title: RMC_EXOs_3D

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description:
Library name: Sample 1
Fetal bovine serum was centrifuged at 4°C, 160,000×g, and 16 hours. Collect the clear liquid on the top layer after centrifuging the fetal bovine serum, and this liquid is the low exosome serum. The 3D culture system was successively circulated internally and externally with enzyme-free and sterile PBS, DMEM, and complete medium containing 10% fetal bovine serum for 24-48 hours. Then, the ASCs were inoculated into the outer circulation culture cylinder of the 3D system and repeatedly tapped until the cells adhered evenly. We would invert the culture tube up and down every 30 minutes, and then connect it to the complete culture medium after 2 hours and 30 minutes. The sugar consumption in the complete culture medium should be checked every other day to replace it with fresh complete culture medium in a timely manner. Then, the supernatant was subjected to gradient centrifugation to harvest exosomes. Briefly, the process involved centrifugation at 4°C for 15 minutes at 300×g, followed by 30 minutes at 2000×g, then 30 minutes at 10000×g, and finally 2 hours at 120000×g.

data_processing:
CASAVA  bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Assembly: reference sequence database was the bovine genome database
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Cervus nippon

source_name: antler

extract_protocol:
The total RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The supernatant was subjected to gradient centrifugation to harvest exosomes. Briefly, the process involved centrifugation at 4°C for 15 minutes at 300×g, followed by 30 minutes at 2000×g, then 30 minutes at 10000×g, and finally 2 hours at 120000×g.

value: antler

value: ASCs

value: antler mesenchymal stem cell

value: WT

value: 3D ASC Exos collected from the supernatant of ASCs in a 3D culture system

tag: batch


title: H07spimpLA2347sclero

status: Public on Dec 02 2025

type: SRA

city: Kiel

first: Severin

last: Einspanier

address: Hermann-Rodewald-Straße 9

department: Department of Plant Pathology and Protection

country: Germany

institute: Christian-Albrechts-University Kiel

description: Library name: sample77

library_source: transcriptomic

data_processing:
We used cutadapt for trimming&quality filtering
rRNA was depleted using STAR, non-mapping reads were used for further analysis
Reads were mapped to each species' reference genome using STAR.
We used featurecounts for read quantification.
FastQC and MultiQC were used for quality assessment.
Assembly: PRJEB5809, PRJCA008297, PRJNA607731, PRJNA727176, PRJNA1210999
Supplementary files format and content: txt-file contaning read counts per gene (not transcript!).

molecule: total RNA

organism: Solanum pimpinellifolium

source_name: leaf

growth_protocol: Per accession, a single plant was grown in standard greenhouse conditions and occasionally propagated by cuttings. For the sequencing experiments, single leaflets were sampled from the plants and incubated in a humid envoironment. Sclerotinia sclerotiorum strain 1980 was gron fresh from sclerotioa on cultivated in potato dextrose agar,at 20°C in the dark.

extract_protocol:
RNA was isolated using the Quick-RNA Plant Kit (ZYMO RESEARCH). We pooled 2x2cm parts of two independent leaves into DNA/RNA-shield (ZYMO RESEARCH). 0.5ng/µL RNA was used for library preparation.
We used the 3' mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12nt) with PCR Add-on and Reamplification Kit V2 for Illumina, and the SIRV-Set 3 for in-house library preparation, following the manufacturers iinstructions.

treatment_protocol: Inoculated leaves were treated my a mycelial suspension. For this, potato dextrose broth medium was inoculated with S. Sclerotiorum agar-plugs and incubated for four days on a rotary shaker (120 rpm). The mixture was then mixed, vaccuum-filtered and diluted to an OD=1. Tween80 was added. Empty PDB was used for the mock-treatment

tag: tissue

value: leaf

tag: genotype

tag: treatment

value: sclero


title: AB.CVID21

city: Vienna

first: Ola

last: Grimsholm

address: Wahringer Gurtel 18-20

department: Pathophysiology and Allergy Research

country: Austria

institute: Medical University of Vienna

description:
Library name: Sample 7
CD27 bright memory cells_CVID

data_processing:
Paired-end sequencing (2 x 75 bp) was performed on an Illumina NextSeq 500. Base calling was done by RTA software and demultiplexing to paired-end FASTQ files was performed with CASAVA (v1.8.2).
Adapter sequences were trimmed using Trimmomatic (v0.39). Filtering parameters were set to SLIDINGWINDOW:4:20 and MINLEN:25.
Reads were aligned to human GRCh38 using STAR (v2.6.1a) in 2-pass mode, and quantified at the gene level with featureCounts (v2.0.6) and Ensembl 110 GTF annotation.
Assembly: human GRCh38/Ensembl 110 GTF
Supplementary files format and content: Tab-delimited text file includes gene raw counts for each sample  obtained with featureCounts v2.0.6

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro kit (QIAGEN).
Library preparation was performed using the Illumina TruSeq Stranded mRNA kit. The protocol included mRNA enrichment with oligo-dT beads, dUTP-based second-strand synthesis for strand specificity, indexing with TruSeq set A, and amplification via a 15-cycle PCR, with AMPure XP bead purification.

treatment_protocol: Naive B cells and CD27bright MBCs were stimulated with 1 μg/mL rhCD40L plus 10 μg/mL anti-IgM/IgG/IgA and 20 ng/mL rhIL-21 or 0.35 μM TLR9 agonist CpG-B ODN2006 for 48 hours in complete medium at a concentration of 2.5x106 cells/mL.

value: peripheral blood

tag: cell type

value: CD27 bright memory cells

value: CVID

value: TLR9 agonist (CpG) for 48 hours


title: 9 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 48h, Replicate 1

city: Louvain-la-Neuve

first: Charles

last: Hachez

address: Croix du Sud 4

department: LIBST

country: Belgium

institute: UCLouvain

data_processing:
Using CLC Genomic Workbench (Qiagen), reads were cleaned and trimmed of adaptors, ambiguous nucleotides, homopolymers in 3’ and 5’ and for quality (PHRED30) and minimum length.
They were then mapped to the N. tabacum TN90 reference genome (GCF_000715135.1_Ntab- TN90_genomic)
Identification of differentially expressed genes (DEGs) was based on normalized gene expression calculated as counts per million mapped reads (CPM), analyzed with a fold change (FC) >1.5 or <0.67 and a p-value <0.05 using Rstudio with EdgeR package (Law et al., 2016)
Assembly: GCF_000715135.1_Ntab- TN90_genomic
Supplementary files format and content: RNAseq Inducible MIXTA results.xlsx is a xls file identifying the differentially expressed genes (DEGs). This is based on normalized gene expression calculated as counts per million mapped reads (CPM), analyzed with a fold change (FC) >1.5 or <0.67 and a p-value <0.05 using Rstudio with EdgeR package.
Supplementary files format and content: "RNAseq_Raw.xlsx" is a xls file giving, for each locus  the normalized gene expression calculated as counts per million mapped reads (CPM) for control (MS4, MS3,MS2) or induced conditions (BE4,BE3,BE2), the calculated fold change compared to control conditions as well as the associated p value.

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: Aerial parts of 9 day-old seedlings

growth_protocol: N. tabacum cv Petit Havana (SR1) was utilized for stable plant transformation. Seeds were surface-sterilized with chlorine gas, sown on half-strength Murashige and Skoog agar plates (4.4 g/L MS basal medium, MP Biochemicals, catalog no. 92610024; 30 g/L sucrose; 8 g/L agar; pH adjusted to 5.6 with KOH), stratified at 4°C for 3 days, and subsequently transferred to a growth chamber with a 16-hour light/8-hour dark cycle, 50 μmol photon/m2/s, at 25 ± 2°C. Selected T2 seeds were sterilized, sown, stratified, and grown under control and β-estradiol-supplemented conditions for 7 days. Aerial parts from 15 seedlings were collected at 4 and 48 hours post-induction for RNA extraction.

extract_protocol:
Tissues were frozen in liquid nitrogen, ground, and RNA was extracted using the Spectrum Plant Total RNA Kit with on-column DNase I digestion.
The RNA-seq libraries were generated and sequenced by Genewiz (Azenta life science) using Illumina NovaSeq sequencing plateform. A minimum of 38 million 150 bp paired-end reads were obtained per sample

value: Aerial parts of 9 day-old seedlings

tag: cultivar

value: Petit Havana

value: B-estradiol 48h

tag: time


title: 9 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 48h, Replicate 3

treatment_protocol: Selected T2 seeds were sterilized, sown, stratified, and grown under control and β-estradiol-supplemented conditions for 7 days. Aerial parts from 15 seedlings were collected at 4 and 48 hours post-induction for RNA extraction.


title: Leaf primordia SR1, Halo-tagged GFP (Negative control), replicate 2

library_source: genomic

data_processing:
The DNA-seq libraries were sequenced by Macrogen using Illumina NovaSeq 6000 sequencing platform. A minimum of 50 million 150 bp paired-end reads were obtained per sample
Using CLC Genomic Workbench (Qiagen), reads were cleaned and trimmed of adaptors, ambiguous nucleotides, homopolymers in 3’ and 5’ and for quality (PHRED30) and minimum length
They were then mapped to the N. tabacum TN90 reference genome (GCF_000715135.1_Ntab- TN90_genomic)
Peak scores (>2) and p-values (<0.05) were then calculated using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench comparing our samples to the negative control (DNA bound to nlsGFP).
Assembly: GCF_000715135.1_Ntab- TN90_genomic
Supplementary files format and content: "DAPseq ZFP8 results.xlsx" and "DAPseq MIXTA results.xlsx" are tab delimited text files giving the calculated Peak scores (>2) and p-values (<0.05) using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench comparing our samples to the negative control (DNA bound to nlsGFP). Peaks of interest were selected based on their proximity to a gene: 3kb upstream of a START codon and 1kb downstream of a STOP codon.
Supplementary files format and content: "DAP_seqZFP8_raw.xlsx" and "DAP_seqMIXTA_raw.xlsx" are tab delimited text files providing for each detected DAPseq Peak the  following information: chromosome, genomic region, peak center, Peak length, Peak shape score and P-value calculated using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench.
Library strategy: DAP-seq

molecule: genomic DNA

source_name: Leaf primordia

extract_protocol:
Leaf primordia harvested from three independent WT plants were flash-frozen, grinded and DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega; A1120).
DNA was fragmented using a sonicating bath for 20 min (Elam S10H Elmasonic) and fragment size was verified on gel.
the DNA fragments were subjected to end-repair (Fast DNA end repair kit, Thermoscientific, K0771), A-tail reaction using Klenow enzyme (NEB, M0212S), ligation to the adaptor (Promega, M1794) and DNA concentration measurement (Qubit dsDNA Assay kit, Qiagen, Q32850). HALO-AmMIXTA, HALO-NtZFP8 and HALO-nlsGFP (negative control) were expressed independently three times using the TnT® Coupled Wheat Germ Extract System (Promega, L41030). Expression was confirmed by Western-blot using Monoclonal Antibody Raised Against the HaloTag® Protein (Promega, G9211) and Goat anti-mouse IgG (H+L) HRP conjugated (Chemicon, AP308P).  Proteins were bound to the 20μl of Magne® HaloTag Beads (Promega, G7882) per sample, washed and put in contact with 1000 ng of DNA for 1h at 25°C. Each replicate of proteins was put in contact with one replicate of DNA. Beads were washed and DNA was eluted in EB at 98°C. Index and adaptor were added to the DNA fragments using Phusion® High-Fidelity DNA polymerase (NEB, M0530L) and NEBNext® Multiplex Oligos for Illumina® primers (NEB, E6440S), and DNA check on gel and was purified using the minelute reaction cleanup kit (Qiagen, 28204)

treatment_protocol: The DAPseq experiment was executed following the protocol from Bartlett et al. (2017) with some small modifications.

