title: Liver, HFD, 7day, rep3

growth_protocol: 8-week-old C57BL/6J male mice were randomized into two groups for the experiment

extract_protocol:
Total RNA was isolated from freshly frozen liver tissues of mice using TriZol reagent.
RNA library for RNA-seq was prepared as following: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments. The first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis.

treatment_protocol: One group was subjected to a HFD feeding for 7 days, while the other group was maintained on a regular chow diet. After the 7-day period, both groups underwent PHx surgery. Samples were then collected 40 hours post-surgery to assess the effects of the dietary conditions and the surgical intervention on the mice.

value: Liver


title: deltaNTR mycLARP6-3

status: Public on Jan 22 2026

type: SRA

city: Oxford

first: Faraz

middle: K.

last: Mardakheh

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: CLIP_NTR_3

library_source: transcriptomic

data_processing:
iCLIP data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were uploaded on the webserver iMAPS (imaps.goodwright.com) for primary iCLIP data analysis. The human genome GRCh38.p13 GENCODE V42 was used with the primary assembly comprehensive annotation. Reads were first trimmed with TrimGalore! (software developed by Felix Krueger), to remove remaining adapters and low-quality reads, then pre-mapped to rRNA and tRNA sequences with Bowtie 2 and discarded. This step ensured that reads mapping to repetitive regions were not misaligned to mRNA. The remaining unmapped reads were then mapped to the genome with STAR. PCR duplicates were removed with UMI-tools based on the presence of identical UMIs in reads mapping to the same position. The exact crosslink position was then identified as the first nucleotide after the experimental barcode, and this data was downloaded from the webserver and processed further offline. The crosslink information was used to call the peaks, which represent the binding sites of LARP6, for each individual replicate. The peak caller Clippy (version 1.5.0) was used with the following settings: rolling mean 15; minimum counts per gene 3; minimum counts per peak 3; prominence 1 (default); peak threshold 0.4 (default). The peaks called for the individual replicates were then combined into one file per mutant by merging the peaks and summing their peak scores using bedtools (version 2.30.0), with the peak scores indicative of the binding strength. Background normalisation was performed by subtracting the peaks that were called in the parental negative control from each combined peak file, using bedtools.
Total RNA-Seq data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were trimmed with TrimGalore! (version 0.6.10) to remove the remaining adapter sequences and low-quality reads. Reads were then mapped to the human genome GRCh38.p13 GENCODE V42 with STAR (version 2.7.10b). Default parameters were used, and gene counts were generated directly from the mapping step by enabling the –quantMode GenerateCounts option. The gene counts from the RNAseq were used for iCLIP data normalisation. The iCLIP peak scores were normalised for transcript abundance according to the following formula: normalised peak score=((peak score)/(gene count)*1000).
Assembly: GRCh38.p13 GENCODE V42
Supplementary files format and content: peaks.bed (iCLIP peak scores)
Supplementary files format and content: .out (INPUT RNA-seq read counts)
Library strategy: iCLIP

molecule: total RNA

organism: Homo sapiens

source_name: Brain

growth_protocol: U-87 MG (PURCHASED FROM ATCC) cells were grown in DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. U-87 MG myc-LARP6 inducible cell lines were grown as above, and myc-LARP6 expression was induced with 60 ng/mL Doxycycline. All cells were maintained in a humidified incubator at 37°C, 5% CO2. Cells were passaged consistently before reaching confluence with Trypsin-EDTA (Gibco), and tested regularly for mycoplasma, using the MycoAlert Mycoplasma Detection Kit (Lonza Bioscience).

extract_protocol:
For iCLIP, cells were UV-C crosslinked, lysed, and subjected to iCLIP as indicated in (https://doi.org/10.1101/2024.09.20.614075). Briefly, 20 million cells per condition were grown in 15 cm dishes and myc-LARP6 mutants were induced with 60 ng/mL doxycycline for 24 hours. Cells were crosslinked on ice at 150 mJ/cm2 at 254 nm in a Hoefer Scientific UV crosslinker to form covalent bonds between RBPs and RNAs that were in direct contact, then scraped in PBS and pelleted. Cell pellets were lysed in iCLIP lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate, cOmplete protease inhibitor cocktail (Roche), 1 mM PMSF), cleared, and diluted to 1 mg/mL in 1 mL volume. Samples were then treated with 0.2 units/mL lysate RNase I (Thermo Scientific, catalogue number EN0602) and 2 μL Turbo DNase (Ambion) for 3 minutes at 37°C to partially digest the RNA. 50 μL Dynabeads Protein G (Invitrogen) per sample were first conjugated with 4 μg (10 μL) mouse anti-myc-tag antibody (Cell Signaling, 9B11) for one hour at RT in a rotating wheel, then added to the samples to perform the immunoprecipitation (IP) for one hour at 4°C in a rotating wheel. After the IP, samples were stringently washed twice with high-salt wash buffer (50 mM Tris-HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate), then once with PNK wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20).
For Input RNA-seq, cells grown under the same conditions as the ones used in the iCLIP experiment was subjected to RNA extraction with TRIzol. The purified RNAs were quantified with the Qubit RNA High-sensitivity assay, and the quality was validated with the Agilent High Sensitivity RNA ScreenTape assay, with all samples having a RIN ≥ 9.3. The whole transcriptome RNAseq library preparation and sequencing was outsourced to Novogene.
For iCLIP, The RNA fragments were dephosphorylated on the beads at the 3’ end, followed by 3’ end ligation of different barcoded adapters, to allow for downstream multiplexing of each replicate into one sample. The samples were then eluted from the beads, run on an SDS-PAGE gel, followed by isolation of the RNA fragments and subsequent library preparation as described previously. The amplified libraries were quantified and validated with the Qubit dsDNA High-sensitivity and Agilent D1000 high sensitivity ScreenTape assays, pooled in an equimolar ratio, and deep sequenced on an Illumina NextSeq 500 instrument, using a single-end 100 nt workflow. Sequencing was performed at the Barts and The London Genome Centre.
For Input RNA-seq, rRNA depletion whole transcriptome sequencing using two protocols (short and long RNAs) was performed by Novogene (https://www.novogene.com/eu-en/services/research-services/transcriptome-sequencing/whole-transcriptome-sequencing/)

