title: MLO_WT2207d60

city: Singapore

first: Matas

last: Vitkauskas

address: 60 Biopolis St.

department: Genome Institute of Singapore

country: Singapore

institute: A*star research entities

data_processing:
Briefly, reads were quality-checked using FASTQC to ensure sequencing quality, and then processed for adaptor and low read quality trimming (TrimGalore v0.6.4). Alignment to human transcriptome NCBI_GRCh38 was carried out with STAR v2.6.1. Gene feature counting was performed using FeatureCount v1.6.4 prior to differential expression analysis with DESeq2.
Assembly: hg38 - GRCh38.p13 (EnsDb.Hsapines.v104 )
Supplementary files format and content: Processed files are the individual matrices from tximport transcript quantification package. They are in .RDS format and were compressed using gzip. Raw files are fastq files.

source_name: H9 cells

growth_protocol: Organoids were generated as previously published [34], [35], with minor modifications. In brief, TrypLE-Express (Life Technologies)-dissociated hPSCs were seeded into a V-bottom 96-well culture plate (Sumitomo Bakelite) in neuronal induction media with the ROCK inhibitor thiazovivin (Calbiochem), which was removed after 24 h. Neuronal induction medium, used for the first three days, contained DMEM/F12:Neurobasal (1:1), N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), and β-mercaptoethanol (0.1%) (all Invitrogen) supplemented with 1 μg/ml heparin (Sigma-Aldrich), 10 μM SB431542 (Stemgent), 200 ng/ml Noggin (Prospec), and 0.8 μM CHIR99021 (Reagents Direct). On day 4, 100 ng/ml SHH-C25II and 100 ng/ml FGF8 (both R&D Systems), along with 0.5 μM purmorphamine (Stemgent), were added for midbrain patterning. On day 7, media was completely removed and organoids were embedded in reduced growth factor Matrigel (Corning) and left to solidify in a 37°C incubator for 30 min, then grown in tissue growth induction medium containing Neurobasal, 1:100 N2 supplement, 1:50 B27 without vitamin A, 1% GlutaMAX, 1% minimum essential media-nonessential amino acid, and 0.1% β-mercaptoethanol supplemented with 2.5 μg/ml insulin (Sigma-Aldrich), 200 ng/ml laminin (Sigma-Aldrich), 100 ng/ml SHH-C25II, and 100 ng/ml FGF8. On day 8, hMLOs were transferred using a wide-bore pipette tip into low-attachment 6-well-plates (Costar) in final differentiation media, consisting of Neurobasal medium, N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), β-mercaptoethanol (0.1%), 10ng/ml BDNF (Peprotech), 10 ng/ml GDNF (Peprotech), 100 μM ascorbic acid (Sigma-Aldrich), and 125 μM db-cAMP (Sigma-Aldrich), and were cultured on orbital shakers for maintenance. For long-term drug treatment of organoids, rotenone (Sigma-Aldrich), L-3,4-dihydroxyphenylalanine (L-DOPA) (Sigma-Aldrich), and N-acetyl cysteine (NAC) (Sigma-Aldrich) was added to culture media at the indicated concentrations.

extract_protocol:
Three to four organoids were used for each dissociation reaction, following manufacturer’s protocol. In brief, 50 units of papain enzyme (Worthington) was activated with 1 mM L-cysteine and 0.5 μM EDTA in Earle's Balanced Salt Solution (EBSS) (Thermo Fisher), and DNase I (Worthington) added. hMLOs were finely chopped with a scalpel and then resuspended in papain enzyme mix. The slurry was incubated at 37°C, 5% CO2 for 45 min on a rotator, and then triturated. Cells were spun down at 300xg for 5 min, and washed twice in EBSS containing ovalbumin (Worthington) and BSA.
Library preparation for RNA-seq was performed by Novogene AIT Singapore, using a directional mRNA library prep kit (NEB) with polyA enrichment. Paired-end 150 nt sequencing was performed on the Illumina NovaSeq, with sequencing depth of at least 30 million read pairs per sample. Datasets were analyzed using the nf-core/RNA-Seq pipeline version 1.4.2 .

value: H9 cells

tag: age


title: mESCs, shBeclin1, replicate 2, Day0

status: Public on Dec 04 2025

type: SRA

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

country: China

institute: wuhan university

description:
Library name: ES shBeclin1_2
q60

library_source: transcriptomic

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using STRA software (version 2.5.3a) with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: shBeclin1_exp.xlsx includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

tag: tissue

value: heart

tag: cell line

tag: cell type

value: mouse Embryonic Stem Cells

tag: genotype

value: WT

tag: treatment

tag: batch


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn75, donor 3

city: Mannheim

first: Guanhao

last: Li

state: Baden-Württemberg

address: Ludolf-Krehl Strasse 13-17

department: Institute of Transfusion Medicine and Immunology

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

data_processing:
FastQC and Cutadapt were used to assess the quality of raw sequencing data (fastq data).
HISAT2 was used to align the cleaned reads to the reference genome (hg38).
FeatureCounts was used to count the number of reads mapping to each gene.
Assembly: GRCh38
Supplementary files format and content: A text file including featureCounts was generated to count the number of reads for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Macrophages

growth_protocol: Monocytes were cultivated for 6 days on the sample disks at a concentration of 2×10^6cells/mL in macrophage serum-free medium X-Vivo 10 (Lonza) supplemented with 5 ng/mL M-CSF (Peprotech, Hamburg, Germany) and cytokines as follows: For M0, no cytokines were added; for M1, 100 ng/mL of IFNγ (Peprotech, Hamburg, Germany) was added; and for M2, 10 ng/mL of IL-4 was added. The cells were cultured in a 37°C incubator with an atmosphere of 7.5% CO2.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I (Omega Bio-tek, Norcross, USA) according to the manufacturer’s instructions. 500ng of total RNA was used for construction of sequencing libraries.
The quality of total RNA samples was checked on BioAnalyzer2100 (G2939BA, Agilent, USA) using Eukaryotic Total RNA Nano Kit (5067-1512, Agilent, USA) according to manufacturer’s protocol. Samples with RNA integrity number (RIN) value >8 were accepted for the library preparation process.
RNA-Seq libraries were prepared from Illumina Stranded mRNA Prep and Ligation Kit (20040534, Illumina, USA) according to the manufacturer’s protocol. Briefly, Oligo(dT) magnetic beads purify and capture the mRNA molecules containing polyA tails. Then the purified mRNA was fragmented and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. In the second strand cDNA synthesis step, dUTP replaces dTTP to achieve strand specificity. The final steps add adenine (A) and thymine (T) bases to fragment ends and ligate adapters. Sequencing runs are performed on an Illumina NextSeq 550 instrument using single-end 75-cycle sequencing by the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (20024906, Illumina, USA).

value: Macrophages


title: mESCs, shBeclin1, replicate 1, Day0

description:
Library name: ES shBeclin1_1
q60


title: Lung, wt_p21_1

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Forward and reverse reads were then aligned to the reference genome index using the Rsubread align function.
Gene counts were quantified using the BAM files generated from this step, featureCounts (v2.0.3).
Assembly: GRCm38 DNA primary assembly
Supplementary files format and content: .txt formatted gene count matrix

source_name: Lung

extract_protocol:
Lungs were homogenised using pellet pestles and RNA extraction was performed using the Isolate II RNA mini kit according to manufacturer’s instruction An input of 100 ng of total RNA was prepared and indexed for illumina sequencing using the TruSeq RNA sample Prep Kit with RiboGlobin depletion as per manufacturer’s instruction. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2 x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit as per manufacturer’s instructions.
1000 ng of the isolated total RNA was globin reduced and TruSeq Stranded kit was used for library preparation.

value: Lung

value: wild-type

value: p21 virus, 3 d.p.i.


title: mESCs, shNT, replicate 2, Day0

description:
Library name: ES shNT_2
q60

value: ES+shNT


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn50, donor 3


title: Macrophages, without stimulation + plastic, donor 4


title: MLO_WT1310d60


title: Lung, quint_mock_4

value: mock virus, 3 d.p.i.


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn25, donor 3


title: Lung, wt_p21_5


title: PC9SENSITIVE-3

city: Nanjing

first: yuxian

last: Qian

address: baiziting no.42

institute: Nanjing medical university

data_processing:
After sequencing by Illumina NovaSeq 6000 sequencer, image analysis, base identification and quality control, Raw reads (Raw Data) were produced. First use Q30 for quality control. Then, cutadapt[1] software (v1.9.3) was used to disconnect low-quality reads and obtain high-quality clean reads. STAR software was used to match clean reads from input library to mouse reference genome (MM10), and then DCC software was used to identify circRNA. The de-coupling reads were compared to the human reference genome using Hisat2 software (v2.0.4). MACS software was then used to identify methylated genes in each sample. Differential methylation gene identification was performed using diffReps software. The peaks located on the exon of mRNA, LncRNA and circRNA were screened by our own procedures and annotated accordingly. The coding genes of differential methylation, LncRNA associated genes and circRNA source genes were analyzed by GO and Pathway, respectively.
Assembly: hg19
Supplementary files format and content: Excel format of methylated sites of circRNAs

extract_protocol:
m6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit (GenSeq).
Utilize NEBNext® The Ultra II Directional RNA Library Prep kit was used to detect Input RNA samples without immunoprecipitation. RNA sequencing library was constructed from IP RNA samples after immunoprecipitation. Analysis by BioAnalyzer 2100 Agilent performs library quality inspection. The Illumina NovaSeq 6000 sequencer was run in 150 bp double-ended mode High-throughput sequencing was performed.
MeRIP-seq

value: lung adenocacinoma cell

value: Vehicle

tag: phenotype

value: SENSITIVE (N)


title: MLO_WT2106d60


title: CD45 positive lung cells IAPA antibody info

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description:
Library name: LSC004_CITESEQ
Used antibody panel added in feature_reference.csv