value: Leaf primordia

tag: expressing

value: Halo-tagged GFP (Negative control)


title: BALF, Others_35

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

country: South Korea

institute: Soonchunhyang University

data_processing:
The raw 16S amplicon sequences were processed by QIIME2 v1.8.0 with default parameters.
We then used SHI7 for trimming Nextera adapters and stitching paired-end reads and performed quality trimming at both ends of the stitched reads until a minimum Phred score of 32 was reached.
The OTUs were determined by de novo clustering of the sequences with a 97% sequence identity cut-off by QIIME
We performed alpha- and beta-diversity analyses in R using the vegan and phyloseq packages.
Based on the OTU table, we calculated the average richness estimate for each alpha-diversity metric (Chao1, observed OTUs, and Shannon).
Supplementary files format and content: OTU.xlsx
Library strategy: 16s rRNA seq

organism: human lung metagenome

source_name: Bronchoalveolar lavage fluid

extract_protocol:
From BALF samples, DNA was extracted by the QIAamp DNA microbiome kit (Qiagen, 51704).
We used Herculase II Fusion DNA Polymerase Nextera XT Index Kit V2, and sequencing instrument model was Illumina MiSeq.

value: Bronchoalveolar lavage fluid

tag: disease state

value: Others

tag: Sex

value: Male

tag: age

tag: bmi


title: CD4TILs, RELB, Donor43

city: Durham

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

country: USA

institute: Duke University

description: Library name: T43 CD4 RELB

data_processing:
Initial data processing was performed on FASTQ files using MiXCR using the present for the SMARTer Human TCR a/b kit
The R package immunarch was used to analyze effective number of types for TCR diversity across samples to account for both number of clones and relative abundance.
Assembly: MiXCR V-, D-, J-, and C- gene segment librar for Homo sapiens
Supplementary files format and content: .tsv files were generated from MiXCR exporClones function. File outputted includes clonotype abundances, nucleotide and amino acid clonotype sequences, Phred qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene regions present in sequence
Library strategy: TCR-Seq

source_name: NSCLC tumor

extract_protocol:
RNA was isolated using Norgen’s Total RNA Purification Plus Kit
Takara’s SMARTer Human TCR a/b Profiling Kit v1 was used to generate TCR-seq libraries. Library generation and purification methods were carried out according to manufacturer protocol.

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

value: RELB


title: BALF, NTM_20

value: NTM


title: DPTILs, RELB, Donor36

description: Library name: T36 DP RELB

value: DP


title: H08spimpLA1332sclero

description: Library name: sample78

value: leaf

value: sclero


title: 9 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 48h, Replicate 2


title: G08spimpLA1332sclero

description: Library name: sample68


title: BALF, Others_34

value: Female


title: CD4TILs, Untransduced, Donor43

description: Library name: T43 CD4 -

value: Untransduced


title: CD8TILs, RELB, Donor36

description: Library name: T36 CD8 RELB


title: CD4TILs, RELB, Donor36

description: Library name: T36 CD4 RELB


title: 9 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 48h, Replicate 1

value: Aerial parts of 9 day-old seedlings

value: Control 48h


title: BALF, NTM_21


title: F07spimpLA2347sclero

description: Library name: sample57


title: BALF, TB_28

value: TB


title: 9 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 48h, Replicate 3

value: Petit Havana


title: BALF, Others_32


title: F08spimpLA1332sclero

description: Library name: sample58


title: BALF, NTM_19


title: CD8TILs, Untransduced, Donor36

description: Library name: T36 CD8 -


title: BALF, Others_31


title: G07spimpLA2347sclero

description: Library name: sample67


title: CD4TILs, Untransduced, Donor36

description: Library name: T36 CD4 -


title: 7 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 4h, Replicate 3

source_name: Aerial parts of 7 day-old seedlings

value: Aerial parts of 7 day-old seedlings

value: B-estradiol 4h


title: BALF, TB_27

value: Bronchoalveolar lavage fluid


title: 7 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 4h, Replicate 1


title: E08spimpLA1332sclero

description: Library name: sample48


title: DPTILs, RELB, Donor49

description: Library name: T49 DP RELB


title: BALF, TB_26

value: Male


title: E07spimpLA2347sclero

description: Library name: sample47


title: DPTILs, Untransduced, Donor49

description: Library name: T49 DP -

value: NSCLC tumor


title: 7 day-old Nicotiana tabacum SR1 seedling, induced by estradiol and collected at 4h, Replicate 2


title: 9 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 48h, Replicate 2


title: D08spimpLA1332mock

description: Library name: sample38

value: mock


title: 7 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 4h, Replicate 3

value: Control 4h


title: CD8TILs, RELB, Donor49

description: Library name: T49 CD8 RELB

value: tumor-infiltrating lymphocytes

value: RELB


title: D07spimpLA2347mock

description: Library name: sample37

value: leaf


title: 7 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 4h, Replicate 2


title: CD8TILs, Untransduced, Donor49

description: Library name: T49 CD8 -


title: BALF, TB_24


title: CD4TILs, RELB, Donor49

description: Library name: T49 CD4 RELB


title: 7 day-old Nicotiana tabacum SR1 seedling, Non induced and collected at 4h, Replicate 1


title: BALF, TB_25


title: C07spimpLA2347mock

description: Library name: sample27


title: CD4TILs, Thy1.1, Donor49

description: Library name: T49 CD4 Thy1.1


title: B08spimpLA1332mock

description: Library name: sample18


title: BALF, NTM_18

value: NTM


title: BALF, NTM_17

value: Female


title: Day 100 marrow from patient 9

city: New York

first: Alan

last: Hanash

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: 9_100_IGO_15877_1_S40

library_source: transcriptomic single cell

data_processing:
Cellranger v.8.0.0 was used for initial processing of the single cell RNA reads.
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 feature matrix

source_name: Bone marrow

extract_protocol:
Viably-frozen bone marrow mononuclear cells were thawed into prewarmed and filtered 1640 RPMI (Gibco, catalog #11875093) with 10% FBS. Cells were suspended in Human FcR Blocking Reagent (Miltenyi Biotec, catalog #130-059-901) diluted in Filtered DPBS (Corning, catalog #21-031-CM) + 0.5% BSA (Fisher, catalog #F2442-500ML) and incubated for 10 minutes at 4ºC. Brilliant Staining Buffer (BD, catalog #563794) and surface antibody mix (CD3 PE-Cy7, Invitrogen catalog#25-0038-42; CD45 BV510, Biolegend catalog #369526, CD56 BUV737, Biolegend catalog #612766; CD19 BV605, Biolegend catalog #302244) was added to the cells in blocking solution and incubated for 30 minutes at room temperature, protected from light. Cells were washed in filtered DPBS + 0.5% BSA and filtered using 30 um filters (Sysmex), before they were resuspended in in filtered DPBS + 2% BSA + DAPI. Cell populations were sorted using Fluorescent Activated Cell Sorting (FACS) on the Aria3 instrument (BD), and the population of interested was selected based on CD45-positivity and FSC-A vs SSC-A size gating to enrich for lymphocytes. Cells were advanced to sequencing in DPBS + 0.04% BSA. Single cell suspensions were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability.
Following QC, samples were loaded onto Chromium Next GEM Chip K (10X Genomics PN 1000286) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 18-23K cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 50 ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq X in a PE28/88 run using the NovaSeq X 25B Reagent Kit (300 cycles) (Illumina). An average of 52K reads was generated per cell.

value: Bone marrow

value: allogeneic hematopoietic cell transplantation


title: CD4TILs, Untransduced, Donor49

description: Library name: T49 CD4 -

value: Untransduced


title: BALF, TB_23

value: TB


title: DPTILs, RELB, Donor50

description: Library name: T50 DP RELB

value: DP


title: CD8TILs, RELB, Donor50

description: Library name: T50 CD8 RELB


title: ko2_Se_d8_sp

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

description: Library name: ko2_Se_d8_sp

data_processing:
for RNA-seq: fastp for trimming, mapping with STAR, indexing bam with samtools, BigWig with deepTools, counting reads with FeatureCouts,                         EdgeR log2 for transforming counts, Identifying Differential Expressed Genes with DESeq2.
for ATAC-seq:  The nfcore/atacseq bioinformatic pipeline (https://nf-co.re/atacseq/2.1.2/ ) was used for the ATAC-seq data analysishttps://nf-co.re/atacseq/2.1.2/. Briefly, after adapter trimming the reads were mapped to the human genome (hg38) using Bowtie2 with default paired-end settings. Next, all non-nuclear reads, and unmapped paired reads were discarded. Duplicated reads were removed with picard MarkDuplicates. Filtering to remove unmapped regions, mitochondrial DNA and blacklisted regions was done using SAMtools. Macs2 was used for broad peak calling and HOMER for peak annotation (annotatePeaks.pl). Motif enrichment analysis was conducted with Homer (findMotifsGenome.pl). The normalized bigWig files, scaled to 1 million mapped reads, were created with BEDTools. Differential accessibility analysis was carried out using DESeq2. IGV platform was used for visualization of bigWig tracks, peaks and differential sites.
for scRNA-seq: The raw scRNA-seq data were processed with bcl2fastq v2.20 to demultiplex samples and convert .bcl files to .fastq format. For initial data processing and some basic analyses 10xGenomics Cell Ranger pipelines and Seurat R package were used.
Assembly: Assembly: genome_hs_38_94/Homo_sapiens.GRCh38.94
Supplementary files format and content: text file, tsv.gz, mtx.gz

source_name: cell line

growth_protocol: Cells cultured in StemFlex (Thermo Fisher Scientific) medium on Geltrex (Thermo Fisher Scientific)-coated plates at 37 °C, under an atmosphere containing 5% CO2. Cells were passaged every 3-4 days using PBS-EDTA.