treatment_protocol: 60 ng/mL Doxycycline for 24hrs.

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Glioblastoma

tag: genotype

value: LARP6 deltaNTR

tag: antibody

value: myc-tag

tag: replicate


title: Liver, chow diet, 7day, rep3

city: china

first: Yao

last: Tao

state: zhejiang

address: zhejiang province

country: China

institute: First Affiliated Hospital, Zhejiang University

data_processing:
In this study, we implemented a series of precise quality control and analysis steps for the sequenced data collected. Initially, Trim Galore version 0.6.1 was used for quality control of raw reads, removing those with Phred quality scores below 20 and lengths less than 35 bp after trimming. Subsequently, these quality-filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using HISAT2 version 2.2.1 with default settings. Post-alignment, duplicates were marked using Sambamba version1.0.1. Quantification of the aligned reads was then conducted using featureCounts version 2.0.2, based on gene IDs from the mouse Gencode version 20. Finally, normalization of read counts and differential gene expression analysis were performed using the R package DESeq2.
Assembly: mm10
Supplementary files format and content: text files of normalized counts for every sample and every gene.

organism: Mus musculus

source_name: Liver


title: CAOV3_Ascites_Rep_3

city: Durham

first: Jen-Tsan Ashley

last: Chi

state: NC

address: 101 Science Dr

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

data_processing:
TrimGalore toolkit
The TrimGalore toolkit was used to trim low quality bases via Cutadapt (removed <20nt reads)
Reads were mapped to the GRCh38v93 version of human genome using the STAR RNA-seq alignment tool
Counts were compiled using the HTSeq tool
DESeq and GSEA were used for normalization, differential expression, and gene enrichment analyses
Assembly: GRCh38v93 human genome
Supplementary files format and content: CSV file includes normalized counts for each sample

source_name: ovary

growth_protocol: CAOV3 and TOV21G cells were maintained in DMEM media, supplied with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed with PBS and RNA was harvested using the Rneasy mini kit (Qiagen). RNA extracts were further treated with the RNAse-free DNAse set (Qiagen). 1 ug of RNA was sent for to the Duke SGT facility for library prep and sequencing
Library was constructed by the Duke SGT facility

treatment_protocol: 2.5 x 10^5 CAOV3 and TOV21G cells were seeded in 1.5 mL of DMEM media supplied with 10% FBS and antibiotics in 6-well plates. 150 uL of ovarian cancer ascites (10%) was added to the cell media and cells were incubated with the ascites for 16 hours.

value: ovary

value: epithelial high grade serous

value: WT

tag: treatment

value: 10% ovarian cancer ascites for 16 hours


title: IDT synthesized fragments (2OMe)

city: Winston-Salem

first: Keith

last: Gagnon

address: 575 Patterson Ave

department: Biochemistry

institute: Wake Forest Baptist Medical Center

description: Library name: IDT synthesized fragments (2OMe)

data_processing:
Reads were called from the POD5 files with Dorado software (v1.0.0) with settings for RNA modifications (RNA basecalling model rna004_130bps_sup@v5.2.0), and aligned to a HIV-1 genome (AF324493.2, included as NL43_AF324493.2_R2R.fasta), producing a BAM file.
modkit was used to generate a bedgraph of each modification, using a command such as: modkit pileup [location_of_BAM] --ref [loc_of_reference] -t 18 --region NL43_AF324493.2_R2R --max-depth 10000000 --bedgraph ./ --filter-threshold .7 --motif DRACH 2 --prefix m6A
Bedgraph files were filtered to remove modification calls at positions with fewer than 10 reads to reduce noise from low-call areas.
Reads unaligned to HIV-1 reference genome were removed from BAM file to reduce file size and protect PLWH data.
Assembly: NL43_AF324493.2_R2R.fasta
Supplementary files format and content: bedgraph files. Tab-seperated text files, one per modification. Columns in file are: column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters 5 | total calls | Number of calls passing filters, both modified and unmodified column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position  int 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 | total calls | Number of calls passing filters, both modified and unmodified column  name  description  type ------------------------------------ 1  chrom  name of reference sequence from BAM header  str 2  start position  0-based start position  int 3  end position  0-based exclusive end position  int 4 fraction modified Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 total calls Number of calls passing filters, both modified and unmodified int

