters were ligated to the RNA. Afterwards, an RT primer including sample-specific barcodes was utilised to perform reverse transcription (RT). Amplification of the cDNA was achieved using a polymerase chain reaction (PCR) with 21 cycles. PCR products were subsequently size selected via AMPure Beads XP (Beckman Coulter, Brea, CA, USA). Size and 449 concentration of the purified PCR products were determined using an Agilent DNA 1000 Kit (Agilent Technologies, Santa Clara, CA, USA) and QubitTM 1X dsDNA High Sensitivity (HS) (ThermoFisher Scientific, Waltham, MA, USA), respectively. Fifteen samples and one performance control sample were pooled in an equimolar fashion in one sequencing library, which was circularized using the MGI Easy circularisation kit. In total, we prepared 8 libraries composed of a total of 120 samples
Samples were sequenced on DNBSEQ-G400RS with DNBSEQ-G400RS High-throughput Sequencing Set (Small RNA FCL SE50) by BGI in Wuhan, China.

value: ear skin

tag: genotype

value: wild-type

value: female

tag: mouse id

tag: location

value: right

tag: group

value: treatment

tag: group 2

value: none experimental ear

tag: timepoint (min)


title: M7a_right-ear_treatment_30min

description: Maus 7 - 30 min

tag: strain


title: M1a_right-ear_treatment_0min

description: Maus 1 -0 min

tag: Sex


title: NDC

tag: treatment

value: 0nM VD treatment control


title: RNA from liver from OldIsoRec1

description:
Old isochronic recovery
liver41

tag: mouse strain

value: liver

tag: age (years)


title: COVID_L14

tag: tissue

value: total lung


title: COVID_L13

value: lung


title: M41_left-ear_treatment_120min_irradiated

description: Li M41 2h B

tag: age

value: left

value: experimental ear


title: RNA from liver from OldIso3

description:
Old isochronic parabiosis
liver33

value: C57BL/6 WT

tag: mouseid


title: RNA from liver from OldIso2

description:
Old isochronic parabiosis
liver32


title: M9a_left-ear_treatment_60min_irradiated

description: RNA Mausohr 9 - 1h


title: COVID_L15


title: RNA from liver from OldIso1

description:
Old isochronic parabiosis
liver31


title: M7a_left-ear_treatment_30min_irradiated

description: RNA Mausohr 7 - 30min


title: COVID_L8


title: COVID_L9


title: AM 175-1

description: Sample 53_T

value: Alveolar macropahges

value: WT

value: no tretament


title: M5a_left-ear_treatment_10min_irradiated

description: RNA Mausohr 5 - 10min


title: COVID_L6


title: M1a_left-ear_treatment_0min_irradiated

description: RNA Mausohr 1 -0h


title: 4-OHT treated cultured microglia 3 (Cre+)

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Cortical

growth_protocol: DMEM, 10% Fetal Bovine Serum (FBS), 1 X Penicillin/Streptomycin. Cells were cultured at 37 degree at 5% CO2.

extract_protocol:
Cells were lyzed with Trisol and RNA was prepared using RNA prep kit (Invitrogen, PureLink RNA kit).
Takara Clontech SMARTer

treatment_protocol: Cells were treated with 1.5μM 4-hydroxytamoxifen (4-OHT) for 2 days before harvest.

value: Cortical

value: Microglia

value: Mouse cortical microglia

value: Cre+


title: RNA from liver from OldIsoRec2

description:
Old isochronic recovery
liver42


title: Control14_M


title: 4-OHT treated cultured microglia 1 (Cre+)


title: M17_left-ear_control_120min

description: Li M17 2h K

value: ear skin

value: wild-type

value: female

value: control


title: 4-OHT treated cultured microglia 2 (Cre+)


title: COVID_L16


title: Control10_M


title: 4-OHT treated cultured microglia 1 (Cre-)

value: Cre-


title: M18_left-ear_control_60min

description: Li M18 1h K

value: none experimental ear


title: 4-OHT treated cultured microglia 2 (Cre-)


title: 4-OHT treated cultured microglia 3 (Cre-)


title: Control13_M

value: lung

value: total lung


title: Control7_M


title: M25_left-ear_control_10min

description: Li M25 K

value: left


title: Maus4_2_control_120min

description: See additional file metaData.tsv.

data_processing:
Single-cell peripheral blood mononuclear cells: Reads were aligned against the mm10 genome (refdata-gex-mm10-2020-A) using the 10x Genomics CellRanger software (v.7.1.0) using a cut-off value of 200 UMIs. For quality-control, SoupX (v.1.6.1) was used to remove ambient cell free mRNA contamination, cells with more than 10% mitochondrial reads, <200 features or >2,500 features were removed using Seurat (v.4.3.0). As a third quality-control step, doublets were removed using DoubletFinder (v.2.0.3) using automatically determined (using the recommended settings) parameters nExp and pK. The samples were normalized using Seurats SCTransform function and aligned using Seurat integration with default settings.
Assembly: mm10
Supplementary files format and content: gene_expression_raw.tsv: Tab-separated file of raw feature counts per cell.
Supplementary files format and content: metaData.tsv: Tab-separated file containing annotation of single-cell data

source_name: blood

extract_protocol:
PBMCs were isolated from heparin blood of four mice using standard Ficoll gradient. Cells 513 were counted in a hemocytometer using Trypan blue for live/dead staining. Viability was >95% for all samples.
Single-cell transcriptome analysis was performed using Chromium Next GEM Single Cell 3' Kit v3.1 (10xGenomics) with 5,000 cells input after the manufacturer’s protocol.
Generated single-cell libraries were sequenced by Novogene on an Illumina NovaSeq using PE150 sequencing.