extract_protocol:
For RNA-seq: WT and GPX2 stem cells derived foregut endoderm and WT, GPX2 KO, WT treated with H2O2 (10nM) and GPX2 KO treated with sodium selenite (100pM) definitive endoderm cells differenced spontaneously for additional 5 days were subjected to RNA-seq.  Total RNA was extracted and purified using Trizol as previously described (Varshney et al., 2017). RNAseq was performed according to the TruSeq RNA Library Prep Kit protocol.
For ATAC-seq: The WT, GPX2 KO definitive endoderm cells differented spontanously  for additional 5 days were subjected to ATAC-seq. Cells  were dispersed to single cells using TrypLE. The 5 x 104 cells were resuspended in 50 µl of cold ATAC-RSB buffer (10mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2,, 0.1% Tween-20, 0.1% NP-40). For nuclei extraction, the cells were incubated with 0.1% digitonin for 3 min at 4 °C and centrifuged at 500 x g for 10 min at 4 °C with the addition of 1 ml ATAC-RSB. The supernatant was discarded, and nuclei were prepared for the transposition reaction. The solution containing transposed fragments was purified using the Zymo DNA Clean & Concentrator (Zymo Research, USA) and the transposed DNA was eluted in 20 μl H2O and stored in -20 °C. Barcoded adapters were added to the transposed fragments by PCR with the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs, USA), according to the producer protocol and after purified with the AMPure XP beads. The samples were 150 bp paired-end sequenced on the NovaSeqX platform.
For scRNA-seq: The WT and GPX2 KO stem cells derived beta cells or early pancreatic progenitors cells were dispersed with Tripsin, washed with 0.1% saponin – 1% BSA – PBS, filtered through 30 μm mesh filter. Afterwards cells were counted using Countess and adjusted to 700-1,200 cells/μl. scRNA-seq was performed with 10xGenomics platform or ScaleBio and Illumina according to the manufacturer's protocol. Libraires were pair-end sequenced with depth of 40,000 reads per cell.
paired-end libraries

value: cell line

value: PSC

value: WT

value: definitive endoderm spontanous differentiaion


title: BALF, NTM_16

value: Bronchoalveolar lavage fluid


title: BALF, Others_30

value: Others


title: A08spimpLA1332mock

description: Library name: sample8

value: mock


title: ko1_Se_d8_sp

description: Library name: ko1_Se_d8_sp


title: C08spimpLA1332mock

description: Library name: sample28


title: Day 100 marrow from patient 26

description: Library name: 26_100_IGO_15877_2_S9


title: H02spenLA2963mock

description: Library name: sample72

organism: Solanum pennellii


title: BALF, NTM_29

value: Male


title: A07spimpLA2347mock

description: Library name: sample7


title: BALF, TB_22


title: CD8TILs, Thy1.1, Donor50

description: Library name: T50 CD8 Thy1.1

value: NSCLC tumor

value: tumor-infiltrating lymphocytes


title: ko2_d8_sp

description: Library name: ko2_d8_sp


title: wt2_h202_d8_sp

description: Library name: wt2_h202_d8_sp


title: G02spenLA2963mock

description: Library name: sample62

value: leaf


title: BALF, Others_29

value: Female


title: CD4TILs, RELB, Donor50

description: Library name: T50 CD4 RELB

value: RELB


title: CD8TILs, Untransduced, Donor50

description: Library name: T50 CD8 -


title: wt1_h202_d8_sp

description: Library name: wt1_h202_d8_sp


title: ko1_d8_sp

description: Library name: ko1_d8_sp


title: CD4TILs, Untransduced, Donor50

description: Library name: T50 CD4 -


title: BALF, Others_28


title: CD4TILs, Thy1.1, Donor50

description: Library name: T50 CD4 Thy1.1


title: G01spenLA1303sclero

description: Library name: sample61

value: sclero


title: DPTILs, Initial, Donor50

description: Library name: T50 DP

value: Initial


title: BALF, Others_27


title: BALF, Others_26


title: CD8TILs, Initial, Donor50

description: Library name: T50 CD8


title: wt1_d8_sp

description: Library name: wt1_d8_sp


title: F02spenLA2963mock

description: Library name: sample52


title: F01spenLA1303sclero

description: Library name: sample51


title: wt2_d8_sp

description: Library name: wt2_d8_sp


title: H01spenLA1303sclero

description: Library name: sample71


title: GPX2_KO_D8

description:
Library name: GPX2_KO_D8
ScaleBio platform did not support export of raw data for this sample.

value: GPX2 KO

value: stem cells derived beta cells differentiation


title: E02spenLA2963mock

description: Library name: sample42


title: CD4TILs, Initial, Donor50

description: Library name: T50 CD4


title: DPTILs, Initial, Donor49

description: Library name: T49 DP

value: DP


title: B07spimpLA2347mock

description: Library name: sample17


title: E01spenLA1303sclero

description: Library name: sample41


title: KO_d8_ATAC_rep2

description: Library name: KO_d8_ATAC_rep2

value: cell line

value: PSC


title: BALF, TB_20

value: TB


title: WT_D8

description:
Library name: WT_D8
ScaleBio platform did not support export of raw data for this sample.

value: WT


title: KO_d8_ATAC_rep1

description: Library name: KO_d8_ATAC_rep1

value: definitive endoderm spontanous differentiaion


title: CD8TILs, Initial, Donor49

description: Library name: T49 CD8


title: CD4TILs, Initial, Donor49

description: Library name: T49 CD4


title: BALF, Others_24

value: Bronchoalveolar lavage fluid

value: Others


title: BALF, NTM_15

value: NTM


title: C02spenLA2963sclero

description: Library name: sample22


title: IB.CVID25

description:
Library name: Sample 22
CD27 bright memory cells_CVID

value: peripheral blood

value: CD27 bright memory cells

value: CVID


title: BALF, Others_25

value: Male


title: BALF, Others_23


title: BALF, Others_22


title: C01spenLA1303mock

description: Library name: sample21

value: leaf

value: mock


title: CD4TILs, Initial, Donor43

description: Library name: T43 CD4

value: NSCLC tumor

value: tumor-infiltrating lymphocytes

value: Initial


title: BALF, TB_21


title: CD8TILs, Initial, Donor43

description: Library name: T43 CD8


title: BALF, TB_19


title: D02spenLA2963sclero

description: Library name: sample32

value: sclero


title: GPX2_KO_D21

description: Library name: GPX2_KO_D21

value: cell line

value: PSC

value: GPX2 KO

value: stem cells derived beta cells differentiation


title: B01spenLA1303mock

description: Library name: sample11


title: B02spenLA2963sclero

description: Library name: sample12


title: CD8TILs, Initial, Donor36

description: Library name: T36 CD8


title: WT_D21

description: Library name: WT_D21

value: WT


title: BALF, Others_21

value: Bronchoalveolar lavage fluid

value: Others

value: Female


title: D01spenLA1303mock

description: Library name: sample31


title: DPTILs, Initial, Donor36

description: Library name: T36 DP

value: DP


title: A02spenLA2963sclero

description: Library name: sample2


title: A01spenLA1303mock

description: Library name: sample1


title: WT_d8_ATAC_rep2

description: Library name: WT_d8_ATAC_rep2

value: definitive endoderm spontanous differentiaion


title: WT_D6_2_sp

description: Library name: WT_D6_2_sp

value: foregut endoderm differantion


title: WT_D6_1_sp

description: Library name: WT_D6_1_sp


title: BALF, TB_17

value: TB

value: Male


title: KO_D6_2_sp

description: Library name: KO_D6_2_sp


title: CD4TILs, Initial, Donor36

description: Library name: T36 CD4

value: NSCLC tumor


title: TRF2, IP

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Quality control was conducted, ensuring that the parameters for unique mapped reads (> 45 million), Non-Redundant Fraction (NRF > 0.65), and FRIP score (> 1) met satisfactory standards for both IP and Input experiments. Raw data files from ChIP-Seq assays were aligned to the human reference genome (GRCh38/hg38) using Bowtie2 v2.3.2 [38]. Peak calling was performed using MACS2 v2.1.0 [39], with a threshold p-value = 0.001, using the input libraries as control. Peaks were annotated with the annotatePeaks.pl function, available within the HOMER software [40]. The peakAnno function of the ChIPseeker v1.36.0 R package [41] was used to retrieve the genomic distribution of ChIP-seq data peaks around the TSS, to calculate peak coverage and for the genomic annotation, which was divided in the following main categories: Promoter, 5’UTR, 3’UTR, Exon, Intron, Distal Intergenic.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: HCT116 cells were cultured in high glucose Dulbecco modified eagle medium (DMEM; Invitrogen, Carlsbad, CA, USA). Medium was supplemented with 10% fetal bovine serum (FBS, Hyclone), 1% L-glutamine (Gibco) and 1% penicillin/streptomycin (Gibco). Cells were maintained at 37 °C with 5% CO2.

extract_protocol:
HCT116 (7 × 10^5) cells were plated and, after 72h, fixed with 1% of formaldehyde. Nuclei were lysed with SDS lysis buffer and lysates were sonicated by using the biorupter (Diagenode Inc., NXT-Dx Belgium). The average length of sonicated chromatin was around 300–400 bp. For each IP, 100 μg of chromatin and 5 μg of anti-TRF2 (NB110-57130, Novus) antibodies were used.
ChIP samples were quantified by the Agilent 2100 Bioanalyzer System (Agilent Technologies) followed by library preparation for sequencing. DNA libraries were generated using the MicroPlex Library Preparation Kit protocol on the IP-Star Compact (Diagenode) apparatus following the manufacturer's instructions. Libraries were quantified using the KAPA Library Quantification Kit (KapaBiosystems) followed by sequencing of 1.8 pM per library in a NextSeq500 illumina system.