library_source: other

data_processing:
CellRanger version 8.0.1 was used to map the reads to the reference genome
Assembly: mm10 Ensembl98
Supplementary files format and content: .h5 files containing count matrices
Supplementary files format and content: feature_reference.csv containing used antibodies in the citeseq library
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Perfused lungs were harvested in complete RPMI (RPMI 1640 (Life-technologies)) supplemented with 10% FCS, nonessential amino acids (Gibco) and HEPES (Gibco) and kept on ice until processing. Single cells were obtained after mechanical dissociated of the lungs and digestion in digestion buffer (PBS, 3% FCS, 2 mg/ml collagenase IV) for 1 h at 37 °C. After incubation, cells were passed through a 100 µm nylon cell strainer and red blood cells were lysed with a red blood cell lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA). Up to 4 million cells per mouse were incubated for 30 min on ice with 50 μL of staining mix in PBS containing 0.04% BSA, TruStain FcX Block (BioLegend, cat 101320), CD45-APC (30-F11), mouse CITE-Seq antibody panel and an unique mouse TotalSeq-C cell hashing antibody (BioLegend) diluted 1:1000. The CITE-Seq panel contains 192 unique oligoconjugated antibodies and isotype controls (TotalSeq™-C). To enable simultaneous processing of multiple biological replicates, we applied a cellular hashing strategy using TotalSeq-C anti-mouse hashtag antibodies specific against mouse CD45 and MHC class I (BioLegend). Briefly, three to four biological replicates (mice) were pooled and labeled with unique hashtag antibodies prior to single-cell processing. Each biological replicate received a distinct TotalSeq-C barcode, allowing downstream demultiplexing and assignment of single-cell transcriptomic and protein expression data to individual mice. FACS-sorted single-cell suspensions were resuspended at an estimated final concentration of 2000 cells/μ, with replicates pooled in equimolar ratios and loaded on a Chromium GemCode Single Cell Instrument (10× Genomics) to generate single-cell Gel beads-in-EMulsion (GEM).
The cDNA libraries were prepared using the GemCode Single Cell 5′ v3 Gel Bead and Library kit, version GEM-X V3 according to the manufacturer's instructions (10x Genomics, User Guide CG000734). Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 5′ gene expression and cell surface protein construction. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the Fragment Analyzer(Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core on the Illumina NovaSeq 6000 platform with a read configuration of 28 cycles for Read 1, 10 cycles for i7 index, 10 cycles for i5 index, and 90 cycles for Read 2, incorporating 1% PhiX as a sequencing control, pooled in an 85:15 ratio for the combined 5′ gene expression and cell surface protein samples, respectively

treatment_protocol: Eight to ten weeks old immunocompetent male C57BL/6NTac mice (internal stock of the Laboratory Animal Centre, KU Leuven) were randomly allocated to experimental groups [Healthy control, influenza only infected mice, Aspergillus only infected mice and IAPA (superinfection influenza + Aspergillus) infected mice]. Mice received a viral challenge via an intranasal instillation of 10 plaque forming units (PFU) mouse-adapted influenza virus A/H3N2/Ishikawa/7/82 or sham (PBS) on day 0 (10 µL per nostril) and orotracheally inoculation with 20 µL of a red-shifted thermostable firefly luciferase A. fumigatus spore solution (CBS144.89 strain (CEA10) isolated from a patient with IPA (17, 81); 5 x 109 conidia/mL) or sham (PBS) under inhalation anesthesia with isoflurane (1.5-2% in 100% oxygen, Primal Critical Care) on day 4.

value: IAPA

tag: library type

value: HTO + ADT


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn100, donor 3


title: MLO_WT1506d60


title: Lung, quad_p21_2


title: Macrophages, IFNgamma stimulation + Ti64_CaP, donor 3


title: CD45 positive lung cells Influenza 4 antibody info

description:
Library name: LSC003_CITESEQ
Used antibody panel added in feature_reference.csv

value: Influenza


title: Lung, quint_mock_3


title: Macrophages, IFNgamma stimulation + Ti64, donor 3


title: CD45 positive lung cells Aspergillus antibody info

description:
Library name: LSC002_CITESEQ
Used antibody panel added in feature_reference.csv

value: Aspergillus


title: Lung, quint_mock_2


title: CD45 positive lung cells healthy control (HC) antibody info

description:
Library name: LSC001_CITESEQ
Used antibody panel added in feature_reference.csv

value: Healthy control (HC)


title: MLO_DJ2207d60

value: H9 cells

value: DJ-1 KO


title: Lung, quint_p21_6


title: MLO_DJ1310d60


title: CD45 positive lung cells IAPA 4 replicates

description: Library name: LSC004_cDNA

library_source: transcriptomic single cell

data_processing:
CellRanger version 8.0.1 was used to map the reads to the reference genome
Assembly: mm10 Ensembl98
Supplementary files format and content: .h5 files containing count matrices
Supplementary files format and content: feature_reference.csv containing used antibodies in the citeseq library

value: mRNA


title: Macrophages, without stimulation + Ti64_CaP_Zn75, donor 3

value: Macrophages


title: Lung, quint_p21_5

value: Lung


title: CD45 positive lung cells Influenza 4 replicates

description: Library name: LSC003_cDNA


title: Macrophages, without stimulation + Ti64_CaP_Zn25, donor 3


title: MLO_DJ1506d60


title: mESCs, shNT, replicate 1, Day0

description:
Library name: ES shNT_1
q60

value: heart

value: mouse Embryonic Stem Cells

value: WT


title: Lung, quad_mock_4

value: mock virus, 3 d.p.i.


title: CD45 positive lung cells Aspergillus 3 replicates

description: Library name: LSC002_cDNA


title: MLO_DJ0307d60


title: Lung, quad_mock_3


title: Macrophages, without stimulation + Ti64_CaP_Zn100, donor 3


title: MLO_WT0307d60


title: CD45 positive lung cells healthy control (HC) 3 replicates

description: Library name: LSC001_cDNA


title: Macrophages, without stimulation + Ti64_CaP, donor 3


title: Lung, quad_mock_2


title: Pooled lung resident T cells from Young_A20, YoungD1cA20, and Aged mice (TCR)

city: San Francisco

first: Nancy

last: Allen

state: CA

address: 513 Parnassus Ave.

department: Medicine

country: USA

institute: UCSF

description:
Library name: Resident_CD3_TCR
10x Genomics

data_processing:
Raw Fastq files were aligned with Cellranger. Demultiplexing was performed in Seurat using HTODemux
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

extract_protocol:
Prior to sacrifice animals were anesthetized and administerd 3ug of fluorescently labeled anti-mouse CD45 (clone 30-F11, BD563890) in 150 uL PBS. After 3 minutes of antibody circulation mice were euthanized with isofluorane. After cardiac perfusion with PBS, mouse lungs were tracheally perfused with a digestion cocktail of Liberase TM (40 ug/mL, Millipore Sigma 5401119001) and Dnase (50 U/ml, Sigma DN25) in HBSS (+Ca+Mg) and removed from the chest. The lung was incubated in digestion cocktail for 45 mins at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cell suspensions were blocked with mouse FcR blocking reagent (Miltenyl Biotec 130-092-575) for 15 minutes and then incubated with the appropriate fluorescently-conjugated antibodies and Biolegend barcode antibodies in sorting buffer for 30 min at 4C. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and DRAQ7 (CST #7406), respectively. The following antibodies were used for staining: anti-CD45 UVC (BD 564279) , anti-CD11b BV605 (BD 563015) and anti-CD3 PECy7 (Biolegend, 100219). FACS was performed on a BD FACS Aria using FACSDiva Software.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

value: T cells

value: Tnfaip3f/f (Young_A20), Dermo1-cre/+;Tnfaip3f/f (Young_D1cA20), and wild-type C57BL/6 (Aged)

value: Homeostasis


title: Macrophages, without stimulation + Ti64, donor 3


title: Pooled lung resident T cells from Young_A20, YoungD1cA20, and Aged mice (Gene_expression)

description:
Library name: Resident_CD3_GEX
10x Genomics


title: human sperm head, donor8_T2, PANDORA-seq

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

institute: university of utah

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: sperm head

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: sperm head

value: 52 years

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: human sperm head, donor7_T2, PANDORA-seq

value: 60 years


title: human sperm head, donor8_T1, PANDORA-seq

value: 38 years


title: Macrophages, without stimulation + plastic, donor 3


title: Lung, quad_p21_5

value: p21 virus, 3 d.p.i.


title: Lung, quad_mock_1


title: Lung, quad_p21_6


title: Macrophages, without stimulation + Ti64_CaP_Zn50, donor 3


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn75, donor 2


title: Pooled lung resident T cells from Young_A20, YoungD1cA20, and Aged mice (Hashtag_oligos)

description:
Library name: Resident_CD3_CSP
10x Genomics


title: MLO_DJ2106d60

value: H9 cells

value: DJ-1 KO


title: Lung resident CD45+ cells from Dermo1-cre/+;Tnfaip3f/f (D1cA20) mice

description: Library name: D1cA20

data_processing:
For scRNA sequencing data was processed using Cell Ranger. For bulk RNA sequencing reads were aligned using HISAT and assembled with Stringtie software to the reference genome Mus musculus, UCSC version mm10
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual. For bulk RNA sequencing data raw counts per gene are listed per sample in comma-separated values (.csv) format.

extract_protocol:
Prior to sacrifice animals were anesthetized and injected retro-orbitally with 3ug of fluorescently labeled anti-mouse CD45 (clone 30-F11, BD563890) in 150 uL PBS. After 3 minutes of antibody circulation mice were euthanized with isofluorane. After cardiac perfusion with PBS, mouse lungs were tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was incubated in digestion cocktail for 1 hour at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cell suspensions were blocked with mouse FcR blocking reagent (Miltenyl Biotec 130-092-575) for 15 minutes and then incubated with the appropriate fluorescently-conjugated antibodies in sorting buffer for 30 min at 4C. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and DRAQ7 (CST #7406), respectively. The following antibodies were used for staining: anti-CD45 UVC (BD 564279), anti-CD31 BV711(BD 740680), anti-Epcam BV711 (Biolegend 118233), anti-Pdgfra APC (Fisher Scientific 50-112-9423). FACS was performed on a BD FACS Aria using FACSDiva Software.
For scRNA sequencing cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.