value: blood

value: PBMCs

tag: agent


title: Control6_M


title: Maus2_2_control_120min

description: See additional file metaData.tsv.


title: M3a_left-ear_control_0min

description: RNA Mausohr 3 unbestrahlt- li


title: Control3_M


title: Maus6_treatment_120min

description: See additional file metaData.tsv.

value: irradiated with NTP


title: M41_right-ear_treatment_120min

description: Re M41 2h B

value: right

value: treatment


title: Control2_M


title: M9a_right-ear_treatment_60min

description: Maus 9 - 1h


title: Maus3_2_treatment_120min

description: See additional file metaData.tsv.


title: M37_left-ear_treatment_30min_irradiated

description: Li M37 30' B

value: experimental ear


title: Raw264.7,Con A,rep3

city: Nanchong

first: Yan

last: Lu

address: 1 Shida Road, Nanchong, Sichuan 637009, P.R. China

institute: China West Normal University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp (version 0.19.7) (parameters: fastp -g -q 5 -u 50 -n 15 -l 150 ) . then mapped to mm10 whole genome using hisat2 v2.0.5 with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Ascites

growth_protocol: Raw264.7 cells were in RPMI-1640 containing 10% FBS and supplemented with 100 U/mL Penicillin and 100μg/mL streptomycin sulfate in a humidified incubator with 5% CO2 at 37℃.

extract_protocol:
Raw264.7 cells were harvested and snap frozen in liquid nitrogen.Then total RNA was extracted using Trizol (Ambion/Invitrogen, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext 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, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR. 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. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) 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 (PE150) were generated.

treatment_protocol: Raw264.7 cells were treated with 10µg/mL N protein of SARS-CoV-2 or Con A (as positive control) for 24 hours. Untreated cells as blank control.

value: Ascites

tag: cell line

value: macrophage

value: WT

value: treated with Con A for 24h


title: Control1_M

tag: cell type


title: M27_left-ear_control_30min

description: Li M27 30' K

value: ear skin

tag: genotype

value: wild-type

value: female


title: M36_left-ear_treatment_10min_irradiated

description: Li M36 10' B

tag: mouse id


title: HUVEC, FICZ-6-5

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
RTA version 2.11.3 running under NextSeq Control Software version 4.0.0 was used for basecalling.
Reads were aligned to Ensemble mouse genome (GRCh37) using Tophat2 (2.0.11)
Gene-based read counts were performed using Rsubread from FeatureCounts
Assembly: hg19
Supplementary files format and content: csv file includes Gene counts for each Sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Cultured in EGM-2 (Lonza), and used at between passages 1-4 for experiments

extract_protocol:
Cells were snap frozen in TRIzol and RNA purified using the TRIzol plus RNA Purification kit (both Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells treated with either 10nM FICZ or DMSO control for 6 hours

value: Human umbilical vein endothelial cells

value: FICZ


title: HUVEC, FICZ-6-4


title: Raw264.7,Con A,rep2


title: HUVEC, FICZ-6-3


title: M38_left-ear_treatment_0min_irradiated

description: Li M38 0h K

tag: location


title: Control5_M

source_name: lung

value: lung

value: total lung


title: M13_right-ear_control_120min

description: Re M13 2h K

tag: group

value: control

value: none experimental ear


title: HUVEC, FICZ-6-2


title: Raw264.7,Con A,rep1


title: Raw264.7,N,rep1

value: treated with 10ug/mL N protein of SARS-CoV-2 for 24h


title: Raw264.7,N,rep2


title: M11_right-ear_control_30min

description: Re M11 30' K

value: right

tag: group 2


title: Raw264.7,N,rep3


title: Raw264.7,control,rep3

value: untreated


title: M5_right-ear_control_60min

description: Re M5 1h

tag: timepoint (min)


title: Raw264.7,control,rep2


title: HUVEC, DMSO-6-4

value: DMSO


title: M15_right-ear_control_10min

description: Re M15 10' K

tag: strain


title: M24_right-ear_control_0min

description: Re M24 direkt K

tag: Sex


title: M20_left-ear_treatment_60min_irradiated

description: Li M20 1h B

value: left

value: treatment

value: experimental ear


title: M19_right-ear_treatment_120min

description: Re M19 2h


title: HUVEC, DMSO-6-2

tag: treatment


title: M20_right-ear_treatment_60min

description: Re M20 1h


title: A549_nsp1_WT_UNC0638_pIC_3_S31_R1

city: Bethesda

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description:
RNA-seq of A549 cells expressing WT and mutant NSP1 and with or without H3K9 methyl transferases inhibitors
A549_NSP1WTvsNSP1K164A/H165A_UNC0638_pIC_gene_exp.diff

data_processing:
bcl2fastq (version 2.20.0) was used to convert bcl sequencing files to fastq files demultiplexing by primer index
cutadapt (version 2.4 with Python 3.7.2) was used to demultiplex ribosome footprinting data and remove adapter sequences
STAR (version 2.7.2b) was used to aligned RNA-Seq and ChIP-Seq data to the human genome. tophat (version 2.1.1) was used to align ribosome footprinting data to the human transcriptome
cuffdiff (cufflinks version 2.2.1) was used to quantify and compare RNA abundance for RNA-Seq and ribosome footprinting data. bedtools (version 2.29.2)  was used to calculate coverage of aligned ChIP-Seq reads
Assembly: hg38

growth_protocol: A549 cells were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS)

extract_protocol: RNA from transfected cells was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, Cat# R2050) according to the manufacturer’s instructions.