value: colon cancer cell line

tag: chip antibody

value: anti-TRF2 (NB110-57130, Novus)


title: WT_d8_ATAC_rep1

description: Library name: WT_d8_ATAC_rep1


title: Wildtype_ChIP_H3K4me3

city: Montreal

first: Luke

last: McCaffrey

state: Quebec

address: 1160 Pine Ave Ouest

department: Oncology

country: Canada

institute: McGill University

description: Library name: Wildtype_ChIP_H3K4me3

data_processing:
Reads were trimmed using Trimmomatic (v0.6.6) using default parameters and then aligned to the hg38 genome using BWA(v0.7.17).
Removal of PCR duplicates was then done using Picard (v2.0.1). MACS2 was then used for peak identification using default parameters and inputs as controls.
Aligned BAM files were used to generate the bigwigs using DeepTools/Homer. The resulting bigwigs were used for metaplot and heatmaps using the computeMatrix and plotHeatmap functions in DeepTools.
Assembly: hg38
Supplementary files format and content: BigWig

organism: Mus musculus

source_name: Prostate

growth_protocol: All human trophoblast stem cells used in this study were procured from the Arima lab (Tohoku Graduate school of Medicine, Japan). Wild-type CT27 (female), CT29 (male) and CT30 (female) cells were derived from first trimester placenta. hTSCs were cultures on 2.5 g/mL laminin-511 (Millipore-Sigma,  CC160-1050UG) pre-coated plates and media was refreshed every two days. Cells were passaged when up to 90% confluent using 30% TrypLE (GibcoTM, 12604021). hTSCs were maintained and cultured in media composing of DMEM-F/12 (Gibco, 11320033) media supplemented with 0.3% BSA (Millipore Sigma, A9205-50ML), 1% Insulin-Transferrin-Selenium-Ethanolamine (GibcoTM, 51500056), 1% Pencillin/Streptomycin, 0.1 mM 2-mercaptoethanol (Thermo Scientific, 21985023), 50 ng/mL EGF (StemCell, 78006.2), ES-qualified fetal bovine serum (Gibco, 20439024), 1.5 g/mL L-ascorbic acid, 2mM CHIR99021 (Cayman Chemical Company, 13122), 0.5 mM A83-01 (Selleck Chemicals, S7692), 1 mM SB431542 (Cayman Chemical Company, 13031), 5 M Y-27632 (Cayman Chemical Company, 10005583) and 0.8 mM Valproic Acid (Millipore Sigma, p6273-100ML).

extract_protocol:
DispaseII digested and trypsinized prostates (4 per condition) were pooled, fixed and crosslinked using 1% paraformaldehyde (diluted in PBS) for 15 minutes. The crosslinking was then quenched using 1 mM of Glycine for 10 minutes. Prostates were then lysed and sonicated using the M220 ultrasonicator (Covaris) in 1 ML tubes with an AFA Fiber and the following conditions ( cycles/burst = 200, Duty Factor = 20%, Peak Intensity Power = 75, time = 10 minutes and temperature = 7 degrees celcius). The sheared DNA was then pre-cleared using magnetic beads for 1 hour. Antibodies were then added to the DNA and incubated overnight at 4 degrees. Magnetic beads were added to each samples. The DNA samples were then eluted and de-crosslinked overnight at 62 degrees. Residual RNA and protein was then removed using RNAseA and proteinaseK and DNA was isolated using the Qiagen PCR purification Kit using manufacturer's instructions.
The eluted DNA from ChIP was used to construct multiplex libraries with the NEBNext Ultra II DNA library Kit using manufacturer’s instructions.

value: Prostate

value: prostate epithelial

value: Wild-Type

value: H3K4me3 (CST CD42D8)


title: BALF, NTM_14

value: NTM


title: Wildtype_ChIP_Lact

description: Library name: Wildtype_ChIP_Lact

value: PanKLa (PTM-1401RM)


title: HCT116 cells with shControl, rep3

data_processing:
The raw sequence reads (FASTQ) were subjected to quality control using FastQC version 0.10.1. Subsequent trimming was conducted with Cutadapt version 1.9.1. The reads were then aligned to the human GRCh38 reference genome using STAR version 2.6.1. FeatureCounts version 1.6.3 was employed to quantify the reads at the gene level. Finally, the DESeq2 package, part of the Bioconductor suite, was utilized to normalize the count data, estimate biological variance, and identify differentially expressed genes. Transcripts with a log2 Fold Change (logFC) greater than 0.58 or lower than −0.58 and adjusted p-value less than 0.05 in shTRF2-infected HCT116 cells vs shControl were considered as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing raw counts for each Sample

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated in triplicate using the same amount of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x75 bp) with NextSeq 500 (Illumina, CA).

value: control


title: BALF, TB_16

value: Bronchoalveolar lavage fluid


title: DPTILs, Initial, Donor43

description: Library name: T43 DP

value: tumor-infiltrating lymphocytes

value: Initial


title: Wildtype_ChIP_Input

description: Library name: Wildtype_ChIP_Input

value: Input


title: Input


title: KO_D6_1_sp

description: Library name: KO_D6_1_sp

value: cell line

value: PSC

value: GPX2 KO

value: foregut endoderm differantion


title: Cast_ChIP_Lact

description: Library name: Cast_ChIP_Lact

value: Male


title: BALF, TB_15

value: TB


title: Preconditiong, FCCP3

city: Columbus

first: Lufang

last: Zhou

state: Ohio

address: 460 W 12th Ave, BRT

institute: Ohio State University

description: Library name: sample 13

data_processing:
Perform alignments with HISAT2 to the reference4
Counting the reads using the HTseq software
Gene expression level analysis
Gene ontology (GO) enrichment analysis
Assembly: hg19
Supplementary files format and content: tab-delilited tex file includes raw counts for each sample

extract_protocol:
total RNA was extracted from cells using the RNeasy Fibrous Tissue Mini Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, thefirst strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis usingeither dUTP for directional library or dTTP for non-directional library.

value: myocyte

value: wildtype

value: Preconditioning+FCCP


title: Preconditiong, FCCP2

description: Library name: sample 12


title: HCT116 cells with shControl, rep2

value: colon cancer cell line


title: Preconditiong, FCCP1

description: Library name: sample 11


title: BALF, NTM_13

value: NTM

value: Female


title: Cast_ChIP_Input

description: Library name: Cast_ChIP_Input

value: Prostate

value: prostate epithelial

value: Wild-Type


title: BALF, NTM_12

value: Bronchoalveolar lavage fluid


title: HCT116 cells with shControl, rep1

value: control


title: HCT116 cells with silencing of TRF, rep3

value: TRF2 silencing


title: Preconditioning 3

description: Library name: sample 9

value: Preconditioning


title: HCT116 cells with silencing of TRF, rep2


title: AB5075 SP RIL-IP replicate C

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

description:
Library name: Sample 4C
RNA after application of RIL-seq

library_source: other

data_processing:
fastq records trimming (cutadapt 2.10)
short reads mapping and wiggle file generation (rilseq 0.78)
chimera mapping and s-chimera reporting (rilseq 0.78)
BED file generation (rilseq .78)
bigwig file generation (deepTools version 3.5.1)
Assembly: A. baumannii AB5075-UW chromosome and 3 plasmids; NZ_CP008706.1, NZ_CP008707.1, NZ_CP008708.1, and NZ_CP008709.1
Supplementary files format and content: Bigwig format for significant chimeric fragments of RILseq samples (Samples 1 - 4)
Supplementary files format and content: Bed format for HemZ-containing chimeras (sample 1 only) and Aar-containing chimeras (sample 3 only).

molecule: other

organism: Acinetobacter baumannii

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.6, samples 3&4 were collected at OD ≈ 2.0.

extract_protocol:
Standard TRI Reagent LS protocol was used for RNA extraction
Samples were subjected to the RIL-seq manipulations to ligate RNAs that interact on Hfq (Melamed et al., 2018).
Final libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.

value: WT

value: Growth:OD ≈ 2.0 in LB

tag: ip antibody

value: anti-VSVG mAb (Sigma #SAB4200695)


title: BALF, NTM_11


title: AB5075 SP RIL-IP replicate B

description:
Library name: Sample 4B
RNA after application of RIL-seq


title: Preconditioning 2

description: Library name: sample 8


title: Control, FCCP3

description: Library name: sample 6

value: FCCP


title: HCT116 cells with silencing of TRF, rep1


title: AB5075 hfq-V SP RIL-IP replicate C

description:
Library name: Sample 3C
RNA after application of RIL-seq

value: hfq-VSVG


title: Control, FCCP2

description: Library name: sample 5

value: myocyte

value: wildtype


title: AB5075 SP RIL-IP replicate A

description:
Library name: Sample 4A
RNA after application of RIL-seq


title: Cast_ChIP_H3K4me3

description: Library name: Cast_ChIP_H3K4me3

value: Male

value: H3K4me3 (CST CD42D8)


title: BALF, TB_14

value: TB

value: Female


title: Lmna Knockdown Dermal Fibroblast ATAC-Seq Rep 2

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

description: ATAC fragments

data_processing:
The ATAC-Seq samples were analyzed with the ENCODE ATAC-seq processing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline, version 0.3.4). The naive overlap peak set from all replicates for a given sample was used. Such peak sets from all samples were concatenated and merged using the bedtools merge command to produce a master peak set across all samples.
Assembly: hg38
Supplementary files format and content: tagAlign files, bigWig files, and peak calls files (narrowPeak) were generated for each technical replicate via the ENCODE ATAC-seq data processing pipeline

source_name: dermal fibroblast

extract_protocol:
10-20,000 normal human dermal fibroblasts before and after Lmna knockdown and human embryonic stem cells were centrifuged at 500xg for 5 min at 4˚C in a fixed angle centrifuge. After removing the supernatant, the cell pellets were re-suspended in 50uL ATAC-Resuspension Buffer (RSB) (500uL 1M Tris-HCl, 100uL 5M NaCl, 150uL 1M MgCl2 in 49.25mL sterile water) with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Samples were pipetted up and down three times to mix, incubated 3 minutes on ice, then diluted in 1mL of ice-cold ATAC-resuspension buffer (RSB) containing 0.1% Tween-20 and centrifuged at 500xg for 10 min at 4˚C to pellet the nuclei.
The supernatants were carefully removed and the pellets were re-suspended in 25 µL of transposase reaction mix (12.5 µL 2x TD buffer, 1.25 µL TN5 transposase (Illumina) and 11.25 µL nuclease-free water). Transposase reactions were carried out by incubating samples at 37˚C for 30 min under mild agitation (300 rpm on a Thermo-mixer C, Eppendorf). Once the incubation was completed, sample tubes were placed on ice and the transposed DNA fragments from each sample were purified using a Qiagen MinElute PCR Purification Kit following manufacture’s protocol. Purified DNA fragments were then amplified for 13 cycles using barcoded PCR primers and NEB Next High Fidelity 2x PCR Master Mix (New England Bio Labs) on a thermal cycler. Double concentrated Ampure beads were used to purify transposed DNA amplicons. The molarity of each DNA library was determined (Agilent 2100 Bioanalyzer), pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp paired-end reads.