title: human sperm head, donor6_T2, PANDORA-seq

value: 43 years


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn50, donor 2

value: Macrophages


title: a9855_32

city: Houston

first: Caleb

middle: A

last: Wood

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Illumina software used for basecalling was performed by Novogene (Beijing, CN)
Raw reads were processed for low quality, adapter related sequences, and high n-% using fastp v0.23.1 and default parameters (Chen et al., 2018). Processed reads were aligned to the most recent mouse genome build (mm39, NCBI). Alignment and gene counts were performed using STAR aligner v2.7.9a (Dobin et al., 2013) with default parameters. A
Transcript counts were generated using STAR aligner v2.7.9a (Dobin et al., 2013) with default parameters.
Normalization for abundance was performed within DESeq2 v.1.32.0 (Love et al., 2014)
Assembly: mm39
Supplementary files format and content: Comma separated variable file of matrix table with raw gene counts for every gene and every sample

source_name: subdissected entorhinal cortex

extract_protocol:
Brains were removed and EC was isolated, flash frozen on dry ice, and RNA was harvested using an RNeasy kit (Qiagen, cat # 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene (Beijing, CN)

value: subdissected entorhinal cortex

tag: Sex

value: M

value: tg/tg

tag: strain

value: Nop-tTA Line S (MMRRC strain #31779) x TRE-GlyCl-YFP Line 9531 (Jax strain #29301)


title: human sperm head, donor6_T1, PANDORA-seq

value: 37 years


title: Lung resident CD45+ cells from Tnfaip3f/f (A20control) mice

description: Library name: A20control

value: Lung


title: Macrophages, IFNgamma stimulation + plastic, donor 3


title: a9847_30


title: Male C57BL/6J mice, LPS/GaIn + TCP3

city: Guangzhou

first: Renjie

last: Cao

address: No. 132, East Tianhe Road

department: School of Pharmaceutical Sciences

institute: Sun-yat sen university

description:
Library name: Sample 6
FPKM.LT5

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm9
Supplementary files format and content: FPKM values for each Sample

source_name: Liver

growth_protocol: All mice were housed in a pathogen-free system, which provides sterile isolator cages with fresh food, water, and bedding weekly.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: Mice were injected intraperitoneally with vehicle (corn oil, Sigma, St. Louis, USA) or 3 mg/kg TCP (Aladdin Biotechnology, Shanghai, China) once daily for 5 days. Two hours after the last injection, the mice were intraperitoneally injected with saline or LPS/GaIn (100 μg/kg and 700 mg/kg, respectively. Sigma, St. Louis, USA)  for 6 hours

value: Liver

value: male

value: Wild type

value: LPS challenge with TCP pretreatment


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn100, donor 2


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn25, donor 2


title: human sperm head, donor5_T2, PANDORA-seq

value: sperm head

value: 57 years

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Male C57BL/6J mice, LPS/GaIn + TCP2

description:
Library name: Sample 5
FPKM.LT3


title: a9845_34

value: Veh


title: human sperm head, donor5_T1, PANDORA-seq

value: 36 years


title: human sperm head, donor4_T2, PANDORA-seq

value: 54 years


title: a9843_28


title: Male C57BL/6J mice, LPS/GaIn + TCP1

description:
Library name: Sample 4
FPKM.LT1


title: Macrophages, IL4 stimulation + Ti64, donor 2

value: Macrophages


title: Macrophages, IL4 stimulation + Ti64_CaP, donor 2


title: Male C57BL/6J mice, LPS/GaIn3

description:
Library name: Sample 3
FPKM.L4

value: LPS challenge with vehicle pretreatment


title: Male C57BL/6J mice, LPS/GaIn2

description:
Library name: Sample 2
FPKM.L3


title: human sperm head, donor7_T1, PANDORA-seq

value: 46 years


title: a9724_24

value: subdissected entorhinal cortex

value: F

value: tg/tg


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn75, donor 2


title: Macrophages, IL4 stimulation + plastic, donor 2


title: a9734_27

value: Nop-tTA Line S (MMRRC strain #31779) x TRE-GlyCl-YFP Line 9531 (Jax strain #29301)


title: a9719_25


title: a9718_26


title: human sperm head, donor2_T2, PANDORA-seq

value: 64 years


title: BM OP-HU3

city: Xi'an

first: Chen

last: Zhang

address: Xinsi road

department: Department of hematology

institute: Tangdu Hospital

data_processing:
CASAVA was used for base-calling.
Clean reads were obtained by removing reads containing adapter, reads containing N base and low quality  through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file include FPKM value for each sample

source_name: femur

growth_protocol: Freshly isolated bone marrow cells were used for total RNA extraction

extract_protocol:
Total RNA was isolated using TRNzol (DP424, TIANGEN) according to the manufacturer’s instructions and used for library preparation.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Mice were treated with or without hindlimb unloading for four weeks.

value: Bone marrow

value: Bone marrow cells

value: WT

value: hindlib unloading


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn50, donor 2


title: human sperm head, donor3_T1, PANDORA-seq

value: sperm head

value: 41 years


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn25, donor 2


title: BM OP-HU2


title: Lung, quad_p21_1

value: Lung

value: p21 virus, 3 d.p.i.


title: a9461_21

value: Veh


title: human sperm head, donor2_T1, PANDORA-seq

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn100, donor 2

value: Macrophages


title: a9455_17


title: a9454_20

value: M


title: human sperm head, donor1_T2, PANDORA-seq

value: 68 years


title: human sperm head, donor3_T2, PANDORA-seq

value: 49 years


title: BM control 3


title: Macrophages, IFNgamma stimulation + Ti64_CaP, donor 2


title: human sperm head, donor1_T1, PANDORA-seq

value: 52 years


title: BM control 2


title: Macrophages, IFNgamma stimulation + plastic, donor 2


title: Male C57BL/6J mice, LPS/GaIn1

description:
Library name: Sample 1
FPKM.L1

value: Liver

value: male

value: Wild type

value: LPS challenge with vehicle pretreatment


title: BM control 1

value: Bone marrow

value: Bone marrow cells

value: WT


title: pbmc, at Post 24h, in POD group

city: Chengdu

first: Juan

last: Wu

state: Sichuan

address: No. 37 Guo Xue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

description: 10x Genomics

data_processing:
CellRanger software (version 7.0.0, 10X Genomics) was used to analyze the sequencing data, and gene expression information for each cell was obtained.
Assembly: Ensembol V105
Supplementary files format and content: Tab-separated values and Matrix files

source_name: pbmc

extract_protocol:
Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll Hypaque density solution. Cells were used only if >80% were viable based on trypan blue staining, in which case they were subjected to single-cell RNA sequencing.
An appropriate volume of peripheral blood mononuclear cells was loaded onto a 10X Genomics Chromium instrument to capture 8000 single cells according to the manufacturer’s instructions for the 10X Genomics Chromium Single-Cell 5’ kit (version 2). Subsequent cDNA amplification and library construction were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150 bp) at LC-Bio Technology (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: pbmc

tag: time

value: Post 24h


title: a9452_22

value: subdissected entorhinal cortex

value: tg/tg

value: Nop-tTA Line S (MMRRC strain #31779) x TRE-GlyCl-YFP Line 9531 (Jax strain #29301)


title: pbmc, at Pre-grugery, in POD group

description: 10x Genomics

value: Pre-grugery


title: Macrophages, without stimulation + Ti64_CaP_Zn75, donor 2

value: Macrophages


title: pbmc, POD group, at Post 24h

description: 10x Genomics


title: treatment 3

city: hangzhou

first: Hui

last: Dang

state: zhejiang

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

description: KO group, replicate biosample 1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to gossypium hirsutum using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: thyroid

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: thyroid

value: TET1 KO

value: KO


title: a9453_23

value: M


title: human sperm head, donor4_T1, PANDORA-seq

value: sperm head

value: 34 years

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: treatment 2

description: KO group, replicate biosample 1


title: BM OP-HU1

value: Bone marrow

value: hindlib unloading


title: a9226_19

value: F


title: pbmc, POD group, at Pre-grugery

description: 10x Genomics

value: pbmc


title: treatment 1

description: KO group, replicate biosample 1


title: a9224_18


title: Macrophages, without stimulation + Ti64_CaP_Zn50, donor 2


title: Macrophages, without stimulation + Ti64_CaP_Zn25, donor 2


title: a9442_14


title: Macrophages, IFNgamma stimulation + Ti64, donor 2


title: Macrophages, without stimulation + Ti64_CaP_Zn100, donor 2


title: pbmc, at Post 24h, in non POD group

description: 10x Genomics

value: Post 24h


title: control 3

description: control group, replicate biosample 1

value: WT


title: pbmc, at Pre-grugery, in non POD group

description: 10x Genomics


title: a8884_12

value: subdissected entorhinal cortex

value: tg/tg


title: control 2

description: control group, replicate biosample 1


title: Macrophages, without stimulation + Ti64_CaP, donor 2


title: pbmc, non POD group, at Post 24h

description: 10x Genomics


title: a8753_4

value: Nop-tTA Line S (MMRRC strain #31779) x TRE-GlyCl-YFP Line 9531 (Jax strain #29301)


title: control 1

description: control group, replicate biosample 1


title: Macrophages, without stimulation + plastic, donor 2

value: Macrophages


title: Macrophages, without stimulation + Ti64, donor 2


title: VNG, wt, I4

city: Philadelphia

first: Chengcheng

last: Jin

state: PA

address: BRB II/III, Room 732-734, 421 Curie Blvd

department: Department of Cancer Biology

institute: University of Pennsylvania

description:
Chromium Next GEM Single Cell 3’ Kit v3.1
wt_barcodes.tsv
wt_features.tsv
wt_matrix

data_processing:
Raw sequencing data for RNA expression were aligned to the mm10 reference mouse transcriptome.
Low-quality cells were filtered and the remaining cells were clustered using the R package Seurat v3
Assembly: mm10
Supplementary files format and content: tab-separated values file includes barcodes
Supplementary files format and content: tab-separated values file includes features
Supplementary files format and content: tab-separated values file includes matrix

source_name: vagal nodose ganglion

extract_protocol:
Vagal nodose ganglions were acutely dissected and dissociated in a solution with liberase and Dnase. Cells were then triturated, filtered, and enriched using Percoll.
Single-cell cDNA libraries were prepared at the Yale Center for Genomic Analysis (YCGA)

value: vagal nodose ganglion

value: PBS, tail vein injection


title: pbmc, non POD group, at Pre-grugery

description: 10x Genomics

value: Pre-grugery


title: VNG, wt, I3


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn25, donor 1


title: K562, non-targeting sgRNA, Rapamycin treated, rep 2

city: Cambridge

first: David

last: Mayhew

state: MA

address: 500 Technology Square, Suite 700

institute: Foghorn Therapeutics

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR (v2.7.3a).
Gene counts were quantified on the GENCODE reference gtf file version 27 using featureCounts from the SubRead package (v2.0.0).
Differential gene expression was calculated from the resultant gene-level counts matrix using the limma-voom method (after TMM normalization) in R (R v4.1.2, limma v3.34.9, Glimma 1.10.0, and edgeR v3.24.0).
Assembly: hg38
Supplementary files format and content: Ensembl_Read_Counts.txt (gene-level read counts table).