treatment_protocol: For transient transfection plasmids were transfected into cells using Lipofectamine 3000 (Invitrogen) according to manufacturer’s instructions. Poly I/C was transfected with the plasmid at 1/10 of the plasmid.

value: epithelial

value: WT

value: poly I/C, UNC0638, FH-NSP1 expression


title: HUVEC, DMSO-6-1


title: M37_right-ear_treatment_30min

description: Re M37 30' B

value: ear skin

value: wild-type

value: female


title: HUVEC, FICZ-6-1

value: Human umbilical vein endothelial cells

value: FICZ


title: BMMCs, Elk4 knockout 1, IgE-DNP/HSA stimulation

city: Hongkong

first: Yuji

last: Huang

address: Road 86 wujin

institute: Shanghai Jiao Tong University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: bone marrow derived mast cells

growth_protocol: Bone marrow cells were obtained by flushing bone marrow from the femurs and tibias of mice. Cells were cultured in BMMC media (RPMI 1640 media containing 2 M L-glutamine, 10% foetal bovine serum, 1 M sodium pyruvate, 0.1 M nonessential amino acids, 100 U/mL penicillin, 100 mg/mL streptomycin, 25 M HEPES, 10 ng/mL IL-3, and 10 ng/mL SCF (PeproTech, Cranbury, NJ)). After 4 to 8 weeks of culture, the BMMCs were stained to confirm surface expression of fluorescein isothiocyanate (FITC)–anti-mCD117 (BioLegend) and red-phycoerythrin–anti-mFcεRI (BioLegend), and >80% of the cells were found to be double positive.

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) after activation.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: 5x105 BMMCs were seeded in 24-well plates and sensitized with anti-DNP-IgE(0.5μg/ml) overnight. On the next day, BMMCs were stimulated for 1 hour at 37°C with 100 ng/mL DNP-HSA antigen.

value: bone marrow derived mast cells

value: knockout

value: IgE-DNP/HSA stimulation


title: BMMCs, Elk4 knockout 2, IgE-DNP/HSA stimulation


title: M36_right-ear_treatment_10min

description: Re M36 10' B

value: right

value: none experimental ear


title: BMMCs, Elk4 knockout 2

value: untreated


title: A549_nsp1_WT_UNC0638_pIC_1_S29_R1


title: HUVEC, DMSO-6-5

value: DMSO


title: BMMCs, Elk4 knockout 1


title: A549_nsp1_WT_DMSO_pIC_3_S19_R1

description:
RNA-seq of A549 cells expressing WT and mutant NSP1 and with or without H3K9 methyl transferases inhibitors
A549_NSP1WTvsNSP1K164A/H165A_DMSO_pIC_gene_exp.diff

value: poly I/C, DMSO, FH-NSP1 expression


title: Day20_CM_Am80_siRARA_siRARB_3

city: Kyoto

first: Yoshinori

last: Yoshida

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

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.26.0) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: hiPSCs derived CM

growth_protocol: For iPSCs, ReproCELL supplemented with bFGF at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, undifferentiated iPSCs were dissociated, and then suspended in StemPro-34 media supplemented with Y-27632 and BMP4. On day 1, media, containing activin A, BMP4 and bFGF, were added. On day 3, the media were changed to differentiation media supplemented with VEGF and IWP-3. On day 7, the media were changed to StemPro-34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were exchanged every 3 days.

extract_protocol:
RNeasy Micro Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

treatment_protocol: To purify cardiomyocytes, CD172a/b-positive and  CD31, CD49a, CD90, CD140b-negative populations were sorted at day20 of the differentiation.  For siRNA experiments, purified CMs were seeded on the plates and siRNAs were  transfected onto the cells. Am 80 or DMSO were administered on the next day. CMs were sorted 2 days after the treatment of siRNAs.