value: dermal fibroblast

tag: disease

value: Hutchinson-Gilford Progeria Syndrome

tag: mutation

value: LMNA Exon 11, heterozygous c.1824C>T (p.Gly608Gly)

tag: transfection

value: Lmna siRNA


title: BALF, Others_20

tag: tissue

value: Bronchoalveolar lavage fluid

value: Others


title: Preconditiong 4

description: Library name: sample 10

tag: genotype

value: Preconditioning


title: AB5075 hfq-V SP RIL-IP replicate B

description:
Library name: Sample 3B
RNA after application of RIL-seq

tag: treatment

value: Growth:OD ≈ 2.0 in LB


title: AB5075 hfq-V SP RIL-IP replicate A

description:
Library name: Sample 3A
RNA after application of RIL-seq

value: anti-VSVG mAb (Sigma #SAB4200695)


title: BALF, Others_18


title: BALF, Others_17


title: Control , FCCP1

description: Library name: sample 4

tag: cell type

value: FCCP


title: BALF, TB_13


title: Normal Dermal Fibroblast ATAC-Seq Rep 1

description: ATAC fragments

value: Normal


title: Control 3

description: Library name: sample 3

value: myocyte

value: control


title: Preconditioning 1

description: Library name: sample 7

value: wildtype


title: AB5075 EP RIL-IP replicate C

description:
Library name: Sample 2C
RNA after application of RIL-seq

value: WT

value: Growth:OD ≈ 0.6 in LB


title: BALF, Others_19

value: Female


title: BALF, TB_12

value: TB

value: Male


title: Control 1

description: Library name: sample 1


title: hESC ATAC-Seq Rep 1

description: ATAC fragments

source_name: embryonic stem cell

value: embryonic stem cell


title: Control 2

description: Library name: sample 2


title: AB5075 EP RIL-IP replicate B

description:
Library name: Sample 2B
RNA after application of RIL-seq


title: hESC ATAC-Seq Rep 2

description: ATAC fragments


title: Normal Dermal Fibroblast ATAC-Seq Rep 2

description: ATAC fragments

value: dermal fibroblast


title: AB5075 EP RIL-IP replicate A

description:
Library name: Sample 2A
RNA after application of RIL-seq


title: CY18-RB183

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

description: 3' mRNA

data_processing:
illumina SureCell software is used for demultiplexing and alignment.
QC checked and the matrices were processed through SEURAT V3 pipeline for downstream analysis.
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: CSV Matrix table with raw gene counts for every gene and every sample

source_name: BM-MSC

extract_protocol:
Cells were thawed from liquid nitrogen storage, washed, filtered and counted for preparing the cell mix with reagents to process for single cell barcoding and library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow

value: Mesenchymal Stromal Cell


title: BALF, Others_15

value: Bronchoalveolar lavage fluid

value: Others


title: AB5075 hfq-V EP RIL-IP replicate B

description:
Library name: Sample 1B
RNA after application of RIL-seq

value: hfq-VSVG

value: anti-VSVG mAb (Sigma #SAB4200695)


title: Ischemia - Vena porta infusion 4

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

data_processing:
.fastq files were quality checked and reads with adapter contamination, over 10% of uncertain nucleotides, or with >50% low quality nucleotides (base quality <5) were removed.
Reads were mapped against the Ensembl 110 Sus scrofa genome using the HISAT2 package
Annotation was performed using the Ensembl Sus scrofa 11.1.110.gtf.gz file
Assembly: assembly 11.1
Supplementary files format and content: raw_counts.txt file is a tab-delimited file with Ensembl gene ID, raw counts after mapping, and annotation

organism: Sus scrofa

source_name: liver

growth_protocol: Cryopreserved human BM-MSC (Fr90 BM-MSC M0121 and BM13; Neostem, New York, USA) were thawed by stepwise dilution and expanded (maximum of 6 passages) in culture medium consisting of alpha-minimum essential medium (MEM)/GLUTAMAX (Gibco, Paisley, UK), 2% fetal bovine serum (Sigma-Aldrich, St. Louis, USA), 1% antibiotic–antimycotic (Gibco) supplemented with 20 ng/mL of recombinant human epidermal growth factor (eBioscience, San Diego, USA) and 10 ng/mL of recombinant human fibroblast growth factor 2 (eBioscience), at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated using the miRNEAsy kit (Qiagen) according to the manufacturer's protocol and eluted in RNAse-free water. Samples were mRNA enriched using oligodT
Library construction was performed at the Novogene sequencing facilities, Cambridge, UK.  In short, purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR. The single strand circle DNA (ssCir DNA) was formatted as the final library.

treatment_protocol: Pigs were sedated and a tracheotomized for intubation and mechanical ventilation. A midline laparotomy was performed and the exposed liver was totally excluded of blood flow for 45 minutes by placing vascular clamps on hepatic artery and veins and the portal vein. After this period of ischemia, MSCs were infused with 3x10E6 MSCs/kg bodyweight either in the portal vein (group Portal) or the hepatic artery (group Arterial). Sham operated animals did not receive any MSCs after clamping (group Control).

value: liver

tag: infused cells

value: human MSCs

value: 45' Ischemia

value: 6 hours reperfusion


title: Ischemia - Vena porta infusion 3


title: CY18-RB177

description: 3' mRNA


title: CY10-179-OT

description: 3' mRNA


title: AB5075 hfq-V EP RIL-IP replicate C

description:
Library name: Sample 1C
RNA after application of RIL-seq


title: BALF, Others_14


title: CY17-RB174

description: 3' mRNA


title: AB5075 hfq-V EP RIL-IP replicate A

description:
Library name: Sample 1A
RNA after application of RIL-seq


title: Ischemia - Vena porta infusion 2


title: BALF, Others_16


title: A549 cells, VILMIR, 10 ng/mL IFN, rep3

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

description:
Library name: KJ204
DNBSEQ-G400C

data_processing:
Complete Genomics RNA-seq reads were mapped against the human genome assembly version 38 (Hg38) using STAR version 2.7.9a. Custom STAR parameters were set as follows: limitOutSAMoneReadBytes: 1000000, outSAMprimaryFlag: AllBestScore, outFilterType: BySJout, alignSJoverhangMin: 8, alignSJDBoverhangMin: 3, outFilterMismatchNmax: 999, alignIntronMin: 20, alignIntronMax: 1000000, alignMatesGapMax: 1000000, outFilterMultimapNmax: 20; otherwise, default STAR parameters were used.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample as generated by STAR

growth_protocol: A549 cell lines were maintained in F-12K media with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from cells following the TRIzol isolation method (Invitrogen). All samples were quantified and assayed to confirm minimum RNA integrity number of at least 9.7 using an Agilent TapeStation 4150.
500 ng of total RNA per sample underwent mRNA capture and was then fragmented at 94°C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using eleven cycles of final amplification (KAPA mRNA HyperPrep Kit, catalog no. KK8580 and KAPA UDI Adapter Kit, catalog no. KK8727). Libraries underwent QC prior to sequencing using an Agilent TapeStation 4150.

treatment_protocol: A549 cells were seeded overnight between 150,000-175,000 cells per well in 12-well plates in 1.5 mL media to reach ~80-90% confluency the next day. The media was then removed, and the cell monolayer was washed with 1X DPBS prior to interferon treatment. Cells were treated with fresh A549 media with or without human IFN-β recombinant protein (R&D Systems™ 8499IF010) at 1 ng/mL or 10 ng/mL for 6 hours.

value: epithelial cell

value: VILMIR overexpression

value: 10 ng/mL IFN-β


title: BALF, TB_11

value: TB


title: Ischemia - Vena porta infusion 1


title: CY17-RB171

description: 3' mRNA


title: BALF, Others_13

value: Female


title: A549 cells, VILMIR, 1 ng/mL IFN, rep3

description:
Library name: KJ203
DNBSEQ-G400C

value: 1 ng/mL IFN-β


title: CY17-RB168

description: 3' mRNA


title: BALF, NTM_09

value: NTM


title: Ischemia - Arteria hepatica infusion 4


title: Ischemia - Arteria hepatica infusion 3


title: CY10-139-OT

description: 3' mRNA

value: Bone Marrow


title: BALF, TB_09


title: A549 cells, Ctrl, 10 ng/mL IFN, rep3

description:
Library name: KJ201
DNBSEQ-G400C

value: Empty vector


title: BALF, NTM_10

value: Bronchoalveolar lavage fluid


title: Ischemia - Arteria hepatica infusion 1


title: A549 cells, Ctrl, 1 ng/mL IFN, rep3

description:
Library name: KJ200
DNBSEQ-G400C


title: Ischemia - Arteria hepatica infusion 2


title: Thalamus, mmpp3, Day7

city: Tianjin

first: Libo

last: Su

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

description:
Library name: Simple9
Column name in raw_counts_All_Samples.txt:mmpp3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Thalamus

extract_protocol:
Total RNA was extracted from tissue or cultured cells using TRIzol reagent (Invitrogen) as per the manufacturer’s protocol, yielding 2 µg, which was used for sequencing library construction. RNA libraries for RNA-seq were prepared using the SMARTER mRNA Seq Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thalamus

value: WT


title: A549 cells, Ctrl, mock, rep3

description:
Library name: KJ199
DNBSEQ-G400C

value: mock


title: BALF, TB_08

value: Male


title: A549 cells, VILMIR, 10 ng/mL IFN, rep2

description:
Library name: KJ198
DNBSEQ-G400C


title: BALF, Others_12

value: Others


title: Thalamus, stroke3, Day7

description:
Library name: Simple6
Column name in raw_counts_All_Samples.txt:stroke3


title: Ischemia-No infusion 2

value: liver

value: 45' Ischemia


title: Ischemia-No infusion 3

value: 6 hours reperfusion


title: A549 cells, VILMIR, 1 ng/mL IFN, rep2

description:
Library name: KJ197
DNBSEQ-G400C

value: epithelial cell

value: VILMIR overexpression


title: Ischemia-No infusion 1


title: A549 cells, VILMIR, mock, rep3

description:
Library name: KJ202
DNBSEQ-G400C


title: No ischemia-No infusion 2

value: No Ischemia

value: no reperfusion


title: BALF, TB_10

value: TB


title: BALF, Others_11


title: A549 cells, VILMIR, mock, rep2

description:
Library name: KJ196
DNBSEQ-G400C


title: Thalamus, stroke1, Day7

description:
Library name: Simple4
Column name in raw_counts_All_Samples.txt:stroke1


title: Thalamus, stroke2, Day7

description:
Library name: Simple5
Column name in raw_counts_All_Samples.txt:stroke2


title: BALF, TB_07


title: No ischemia-No infusion 1a


title: BALF, NTM_08

value: NTM

value: Female


title: A549 cells, Ctrl, 10 ng/mL IFN, rep2

description:
Library name: KJ195
DNBSEQ-G400C

value: Empty vector

value: 10 ng/mL IFN-β


title: BALF, Others_10

value: Bronchoalveolar lavage fluid


title: Thalamus, mmpp2, Day7

description:
Library name: Simple8
Column name in raw_counts_All_Samples.txt:mmpp2