growth_protocol: K562 cells (ATCC: CCL-243) were cultured at 37C 5%CO2 in Iscove's Modified Dulbecco's Medium supplemented with 1X GlutaMAX and 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) from frozen cell pellets previously washed with PBS. 1 μg RNA per sample was used as input material.
Sequencing libraries were generated at Novogene using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations, index codes were added to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.

treatment_protocol: K562 cells (1x10^6) were treated with DMSO or rapamycin (10 nM) for 24 h.

value: K562-FIRE (Lv EF1a dCas9 2A Blast; EF1a MS2-Fkbp(1x) 2A Hygro; Lv EF1a SS18-Frb PGK Puro)

value: non-targeting sgRNA

value: Rapamycin


title: a8751_7


title: K562, non-targeting sgRNA, DMSO treated, rep 2

value: DMSO


title: a8749_5

value: Veh


title: VNG, wt, I2


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn50, donor 1


title: K562, non-targeting sgRNA, Rapamycin treated, rep 1


title: a8744_3

value: M


title: a7928_2

value: F


title: VNG, wt, I1


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn75, donor 1


title: K562, HBG1 promoter sgRNA, Rapamycin treated, rep 3

value: HBG1 promoter sgRNA


title: a8881_15


title: VNG, kp3, R3

description:
Chromium Next GEM Single Cell 3’ Kit v3.1
kp3_barcodes.tsv
kp3_features.tsv
kp3_matrix

value: KP lung tumor, tail vein injection


title: a7922_1


title: Macrophages, IL4 stimulation + Ti64_CaP, donor 1


title: VNG, kp3, R2

value: WT


title: K562, HBG1 promoter sgRNA, DMSO treated, rep 3


title: Macrophages, IL4 stimulation + Ti64_CaP_Zn100, donor 1


title: Prostate cancer tissue, prostate cancer patient3,rep3

city: Suzhou

first: Ouyang

last: Jun

address: No.899 Pinghai Road,Gusu District

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample6

data_processing:
Base calling were converted to FASTQ format using BaseSpace (Illumina).
Assembly: hg38
Supplementary files format and content: The Excel file contains FPKM values for each sample.

source_name: Prostate cancer tissue

extract_protocol:
RNA was extracted from TRIzol reagent following the manufacturer’s protocol.
1 μg of total RNA was used for subsequent library preparation. RNA libraries for RNA sequencing were prepared using the SMARTer Stranded RNA-Seq Kit

value: Prostate cancer tissue

value: Human Prostate Cancer


title: K562, HBG1 promoter sgRNA, Rapamycin treated, rep 2


title: Macrophages, IL4 stimulation + Ti64, donor 1


title: Prostate cancer tissue, prostate cancer patient2,rep2

description: Library name: Sample5


title: K562, HBG1 promoter sgRNA, DMSO treated, rep 2


title: VNG, kp3, I1


title: Prostate cancer tissue, prostate cancer patient1,rep1

description: Library name: Sample4


title: VNG, kp3, R1


title: Macrophages, IL4 stimulation + plastic, donor 1


title: K562, HBG1 promoter sgRNA, Rapamycin treated, rep 1


title: M WT NX 5

city: Madison

first: Jyoti

last: Watters

state: WI

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Following sequencing, sequences were aligned by Novogene to the reference genome using HISAT2 software
Assembly: Reference genome: GRCm38/mm10
Supplementary files format and content: tab-delimited rext file includes raw counts for each sample
Supplementary files format and content: tab-delimited rext file includes RPKM values for each sample

source_name: microglia

extract_protocol:
Cd11b+ Microglia were immunomagnetically isolated from the cerebrum.
RNA was isolated with TriReagent and sent to Novogene for library construction.

value: microglia

value: Wildtype

value: Normoxia


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn75, donor 1

data_processing:
FastQC and Cutadapt were used to assess the quality of raw sequencing data (fastq data).
HISAT2 was used to align the cleaned reads to the reference genome (hg38).
FeatureCounts was used to count the number of reads mapping to each gene.
Assembly: GRCh38
Supplementary files format and content: A text file including featureCounts was generated to count the number of reads for each sample.

value: Macrophages


title: Prostate cancer adjacent tissue, prostate cancer patient3,rep3

description: Library name: Sample3

source_name: Prostate cancer adjacent tissue

value: Prostate cancer adjacent tissue


title: K562, HBG1 promoter sgRNA, DMSO treated, rep 1

value: K562-FIRE (Lv EF1a dCas9 2A Blast; EF1a MS2-Fkbp(1x) 2A Hygro; Lv EF1a SS18-Frb PGK Puro)


title: M WT NX 4


title: Prostate cancer adjacent tissue, prostate cancer patient2,rep2

description: Library name: Sample2


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn100, donor 1


title: A1726-2_SRPBM

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
The fragments of genes were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization.
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software

source_name: lymph node/skin tissue

extract_protocol:
Total RNA was extracted from FFPE tissues followed by library preparation according to Illumina standard instruction (SMARTer Stranded Total RNA-Seq Kit v2).
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina NovaSeq6000.

value: lymph node/skin tissue

value: Sintilimab with P-GEMOX chemotherapy

value: Drug-sensitivity


title: Prostate cancer adjacent tissue, prostate cancer patient1,rep1

description: Library name: Sample1


title: 301032_SRPBM


title: M WT NX 2


title: Macrophages, IFNgamma stimulation + Ti64_CaP, donor 1

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I (Omega Bio-tek, Norcross, USA) according to the manufacturer’s instructions. 500ng of total RNA was used for construction of sequencing libraries.
The quality of total RNA samples was checked on BioAnalyzer2100 (G2939BA, Agilent, USA) using Eukaryotic Total RNA Nano Kit (5067-1512, Agilent, USA) according to manufacturer’s protocol. Samples with RNA integrity number (RIN) value >8 were accepted for the library preparation process.
RNA-Seq libraries were prepared from Illumina Stranded mRNA Prep and Ligation Kit (20040534, Illumina, USA) according to the manufacturer’s protocol. Briefly, Oligo(dT) magnetic beads purify and capture the mRNA molecules containing polyA tails. Then the purified mRNA was fragmented and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. In the second strand cDNA synthesis step, dUTP replaces dTTP to achieve strand specificity. The final steps add adenine (A) and thymine (T) bases to fragment ends and ligate adapters. Sequencing runs are performed on an Illumina NextSeq 550 instrument using single-end 75-cycle sequencing by the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (20024906, Illumina, USA).


title: 466639_SRPBM


title: Colon, tumor33

city: Seoul

first: Min Seob

last: Kwak

address: 892, Dongnam-ro, Gangdong-gu

country: South Korea

institute: Kyung Hee university

description:
Library name: Sample66
21-F-TN-0041

data_processing:
Using the Illumina Hiseq 2500, the raw data were generated and their Low-quality reads and adapter sequences were trimmed by Trimmomatic v0.38.
Using the StringTie v2.2.0, transcripts and genes were assembled from the aligned reads, followed by read alignment and quantification by HISAT v2.2.1.
Adapter sequences were trimmed by Trimmomatic v0.38.
Using the StringTie v2.2.0, transcripts and genes were assembled from the aligned reads, followed by read alignment and quantification by HISAT v2.2.1.
Genes less than 100 counts per million were filtered out and the counts were normalized with calcNormFactors function.
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, raw count
Supplementary files format and content: All counts were inserted on tab-delimited file.

source_name: Colon

extract_protocol:
Total RNA was extracted from colonic tissue samples using TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and by RNase-free agarose gel electrophoresis.
We performed RNA sequencing on the samples of included patients using SureSelectXT RNA Direct Library Preparation Kit.

value: Colon

tag: disease state

value: Tumor


title: 1617630_SRPBM


title: Macrophages, IFNgamma stimulation + Ti64, donor 1

first: Guanhao

last: Li

institute: Medical Faculty Mannheim, Heidelberg University


title: M WT NX 1


title: Colon, tumor31

description:
Library name: Sample64
21-F-TN-0038


title: M 5X NX 5


title: Macrophages, IFNgamma stimulation + plastic, donor 1


title: M 5X NX 4


title: Colon, tumor30

description:
Library name: Sample63
21-F-TN-0037


title: 444324_SRPBM

value: Drug-resistance


title: 395942_SRPBM


title: M 5X NX 3


title: Macrophages, without stimulation + Ti64_CaP_Zn75, donor 1


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn50, donor 1


title: M WT NX 3


title: M 5X NX 2


title: Macrophages, IFNgamma stimulation + Ti64_CaP_Zn25, donor 1


title: Colon, tumor28

description:
Library name: Sample61
21-F-TN-0026


title: PA1509363_SRPBM


title: Macrophages, without stimulation + Ti64_CaP_Zn25, donor 1


title: Colon, tumor32

description:
Library name: Sample65
21-F-TN-0039


title: Colon, tumor26

description:
Library name: Sample59
21-F-TN-0017


title: M WT IH 5

value: Intermittent Hypoxia


title: LSECs_4H

city: Beijing

first: Yi

last: Long

address: Jinchun Road

institute: Tsinghua university

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high qualit
Clean reads were mapped to GRCh38 using Hisat2.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include fpkm values for each sample

extract_protocol:
Total RNA was extracted by using Trizol reagent. Around 1000 ng of total RNA was used for the construction of sequencing libraries according to standard Illumina protocols.
RNA libraires for RNA-seq were prepared using VAHTS Universal V6 RNAseq Library Prep Kit for Illumina ® (NR604-01/02).