tag: experiment

value: siRNA

tag: sirna

value: RARA+RARB


title: Day20_CM_Am80_siRARA_3

value: RARA


title: M19_left-ear_treatment_120min_irradiated

description: Li M19 2h B

tag: tissue

value: left

value: treatment

value: experimental ear


title: M38_right-ear_treatment_0min

description: Re M38 0h K

value: ear skin

value: wild-type

tag: age

value: female


title: Day20_CM_DMSO_siRARA_3


title: Raw264.7,control,rep1

value: Ascites

value: macrophage

value: WT


title: HUVEC, DMSO-6-3

value: Human umbilical vein endothelial cells


title: A549_nsp1_WT_DMSO_pIC_2_S18_R1

first: Markus

value: epithelial


title: BMMCs, heterozygous 2, IgE-DNP/HSA stimulation

value: bone marrow derived mast cells

value: heterozygous

value: IgE-DNP/HSA stimulation


title: A549_nsp1_WT_DMSO_pIC_1_S17_R1

value: poly I/C, DMSO, FH-NSP1 expression


title: BMMCs, heterozygous 1, IgE-DNP/HSA stimulation


title: BMMCs, heterozygous 2

value: untreated


title: A549_nsp1_WT_UNC0638_pIC_2_S30_R1

value: poly I/C, UNC0638, FH-NSP1 expression


title: M33_right-ear_treatment_120min

description: Re M33 2h B

value: right

value: none experimental ear


title: M31_right-ear_treatment_60min

description: Re M31 1h B

value: treatment


title: Day20_CM_Am80_siRARB_3

value: siRNA

value: RARB


title: BMMCs, heterozygous 1


title: M29_right-ear_treatment_30min

description: Re M29 30' B

value: ear skin

value: wild-type

value: female


title: A549_nsp1_K164A/H165A_UN_pIC_2_S33_R1

value: WT

value: poly I/C, UNC0638, FH-NSP1 K164A/H165A expression


title: Day20_CM_DMSO_siRARA_siRARB_3

value: DMSO

value: RARA+RARB


title: Day20_CM_DMSO_siRARB_3


title: Day20_CM_Am80_siNC_3

value: NC


title: M39_right-ear_treatment_0min

description: Re M39 0h B


title: Day20_CM_DMSO_siNC_3


title: BMMCs, wild type 1, IgE-DNP/HSA stimulation

value: bone marrow derived mast cells

value: IgE-DNP/HSA stimulation


title: M33_left-ear_treatment_120min_irradiated

description: Li M33 2h B

value: left

value: experimental ear


title: BMMCs, wild type 2

value: untreated


title: M31_left-ear_treatment_60min_irradiated

description: Li M31 1h B


title: A549_nsp1_K164A/H165A_DMSO_pIC_3_S22_R1

value: epithelial

value: poly I/C, DMSO, FH-NSP1 K164A/H165A expression


title: A549_nsp1_K164A/H165A_UN_pIC_1_S32_R1


title: A549_nsp1_K164A/H165A_DMSO_pIC_2_S21_R1


title: Day20_CM_DMSO_siRARA_siRARB_2

value: siRNA


title: BMMCs, wild type 1


title: M29_left-ear_treatment_30min_irradiated

description: Li M29 30' B

value: treatment


title: A549_nsp1_K164A/H165A _DMSO_pIC_1_S20_R1


title: Day20_CM_Am80_siRARA_2

value: RARA


title: MUC29186

first: Stefan

last: Engelhardt

description: single cell hashtag oligonucleotide (HTO) multiplexing library

library_source: other

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
cellranger v6.0.1 for alignment, filtering, barcode counting, UMI counting, demultiplexing of HTOs
Assembly: GRCm39; vM27
Supplementary files format and content: raw gene counts in txt.format

molecule: other

extract_protocol:
Primary cells from lung were digested using an enzyme cocktail (CollageaseII/DispaseII /DNAseI) and subjected lung cell suspension to CD45-based MACS to leukocytes and non-leukocytes. Cells were multiplexed from three different animals in each group and the proportion of CD45+ cells were reduced to 50% to avoid oversampling. Several washing steps were performed before performing GEM production.
Barcoding and library preparation was done using Chromium single cell 3’ Kit (v2, 10x Genomics).

value: lung

value: Lung cell suspension

tag: disease state

value: bleomycin

tag: timepoint

value: 14 days after bleomycin

tag: index


title: M39_left-ear_treatment_0min_irradiated

description: Li M39 0h B

value: ear skin

value: wild-type

value: female


title: M13_left-ear_control_120min

description: Li M13 2h K

value: control

value: none experimental ear


title: primary CRC24.T

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to mouse genome build GRCh38/hg38  using using START version 2.5.3a. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (version 1.6.4) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package (version 4.0.5).
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: primary colorectal cancer

extract_protocol:
RNA was extracted from dissociated healthy, peritumoral and tumor samples using the ARCTURUS™ PicoPure™ RNA Isolation Kit (Thermofisher).
Libraries were prepared for sequencing using SMART-Seq v4 ultra-low RNA kit (Takara Bio)

value: colon

tag: tissue type

value: tumor


title: A549_nsp1_K164A/H165A_UN_pIC_3_S34_R1

tag: cell line

tag: cell type

tag: genotype

value: WT

value: poly I/C, UNC0638, FH-NSP1 K164A/H165A expression


title: Day20_CM_DMSO_siRARA_2

value: DMSO


title: primary CRC24.P

value: peritumor


title: MUC29184

city: Munich

address: Biedersteiner Str. 29

institute: Technical University Munich

value: pbs


title: Day20_CM_Am80_siRARB_2

value: siRNA

value: RARB


title: primary CRC24.H

value: non-neoplastic


title: M5_left-ear_control_60min

description: Li M5 1h

tag: mouse id

tag: location

value: left

tag: group


title: Day20_CM_DMSO_siRARB_2


title: BMMCs, wild type 2, IgE-DNP/HSA stimulation

value: bone marrow derived mast cells

value: IgE-DNP/HSA stimulation


title: Day20_CM_Am80_siRARA_siRARB_2

value: RARA+RARB


title: MUC29183

tag: strain

value: lung

value: Lung cell suspension

value: control oligo

value: 14 days after bleomycin


title: M11_left-ear_control_30min

description: Li M11 30' K

value: ear skin

value: wild-type

tag: Sex

value: female

value: control

tag: group 2

value: none experimental ear

tag: timepoint (min)


title: primary CRC23.T

value: colon

value: tumor


title: primary CRC23.P

value: peritumor


title: MUC29182_3

description:
single cell 3' mRNA library (10x Genomics)
Bleo21_barcodes.tsv.gz
Bleo21_features.tsv.gz
Bleo21_matrix.mtx.gz

value: bleomycin

tag: treatment


title: M15_left-ear_control_10min

description: Li M15 10' K

tag: tissue

value: left


title: Day20_CM_Am80_siNC_2

tag: experiment

value: siRNA

tag: sirna

value: NC


title: primary CRC23.H

value: non-neoplastic


title: Day20_CM_Am80_siRARA_siRARB_1

value: RARA+RARB


title: M23_right-ear_treatment_0min

description: Re M23 0h

tag: age

value: right

value: treatment


title: Day20_CM_DMSO_siNC_2

value: DMSO


title: primary CRC22.T


title: MUC29182_1

value: lung

value: Lung cell suspension

tag: disease state

tag: timepoint

value: 14 days after bleomycin

tag: index


title: Day20_CM_DMSO_siRARA_siRARB_1


title: primary CRC22.P

tag: tissue type


title: Day20_CM_Am80_siRARA_1

value: RARA


title: MUC29185

tag: cell type

value: control oligo


title: M14_left-ear_treatment_120min_irradiated

description: Li M14 2h B

value: ear skin

tag: genotype

value: wild-type

value: female

tag: mouse id

value: experimental ear


title: MUC29182_2

value: bleomycin


title: M10_left-ear_treatment_60min_irradiated

description: Li M10 1h B

tag: location

value: left

tag: group


title: MUC29181_4

description:
single cell 3' mRNA library (10x Genomics)
BleoC_barcodes.tsv.gz
BleoC_features.tsv.gz
BleoC_matrix.mtx.gz