value: Thalamus

value: WT


title: Thalamus, sham3, Day7

description:
Library name: Simple3
Column name in raw_counts_All_Samples.txt:sham3


title: Thalamus, mmpp1, Day7

description:
Library name: Simple7
Column name in raw_counts_All_Samples.txt:mmpp1


title: BALF, NTM_07


title: A549 cells, Ctrl, 1 ng/mL IFN, rep2

description:
Library name: KJ194
DNBSEQ-G400C

value: 1 ng/mL IFN-β


title: KhES_Blastoid_D4_sample2

city: Kyoto

first: Kaori

last: Mutsuda-Zapater

address: Yoshidahonmachi, Sakyo Ward

country: Japan

institute: Kyoto university

description:
Library name: KhES_D4_2_2025
mRNA-seq (polyA+) data from blastoids derived from KhES1 cultured inDMEM with 10% FBS in hydrogel, sample 2

data_processing:
Chromium barcodes were used for demultiplexing by using CellRanger program (10x Genomics; v9.0.0, https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Alignment and UMI counting were performed using CellRanger to map sequencing reads to a custom version of the Ensembl GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Gene expression values were calculated with the Cell Ranger Count v9.0.0 pipeline

organism: Homo

growth_protocol: hESCs were handled following the guidelines provided by the ethical committee of Kyoto University (Approved #ES3-9 and ES3-29). Prior to culturing, 1.3% (v/v) hESC-certified Matrigel (Corning, NY, USA) in DMEM/F12 medium was used to coat the culture dishes. After 24 h at 4˚C, the excess Matrigel was removed, and the coated dish was washed with fresh DMEM/F12 medium. mTeSR-1 medium was used for the daily culturing of hPSCs. For passaging, cells were dissociated with TrypLE Express (Life Technologies, Carlsbad, CA, USA) for 3 min at 37 ˚C. The cells were centrifuged at 150 × g for 3 min, resuspended in mTeSR-1 medium and counted using a NucleoCounter NC-200 (Chemetec, Baton Rouge, LA, USA). mTeSR-1 medium containing 10 µM of Y27632 was used to prevent the apoptosis of the dissociated hPSCs on the first two days. mTeSR-1 medium without Y27632 was used on the subsequent days, with daily medium change. The cells were maintained in an incubator at 37°C with 5% (v/v) CO2.

extract_protocol:
Dissociated cells were introduced to the Chromium controller (10x Genomics, Pleasanton, CA, USA) for encapsulation, following the manufacture’s instruction (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)).
StepOnePlus (Applied Biosystems)

treatment_protocol: hPSCs cultured on Matrigel-coated dishes with mTeSR-1 medium were harvested with TrypLE Express for 3 min at 37°C. The dissociated hPSCs were resuspended in high-glucose DMEM supplemented with 10% (v/v) FBS and 10 µM of Y27632, and then transferred to Aggrewell 400 (Stem Cell Technologies) at 1.2 × 10^6 cells per well. After 24 h at 37°C with 5% (v/v) CO2, the hPSC aggregates were resuspended in a hydrogel solution {DMEM with 10%[w/v] PNIPAAm-β-PEG hydrogel at 4°C. 260 µL of the hPSC aggregate suspension with the hydrogel were transferred into each well of a 24-well plate, to which high-glucose DMEM supplemented with 10% (v/v) FBS and 10 µM of Y27632 was added. Medium was changed daily and the aggregates were maintained at 37°C with 5% (v/v) CO2 for 4 days.

tag: condition

value: DMEM with 10% FBS in hydrogel

value: Embryonic stem cells


title: Thalamus, sham2, Day7

description:
Library name: Simple2
Column name in raw_counts_All_Samples.txt:sham2


title: BALF, TB_06

value: Male


title: A549 cells, Ctrl, mock, rep2

description:
Library name: KJ193
DNBSEQ-G400C

value: mock


title: Thalamus, sham1, Day7

description:
Library name: Simple1
Column name in raw_counts_All_Samples.txt:sham1


title: BALF, Others_09

value: Others


title: A549 cells, VILMIR, 10 ng/mL IFN, rep1

description:
Library name: KJ192
DNBSEQ-G400C

value: epithelial cell

value: VILMIR overexpression


title: SiPiezo2

city: Nanjing

first: yujia

last: xue

address: Longmian Avenue 639

institute: China Pharmaceutical University

description: Library name: sample2

data_processing:
Removing reads containing adapters;
Removing reads containing more than 10% of unknown nucleotides (N); Removing reads containing adapters;Removing reads containing more than 10% of unknown nucleotides (N); Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
BWA (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak B WA[1] (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak  scanning.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on forward and reverse strands centered around the binding site. SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value<1e-5. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number were displayed.
Assembly: mm10
Supplementary files format and content: NC-vs-siPIEZO2.final.anno.txt

source_name: heart

extract_protocol:
ATAC DNA Extract Beads intended for DNA extraction by using Hyperactive ATAC-Seq Library Prep Kit for Illumina-TD711
ATAC DNA Clean Beads is used for library purification.10 ng of DNA was used as startnig material for input amout. Libraries were amplified using 10 cycles on thr thermocycle.

value: heart

value: primary cardiac fibroblasts


title: G06shabroLA1721sclero

city: Kiel

first: Severin

last: Einspanier

address: Hermann-Rodewald-Straße 9

institute: Christian-Albrechts-University Kiel

description: Library name: sample66

data_processing:
We used cutadapt for trimming&quality filtering
rRNA was depleted using STAR, non-mapping reads were used for further analysis
Reads were mapped to each species' reference genome using STAR.
We used featurecounts for read quantification.
FastQC and MultiQC were used for quality assessment.
Assembly: PRJEB5809, PRJCA008297, PRJNA607731, PRJNA727176, PRJNA1210999
Supplementary files format and content: txt-file contaning read counts per gene (not transcript!).

organism: Solanum habrochaites

extract_protocol:
RNA was isolated using the Quick-RNA Plant Kit (ZYMO RESEARCH). We pooled 2x2cm parts of two independent leaves into DNA/RNA-shield (ZYMO RESEARCH). 0.5ng/µL RNA was used for library preparation.
We used the 3' mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12nt) with PCR Add-on and Reamplification Kit V2 for Illumina, and the SIRV-Set 3 for in-house library preparation, following the manufacturers iinstructions.

value: leaf

value: sclero


title: NC

description: Library name: sample1

value: TGF-b


title: BALF, TB_05

data_processing:
The raw 16S amplicon sequences were processed by QIIME2 v1.8.0 with default parameters.
We then used SHI7 for trimming Nextera adapters and stitching paired-end reads and performed quality trimming at both ends of the stitched reads until a minimum Phred score of 32 was reached.
The OTUs were determined by de novo clustering of the sequences with a 97% sequence identity cut-off by QIIME
We performed alpha- and beta-diversity analyses in R using the vegan and phyloseq packages.
Based on the OTU table, we calculated the average richness estimate for each alpha-diversity metric (Chao1, observed OTUs, and Shannon).
Supplementary files format and content: OTU.xlsx
Library strategy: 16s rRNA seq

extract_protocol:
From BALF samples, DNA was extracted by the QIAamp DNA microbiome kit (Qiagen, 51704).
We used Herculase II Fusion DNA Polymerase Nextera XT Index Kit V2, and sequencing instrument model was Illumina MiSeq.

value: TB


title: H05shabroLA2167sclero

description: Library name: sample75


title: A549 cells, Ctrl, 10 ng/mL IFN, rep1

description:
Library name: KJ189
DNBSEQ-G400C

value: Empty vector

value: 10 ng/mL IFN-β


title: BALF, Others_08

value: Bronchoalveolar lavage fluid

value: Female


title: T-S

description: Library name: sample6

data_processing:
Removing reads containing adapters;
Removing reads containing more than 10% of unknown nucleotides (N); Removing reads containing adapters;Removing reads containing more than 10% of unknown nucleotides (N); Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
BWA (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak B WA[1] (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak  scanning.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on forward and reverse strands centered around the binding site. SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
MACS (version: macs14)( -p 1e-3 -m 10,30) is a computational method that was designed to identify read-enriched regions from ChIP-seq data. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value<1e-5. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number were displayed.
Assembly: mm10
Supplementary files format and content: *.final.anno.txt

extract_protocol:
ConA Beads Pro intended for nucleus binding and DNA Extract Beads Pro intended for DNA extraction by using Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro TD904
VAHTS DNA Clean Beads (Vazyme #N411) is used for library purification.10 ng of DNA was used as startnig material for input amout. Libraries were amplified using 10 cycles on thr thermocycle.


title: BALF, NTM_06

value: NTM


title: SI-S

description: Library name: sample5

value: TGF-b+SiSRF


title: NC-S

description: Library name: sample4

value: NC


title: A549 cells, VILMIR, 1 ng/mL IFN, rep1

description:
Library name: KJ191
DNBSEQ-G400C

value: 1 ng/mL IFN-β


title: KhES_Blastoid_D4_sample1

description:
Library name: KhES_D4_1_2025
mRNA-seq (polyA+) data from blastoids derived from KhES1 cultured inDMEM with 10% FBS in hydrogel, sample 1

value: DMEM with 10% FBS in hydrogel

value: Embryonic stem cells


title: A549 cells, Ctrl, mock, rep1

description:
Library name: KJ187
DNBSEQ-G400C

value: epithelial cell

value: mock


title: F06shabroLA1721sclero

description: Library name: sample56


title: A549 cells, Ctrl, 1 ng/mL IFN, rep1

description:
Library name: KJ188
DNBSEQ-G400C


title: G05shabroLA2167sclero

description: Library name: sample65


title: H06shabroLA1721sclero

description: Library name: sample76


title: F05shabroLA2167sclero

description: Library name: sample55


title: T-T

description: Library name: sample3

value: heart

value: primary cardiac fibroblasts


title: BALF, Others_07

value: Others

value: Male


title: E06shabroLA1721sclero

description: Library name: sample46

value: leaf

value: sclero


title: A549 cells, VILMIR, mock, rep1

description:
Library name: KJ190
DNBSEQ-G400C

value: VILMIR overexpression


title: BALF, Others_06

value: Bronchoalveolar lavage fluid


title: BALF, NTM_05

value: Female


title: SI-T

description: Library name: sample2

value: TGF-b+SiTAZ


title: E05shabroLA2167sclero

description: Library name: sample45


title: BALF, NTM_04

value: NTM


title: Y2

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

description: Library name: Sample 8

data_processing:
Reads were trimmed using trim_galore
mapping mapped to hg38  use STAR
gene count matrix were create by featureCounts
RSEM  was used on the RNA-Seq data to caulate TPM
Assembly: mm10
Supplementary files format and content: RSEM genes.results file