organism: Human immunodeficiency virus 1

source_name: Synthesized

growth_protocol: Jurkat cells (HIV repository) were cultured in RPMI-1640 medium supplemented with 10% FBS, 1x P/S, and non-essential amino acids (NEAA).  CD4+ T cells were harvested from whole blood tubes from unidentified healthy donors or leukopaks (Red Cross Blood). Negative cell separation was conducted following the vendors protocol with EasySep Direct Human CD4+ T cell Isolation Kits or RosetteSep Human CD4+ T cell Enrichment Cocktail (Stem Cell Technologies) with Lymphoprep (Stem Cell Technologies) as density medium, respectively. Before infection, we activated T cells by adding anti-CD3 and anti-CD28 antibodies along with IL-2.

extract_protocol:
Total RNA was harvested via TRIZol (Invitrogen), using the manufacturer's protocol.
After extraction, total RNA was divided, and approximately 15-20 μg was used for poly-A selection and RNaseH ribosomal RNA depletion. For poly-A selection, the NEBNext High Input Poly(A) mRNA Isolation Module (E3370S) was used according to the manufacturer's protocol. For the RNaseH treatment, total RNA was hybridized with DNA oligonucleotides complementary to rRNA. The solution was heated to 95°C and slow cooled to 65°C to enable oligonucleotide hybridization. RNase H (McLabs, HTRH-200) was added (200 U) and the solution incubated at 65°C for 5 min to degrade rRNA. DNA was then degraded using 150 U of Turbo DNase (Invitrogen, AM2239) at 37°C for 20 min. RNA was then purified using AMPure XP beads. A polyadenylation reactions was performed using E. coli Poly(A) Polymerase (New England Biolabs, M0276L).  The final library was loaded on a PromethION RNA flow cell (FLO-PRO004RA) and sequenced on a PromethION P2 solo using MinKNOW (v. 24.06.10) with POD5 and live base-calling on.

treatment_protocol: Jurkat cells: When infecting with replicative NL4-3 and pHIVdEnv-GFP, we used a high cell density of ~2.5 x 106 cells/mL with a working concentration of HIV p24 (determined by ELISA) of 500-600 ng/mL. Cells were harvested at 45-48 h post-infection.  CD4+ T cells: Activation was confirmed 3 days post-treatment by measuring CD4+/CD69+ double-positive cell percentage by flow cytometry.  Day 0, isolate CD4+ T cells from blood and activate T cells  Day 3: test activation % and infect CD4+ T cells with WT-HIV.  Day 4: TRIUMEQ cART treatment when applicable  Day 6: harvest CD4+ T cells for TRIzol lysis as well as quantify infection rate by flow cytometry with KC57 antibody  cART treatment: To model current cART therapy, we added TRIUMEQ with the respective concentrations for each of the antiretrovirals based on reported plasma levels: ABC 140 ng/mL, 3TC 670 ng/mL, DTG 3.9 ug/mL.

value: Synthesized


title: PHx

library_source: transcriptomic single cell

data_processing:
After sequencing with the 10X Genomics platform and processing by Berry Genomics, the FASTQ files were analyzed using the Cell Ranger software. Cell Ranger aligned the reads to a reference genome and processed barcodes to identify and quantify individual cells. Next, normalization of data was conducted to compensate for variable sequencing depths across cells. The Seurat package was used for further downstream analysis, incorporating Harmony for dimensionality reduction and UMAP for visual data representation.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

growth_protocol: 8-week-old C57BL/6J mice underwent 2/3 PHx surgery to simulate liver regeneration. A control group was subjected to a sham operation. At 48 hours post-surgery, liver cells were harvested from both PHx and sham-operated mice for single-cell RNA sequencing using the 10X Genomics platform.

extract_protocol:
Liver tissues from C57BL/6J mice, collected 60 hours after PHx or sham surgery, underwent enzymatic digestion to create a single-cell suspension. This suspension was then processed for single-cell RNA sequencing using the 10X Genomics platform. Sequencing involved reverse transcription, amplification, and sequencing of each cell's RNA.
Single-cell RNA sequencing was performed following Berry Genomics' protocols. This involved preparing liver cell samples isolated post-surgery, constructing sequencing libraries, and processing through high-throughput sequencing platforms like HiSeq2500 and NovaSeq. The data obtained were then transformed into FASTQ files post primary quality control, which filtered low-quality reads and removed adapters, ensuring high-quality datasets for analysis. Key quality control measures included assessing raw reads, bases, Q20, Q30, and GC content, guaranteeing the integrity and reliability of the sequencing data. This protocol facilitated a detailed examination of liver cell populations post partial hepatectomy.