tag: strain


title: Day20_CM_DMSO_siRARA_1

value: siRNA


title: primary CRC22.H

value: colon

value: non-neoplastic


title: MUC29181_3


title: primary CRC20.T

value: tumor


title: M12_left-ear_treatment_30min_irradiated

description: Li M12 30' B

tag: Sex

value: treatment

tag: group 2


title: Day20_CM_Am80_siRARB_1

tag: treatment

value: RARB


title: M16_left-ear_treatment_10min_irradiated

description: Li M16 10' B

tag: tissue

tag: timepoint (min)


title: MUC29182_4

value: lung


title: MUC29181_2

value: Lung cell suspension


title: primary CRC20.P

value: peritumor


title: M23_left-ear_treatment_0min_irradiated

description: Li M23 0h B


title: Day20_CM_DMSO_siRARB_1

tag: experiment

value: DMSO

tag: sirna


title: Day20_CM_Am80_siNC_1

value: NC


title: M24_left-ear_control_0min

description: Li M24 direkt K

value: ear skin

tag: age

value: control

value: none experimental ear


title: primary CRC20.H


title: MUC29180_4

description:
single cell 3' mRNA library (10x Genomics)
Sham21_barcodes.tsv.gz
Sham21_features.tsv.gz
Sham21_matrix.mtx.gz

tag: disease state

value: pbs

tag: timepoint

value: 14 days after bleomycin


title: M7_right-ear_control_120min

description: Re M7 K

value: wild-type

value: female

value: right


title: M9_right-ear_control_60min

description: Re M9 1h K


title: MUC29180_3

tag: index


title: Day20_CM_DMSO_3

description: 2_day20CM_Am80DMSO_DESeq2.normalized.xlsx


title: M2_right-ear_control_30min

description: Re M2 30'


title: primary CRC18.P

value: colon

tag: tissue type


title: primary CRC18.H

value: non-neoplastic


title: MUC29180_2

tag: cell type


title: MUC29180_1


title: MUC29181_1

value: bleomycin

value: control oligo


title: primary CRC17.H


title: M1_right-ear_control_10min

description: Re M1 10'

tag: genotype

tag: mouse id


title: Day20_CM_DMSO_2


title: primary CRC18.T

value: tumor


title: M21_right-ear_control_0min

description: Re M21 direkt K

tag: location

tag: group


title: MUC29179_4

description:
single cell 3' mRNA library (10x Genomics)
ShamC_barcodes.tsv.gz
ShamC_features.tsv.gz
ShamC_matrix.mtx.gz

tag: strain

value: lung

value: Lung cell suspension


title: Day20_CM_DMSO_siNC_1

value: siRNA

value: DMSO


title: Day20_CM_Am80_2


title: primary CRC16.T


title: MUC29179_3


title: primary CRC16.P

value: peritumor


title: Day20_CM_DMSO_1


title: primary CRC16.H


title: MUC29179_2


title: Day20_CM_Am80_1


title: M14_right-ear_treatment_120min

description: Re M14 2h

value: ear skin

tag: Sex

value: treatment

tag: group 2


title: M12_right-ear_treatment_30min

description: Re M12 30'

tag: tissue

value: none experimental ear


title: M10_right-ear_treatment_60min

description: Re M10 1h

tag: timepoint (min)


title: primary CRC15.T


title: Day20_CM_FUCCI_Green_2

description: 1_day20CM_FUCCI_subpopulations_DESeq2.normalized.xlsx

tag: experiment

value: isolated FUCCI subpopulations

tag: treatment

tag: fucci subpopulation

value: Green (Kusabira-Orange(-) and Azami-Green(+))


title: M16_right-ear_treatment_10min

description: Re M16 10'

value: wild-type

tag: age

value: female


title: M7_left-ear_control_120min

description: Li M7 K

value: left

value: control


title: Day20_CM_FUCCI_Red_2

value: Red (Kusabira-Orange(+) and Azami-Green(-))


title: Day20_CM_FUCCI_White_2

value: White (Kusabira-Orange(-) and Azami-Green(-))


title: primary CRC15.H

value: colon

value: non-neoplastic


title: primary CRC15.P


title: M9_left-ear_control_60min

description: Li M9 1h K


title: MUC29179_1

value: lung

value: Lung cell suspension

tag: disease state

value: pbs

value: control oligo

tag: timepoint

value: 14 days after bleomycin


title: Day20_CM_FUCCI_White_1

value: DMSO


title: Day20_CM_FUCCI_Green_1


title: primary CRC14.P

tag: tissue type

value: peritumor


title: M2_left-ear_control_30min

description: Li M2 30'