value: Liver

value: LSEC cell line

value: Endothelial cell

value: 20mmHg hydrostatic pressure treated 4 hours


title: M WT IH 4

value: microglia


title: Macrophages, without stimulation + Ti64_CaP, donor 1

city: Mannheim

address: Ludolf-Krehl Strasse 13-17


title: LSECs_24H

value: 20mmHg hydrostatic pressure treated 24 hours


title: 430313B_SRPBM


title: Colon, tumor25

description:
Library name: Sample58
21-F-TN-0016


title: Macrophages, without stimulation + Ti64_CaP_Zn100, donor 1


title: Macrophages, without stimulation + Ti64, donor 1


title: LSECs_NC

value: NC

value: without hydrostatic pressure treatment


title: LSEC_shGPR116_HP


title: Macrophages, without stimulation + plastic, donor 1

value: Macrophages


title: M WT IH 2

value: Wildtype


title: Colon, tumor29

description:
Library name: Sample62
21-F-TN-0036


title: Macrophages, without stimulation + Ti64_CaP_Zn50, donor 1


title: M WT IH 3


title: Colon, tumor23

description:
Library name: Sample56
21-F-TN-0010


title: LSEC_shGPR116_NP

value: Non hydrostatic pressure treatment


title: Colon, tumor22

description:
Library name: Sample55
20-F-TT-0060


title: M WT IH 1


title: LSEC_shControl_HP


title: human sperm head, donor47, PANDORA-seq

description: Library name: ZK7T

source_name: Sperm head

extract_protocol:
For smallRNA-seq, total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Sperm head

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: 40 years


title: M 5X NX 1

value: Normoxia


title: Colon, tumor21

description:
Library name: Sample54
20-F-TT-0059

value: Colon

value: Tumor


title: M 5X IH 5

value: Intermittent Hypoxia


title: human sperm head, donor45, PANDORA-seq

description: Library name: ZD0S

value: 25 years


title: LSEC_shControl_NP

value: Liver

value: LSEC cell line

value: Endothelial cell


title: M 5X IH 4

value: microglia


title: Colon, tumor20

description:
Library name: Sample53
20-F-TT-0054


title: M 5X IH 3


title: human sperm head, donor44, PANDORA-seq

description: Library name: YU26

value: 45 years


title: right eye (migrant), 44 dpf, rep4

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

description: Library name: 22d_lib_RRBS

library_source: genomic

data_processing:
The RRBS sequenced reads were aligned using BSMAP v2.90
Assembly: ASM1334776v1
Supplementary files format and content: txt files include methylation level at each citosine performed using the methratio.py script from BSMAP software.

molecule: genomic DNA

organism: Scophthalmus maximus

source_name: Eye

extract_protocol:
DNA was extracted and purified using the QIAGEN Genomic DNA kit (Qiagen, Germany), in accordance with the manufacturer's instructions.
The Diagenode Premium RRBS kit (Diagenode Inc., USA) was used in accordance with the manufacturer's instructions. The DNA from all samples was subjected to bisulfite conversion by MspI enzyme digestion, resulting in a total of 100 ng of DNA targeted for CCGG sites. The resulting DNA fragments were purified using AMPure XP Beads (Beckman-Coulter, USA), and their concentration was determined using a Qubit High Sensitivity assay (ThermoFisher Scientific, USA).

value: Eye


title: human sperm head, donor43, PANDORA-seq

description: Library name: W6C9

value: 33 years


title: Colon, tumor24

description:
Library name: Sample57
21-F-TN-0015


title: Colon, tumor19

description:
Library name: Sample52
20-F-TT-0053


title: Colon, tumor18

description:
Library name: Sample51
20-F-TN-0075


title: right eye (migrant), 44 dpf, rep2

description: Library name: 20d_lib_RRBS


title: Colon, tumor17

description:
Library name: Sample50
20-F-TN-0072


title: human sperm head, donor42, PANDORA-seq

description: Library name: VX6C

value: 36 years


title: M 5X IH 1


title: right eye (migrant), 44 dpf, rep1

description: Library name: 19d_lib_RRBS


title: human sperm head, donor46, PANDORA-seq

description: Library name: ZG5B

value: 42 years


title: Colon, tumor16

description:
Library name: Sample49
20-F-TN-0062


title: F 5X IH 1


title: human sperm head, donor41 PANDORA-seq

description: Library name: VX1Y

value: Sperm head

value: 46 years


title: Colon, tumor15

description:
Library name: Sample48
20-F-TN-0061


title: F 5X IH 2


title: right eye (migrant), 21 dpf, rep4

description: Library name: 18d_lib_RRBS


title: human sperm head, donor40, PANDORA-seq

description: Library name: VW9T

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: human sperm head, donor39, PANDORA-seq

description: Library name: U91Z

value: 48 years


title: F 5X IH 3


title: right eye (migrant), 21 dpf, rep3

description: Library name: 17d_lib_RRBS


title: Colon, tumor14

description:
Library name: Sample47
21-F-TT-0040

value: Colon


title: right eye (migrant), 44 dpf, rep3

description: Library name: 21d_lib_RRBS


title: right eye (migrant), 21 dpf, rep2

description: Library name: 16d_lib_RRBS


title: human sperm head, donor38, PANDORA-seq

description: Library name: SY3T

value: 26 years


title: right eye (migrant), 21 dpf, rep1

description: Library name: 15d_lib_RRBS


title: F 5X IH 5

value: Intermittent Hypoxia


title: Colon, tumor12

description:
Library name: Sample45
21-F-TT-0038

value: Tumor


title: Colon, tumor27

description:
Library name: Sample60
21-F-TN-0025


title: right eye (migrant), 13 dpf, rep2

description: Library name: 14d_lib_RRBS


title: Colon, tumor13

description:
Library name: Sample46
21-F-TT-0039


title: M 5X IH 2


title: F WT IH 1

value: Wildtype


title: Colon, tumor11

description:
Library name: Sample44
21-F-TT-0037


title: F WT IH 2


title: human sperm head, donor35, PANDORA-seq

description: Library name: PV5D


title: right eye (migrant), 13 dpf, rep1

description: Library name: 12d_lib_RRBS


title: Colon, tumor10

description:
Library name: Sample43
21-F-TT-0036


title: human sperm head, donor34, PANDORA-seq

description: Library name: PI63

value: 41 years


title: F WT IH 3


title: left eye (non-migrant), 44 dpf, rep3

description: Library name: 10i_lib_RRBS


title: Colon, tumor9

description:
Library name: Sample42
21-F-TT-0035


title: Colon, tumor8

description:
Library name: Sample41
21-F-TT-0033


title: F WT IH 4


title: F 5X IH 4


title: F WT IH 5


title: human sperm head, donor31, PANDORA-seq

description: Library name: OY3Y

value: 35 years


title: human sperm head, donor37, PANDORA-seq

description: Library name: SY3L


title: Colon, tumor7

description:
Library name: Sample40
21-F-TT-0032


title: human sperm head, donor32, PANDORA-seq

description: Library name: OYN4

value: 40 years


title: left eye (non-migrant), 44 dpf, rep2

description: Library name: 9i_lib_RRBS


title: left eye (non-migrant), 44 dpf, rep1

description: Library name: 8i_lib_RRBS


title: F 5X NX 5

value: microglia

value: Normoxia


title: Colon, tumor6

description:
Library name: Sample39
21-F-TT-0031


title: left eye (non-migrant), 21 dpf, rep4

description: Library name: 7i_lib_RRBS

value: Eye


title: Colon, tumor5

description:
Library name: Sample38
21-F-TT-0030


title: human sperm head, donor36, PANDORA-seq

description: Library name: QG7P


title: left eye (non-migrant), 21 dpf, rep3

description: Library name: 6i_lib_RRBS


title: human sperm head, donor30, PANDORA-seq

description: Library name: NG6Q

value: 33 years


title: F 5X NX 4


title: left eye (non-migrant), 44 dpf, rep4

description: Library name: 11i_lib_RRBS


title: Colon, normal33

description:
Library name: Sample37
21-F-TT-0028

value: Normal


title: human sperm head, donor28, PANDORA-seq

description: Library name: LI6X

value: Sperm head


title: left eye (non-migrant), 21 dpf, rep2

description: Library name: 5i_lib_RRBS


title: F 5X NX 3


title: F 5X NX 2


title: Colon, normal32

description:
Library name: Sample36
21-F-TT-0027


title: left eye (non-migrant), 21 dpf, rep1

description: Library name: 4i_lib_RRBS


title: F 5X NX 1


title: human sperm head, donor27, PANDORA-seq

description: Library name: JT37

value: 42 years


title: human sperm head, donor29, PANDORA-seq

description: Library name: N22T

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: 47 years


title: human sperm head, donor33, PANDORA-seq

description: Library name: P7NV

value: 27 years


title: left eye (non-migrant), 13 dpf, rep3

description: Library name: 3i_lib_RRBS


title: human sperm head, donor26, PANDORA-seq

description: Library name: JK0P

value: 36 years


title: F WT NX 1


title: left eye (non-migrant), 13 dpf, rep2

description: Library name: 2i_lib_RRBS


title: left eye (non-migrant), 13 dpf, rep1

description: Library name: 1i_lib_RRBS


title: F WT NX 2


title: Colon, normal28

description:
Library name: Sample32
21-F-TT-0020

value: Colon


title: human sperm head, donor25, PANDORA-seq

description: Library name: J8YP


title: F WT NX 3


title: Pges-1deltaB, refed, chronic, rep3

city: Davis

first: Nicolas

last: Seban

address: 1544 Newton Court

institute: UC Davis

description: Library name: 18idG180Rrp3-5G180R_S98_L001_R1_001Aligned.sortedByCoord.out.bam

data_processing:
Reads from RNA-seq were aligned to the C. elegans genome (celegans-ensembl-wbcel235-r67) using STAR (version 2.6.1d).
The celegans-ensembl-wbcel235-r67 knownGene annotation track and aligned reads were used to generate quality control information using the full RSeQC tool suite.
Samples that exhibited strong 3′ _bias using geneBody_coverage.py or poor exon distribution using read_distribution.py were discarded.
Reads were quality checked by FastQC to ensure high quality datasets.
Assembly: celegans-ensembl-wbcel235-r67
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: Ribo-Seq

organism: Caenorhabditis elegans

source_name: Intestine

growth_protocol: 3 days on high-growth media

extract_protocol:
Ribo-TRAPseq adapted protocol (McLachlan 2019)
NEBNext® Ultra™ Directional RNA Library Prep Kit

treatment_protocol: Acute: 30min fasting, 30min re-feeding (after 30min fast); Chornic:180min fasting, 90min re-feeding (after 180min fast)

value: Intestine

value: Chronic Refed


title: human sperm head, donor24, PANDORA-seq

description: Library name: J561

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

value: 37 years


title: Pges-1deltaB, refed, chronic, rep2

description: Library name: 17idG180Rrp2-5G180R_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: F WT NX 4

value: Wildtype


title: human sperm head, donor23, PANDORA-seq

description: Library name: IM6U

value: 44 years


title: Colon, normal27

description:
Library name: Sample31
21-F-TT-0018


title: human sperm head, donor22, PANDORA-seq

description: Library name: IE1C

value: 25 years


title: AE9a leukemia cells, EBM, rep3

city: Tianjin

first: Yishuang

address: 288 Nanjing Road, Tianjin 300020, P. R. China

institute: State Key Laboratory of Experimental Hematology

data_processing:
The data we submitted are raw data. Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: bone marrow

growth_protocol: Leukemia cells were maintained in IMDM with 10% FBS before and after cell sorting.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (QIAGEN).
Libraries were prepared with  the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7775L).