source_name: blood

extract_protocol:
RNA extraction by Zymo Research Direct-zol RNA Microprep Kits
Library construction was performed according to manufacturer’s recommendations for NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: blood

value: PBMC

value: wild type

value: Y


title: NC-T

description: Library name: sample1

value: NC


title: BALF, TB_18

city: Asan

last: Gim

address: 22 Suncheonhyang-ro

institute: Soonchunhyang University

value: TB


title: D06shabroLA1721mock

description: Library name: sample36

source_name: leaf

value: mock


title: Y1

description: Library name: Sample 7


title: BALF, Others_05


title: CRE3

description: Library name: sample6

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using C
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork (parame ters-mismath cost: 2 insertion cost: 3 deletion cos st 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested usina Rneasy mini plus kit(Qiagen)13 uaof total RNA was used for the construction of seauencina libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

value: Fibroblast

value: Tet3 knockout

value: TGF-b


title: BALF, Others_04

value: Others


title: WT3

description: Library name: Sample 6

value: WT


title: CRE2

description: Library name: sample5


title: Y3

description: Library name: Sample 9


title: C06shabroLA1721mock

description: Library name: sample26

value: leaf


title: WT2

description: Library name: Sample 5


title: BALF, NTM_03

value: Bronchoalveolar lavage fluid

value: Female


title: BALF, TB_04


title: WT1

description: Library name: Sample 4


title: C05shabroLA2167mock

description: Library name: sample25


title: GFP3

description: Library name: sample3

value: Control


title: GFP2

description: Library name: sample2


title: ct3

description: Library name: Sample 3

value: blood

value: ct


title: BALF, NTM_02

value: NTM


title: B06shabroLA1721mock

description: Library name: sample16


title: BALF, NTM_01


title: B05shabroLA2167mock

description: Library name: sample15


title: GFP1

description: Library name: sample1


title: A06shabroLA1721mock

description: Library name: sample6


title: ct2

description: Library name: Sample 2

value: PBMC

value: wild type


title: ct1

description: Library name: Sample 1


title: osteocyte，mut3

city: Chongqing

first: Yujiao

last: Liu

state: Chongqing

address: No.1 Xueyuan Road, Yuzhong District

department: College of Laboratory Medicine,

institute: Chongqing Medical University

description:
Library name: Sample 6
mut3

data_processing:
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions .
messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly.
Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles.
After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.
Assembly: Illumina® Stranded mRNA Prep, Ligation
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: bone

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

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: No treatment

value: bone

value: primary osteocyte

value: osteocyte

value: Wnt signaling activated osteocyte

tag: batch


title: D05shabroLA2167mock

description: Library name: sample35

value: mock


title: BALF, Others_03

first: Jeong-An

tag: disease state


title: Age12-3

first: Wei

last: Yu

address: No. 83, Xinqiaozheng Street, Shapingba District, Chongqing, China

institute: The Second Affiliated Hospital of Army Military Medical University of the People's Liberation Army of China

description: Library name: Sample 9

data_processing:
High-quality transcriptome data were obtained by paired-end sequencing using the DNBSEQ-T7 sequencing platform, which removes valid reads after adapter self-association and low-quality bases and reads.
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRCm39 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cochlear tissue

extract_protocol:
RNA-seq assays were performed by Wuhan Ruixing Biotechnology Co.,Ltd (http://www.rxbio.cc). For each sample, 1 μg of total RNA was treated with RQ1 DNase (M6101，Promega，USA) to remove DNA before used for directional RNA-seq library preparation by VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605,Vazyme,China) for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads（N401,Vazyme, China）. Fragmented RNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323,Vazyme,China)，the ligated products were amplified，purified，quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to DNBSEQ-T7 system for 150 nt paired-end sequencing.

value: cochlear tissue


title: A05shabroLA2167mock

description: Library name: sample5


title: BALF, TB_03

value: TB

tag: Sex

value: Male


title: CRE1

description: Library name: sample4

value: heart

value: Fibroblast

value: Tet3 knockout

value: TGF-b


title: BALF, Others_02

value: Bronchoalveolar lavage fluid

value: Others

value: Female

tag: age


title: osteocyte，mut2

description:
Library name: Sample 5
mut2


title: osteocyte，mut1

description:
Library name: Sample 4
mut1


title: Age12-1

description: Library name: Sample 7


title: wt cultivated in mvcmii

city: Trondheim

first: Luciana

last: Fernandes de Brito

address: Kjemi 3, 3.237, Gløshaugen, Sem Sælandsvei 6/8

department: Department of Biotechnology and food science

country: Norway

institute: Norwegian University of Science and Technology

description: Library name: wtmvcmii

data_processing:
Prior to mapping of the generated reads onto the reference genome, the RNA sequencing raw sequences were trimmed using the tool Trimmomatic version 0.4 to a minimal length of 35 base pairs. The trimmed reads were mapped to the B. methanolicus MGA3 reference sequences of the chromosome as well as the two plasmids pBM19 and pBM69 (GenBank accession numbers CP007739, CP007741, and CP007740, respectively) using the software for short read alignment Bowtie2
Assembly: References GenBank accession numbers CP007739, CP007741, and CP007740
Supplementary files format and content: Transcript abundances from pooled triplicates of samples wtmvcm and wtmvcmii were mapped onto the chromosome of MGA3 and the plasmids pBM19 and pBM69. The processed data are provided in the files TPM_Chr-raw.xls, TPM_pBM19-raw.xls, and TPM_pBM69-raw.xls, each containing data corresponding to a single reference sequence. Within each file, transcript abundance is given for either the wtmvcm (MVcM1) or wtmvcmii (PM101) track.

organism: Bacillus methanolicus

source_name: bacterial cell culture

growth_protocol: B. methanolicus strains were pre cultured at 50°C and 200 rpm in 500 mL flasks containing MVcMY, which is MvcM medium supplied with 250 mg/L yeast extract. Main cultures grew in Eppendorf New Brunswick Innova 42R incubators in 250 ml flasks. The defined growth media was MVcM or MVcMii.

extract_protocol:
Total RNA extraction from B. methanolicus MGA3 cells was performed using the NucleoSpin RNA isolation kit (Machery-Nagel, Düren, Germany) and the RNase-free DNase set (Qiagen, Hilden, Germany), following the manufacturer's instructions.
Libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero. Sequencing was carried out with a NovaSeq 6000 platform with sequencing strategy paired-end 150 bp reads generating 3G per sample.

treatment_protocol: We conducted differential gene expression analysis through RNA sequencing, comparing the transcriptomes of B. methanolicus MGA3 growing in either MVcM or MVcMii.

value: bacterial cell culture

value: wild-type

value: glutamate overproducer

value: Pooled triplicates


title: wt cultuvated in mvcm

description: Library name: wtmvcm

value: wild-type behavior


title: H10slycoLA2951sclero

description: Library name: sample80

organism: Solanum lycopersicoides

value: leaf

value: sclero


title: Age8-3

description: Library name: Sample 6

value: cochlear tissue


title: BALF, Others_01

source_name: Bronchoalveolar lavage fluid

tag: bmi


title: osteocyte，WT3

description:
Library name: Sample 3
wt3

value: bone

tag: cell line

value: primary osteocyte

value: osteocyte

value: WT


title: BALF, TB_02

value: TB

value: Male


title: osteocyte，WT2

description:
Library name: Sample 2
wt2


title: Age8-2

description: Library name: Sample 5


title: H09slycoLA2777sclero

description: Library name: sample79


title: osteocyte，WT1

description:
Library name: Sample 1
wt1


title: Lmna Knockdown Dermal Fibroblast ATAC-Seq Rep 1

description: ATAC fragments

value: dermal fibroblast

value: Hutchinson-Gilford Progeria Syndrome

value: LMNA Exon 11, heterozygous c.1824C>T (p.Gly608Gly)

value: Lmna siRNA


title: BALF, TB_01

value: Bronchoalveolar lavage fluid


title: G09slycoLA2777sclero

description: Library name: sample69


title: Bell_W, rep3

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

institute: Yonsei University

description:
Library name: Sample 24
Bell_W3

data_processing:
Experimental Method(RNA QC/Library construction/sequencing) The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA). Namely, mRNA molecules were purified and fragmented from 1μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×151bp) using Illumina NovaSeq6000 (Illumina, CA, USA).
Transcriptome data analysis Filtering The quality of the reads was checked using FastQC (v0.12.1), which helped in understanding the basic quality metrics, including sequence quality scores, GC content, N content, length distribution, and duplication levels. Adapter sequences and the ends of the reads with a Phred quality score of less than 15 were trimmed, and simultaneously, reads shorter than 36 bp were removed using Trimmomatic (v0.39).
Sequence alignment Filtered reads were mapped to the reference genome of the species using the Bowtie aligner (v1.2.3).
Gene expression estimation Read count values were obtained using Subread (v2.0.3).
Differential Expressed gene (DEG) analysis Based on the estimated read counts from the previous step, normalization factors were calculated using the iterative DESeq2 (v1.40.2) method. Q-values were calculated from the p-values using the p.adjust function of the R package with default parameter settings. Differentially expressed genes (DEGs) were identified based on a q-value threshold of less than 0.05 to correct for errors caused by multiple testing.
Assembly: Gene Ontology (GO) analysis The GO database provides a set of hierarchical controlled vocabulary classified into three categories: Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). For the functional characterization of the DEGs, a GO-based trend test was carried out using the R package called clusterProfiler (v4.8.3) through the Wallenius non-central hypergeometric distribution. Genes with P-values < 0.05 following the test were regarded as statistically significant.
Supplementary files format and content: GRCm39.107
Supplementary files format and content: tab-delimited text files include ReadCount values for each Sample

source_name: mesenchymal cells

extract_protocol:
Tooth germs at cap and bell stage were dissected from mouse mandible. The tooth germs from mouse mandible at cap and bell stage were divide two region with lingual and buccal part with 30 gauge fine needle. Furthermore, Lingual part of tooth germs and buccal part of tooth germs were cultured in vitro for 2 days. The mesenchymal cells were isolated from each tooth germ with dispaseII. The total RNA was extracted with TRIzol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mesenchymal cells


title: Ctr-3

description: Library name: Sample 3


title: F10slycoLA2951sclero

description: Library name: sample60


title: Age12-2

description: Library name: Sample 8


title: Bell_W, rep2

description:
Library name: Sample 23
Bell_W2


title: Ctr-2

description: Library name: Sample 2


title: Bell_W, rep1

description:
Library name: Sample 22
Bell_W1


title: Ctr-1

description: Library name: Sample 1


title: Bell_B, rep3

description:
Library name: Sample 21
Bell_B3


title: F09slycoLA2777sclero

description: Library name: sample59


title: Plasma_1078_Control

type: RNA

city: Porto Alegre

first: Santiago Alonso

last: Tobar Leitao

state: Rio Grande do Sul

address: Rua Ramiro Barcelos 2350

department: Experimental Research Center

country: Brazil

institute: Hospital de Clínicas de Porto Alegre

hyb_protocol: Samples were hybridized overnight using the GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA) at 48°C. The arrays were then washed and stained in the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).The signal values were evaluated using the Expression Console Software (EC) v1.2 (Affymetrix by Thermo Fisher Scientific). Intensity values (presence/absence values) and signal histograms of each hybridization were quality-checked.