value: ear skin

value: none experimental ear


title: PMN_WT_B_HIC

city: Philadelphia

first: Alexandra

last: Zezulin

address: 421 Curie Blvd 544 BRB II/III

institute: University of Pennsylvania

data_processing:
Hi-C data was first demultiplexed by Bcl2Fastq v2.20 and then processed using software HiCPro v3.1.0. The ligation sites were obtained by running HiCPro utils script digest_genome.py with option ‘-r ^GATC,G^ANTC’. The reads were aligned to mm10 mouse genome. HiCPro was executed in a sequential mode with modules -s mapping -s proc_hic -s quality_checks for each sample. Valid pairs from different biological replicates were then put into the same folder followed up by running -s merge_persample. The contact matrices were constructed by running -s build_contact_maps and normalized by running -s ice_norm modules. The contact matrix was built in 50-kb resolution for downstream analysis. Hi-C compartments were identified at 50-kb resolution using a “sliding window” strategy. First, the expected matrix was calculated by averaging Hi-C contacts at the same distance. Then, the observed/expected matrix was obtained by summing the observed Hi-C contacts within a window of 500 kb centered at each bin divided by the sum of expected Hi-C contacts in the same window. The observed/expected matrix was then transformed into a Pearson’s correlation matrix. The principal components were then obtained by calculating the covariance matrix of the Pearson’s correlation matrix followed by eigenvector decomposition with the ‘eigen’ function in R. PC1 was used to assign the A and B compartment: regions with positive PC1 values corresponded to the A compartment and negative values corresponded to the B compartment based on their association with gene density.
Assembly: mm10
Supplementary files format and content: The iced.matrix files provided are outputs of the ice_norm module of HiCPro and are normalized contacts between any pair of genomic bins
Supplementary files format and content: The bed file provided genomic coordinates of each bin of the genome for the iced.matrix files

source_name: BM Neutrophils

extract_protocol:
3 million cells were sorted from BM and Hi-C experiments were performed according to the Arima-Hi-C protocol (A510008).
NEBNext Ultra II DNA library Prep kit was used for sequencing library preparation. Briefly, proximally-ligated DNA was fragmented, and an adaptor was added followed by limited-cycle PCR to enrich and add an index to the fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on the NovaSeq 6000.

treatment_protocol: Cells were harvested and were sorted on the same day as harvest

tag: isoloation markers

tag: developmental stage

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Control (Runx1f/f)


title: GMP_WT_B_HIC

source_name: BM GMPs

extract_protocol:
200,000 cells were sorted from BM and Hi-C experiments were performed according to the Arima-Hi-C protocol (A510008).
NEBNext Ultra II DNA library Prep kit was used for sequencing library preparation. Briefly, proximally-ligated DNA was fragmented, and an adaptor was added followed by limited-cycle PCR to enrich and add an index to the fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on the NovaSeq 6000.

value: Lin- cKIT+Sca1-CD16/32+CD150-

tag: genotype


title: PMN_WT_A_HIC


title: PMN_KO_A_HIC

value: Runx1f/f; Cebpa-Cre +


title: PMN_KO_B_HIC


title: M1_left-ear_control_10min

description: Li M1 10'

value: wild-type

value: female

tag: mouse id

tag: location

value: left

value: control


title: primary CRC14.H

value: colon

value: non-neoplastic


title: Day20_CM_FUCCI_Red_1

value: isolated FUCCI subpopulations

value: Red (Kusabira-Orange(+) and Azami-Green(-))


title: primary CRC14.T

value: tumor


title: GMP_WT_A_HIC

tag: strain


title: primary CRC13.T


title: M21_left-ear_control_0min

description: Li M21 direkt K

tag: Sex

tag: group


title: primary CRC13.P

tag: tissue

value: peritumor


title: M8_right-ear_treatment_120min

description: Re M8 2h

value: ear skin

value: right

value: treatment

tag: group 2

tag: timepoint (min)


title: M4_right-ear_treatment_30min

description: Re M4 30'

value: none experimental ear


title: GMP_KO_A_HIC

value: Adult (4-6 weeks old)

value: Bone Marrow


title: primary CRC13.H


title: RNA-seq of Ahr cKO dextran treated SI ILC3 Sample 5

city: Gainesville

first: Liang

last: Zhou

state: Fl

address: 2015 SW 16th Ave

institute: University of Florida

description: RNA-seq of Ahr cKO treated SI ILC3 Sample 2

data_processing:
FastQC (v0.11.5) was used to ensure high per-base sequence quality of reads. Sequenced reads were mapped and raw count values quantified with STAR78 to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25). Differentially expressed genes (max FPKM ≥ 1, fold change ≥ 1.5, q-value ≤ 0.05) were identified by DESeq2 (v1.26.0) analysis. Gene Set Enrichment Analysis (GSEA) was performed for Gene Ontology (GO) analysis. Log2 transformed FPKM values were used for principal component analysis in R (v3.6.2) with the prcomp function and then visualized using the factoextra package (v1.0.7). Heatmaps were created using the R package pheatmap (v1.0.12).
Assembly: mm10
Supplementary files format and content: Raw_Counts.txt

source_name: SI

extract_protocol:
RNA was extracted using the RNAeasy Micro Kit (TaKaRa), followed by complementary DNA (cDNA) generation with the SMART-Seq® HT Kit (TaKaRa).
Sequencing libraries were generated with the Nextera® XT DNA Library Preparation Kit (Illumina), and sequenced on the Illumina HiSeq 2500 instrument.

treatment_protocol: ILC3 cells (Lin–CD90hiCD45lo) were FACS-sorted from the gut of indicated mice.

value: SI

tag: cell type

value: Ahr F/F Rorc-cre

tag: treatment

value: Treated


title: RNA-seq of Ahr cKO dextran treated SI ILC3 Sample 6

description: RNA-seq of Ahr cKO treated SI ILC3 Sample 3


title: Normal, Wild Type, Lineage Negative BM Tissue, 4

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

data_processing:
Gene specific analysis was performed using Partek® Flow® software, v10.0. In Partek Flow, alignment was performed  using “STAR” aligner and quantification was done using “Quantify to annotation model (Partek E/M)”. Normalization was performed using “Poscounts (Deseq2 only)” method. Low expressing genes were filtered by removing features/genes with geometric mean of 10 or lower for all samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized DeSeq2(poscount) values for each Sample.