title: cultured cortical astrocyte, hM4Di, 90min, 2

city: Sendai

first: Momono

last: Segawa

state: Miyagi

address: Katahira 2-1-1, Aoba-ku

department: Graduate School of Life Sciences

country: Japan

institute: Tohoku University

description: Library name: Sample2

data_processing:
The raw data underwent quality control with fastp (v0.23.4), followed by alignment to the mouse genome (mm39) with Salmon (v1.8.0).
Gene count matrices and TPM matrices  were generated using the tximport (v1.34.0) and TxDb.Mmusculus.UCSC.mm39.knownGene (v3.20.0) libraries in R.
Assembly: mm39
Supplementary files format and content: csv file includes raw counts for each sample in 90-min group
Supplementary files format and content: csv file includes raw counts for each sample in 3-days group

source_name: brain

growth_protocol: Cells were plated onto plates pretreated with poly-L-lysine (Sigma-Aldrich, #P2336) at 37°C under 5% CO₂, using high-glucose Dulbecco’s Modified Eagle Medium (DMEM, Wako) supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin (PS, Wako). Cells were transferred to new dishes before confluence.

extract_protocol:
Total RNA was collected from cultured astrocytes after 90 minutes after DCZ application, using Phenol-chloroform based RNA extraction. For, experiment aimed at assessing the long-term effect of DREADD stimulation, the cells were treated with DCZ for 90 min and the medium was replaced to a fresh medium without DCZ. Then, the RNA was collected from the culture three days after.
RNA libralies for RNA-seq were prepared by Novogene. Briefly, the purified total RNA samples underwent mRNA purification, poly-A mRNA enrichment library preparation.

treatment_protocol: Plasmid transfection was performed using HilyMax reagent (Dojindo) according to the manufacturer’s instructions. The medium was replaced to a fresh medium on the next day of transfection. Cultured astrocytes were treated with DCZ (8μM, Deschloroclozapine dihydrochloride; MedChemExpress, #HY-42110A) for 90 min, seven days after plasmid transfection.

value: brain

value: cultured cortical astrocyte

value: hM4Di + DCZ, 90min


title: Damha synthesized fragment (m6A)

description:
Library name: damha synthesized fragment (m6A)
Aligned against damha_reference.fasta, rather than full HIV-1 reference.


description: Library name: IDT synthesized fragment (asp gene, Inosine)


title: Full-length mycLARP6-3

description: Library name: CLIP_FL_3

value: LARP6 FL


title: Damha synthesized fragment (unmodified)

description:
Library name: damha synthesized fragment (unmodified)
Aligned against damha_reference.fasta, rather than full HIV-1 reference.


title: CAOV3_Ascites_Rep_2


title: sham


title: U87 Control-3

description: Library name: CLIP_U87_3


title: t7inVitro HIV full Psi

description: Library name: t7inVitro HIV full Psi

source_name: IVT

value: IVT


title: deltaCTR mycLARP6-2

description: Library name: CLIP_CTR1_2

value: LARP6 deltaCTR


title: 8 rep3

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

description:
Library name: sample6
fpkm_8 rep3

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5) . The expression level of genes was calculated by RSEM (v1.3.1)
StringTie (v2.2.1) was used to reconstruct transcripts, and Cuffmerge was used to integrate the assembled transcripts. Cuffcompare was used to compare the integrated transcripts to a reference annotation. The transcripts with class code types u, i, o, j were selected as new transcripts. The protein-coding potential of new transcripts was predicted by CPC (v0.1).
Using public database (KEGG, GO, etc.) to annotate the genes.
Assembly: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: liver

value: human hepatic stellate cells

value: TGF-β1 + 20 μM 8


title: CAOV3_Control_Rep_3


title: 8 rep2

description:
Library name: sample5
fpkm_8 rep2


title: t7inVitro HIV full m5C

description: Library name: t7inVitro HIV full m5C


title: deltaNTD mycLARP6-2

description: Library name: CLIP_NTD_2

value: Brain

value: Glioblastoma

value: LARP6 deltaNTD


title: deltaLa-Mod mycLARP6-2

description: Library name: CLIP_LaMod_2

value: LARP6 deltaLa-module

value: myc-tag


title: CAOV3_Control_Rep_2

value: ovary

value: epithelial high grade serous

value: WT


title: cultured cortical astrocyte, hM3Dq, 90min, 1

description: Library name: Sample4

value: brain

value: hM3Dq + DCZ, 90min


title: DMSO Model rep3

description:
Library name: sample3
fpkm_Model rep3

value: TGF-β1 + DMSO


title: CAOV3_Ascites_Rep_1

value: 10% ovarian cancer ascites for 16 hours


title: t7inVitro HIV full m6A

description: Library name: t7inVitro HIV full m6A

value: IVT


title: deltaNTR mycLARP6-2

description: Library name: CLIP_NTR_2

value: LARP6 deltaNTR


title: 14H CD4+ HIV Virion

description: Library name: 14H CD4+ HIV Virion

value: T cells

value: HIV-1 infection


title: 8 rep1

description:
Library name: sample4
fpkm_8 rep1

value: liver

value: human hepatic stellate cells

value: TGF-β1 + 20 μM 8


title: CAOV3_Control_Rep_1


title: nup50c nup82 nup136-1

city: WeiFang

first: Xiangyun

last: Yang

state: ShanDong

address: 699 Binhu Road, 699 Binhu Road, Xiashan District

institute: Institute of Advance Agricultural Sciences, Peking University

description: Library name: sample 15

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 9-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: whole seedlings