treatment_protocol: We performed RNA-seq analyses on leukemia cells isolated from collagenase treated bone (endosteal BM, EBM) and from conventional flushed BM (central BM, CBM) ofAE9a leukemia mice.

value: bone marrow

value: leukemia cells

value: mRNA

value: collagenase treated bone (endosteal BM,EBM)


title: Colon, normal26

description:
Library name: Sample30
21-F-TT-0017

value: Normal


title: AE9a leukemia cells, EBM, rep2


title: Colon, normal30

description:
Library name: Sample34
21-F-TT-0023


title: human sperm head, donor21, PANDORA-seq

first: Qi

institute: university of utah

description: Library name: HG9H

value: Sperm head

value: 43 years


title: Pges-1deltaB, refed, chronic, rep1

description: Library name: 16idG180Rrp1-5G180R_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: Colon, normal31

description:
Library name: Sample35
21-F-TT-0024


title: Colon, normal25

description:
Library name: Sample29
21-F-TT-0015


title: human sperm head, donor20, PANDORA-seq

description: Library name: EL9H

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: AE9a leukemia cells, EBM, rep1


title: Colon, normal24

description:
Library name: Sample28
21-F-TT-0014


title: Pges-1deltaB, starve, chronic, rep3

description: Library name: 15idG180Srp3-4G180S_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Starve


title: human sperm head, donor19,  PANDORA-seq

description: Library name: DX1E

value: 34 years


title: AE9a leukemia cells, CBM, rep3

value: conventional flushed BM (central BM,CBM)


title: Pges-1deltaB, starve, chronic, rep2

description: Library name: 14idG180Srp2-4G180S_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Intestine


title: Colon, normal29

description:
Library name: Sample33
21-F-TT-0022

value: Colon


title: Colon, normal23

description:
Library name: Sample27
21-F-TT-0013


title: Pges-1deltaB, starve, chronic, rep1

description: Library name: 13idG180Srp1-4G180S_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: Colon, normal22

description:
Library name: Sample26
21-F-TT-0012


title: human sperm head, donor18, PANDORA-seq

description: Library name: DP83


title: Pges-1deltaB, fed, chronic, rep3

description: Library name: 12idG180Frp3-3G180F_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Fed


title: Colon, normal21

description:
Library name: Sample25
21-F-TT-0011


title: human sperm head, donor17,  PANDORA-seq

description: Library name: CP7S

value: 35 years


title: CAPK, SETD8 WT, Rep4, RNA

city: Boston

first: Zvi

middle: I

last: Cramer

address: 30 Caldwell St

data_processing:
Raw counts of transcripts were derived from fastq files mapped against Gencode M29 release with Salmon using standard settings. The resulting matrix was used as input for DESeq2 normalization and analysis
Assembly: GRCm39
Supplementary files format and content: comma-separated text files include raw counts for each sample
Supplementary files format and content: comma-separated text files include normalized counts generated by median of ratios method by Deseq2 for each sample

source_name: Colorectal Apc, Trp53, Kras Mutant

extract_protocol:
Trizol
Library construction was performed by Novogene, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Colorectal Apc, Trp53, Kras Mutant

value: Colorectal adenocarcinoma

value: SETD8 WT


title: Colon, normal20

description:
Library name: Sample24
21-F-TT-0007


title: human sperm head, donor16, PANDORA-seq

city: Salt Lake City

last: Chen

description: Library name: CN0E

value: 45 years


title: Pges-1deltaB, fed, chronic, rep1

description: Library name: 10idG180Frp1-3G180F_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: human sperm head, donor15,  PANDORA-seq

description: Library name: BB5N

value: 41 years


title: Colon, normal19

description:
Library name: Sample23
21-F-TT-0006


title: Pges-1deltaB, refed, acute, rep3

description: Library name: 09idG030Rrp3-2G030R_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Acute Refed


title: human sperm head, donor14, PANDORA-seq

description: Library name: AB6M

value: 39 years


title: Colon, normal18

description:
Library name: Sample22
21-F-TT-0005

value: Normal


title: CAPK, SETD8 WT, Rep2, RNA


title: human sperm head, donor13, PANDORA-seq

description: Library name: 9IN0

value: Sperm head

value: 42 years


title: CAPK, SETD8 WT, Rep1, RNA


title: Colon, normal17

description:
Library name: Sample21
21-F-TT-0004


title: Colon, normal16

description:
Library name: Sample20
21-F-TT-0003


title: human sperm head, donor12, PANDORA-seq

description: Library name: 91KW

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: 37 years


title: CAPK, SETD8 T140D, Rep4, RNA

value: SETD8 T140D


title: Pges-1deltaB, starve, acute, rep3

description: Library name: 06idG030Srp3-1G030S_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Intestine

value: Acute Starve


title: CAPK, SETD8 T140D, Rep3, RNA


title: AE9a leukemia cells, CBM, rep1

value: bone marrow

value: leukemia cells

value: mRNA

value: conventional flushed BM (central BM,CBM)


title: human sperm head, donor11,  PANDORA-seq

description: Library name: 8DR6


title: Colon, normal15

description:
Library name: Sample19
21-F-TT-0002

value: Colon


title: Pges-1deltaB, fed, chronic, rep2

description: Library name: 11idG180Frp2-3G180F_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Fed


title: human sperm head, donor10, PANDORA-seq

description: Library name: 88Q1

value: 45 years


title: CAPK, SETD8 T140D, Rep2, RNA

value: Colorectal Apc, Trp53, Kras Mutant

value: Colorectal adenocarcinoma


title: Colon, normal14

description:
Library name: Sample18
21-F-TN-0089

value: Normal


title: Pges-1deltaB, starve, acute, rep2

description: Library name: 05idG030Srp2-1G030S_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: CAPK, SETD8 WT, Rep3, RNA

value: SETD8 WT


title: Pges-1deltaB, starve, acute, rep1

description: Library name: 04idG030Srp1-1G030S_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: CAPK, SETD8 T140D, Rep1, RNA


title: Colon, normal13

description:
Library name: Sample17
21-F-TN-0088


title: Pges-1deltaB, fed, acute, rep3

description: Library name: 03idG030Frp3-0G030F_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Acute Fed


title: human sperm head, donor8, PANDORA-seq

description: Library name: 6A01

value: Sperm head

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: 34 years


title: CAPK, SETD8 WT, Rep2, ChIP, H4K20me1

data_processing:
Sequencing reads were aligned to the mouse genome GCRm38 using Bowtie2 with default settings
Resulting SAM files were filtered for uniquely mapped reads and converted to BAM files, which were then sorted and marked for duplicate reads using SAMtools
Technical replicates were then merged and peak calling was performed on merged BAM files using Epic2 with default settings
Bigwig files were generated with deepTools bamcoverage with RPGC normalization and binSize of 50. Bigwig files were then normalized by input samples using bigwigCompare
Assembly: GRCm38
Supplementary files format and content: BED with epic2 peaks

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature than sonicated with a Covaris S220 sonicator
ChIP-seq libraries were prepped using a NEBNext Ultra II DNA Library Prep Kit with NEBNext multiplex oligos for multiplexing


title: Colon, normal12

description:
Library name: Sample16
21-F-TN-0086


title: Pges-1deltaB, fed, acute, rep2

description: Library name: 02idG030Frp2-0G030F_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Intestine


title: human sperm head, donor7,  PANDORA-seq

description: Library name: 5RP9

value: 27 years


title: Pges-1deltaB, refed, acute, rep2

description: Library name: 08idG030Rrp2-2G030R_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Acute Refed


title: CAPK, SETD8 WT, Rep2, ChIP, Input


title: human sperm head, donor6, PANDORA-seq

description: Library name: 5KW5

value: 36 years


title: Pges-1deltaB, refed, acute, rep1

description: Library name: 07idG030Rrp1-2G030R_S98_L001_R1_001Aligned.sortedByCoord.out.bam


title: Ppho-1, refed, chronic, rep3

description: Library name: 18idP180Rrp3-5P180R_S18_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Refed


title: Colon, normal10

description:
Library name: Sample14
21-F-TN-0083


title: human sperm head, donor5,  PANDORA-seq

description: Library name: 4M9C

value: 26 years


title: Colon, normal9

description:
Library name: Sample13
21-F-TN-0082

value: Colon


title: CAPK, SETD8 WT, Rep1, ChIP, Input


title: Colon, normal11

description:
Library name: Sample15
21-F-TN-0085


title: Ppho-1, refed, chronic, rep2

description: Library name: 17idP180Rrp2-5P180R_S17_R1_001Aligned.sortedByCoord.out.bam


title: CAPK, SETD8 WT, Rep1, ChIP, H4K20me1


title: AE9a leukemia cells, CBM, rep2

value: bone marrow

value: leukemia cells

value: mRNA

value: conventional flushed BM (central BM,CBM)


title: Colon, normal8

description:
Library name: Sample12
21-F-TN-0080

value: Normal


title: human sperm head, donor3,  PANDORA-seq

description: Library name: 322M


title: Ppho-1, refed, chronic, rep1

description: Library name: 16idP180Rrp1-5P180R_S16_R1_001Aligned.sortedByCoord.out.bam


title: human sperm head, donor9,  PANDORA-seq

description: Library name: 83PN

value: 51 years


title: Colon, normal7

description:
Library name: Sample11
21-F-TN-0078


title: Ppho-1, starve, chronic, rep3

description: Library name: 15idP180Srp3-4P180S_S15_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Starve


title: human sperm head, donor4, PANDORA-seq

description: Library name: 3DF9

value: Sperm head

value: 33 years


title: human sperm head, donor2, PANDORA-seq

description: Library name: 1KC2

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Colon, normal6

description:
Library name: Sample10
21-F-TN-0077


title: CAPK, SETD8 T140D, Rep2, ChIP, H4K20me1

value: Colorectal Apc, Trp53, Kras Mutant

value: Colorectal adenocarcinoma

value: SETD8 T140D


title: CAPK, SETD8 T140D, Rep1, ChIP, Input


title: Pges-1deltaB, fed, acute, rep1

description: Library name: 01idG030Frp1-0G030F_S98_L001_R1_001Aligned.sortedByCoord.out.bam