source_name: BM Tissue

growth_protocol: All mouse genotypes(Wild type, NUP98-NSD1/FLT3-ITD) were maintained from birth in mice facility.

extract_protocol:
Total RNA was isolated from leukemic NUP98-NSD1/FLT3-ITD bone marrow and Wild Type bone marrow using TRIzol reagent following the manufacturer’s recommended protocol
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA library Prep protocol.

value: BM Tissue

value: Wild Type


title: M3_right-ear_treatment_10min

description: Re M3 10'

value: wild-type

tag: age

value: female


title: primary CRC05.T

value: colon


title: RNA-seq of Ahr cKO untreated SI ILC3 Sample 3

value: Ahr F/F

value: Untreated


title: Normal, Wild Type, Lineage Negative BM Tissue, 3


title: primary CRC05.P

value: peritumor


title: RNA-seq of Ahr cKO untreated SI ILC3 Sample 2


title: M22_right-ear_treatment_0min

description: Re M22 0h

value: ear skin


title: Normal, Wild Type, Lineage Negative BM Tissue, 2


title: RNA-seq of Ahr cKO untreated SI ILC3 Sample 1


title: Normal, Wild Type, Lineage Negative BM Tissue, 1


title: primary CRC05.H

value: non-neoplastic


title: primary CRC04.T

value: tumor


title: Tc_3

data_processing:
Single-end run (SE50) run was performed using a HiSeq2500, MiSeq or a NextSeq 500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: mm10
Supplementary files format and content: raw microRNA counts in txt.format

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions or the cell lysate was used.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: lung

value: T-cells

value: WT

value: no treatment


title: M4_left-ear_treatment_30min_irradiated

description: Li M4 30' B

value: left

value: treatment

value: experimental ear


title: M8_left-ear_treatment_120min_irradiated

description: Li M8 2h B


title: GMP_KO_B_HIC

value: Lin- cKIT+Sca1-CD16/32+CD150-

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Runx1f/f; Cebpa-Cre +


title: Normal, Wild Type, Whole BM Tissue, 4

value: BM Tissue

value: Wild Type


title: primary CRC04.P

value: colon

value: peritumor


title: Day20_CM_Am80_3

tag: experiment

value: DMSO


title: Tc_2


title: Normal, Wild Type, Whole BM Tissue, 3


title: M3_left-ear_treatment_10min_irradiated

description: Li M3 10' B

value: ear skin

value: wild-type

value: female


title: RNA-seq of Ahr cKO dextran treated SI ILC3 Sample 4

description: RNA-seq of Ahr cKO treated SI ILC3 Sample 1

source_name: Si

value: Si

value: Ahr F/F Rorc-cre

value: Treated


title: Normal, Wild Type, Whole BM Tissue, 2


title: primary CRC04.H

value: non-neoplastic


title: IM_3

value: lung

value: Interstitial macrophages

value: WT

value: no treatment


title: IM_2


title: primary CRC03.T

value: tumor


title: Normal, Wild Type, Whole BM Tissue, 1

value: BM Tissue


title: primary CRC03.P


title: IM_1


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 7


title: M50_right-ear_control_0min

description: Re M50 0h K gefällt

value: right

value: control

value: none experimental ear


title: M47_right-ear_control_10min

description: Re M47 10' gefällt


title: primary CRC03.H

value: colon


title: AM_3

value: Alveolar macrophages


title: liver metastasis CRC73

source_name: liver metastasis from colorectal cancer

extract_protocol:
RNA was extracted from OCT-embedded samples using AllPrep DNA/RNA Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease state

value: metastasis


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 6


title: AM_2


title: AM_1


title: M50_left-ear_control_0min

description: Li M50 0h K gefällt

value: ear skin

value: wild-type

value: female

value: left


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 5


title: M22_left-ear_treatment_0min_irradiated

description: Li M22 0h B

value: treatment

value: experimental ear


title: M47_left-ear_control_10min

description: Li M47 10' gefällt


title: liver metastasis CRC71


title: liver metastasis CRC65


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 4


title: LT_D0_3

value: lung

value: WT


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 3


title: M32_right-ear_control_120min

description: Re M32 2h K gefällt


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 2


title: LT_D0_2


title: liver metastasis CRC62


title: liver metastasis CRC61.2


title: M42_right-ear_control_120min

description: Re M42 2h K gefällt


title: LT_D0_1


title: AML, NUP98NSD1/FLT3ITD, BM Tisssue, 1


title: M35_right-ear_control_30min

description: Re M35 30' K gefällt


title: liver metastasis CRC61


title: RUNX1_CUT_IgG

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) or the E. coli K12 genome using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches and MAPQ equal or greater than 30 were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling with the following parameters: narrow, q: 0.05. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0. The following parameters were used: normalized to Bins Per Million mapped reads (BPM bin size: 50. IGV or UCSC genome browser was used for visualization.
Assembly: mm10
Supplementary files format and content: BigWig files provided are normalized tracks of merged replicates
Library strategy: CUT&RUN

extract_protocol:
Cells were sorted from the bone marrow. CUT&RUN reactions were performed using 200,000 FACS-sorted cells.
Libraries were constructed using NEBNext Ultra II DNA Kit. Libraries were size-selected at 150-350 bp  by AMPure XP beads. Libraries were quantified with KAPA, qPCR, and bioanalyzer prior to paired-end sequencing.