value: nup50c nup82 nup136 mutant


title: nup82 nup136-2

description: Library name: sample 14

value: nup82 nup136 mutant


title: deltaCTR mycLARP6-1

description: Library name: CLIP_CTR1_1

value: Brain

value: Glioblastoma

value: LARP6 deltaCTR

value: myc-tag


title: U87 Control-2

description: Library name: CLIP_U87_2

value: WT


title: Full-length mycLARP6-2

description: Library name: CLIP_FL_2

value: LARP6 FL


title: DMSO Model rep2

description:
Library name: sample2
fpkm_Model rep2

value: TGF-β1 + DMSO


title: nup82 nup136-1

description: Library name: sample 13


title: deltaLa-Mod mycLARP6-1

description: Library name: CLIP_LaMod_1

value: LARP6 deltaLa-module


title: MCT_MN_3

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Sample 11

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl 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.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include Counts for each Sample
Supplementary files format and content: txt files include Counts for each Sample

organism: Rattus

source_name: atria

growth_protocol: Rats were randomly assigned to four experimental groups: Saline + Vehicle, Monocrotaline (MCT) + Vehicle, and MCT + MnTBAP.

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

treatment_protocol: The pulmonary arterial hypertension (PAH) model was established on day 0 via intraperitoneal injection of MCT at a dose of 60 mg/kg. Starting two days prior to MCT administration and continuing until day 28 post-injection, MnTBAP (10 mg/kg) was administered intraperitoneally every other day.Total RNA was isolated with TRIzol (Invitrogen) from heart organs (n=4 per group) at each time point according to manufacturer’s instructions.

value: atria

tag: strain

value: Sprague-Dawley

value: MCT + MnTBAP


title: P6S PLWH

description:
Library name: P6S PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.

source_name: blood

value: blood

value: T cells


title: 10D CD4+ HIV

description: Library name: 10D CD4+ HIV

value: HIV-1 infection


title: DMSO Model rep1

description:
Library name: sample1
fpkm_Model rep1

value: liver

value: human hepatic stellate cells


title: 13B P8C PLWH

description:
Library name: 13B P8C PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.


title: MCT_MN_4

description: Library name: Sample 12


title: nup50c nup136-2

description: Library name: sample 12

value: whole seedlings

value: nup50c nup136 mutant


title: t7inVitro HIV unmodified

description: Library name: t7inVitro HIV unmodified

value: IVT


title: deltaNTD mycLARP6-1

description: Library name: CLIP_NTD_1

value: Brain

value: Glioblastoma

value: LARP6 deltaNTD


title: deltaNTR mycLARP6-1

description: Library name: CLIP_NTR_1

value: LARP6 deltaNTR

value: myc-tag


title: MCT_MN_2

description: Library name: Sample 10


title: nup50c nup82 nup136-2

description: Library name: sample 16

value: nup50c nup82 nup136 mutant


title: P5S2 PLWH

description:
Library name: P5S2 PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.


title: mouse NK cells, antiNK1.1 + IL-12 stimulated, STAT4, rep1

city: New York

first: Hyunu

last: Kim

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: mNK_400k_STAT4_aNK11IL12_1

library_source: genomic

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie 2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as a control using narrow peak parameters with cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
The peak atlas was generated by merging via union of peaks called by each sample after filtering out bottom 25% of peaks by MACS2 calculated qValue. Resulting peak atlas was further filtered to only retain peaks that were called by two or more replicates within each sample group, as well as peaks that do not overlap the Encode’s DAC Exclusion List Regions (ENCFF547MET).
Assembly: mm10
Supplementary files format and content: NK_peakatlas_normCounts.tsv
Supplementary files format and content: CD8T_peakatlas_normCounts.tsv
Library strategy: CUT&Run

molecule: genomic DNA

source_name: NK

extract_protocol:
Following CUT&RUN preparation, DNA was extracted using the Qiagen MinElute Kit.
For library preparation, we used the KAPA Hyper Prep Kit and followed the kit's instructions. Amplification cycle number was determined by running qPCR after 4 cycles of amplification and assessing required additional cycles.

treatment_protocol: NK cells were stimulated with aNK1.1 for 3h (or unstimulated as control), sorted, and stimulated for 1h with IL-12. OT-1 CD8+ T cells were stimulated with the respective peptide ((presented by splenocytes) for 16h, sorted, and stimulated for 1h with IL12.