value: Intestine

value: Acute Fed


title: CAPK, SETD8 T140D, Rep2, ChIP, Input


title: HUM-FIA-3_S60

city: College Station

first: Ivan

last: Rusyn

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

description:
Library name: HUM-FIA-3_S60
normcounts_human.csv
qc_hash_human.csv

data_processing:
The gene count matrices were generated from paired-end reads with 2 lanes per sample with ~150 base pairs (bp).
The reads from the 2 lanes for each sample were combined to generate a single fastq file.
Reads were quality trimmed using fastp (version 0.23.2) with the following steps: (1) automatic detection of adapter sequences for paired-end reads, (2) trimming of homopolymer stretches, and (3) removal of bases with Phred quality scores below 20 (Chen et al., 2018).
Reads were aligned to the species-specific genome assembly using STAR version 2.7.10b (Dobin et al. 2013). Aligned reads were sorted with SAMtools version 1.14 (Danecek et al. 2021), and gene-level counts were generated using HTSeq version 2.0.1 (Anders et al. 2014).
Samples with fewer than 1 million total counts or with uniquely mapped reads below 50% were excluded from further analysis. For transcript-level quality control, transcripts that were not expressed across the entire sample set for each species were removed. The Bioconductor package DESeq2 (Love et al., 2014) was used to perform within-species normalization and differential expression analysis across all experimental conditions.
Assembly: Reads from dog, monkey, human, and rat were mapped to the ROS_Cfam_1.0, Macaca_fascicularis_6.0, GRCh38, and mRatBN7 genome assemblies, respectively, using STAR. Gene annotations from Ensembl GTF files corresponding to each assembly were used for quantification.
Supplementary files format and content: normcounts_* files contain normalized count data using DESeq2 R package (Love et al., 2014) for each species
Supplementary files format and content: qc_hash* files contain meta data of the qc-passed samples for each species

source_name: hepatocytes

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the Direct-zol RNA Miniprep (Zymo, USA) following the manufacturer’s protocol with slight modifications detailed here. MPS Scaffolds from each experiment were preserved in RNAlater at -80°C until RNA extraction. On the day of extraction, samples were thawed at room temperature, and each scaffold was cut into two pieces before transferring to a 1.5 mL microcentrifuge tube. Next, 700 µL of TRIzol reagent was added to the samples, which were then incubated at room temperature for 20 minutes. During incubation, the samples were vortexed for 30 seconds every 5 minutes to ensure complete lysis. The scaffolds were removed from the microcentrifuge and the RNA was precipitated using equal volume of 100% molecular grade ethanol, then transferred to a Zymo-Spin™ IICR column. The remainder of the extraction was performed according to the standard protocol. RNA was eluted in 60 uL of DNAase/RNAse free water.
mRNA was isolated from 150ng total RNA using a Nextflex Poly-A Selection kit. Unique dual indexed cDNA libraries were prepared on a Sciclone NGSx liquid handler, using a Nextflex Rapid Directional RNA 2.0 kit miniaturized to 2/5 reaction volume. Optimal PCR cycle count was empirically determined to be 17 by cycling a pool of samples to the plateau phase on a real-time PCR machine. The concentration of libraries was determined using a Molecular Devices (San Jose, CA) Spectramax M2 fluorescent plate reader and Thermo Fisher Scientific (Waltham, MA) Picogreen Assay. Libraries were then pooled by equal mass using a Janus Mini liquid handler. The libraries were pooled by equal mass. The pool was sequenced on a Illumina (San Diego, CA) NovaSeq X+ 1.5B flowcell using the 2x150 bp recipe.

value: hepatocytes

value: fialuridine


title: CAPK, SETD8 T140D, Rep1, ChIP, H4K20me1


title: Ppho-1, starve, chronic, rep1

description: Library name: 13idP180Srp1-4P180S_S13_R1_001Aligned.sortedByCoord.out.bam


title: human sperm head, donor1,  PANDORA-seq

description: Library name: 1CM5

value: 35 years


title: brain, Mouse brain endothelial cells, CTRL, Sham, replicate 4

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Reads were mapped onto the mouse genome using STAR v. 2.7.8a
Counts were extracted with the STAR program using the GENCODE GRCm38 annotation v. M12
Differential gene expression analysis was performed using the R package DESeq2
Assembly: GRCm38 p5
Supplementary files format and content: raw counts from mapping, tab separated values file

source_name: brain

extract_protocol:
RNA from freshly FACsorted  brain endothelial cells (DAPI-, CD45-, CD31+) was isolated using NucleoSpin® RNA XS columns (MACHEREY-NAGEL) without carrier RNA, eluted in ultrapure water
RNA libraries were prepared using SMART-Seq® Ultra Low Input RNA kit (TaKaRa).

treatment_protocol: Sham or 30 min MCAo surgery 72 hours prior RNA extraction.

value: brain

value: endothelial cell

value: CTRL

value: Sham

tag: replicate


title: Ppho-1, fed, chronic, rep3

description: Library name: 12idP180Frp3-3P180F_S12_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Fed


title: HUM-FIA-2_S59

description:
Library name: HUM-FIA-2_S59
normcounts_human.csv
qc_hash_human.csv


title: brain, Mouse brain endothelial cells, CTRL, Sham, replicate 3


title: Colon, tumor4

description:
Library name: Sample8
21-F-TN-0071

value: Colon

value: Tumor


title: Ppho-1, fed, chronic, rep2

description: Library name: 11idP180Frp2-3P180F_S11_R1_001Aligned.sortedByCoord.out.bam


title: HUM-FIA-1_S58

description:
Library name: HUM-FIA-1_S58
normcounts_human.csv
qc_hash_human.csv


title: brain, Mouse brain endothelial cells, CTRL, Sham, replicate 2


title: Colon, tumor2

description:
Library name: Sample6
21-F-TN-0067


title: Ppho-1, fed, chronic, rep1

description: Library name: 10idP180Frp1-3P180F_S10_R1_001Aligned.sortedByCoord.out.bam


title: brain, Mouse brain endothelial cells, CTRL, Sham, replicate 1


title: Ppho-1, refed, acute, rep3

description: Library name: 09idP030Rrp3-2P030R_S9_R1_001Aligned.sortedByCoord.out.bam

value: Acute Refed


title: Colon, tumor1

description:
Library name: Sample5
21-F-TN-0063


title: HUM-D8-2_S8

description:
Library name: HUM-D8-2_S8
normcounts_human.csv
qc_hash_human.csv


title: Ppho-1, starve, chronic, rep2

description: Library name: 14idP180Srp2-4P180S_S14_R1_001Aligned.sortedByCoord.out.bam

value: Chronic Starve


title: Ppho-1, refed, acute, rep2

description: Library name: 08idP030Rrp2-2P030R_S8_R1_001Aligned.sortedByCoord.out.bam


title: Ppho-1, refed, acute, rep1

description: Library name: 07idP030Rrp1-2P030R_S7_R1_001Aligned.sortedByCoord.out.bam


title: brain, Mouse brain endothelial cells, CTRL, MCAo, replicate 4

value: MCAo


title: HUM-D8-1_S7

description:
Library name: HUM-D8-1_S7
normcounts_human.csv
qc_hash_human.csv


title: Colon, normal4

description:
Library name: Sample4
21-F-TN-0062

value: Normal


title: brain, Mouse brain endothelial cells, CTRL, MCAo, replicate 3


title: HUM-D4-3_S6

description:
Library name: HUM-D4-3_S6
normcounts_human.csv
qc_hash_human.csv


title: Colon, normal2

description:
Library name: Sample2
21-F-TN-0046


title: Ppho-1, starve, acute, rep3

description: Library name: 06idP030Srp3-1P030S_S6_R1_001Aligned.sortedByCoord.out.bam

value: Acute Starve


title: brain, Mouse brain endothelial cells, CTRL, MCAo, replicate 2


title: Colon, tumor3

description:
Library name: Sample7
21-F-TN-0070


title: Colon, normal5

description:
Library name: Sample9
21-F-TN-0075


title: Colon, normal3

description:
Library name: Sample3
21-F-TN-0060


title: brain, Mouse brain endothelial cells, CTRL, MCAo, replicate 1


title: HUM-D14-3_S12

description:
Library name: HUM-D14-3_S12
normcounts_human.csv
qc_hash_human.csv


title: Colon, normal1

description:
Library name: Sample1
21-F-TN-0045


title: brain, Mouse brain endothelial cells, YT-iKO, Sham, replicate 4

value: YT-iKO


title: HUM-D8-3_S9

description:
Library name: HUM-D8-3_S9
normcounts_human.csv
qc_hash_human.csv


title: HUM-D4-2_S5

description:
Library name: HUM-D4-2_S5
normcounts_human.csv
qc_hash_human.csv


title: Ppho-1, starve, acute, rep2

description: Library name: 05idP030Srp2-1P030S_S5_R1_001Aligned.sortedByCoord.out.bam

value: Intestine


title: HUM-D14-2_S11

description:
Library name: HUM-D14-2_S11
normcounts_human.csv
qc_hash_human.csv

value: hepatocytes


title: HEK293 cells, GSK-A1, bio rep3

city: Bethesda

first: Tamas

last: Balla

email: matthew.menold@nih.gov, ryan.dale@nih.gov, ballat@mail.nih.gov, kimyj@mail.nih.gov

state: MD

address: 6 Center Dr

institute: National Institute of Child Health and Human Development

description:
Library name: A-3
Column name in counts.tsv: A-3

data_processing:
After sequencing and demultiplexing, raw reads were adapter- and quality-trimmed using cutadapt (v5.1).
Trimmed reads were aligned to the GRCh38.p13 reference genome (GENCODE v46) using STAR (v2.7.11b).
Gene-level counts were generated with featureCounts (Subread v2.1.1) using the GENCODE v46 annotation.
Differential expression analysis between A1 and control conditions was performed in R using DESeq2 (v1.38.0). Technical replicate counts were averaged.
Assembly: GRCh38.p13
Supplementary files format and content: Library-size normalized counts from DESeq2 are provided in counts.tsv, including gene symbols (where available), Ensembl IDs, and technical replicate-collapsed counts for each biological replicate.