value: Lin- cKIT+Sca1-CD16/32+CD150-

value: Adult (4-6 weeks old)

value: Bone Marrow

value: Control (Runx1f/f)

tag: chip antibody

value: IgG negative control (ABIN101961)


title: M42_left-ear_control_120min

description: Li M42 2h K gefällt

extract_protocol:
The ears were immersed in RNAlater for 12 hours at 4°C and subsequently frozen at -80°C. RNA was isolated using miRNeasy Mini kit (Qiagen, Hilden, Germany) after manufacturers recommendations. RNA quantity and quality was determined using Nanodrop (ThermoFisher Scientific, Waltham, MA, USA) and Bioanalyzer RNA Nano Chip Kit (Agilent Technologies, Santa Clara, CA, USA). Mean RNA Integrity Number (RIN) of the samples was 8.2 ± 0.9.
SmallRNA sequencing libraries were prepared using MGIEasy Small RNA Library Prep Kit on the high-throughput MGI SP-960 sample prep system (MGI Tech, Shenzhen, China). According to the manufacturer's protocols, the 3’- and 5’-adapters were ligated to the RNA. Afterwards, an RT primer including sample-specific barcodes was utilised to perform reverse transcription (RT). Amplification of the cDNA was achieved using a polymerase chain reaction (PCR) with 21 cycles. PCR products were subsequently size selected via AMPure Beads XP (Beckman Coulter, Brea, CA, USA). Size and 449 concentration of the purified PCR products were determined using an Agilent DNA 1000 Kit (Agilent Technologies, Santa Clara, CA, USA) and QubitTM 1X dsDNA High Sensitivity (HS) (ThermoFisher Scientific, Waltham, MA, USA), respectively. Fifteen samples and one performance control sample were pooled in an equimolar fashion in one sequencing library, which was circularized using the MGI Easy circularisation kit. In total, we prepared 8 libraries composed of a total of 120 samples
Samples were sequenced on DNBSEQ-G400RS with DNBSEQ-G400RS High-throughput Sequencing Set (Small RNA FCL SE50) by BGI in Wuhan, China.

value: control

value: none experimental ear


title: M45_right-ear_control_0min

description: Re M45 0h K gefällt

value: right


title: HN9.10 cells treated with 100 nmol/L ceramide, replicate 3 [2-2c_S2]

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

institute: Università degli Studi di Udine

data_processing:
Quality control for raw sequencing reads was performed using the FastQC (v0.11.9) and MultiQC (v1.4)
Reads had very good quality and no correction was required. Cutadapt (ver 1.15) was used to remove the 3’adapter, primer and other types of unwanted sequences.
Alignment of reads was conducted with STAR (v2.5.3a) using the mouse genome assembly GRCm38 (mm10) with reference annotation; reads were assigned to a miRNA based on GENCODE annotations and via the STAR function “quantMode TranscriptomeSAM GeneCounts”.
Differential expression analysis was performed using gene raw counts, within the R/Bioconductor DESeq2 package; we estimated the dispersion parameter for each library using the biological group dispersion.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Immortalized hippocampal neurons HN9.10e were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin, and 2.5 μg/mL amphotericin B. Cells were maintained at 37 °C in a saturating humidity atmosphere containing 95% air and 5% CO2.

extract_protocol:
Exosome Isolation: Exosomes released in the culture medium from untreated HN9.10e cells (control sample) and Cer-treated HN9.10e cells (experimental sample) were isolated after 48 hours of treatment. The supernatant was centrifuged at 2000g x 30 min, filtered with 0.22µm filter unit (MILLEX-GS from Millipore, Molsheim, France), in order to remove larger extracellular vesicles and apoptotic bodies, and concentrated with Pierce™ Protein Concentrators PES, 100K MWCO from Thermo Scientific™. Then, the retained in the filter was used to isolate exosomes with “total exosome isolation” kit from Invitrogen-Thermo Fisher Scientific (Waltham, MA, USA) by following the instructions of the company. Exosomal miRNA Isolation: The exosomes-containing pellet was resuspended in 200ul of PBS buffer, quantified using the Exosome Quantitation Kit (System Biosciences) and stored at −80 °C until use. Total RNA was extracted from 5×1010 exosomes using mirVana miRNA Isolation kit (Life Technologies) and miRNA concentration was determined by Qubit microRNA assay kit (Invitrogen).
Sequencing libraries were prepared based on the QIAseq miRNA library kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions. Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Quantified libraries were mixed at an equimolar ratio and sequenced on single-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA).

treatment_protocol: To study the effect of ceramide on cell differentiation and exosome release, ceramide was added to the culture medium at the 100 nmol/L concentration corresponding to the amount of ceramide present in exosomes released under vitamin D3 treatment, as previously reported (Conte et al., 2021). To investigate the effect of exosomes released under ceramide treatment on cell differentiation, exosomes were added to the culture medium with increasing concentration of exosomes (protein concentration from 200 to 300 µg/106 cells), considering that 1x106 cells were able to release exosomes corresponding to 250 µg protein.

tag: cell line

value: Immortalized hippocampal neurons

value: 100 nmol/L ceramide

tag: molecule subtype

value: Exosomal miRNA


title: liver metastasis CRC60

value: liver

value: metastasis


title: M35_left-ear_control_30min

description: Li M35 30' K

value: ear skin

tag: genotype

value: wild-type

value: female

value: left


title: HN9.10 cells treated with 100 nmol/L ceramide, replicate 1 [2-2_S1]

value: WT


title: liver metastasis CRC58


title: M26_left-ear_control_10min

description: Li M26 10' K

tag: mouse id


title: liver metastasis CRC59