data_processing: Raw data were pre-processed using the Robust Multiarray Average (RMA) method, which applies background correction, log2 transformation, and quantile normalization. The batch effect was adjusted with Surrogate Variable Analysis through the sva R package

label: biotin

source_name: Plasma, Control

label_protocol: Total RNA (160 ng), including miRNAs, was biotin-labeled using the FlashTagTM Biotin HSR RNA Labeling kit (Affymetrix, Genisphere, Hatfield, PA, USA)

extract_protocol: Total RNA was extracted from 396 μL of plasma spiked-in with 4 μL of cel-miR-39-3p. Then, 1.2 mL of Trizol LS reagent was added and incubated for 5 minutes. Next, 0.32 mL of chloroform was added, incubated for 15 minutes, and centrifuged at 12,000 x g at 4ºC for 15 minutes. Then, we removed the supernatant, added 0.8 mL of isopropyl alcohol, incubated for 10 minutes, and centrifuged at 12,000 x g at 4ºC for 10 minutes. After removing the isopropyl alcohol, 1.6 mL of 75% ethanol was added and centrifuged at 7,500 x g, at 4ºC, for 5 minutes. Dry for 10 minutes and resuspend in 16 uL of RNase-free water, placed in a dry bath at 58ºC for 10 min. The concentration of total RNA was determined by spectrophotometric analysis (NanoDrop 1000, Thermo Scientific, Wilmington, DE, USA).

value: male

value: plasma

value: Control


title: Control - DBDB Aldo 7

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

description:
Library name: 2624
2624

data_processing:
Cleaned reads were aligned to reference genomes (mouse: GRCm38/mm10) using STAR37 with de novo junction discovery and summarized at the gene level using featureCounts. Differential expression analysis was completed using DESeq2 using the standard workflow. Batch correction for different sequencing runs between HFpEF models was performed using limma’s removeBatchEffect function using the standard workflow.
Assembly: mm10
Supplementary files format and content: Normalized count matrix of all genes for all samples following batch correction for sequencing run.

source_name: Whole heart

extract_protocol:
Total RNA was extracted from whole-heart lysates using TRIzol and the Qiagen RNeasy kit according to the manufacter's specifications.
RNA-sequencing from whole-heart lysates was performed by BGI Genomics using their standard preparation of PolyA RNA using paired-end 100 nucleotide sequencing with 40 million reads.

treatment_protocol: Adult wild-type (WT, strain #000664) and Leprdb/db (strain #000697) C57BL/6J mice were obtained from The Jackson Laboratory. Animals had unlimited access to sterilized water and food, and were housed in an enriched environment with standard bedding and nesting material, under a 12/12 h day-night cycle in a humidity (40–60%) and temperature (20–22°C) controlled facility. HFpEF was studied in two contemporary two-hit models (Fig. 1A). First, WT mice (10-week-old) were fed with HFD (60 kcal% fat, D12492, Research Diets) and drinking water was supplemented with L-NG-nitroarginine methyl ester (L-NAME, 0.5 g/L, Sigma-Aldrich) for 15 weeks. Age-matched control mice were fed with the standard chow used in the Jackson Laboratory chow (Lab Diet, 5k52). Second, osmotic minipumps (Alzet, 2004) were implanted subcutaneously in 12-wk-old mice that delivered a continuous infusion of d-aldosterone (0.3 μg/h) for 4 weeks in db/db mice. Sham control WT mice were implanted with minipumps filled with vehicle only (saline with 5% ethanol). These mice were fed with normal chow (Teklad, 2918). No difference in cardiac morphometry, echocardiography, cellular electrophysiology, and intracellular Ca2+ handling was found between the two control groups of animals.

value: Whole heart

value: female

value: Control - DBDB Aldo

tag: sequencing run


title: Plasma_1077_Control


title: Plasma_184_ObeseHF

source_name: Plasma, ObeseHF

value: ObeseHF


title: Bell_B, rep2

description:
Library name: Sample 20
Bell_B2


title: G10slycoLA2951sclero

description: Library name: sample70

value: leaf

value: sclero


title: Control - DBDB Aldo 5

description:
Library name: 2621
2621


title: Bell_B, rep1

description:
Library name: Sample 19
Bell_B1


title: E09slycoLA2777sclero

description: Library name: sample49


title: D10slycoLA2951mock

description: Library name: sample40

value: mock


title: Control - DBDB Aldo 6

description:
Library name: 2623
2623


title: Bell_L, rep3

description:
Library name: Sample 18
Bell_L3


title: D09slycoLA2777mock

description: Library name: sample39


title: Age8-1

description: Library name: Sample 4

value: cochlear tissue


title: Treated - DBDB Aldo 8

description:
Library name: 2618
2618

value: Treated - DBDB Aldo


title: Plasma_1076_Control


title: Bell_L, rep2

description:
Library name: Sample 17
Bell_L2


title: C10slycoLA2951mock

description: Library name: sample30


title: Plasma_1074_Control


title: Plasma_1073_Control


title: Treated - DBDB Aldo 7

description:
Library name: 2615
2615


title: Plasma_154_ObeseHF


title: Bell_L, rep1

description:
Library name: Sample 16
Bell_L1


title: C09slycoLA2777mock

description: Library name: sample29


title: Treated - DBDB Aldo 6

description:
Library name: 2613
2613


title: Cap_B_2D, rep3

description:
Library name: Sample 15
Cap_B3_2D


title: B10slycoLA2951mock

description: Library name: sample20


title: Plasma_129_ObeseHF


title: Treated - DBDB Aldo 5

description:
Library name: 2612
2612


title: Plasma_151_LeanHF

source_name: Plasma, LeanHF

value: LeanHF


title: B09slycoLA2777mock

description: Library name: sample19


title: Cap_B_2D, rep2

description:
Library name: Sample 14
Cap_B2_2D


title: Control - DBDB Aldo 4

description:
Library name: 986
986


title: Cap_B_2D, rep1

description:
Library name: Sample 13
Cap_B1_2D


title: E10slycoLA2951sclero

description: Library name: sample50


title: A10slycoLA2951mock

description: Library name: sample10


title: Control - DBDB Aldo 3

description:
Library name: 985
985


title: Control - DBDB Aldo 2

description:
Library name: 981
981


title: Cap_L_2D, rep3

description:
Library name: Sample 12
Cap_L3_2D


title: A09slycoLA2777mock

description: Library name: sample9


title: Plasma_115_LeanHF


title: H04schilLA4107sclero

description: Library name: sample74

organism: Solanum chilense


title: Control - DBDB Aldo 1

description:
Library name: 980
980


title: Plasma_1024_Control


title: H03schilLA3111sclero

description: Library name: sample73


title: Plasma_116_LeanHF


title: Cap_L_2D, rep2

description:
Library name: Sample 11
Cap_L2_2D


title: Treated - DBDB Aldo 4

description:
Library name: 962
962


title: Plasma_1028_Control


title: Treated - DBDB Aldo 3

description:
Library name: 961
961


title: G04schilLA4107sclero

description: Library name: sample64


title: Cap_B, rep3

description:
Library name: Sample 9
Cap_B3


title: Cap_B, rep2

description:
Library name: Sample 8
Cap_B2


title: G03schilLA3111sclero

description: Library name: sample63


title: Plasma_105_ObeseHF


title: Cap_B, rep1

description:
Library name: Sample 7
Cap_B1


title: F04schilLA4107sclero

description: Library name: sample54


title: Treated - DBDB Aldo 1

description:
Library name: 6B
6B


title: Plasma_101_ObeseHF


title: Cap_L, rep3

description:
Library name: Sample 6
Cap_L3


title: Cap_L_2D, rep1

description:
Library name: Sample 10
Cap_L1_2D


title: F03schilLA3111sclero

description: Library name: sample53


title: Treated - HFD-Lname 4

description:
Library name: 8
8

value: Treated - HFD-Lname


title: Cap_L, rep2

description:
Library name: Sample 5
Cap_L2


title: Plasma_98_LeanHF


title: Treated - HFD-Lname 3

description:
Library name: 7
7


title: Plasma_128_ObeseHF


title: Cap_L, rep1

description:
Library name: Sample 4
Cap_L1


title: E04schilLA4107sclero

description: Library name: sample44


title: E03schilLA3111sclero

description: Library name: sample43


title: Treated - HFD-Lname 2

description:
Library name: 6
6


title: Plasma_93_LeanHF


title: Plasma_1016_Control


title: Cap_W, rep3

description:
Library name: Sample 3
Cap_W3


title: Treated - HFD-Lname 1

description:
Library name: 5
5


title: Treated - DBDB Aldo 2

description:
Library name: 7B
7B


title: Cap_W, rep2

description:
Library name: Sample 2
Cap_W2


title: D03schilLA3111mock

description: Library name: sample33


title: Plasma_103_LeanHF


title: Control - HFD-Lname 4

description:
Library name: 4
4

value: Control - HFD-LName


title: Cap_W, rep1

description:
Library name: Sample 1
Cap_W1


title: Plasma_74_LeanHF


title: Control - HFD-Lname 3

description:
Library name: 3
3


title: PEM-Control-3

city: Jinan

first: Wen

address: 6699 Qingdao Road

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

data_processing:
RNA-Seq
Assembly: mm9
Supplementary files format and content: PEM-CKO-vs-PEM-Control-all.gene.xls file includes raw counts for each sample

source_name: Peritoneal

extract_protocol:
Total RNA was harvested and 1.5ug total RNA was used for the construction of sequcing libraries
RNA-Seq

value: Peritoneal

value: Peritoneal macrophages (PEMs)

value: macrophages

value: Tim-4 knockout

value: lps


title: C03schilLA3111mock

description: Library name: sample23


title: Control - HFD-Lname 2

description:
Library name: 2
2

value: Whole heart

value: male


title: PEM-Control-2


title: Plasma_66_LeanHF

value: plasma


title: Plasma_59_LeanHF


title: D04schilLA4107mock

description: Library name: sample34


title: B04schilLA4107mock

description: Library name: sample14


title: PEM-Control-1