source_name: HEK293 cells

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 and 37C

extract_protocol:
RNA was purified from frozen cells using RNeasy kits.Total RNA was checked for overall quality with an Agilent bioanalyzer RNA nano chip and processed into barcoded Illumina sequencing libraries with a TruSeq stranded RNA kit.
Libraries were quantitated via Qubit and pooled, then sequencing was performed on an Illumina HiSeq 2500.

treatment_protocol: Confluent cells were treated with 100 nM GSK-A1 inhibitor for 24 hours

value: HEK293 cells


title: Ppho-1, starve, acute, rep1

description: Library name: 04idP030Srp1-1P030S_S4_R1_001Aligned.sortedByCoord.out.bam


title: brain, Mouse brain endothelial cells, YT-iKO, Sham, replicate 3


title: HUM-D14-1_S10

description:
Library name: HUM-D14-1_S10
normcounts_human.csv
qc_hash_human.csv


title: Ppho-1, fed, acute, rep3

description: Library name: 03idP030Frp3-0P030F_S3_R1_001Aligned.sortedByCoord.out.bam

value: Acute Fed


title: HEK293 cells, GSK-A1, bio rep1

description:
Library name: A-1
Column name in counts.tsv: A-1


title: HEK293 cells, GSK-A1, bio rep2

description:
Library name: A-2
Column name in counts.tsv: A-2


title: Ppho-1, fed, acute, rep2

description: Library name: 02idP030Frp2-0P030F_S2_R1_001Aligned.sortedByCoord.out.bam


title: brain, Mouse brain endothelial cells, YT-iKO, Sham, replicate 1

value: brain


title: HEK293 cells, Ctrl, bio rep3

description:
Library name: Ctrl‑3
Column name in counts.tsv: Ctrl-3

value: DMSO


title: brain, Mouse brain endothelial cells, YT-iKO, MCAo, replicate 4

value: endothelial cell


title: HUM-D0-3_S3

description:
Library name: HUM-D0-3_S3
normcounts_human.csv
qc_hash_human.csv


title: Ppho-1, fed, acute, rep1

description: Library name: 01idP030Frp1-0P030F_S1_R1_001Aligned.sortedByCoord.out.bam


title: HEK293 cells, Ctrl, bio rep2

description:
Library name: Ctrl‑2
Column name in counts.tsv: Ctrl-2


title: AB_20, Tumor_chemo_Adjuvantfishoil

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

data_processing:
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions. All samples were sequenced on an Illumina NextSeq 500 with high throughput 2x150 nt (paired-end sequencing) run.
Illumina CASAVA 1.9 with default parameters was used for base-calling and de-multiplexing. Trim Galore v.0.4.1 was used to trim the adapters. FastQC v.0.11.4 was used to check the quality of the sequenced reads. Tophat 2.0.10 and Bowtie2 were used to match the trimmed sequences to the rat reference genome. The rat genome (Rnor 6, Ensembl) was used as a reference genome and was downloaded from the iGENOME website. Sequences that were aligned were saved as .sam files, which were subsequently transformed to .bam files and used for further data processing.
Assembly: rnor6.0
Supplementary files format and content: tab-delimited file includes the raw counts for each sample

organism: Rattus norvegicus

source_name: Skeletal muscle tissue

extract_protocol:
The MagMax-96 total RNA isolation Kit (Ambion, Austin, TX, USA) was used to extract total RNA from gastrocnemius muscle (10 mg / n>5 per group) according to the manufacturer's protocol. The quantity and quality of extracted RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA Integrity Number (RIN) from Bioanalyzer were >9.0, indicating high quality of RNA isolated from muscle biopsies, and these were subjected to NGS analysis.
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions.

value: Fischer 344

value: Gastrocnemius

value: Skeletal muscle tissue

value: chemo

tag: diet

value: diet containing fish oil

value: female


title: HUM-D0-1_S1

description:
Library name: HUM-D0-1_S1
normcounts_human.csv
qc_hash_human.csv


title: brain, Mouse brain endothelial cells, YT-iKO, MCAo, replicate 3

value: MCAo


title: HUM-D0-2_S2

description:
Library name: HUM-D0-2_S2
normcounts_human.csv
qc_hash_human.csv


title: HEK293 cells, Ctrl, bio rep1

description:
Library name: Ctrl‑1
Column name in counts.tsv: Ctrl-1


title: NPDM8_PDDM

city: Yangsan

first: Haeseul

last: Lee

address: 49 Busandaehak-ro

institute: Pusan National University

description:
Library name: NPDM 8
Plasma exosomal RNA from PDDM subject

data_processing:
Sequencing adapters were trimmed, and quality control was performed using standard pipelines. Reads were aligned to the human reference genome (GRCh38) using a suitable aligner, and miRNAs were annotated based on miRBase v22.1 and RNAcentral v14.0.
Assembly: GRCh38
Supplementary files format and content: The processed data files are provided in CSV format and contain RPM-normalized expression values for each small RNA species across all samples. Separate files are included for different RNA types, including miRNA, piRNA, scRNA, snoRNA, snRNA, tRNA, vaultRNA, and YRNA. Each file includes RNA identifiers and sample-wise RPM values generated from the same sequencing dataset using a consistent analysis pipeline.

source_name: plasma

extract_protocol:
Total RNA was extracted from isolated plasma exosomes using the miRNeasy Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.
Small RNA libraries were constructed using the SMARTer smRNA-Seq Kit for Illumina (Takara Bio, Shiga, Japan), according to the manufacturer’s protocol.

value: plasma


title: NPDM17_PDDM

description:
Library name: NPDM 17
Plasma exosomal RNA from PDDM subject


title: AB_18, Tumor_chemo_Adjuvantfishoil


title: brain, Mouse brain endothelial cells, YT-iKO, MCAo, replicate 2


title: HUM-CPZ-2_S53

description:
Library name: HUM-CPZ-2_S53
normcounts_human.csv
qc_hash_human.csv

value: chlorpromazine


title: HUM-CPZ-3_S54

description:
Library name: HUM-CPZ-3_S54
normcounts_human.csv
qc_hash_human.csv


title: b_19, Tumor_chemo_Adjuvantfishoil


title: brain, Mouse brain endothelial cells, YT-iKO, MCAo, replicate 1

value: YT-iKO


title: AB_16, Tumor_chemo_Adjuvantfishoil


title: HUM-CPZ-1_S52

description:
Library name: HUM-CPZ-1_S52
normcounts_human.csv
qc_hash_human.csv


title: NPDM2_PDDM

description:
Library name: NPDM 2
Plasma exosomal RNA from PDDM subject


title: AB_17, Tumor_chemo_Adjuvantfishoil


title: Splenic CD11b+ cells, R3

city: Shanghai

first: Youming

last: Zhang

address: Jimo Road 150, Shanghai 200120, PR China

institute: Shanghai East Hospitol

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ). Clean reads were aligned to the Ensembl GRCm39 using STAR.
Assembly: Ensembl GRCm39
Supplementary files format and content: csv file includes raw counts for each sample

source_name: spleen

extract_protocol:
Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany).
Strand-specific libraries were constructed using the TruSeq RNAsample preparation kit (Illumina, USA), and sequencing was carriedout using the Illumina Novaseq 6000 instrument.

value: spleen

value: primary cells

value: splenic CD11b+ cells

value: WT

value: MI+RDN


title: brain, Mouse brain endothelial cells, YT-iKO, Sham, replicate 2

value: brain

value: Sham


title: Splenic CD11b+ cells, R2


title: HUM-CON-3_S51

description:
Library name: HUM-CON-3_S51
normcounts_human.csv
qc_hash_human.csv

value: hepatocytes

value: DMSO control


title: HUM-CON-2_S50

description:
Library name: HUM-CON-2_S50
normcounts_human.csv
qc_hash_human.csv


title: NPDM7_PDDM

description:
Library name: NPDM 7
Plasma exosomal RNA from PDDM subject


title: AB_15, Tumor_chemo_Adjuvantfishoil

value: Fischer 344

value: Gastrocnemius

value: Skeletal muscle tissue


title: AB_14, Tumor_chemo_Adjuvantfishoil

value: chemo

value: diet containing fish oil

value: female


title: Splenic CD11b+ cells, R1


title: NPDM4_PDDM

description:
Library name: NPDM 4
Plasma exosomal RNA from PDDM subject

value: plasma


title: Splenic CD11b+ cells, M3

value: MI


title: NPDM3_PDDM

description:
Library name: NPDM 3
Plasma exosomal RNA from PDDM subject


title: AB_13, Tumor_chemo_Adjuvantfishoil


title: HUM-CON-1_S49

description:
Library name: HUM-CON-1_S49
normcounts_human.csv
qc_hash_human.csv


title: HUM-BOS-3_S57

description:
Library name: HUM-BOS-3_S57
normcounts_human.csv
qc_hash_human.csv

value: bosentan


title: AB_12, Tumor_nochemo_control

value: no chemo

value: control


title: NPDM18_PDDM

description:
Library name: NPDM 18
Plasma exosomal RNA from PDDM subject


title: NPDM16_PDDM

description:
Library name: NPDM 16
Plasma exosomal RNA from PDDM subject


title: Splenic CD11b+ cells, M1

value: spleen

value: primary cells

value: splenic CD11b+ cells

value: WT


title: HUM-BOS-2_S56

description:
Library name: HUM-BOS-2_S56
normcounts_human.csv
qc_hash_human.csv

value: hepatocytes


title: mouse sperm head, 90-week, traditional sncRNA-seq, rep4

source_name: sperm head

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: sperm head

value: 90 weeks

value: The 15-50nt RNAs were sequenced with standard protocols.


title: NPDM15_PDDM

description:
Library name: NPDM 15
Plasma exosomal RNA from PDDM subject


title: AB_11, Tumor_nochemo_control

value: Fischer 344

value: Gastrocnemius

value: Skeletal muscle tissue


title: AB_10, Tumor_nochemo_control

value: female


title: HUM-BOS-1_S55

description:
Library name: HUM-BOS-1_S55
normcounts_human.csv
qc_hash_human.csv


title: mouse sperm head, 90-week, traditional sncRNA-seq, rep3


title: AB_9, Tumor_nochemo_control


title: AB_8, Tumor_nochemo_control


title: mouse sperm head, 90-week, traditional sncRNA-seq, rep2