value: NK

tag: cell count

tag: stimulation

tag: batch id


title: nup50c nup136-1

description: Library name: sample 11


title: Jurkat Combined Antisense

description: Library name: Jurkat Combined Antisense

source_name: Jurkat

value: Jurkat

value: HIV-1 infection, cART treatment


title: MCT_MN_1

description: Library name: Sample 9

value: atria

value: Sprague-Dawley

value: MCT + MnTBAP


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma PDX

first: Cristina

last: Antonescu

address: 1275 York Avenue

description:
Library name: RMS_PDX
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human hg20
Supplementary files format and content: tab-separated barcode, matrix and feature files

molecule: nuclear RNA

source_name: rhabdomyosarcoma

extract_protocol:
Tissue dissociation and nuclei isolation from frozen tumor samples were performed using the Singulator 1 device and citric acid preservation. The isolated tumor nuclei were washed in wash buffer containing RNase inhibitor and sorted by FACS using 7AAD as marker.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics). The polyA RNA from the nuclear lysate was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. The pooled barcoded DNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected and for subsequent library construction. During library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: rhabdomyosarcoma

value: MYOD1 L122R


title: Seq-Scope-X-Liver

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description:
Library name: Seq-Scope-X-Liver
Seq-Scope-X-Liver

data_processing:
Seq-Scope-X transcriptome data were processed using the Seq-Scope pipeline with adjustments for experimentally determined expansion factors, following the NovaScope and NEDA workflows. Processing included generation of spatial barcode maps, alignment to reference genomes, construction of spatial gene expression matrices, and clustering using Seurat v5.  Spatial factor discovery was performed using Latent Dirichlet Allocation, and FICTURE was used to project cell-type factors into raw pixel space. Microscopy images, which lacked fiducial markers, were aligned to transcriptomic data using QGIS and further processed with CellProfiler and Photoshop. Differential expression, clustering, and integration analyses were conducted on hexagonally binned data to enable spatial and functional interpretation.
Other data could be found at Deep Blue Repository at (https://doi.org/10.7302/kj26-7j44)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz Digital Gene Expression Data in Matrix Market Format
Supplementary files format and content: transcripts.sorted.tsv.gz Spatial Digital Expression Spreadsheet
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

growth_protocol: Mouse liver, colon, and spleen tissues were collected from 8-week-old male C57BL/6 wild-type mice, and brain tissue was obtained from a 6-month-old male mouse. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Michigan (protocol PRO00011369).  Human tonsil tissue was obtained from the UCLA Pathology Biobank as a discarded surgical specimen from an adult patient with chronic tonsillitis. The sample was fully de-identified prior to acquisition and classified as IRB-exempt under institutional and federal guidelines, with no access to identifiable patient information.

extract_protocol:
Fresh frozen tissues were cryosectioned, mounted on charged slides, fixed with formaldehyde, and permeabilized with methanol. Anchor probes were hybridized in a formamide-containing buffer under humidified conditions. Tissues were then embedded in a polyacrylate-based monomer solution, polymerized, and cleared using digestion buffer with Proteinase K.
Tissue expansion was performed by incubation in diluted SSC, and DAPI staining was used to assess tissue integrity. Expanded gels were trimmed for imaging and alignment, then placed onto Seq-Scope Chips. Probe release and transcript transfer were achieved by heat incubation, followed by standard Seq-Scope library preparation, omitting tissue digestion as tissues were not directly attached to the chip.

treatment_protocol: For spatial proteomic analysis, tissues were permeabilized with methanol, blocked with a BSA-containing solution, and incubated overnight with TotalSeq™-A oligonucleotide-tagged antibody cocktails. After washing and post-fixation, tissues were processed using the same embedding, clearing, and expansion steps as in the transcriptome workflow.  Library preparation was modified to capture antibody-bound DNA oligonucleotides. Following reverse transcription, antibody tag libraries were eluted, purified, amplified by AT-PCR and indexing PCR, size-selected to isolate ~250 bp fragments, and sequenced on an Illumina NovaSeq-X platform.

value: liver

value: Normal


title: U87 Control-1

description: Library name: CLIP_U87_1

value: WT


title: 11CI Jurkat HIV-GFP + cART

description: Library name: 11CI Jurkat HIV-GFP + cART

value: T cells


title: MCT_3

description: Library name: Sample 7

value: MCT + Vehicle


title: MCT_2

description: Library name: Sample 6


title: Jurkat HIV-GFP + 0uM STM2457

description: Library name: Jurkat HIV-GFP + 0uM STM2457

value: HIV-1 infection, STM2457 treatment


title: nup136-1

description: Library name: sample 7

value: whole seedlings

value: nup136 mutant


title: Full-length mycLARP6-1

description: Library name: CLIP_FL_1

value: Brain

value: Glioblastoma

value: LARP6 FL

value: myc-tag


title: MCT_4

description: Library name: Sample 8

value: atria


title: nup50c nup82-2

description: Library name: sample 10

value: nup50c nup82 mutant


title: nup136-2

description: Library name: sample 8


title: 11BH Jurkat HIV-GFP (PAS Only)

description: Library name: 11BH Jurkat HIV-GFP (PAS Only)

value: Jurkat

value: HIV-1 infection


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma treated primary responsive B

description:
Library name: RMS_475
10x Genomics

value: rhabdomyosarcoma

value: MYOD1 L122R


title: MCT_1

description: Library name: Sample 5

value: Sprague-Dawley


title: nup82-1

description: Library name: sample 5

value: nup82 mutant


title: nup82-2

description: Library name: sample 6


title: 11BH Jurkat HIV-GFP

description: Library name: 11BH Jurkat HIV-GFP

value: T cells


title: 11BH Jurkat HIV-GFP (RNaseH Only)

description: Library name: 11BH Jurkat HIV-GFP (RNaseH Only)


title: Con_4

description: Library name: Sample 4

value: Saline + Vehicle


title: nup50c-2

description: Library name: sample 4

value: nup50c mutant


title: 11F Jurkat HIV-GFP + cART

description: Library name: 11F Jurkat HIV-GFP + cART

value: HIV-1 infection, cART treatment


title: WT-2

description: Library name: sample 2

value: whole seedlings

value: wild type


title: WT-1

description: Library name: sample 1


title: Jurkat HIV-GFP + 30uM STM2457

description: Library name: Jurkat HIV-GFP + 30uM STM2457

value: HIV-1 infection, STM2457 treatment


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma recurrent metastatic

description:
Library name: RMS_211_2
10x Genomics


title: Con_2

description: Library name: Sample 2


title: 7E Jurkat HIV-GFP + cART

description: Library name: 7E Jurkat HIV-GFP + cART


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma treated primary responsive

description:
Library name: RMS_41_B
10x Genomics


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma treated primary resistant B

description:
Library name: RMS_469
10x Genomics


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma treated primary resistant

description:
Library name: RMS_31_2
10x Genomics


title: nup50c-1

description: Library name: sample 3


title: wild-type sample

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Biomedical Computing

country: South Korea

institute: Korea Institute of Science and Technology Information

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gnee counting and aggregation were made using the Cell Range software v5.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Forebrain

extract_protocol:
Mouse forebrains were placed in 15-ml tubes (VWR, 21008-103) filled with Hibernate E (Gibco, A1247601), B27 (Invitrogen, 17504-044), and GlutaMax (Invitrogen, 35050-061) (HEB) media. Two forebrains were combined for each genotype. The HEB media from the tissue were transferred and saved in a new 15-ml tube, leaving only enough medium to cover the tissue. Subsequently, 1 ml of Papain solution (BrainBits, PAP/HE) was added to the tissue, which was then incubated at 37 °C for 20 min. During incubation, the tissue was gently swirled three times to ensure thorough mixing. After incubation, the Papain solution was carefully removed, taking care not to disturb the tissue at the bottom, while leaving only enough solution to cover the tissue. The previously saved HEB medium was added to the tissue. To triturate the tissue, the tissue with the medium was aspirated into a fire-polished silanized Pasteur pipette (BrainBits, FPP) and immediately dispensed back into the tube, ensuring no air bubbles formed. This process was repeated ten times. Subsequently, the tissue debris was allowed to settle for one min. The supernatant containing the cells was then transferred to a new 15-ml tube, leaving the tissue debris at the bottom. The cells were centrifuged at 200 rcf for 2 min at room temperature. Following the centrifugation, the supernatant was carefully removed without disturbing the cell pellet, leaving only enough media to cover the cell pellet (approximately 50 L). Using a regular-bore pipette tip, the cell pellet was resuspended in 3 ml of cold neuronal culture medium (BrainBits, NbActiv1) by gently pipetting until the cells were fully resuspended. The cell suspension was then passed through a 30 m MACS SmartStrainer (Miltenyi, 130-098-458) and the cell concentration was determined using a Countess II Automated Cell Counter (Thermo Fisher Scientific). The target final cell concentration aimed for was between 700–1,200 cells/L.
Libraries were prepared using Chromium Next GEM Single Cell 3’ RNA library v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: Forebrain

tag: developmental stage

value: Embryo (E18.5)

value: WT


title: 7C Jurkat HIV-GFP

description: Library name: 7C Jurkat HIV-GFP


title: Cyfip2 knockout sample

description: 10x Genomics

value: Cyfip2 knockout


title: Con_3

description: Library name: Sample 3

value: atria


title: nup50c nup82-1

description: Library name: sample 9

value: nup50c nup82 mutant


title: EndoC-βH1, treated with Hu1107 ctrl-EVs

status: Public on Jan 21 2026

city: Duarte

first: James

last: Figarola

state: CA

address: 1500 E. Duarte Road

department: Diabetes-Metabo Res Inst-BRI

institute: City of Hope

description: Library name: Ctrl_EV_1107

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 with a single read mode of 51 cycles. HiSeq Real-Time Analysis (RTA) 2.2.38 software was used to process the image analysis.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreas

growth_protocol: EndoC-βH1 cells were cultured onto 1% ECM-fibronectin (2 µg/ml) coated culture wells in DMEM that contained 5.6 mM D-glucose, 2% Fatty Acid Free heat shock BSA powder, 50 µM 2-mercaptoethanol, 10 mM nicotinamide, 5.5 µg/ml transferrin, 6.7 ng/ml sodium selenite, and 100 U/ml penicillin, 100 μg/ml streptomycin. All culture cells were incubated at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA extraction was performed using the RNeasy Micro Kit or Mini Kit according to the manufacturer’s instructions.
RNA sequencing libraries were prepared with the Kapa mRNA HyperPrep Kit (Kapa Biosystems, KR1352) according to the manufacturer's protocol, and the final libraries were validated using the Agilent Bioanalyzer DNA High Sensitivity Kit (Agilent, 5067-4626) and quantified with a Qubit Fluorometer (Thermo Fisher)

treatment_protocol: EndoC-βH1 cells were treated for 48h with EVs isolated from vehicle- or cytokine- treated primary ductal cells from human pancreas.

value: Pancreas

value: Human beta cell line

value: Ctrl-EV, 48h


title: EndoC-βH1, treated with Hu1145 ctrl-EVs

description: Library name: Ctrl_EV_1145


title: EndoC-βH1, treated with Hu1145 cyto-EVs

description: Library name: Cryo_EV_1145

value: Cyto-EV, 48h


title: EndoC-βH1, treated with Hu1112 ctrl-EVs

description: Library name: Ctrl_EV_1112


title: FRSK_b-END(1-9)

type: RNA

city: Nagakute-shi

first: Hiroyuki

last: Yamamoto

state: Aichi

address: 2-9 Katahira

institute: Aichi Shukutoku University

hyb_protocol: Arrays were incubated at 45 °C for 16 hours at 60 rpm using the GeneChip™ Hybridization Oven 645, according to the protocol provided with the kit.

scan_protocol: Array scanning was performed using the GeneChip™ Scanner 3000 7G in accordance with the manufacturer's instructions.

data_processing: Image quantification and normalization were performed using Expression Console™ Software (Thermo Fisher Scientific, Inc.). To assess array quality, Transcriptome Analysis Console (TAC) software was used. Raw expression values were obtained directly from .CEL files and preprocessed using SST-RMA normalization. method.

label: biotin

organism: Rattus norvegicus

source_name: rat FRSK cells

label_protocol: Fragmented and labeled cDNA samples were prepared using the GeneChip™ WT PLUS Reagent Kit, according to the manufacturer's protocol.

growth_protocol: 10% FBS DMEM, Cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted using theTriPure Isolation Reagent (Roche Life Science).

treatment_protocol: FRSK cells were seeded onto 10-cm culture dishes at a density of 1 × 10⁶ cells per dish and cultured under static conditions to allow for cell attachment. Following attachment, cells were treated with 100 nM of either Met-ENK or β-END(1–9) and incubated for 24 h.

value: Fetal rat skin keratinocyte cell


title: EndoC-βH1, treated with Hu1112 cyto-EVs

description: Library name: Cryo_EV_1112


title: DKO_Dlx2

city: Los Angeles

first: Mingyi

last: Zhang

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description:
Library name: DKO_Dlx2
Epicypher

data_processing:
fastq files were trimmed for adapters and low-quality sequences using Galore and subsequently mapped to the mouse mm10 reference genome using Bowtie2 with default parameters.
PCR duplicates were marked using Picard.
Coverage tracks were generated using the bamCoverage tool from deepTools with the RPKM normalization method, and peak calling was conducted using MACS2.
Peak annotation was performed with ChIPseeker (RStudio) to annotate peaks.
Assembly: mm10
Supplementary files format and content: Bigwig files
Library strategy: CUT&Run

source_name: incisor mesenchyme

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Freshly collected proximal mouse incisor from DKO mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes . The prepared cells were tested for viability before process the extraction. Cells viability  higher than 80% were used for nucleis extranction for the scATACseq.
Library was performed according to the manufacter's introduction (Epicypher).

treatment_protocol: 20ml/ml concentrated tamxifen was administered to mice via intraperitoneal injection at a dosage of 1.5mg/10g body weight

value: incisor mesenchyme


title: EndoC-βH1, treated with Hu1107 cyto-EVs

description: Library name: Cryo_EV_1107


title: MYOD1 L122R mutant spindle cell sclerosing rhabdomyosarcoma recurrent

description:
Library name: RMS_3_2
10x Genomics

value: rhabdomyosarcoma

value: MYOD1 L122R


title: 11E Jurkat HIV-GFP

description: Library name: 11E Jurkat HIV-GFP

value: Jurkat

value: T cells

value: HIV-1 infection


title: Con_1

description: Library name: Sample 1

value: Sprague-Dawley

value: Saline + Vehicle


title: FRSK_control


title: l02-3 [small RNA]

city: suzhou

first: zhixian

last: ding

state: province

address: No. 125, West Huaihe Road, Yongqiao District

institute: Wanbei Coal Electric Group General Hospital,

description:
Library name: SAMPLE9
L02_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: gene_tpm_anno.txt

growth_protocol: The human hepatocellular carcinoma cell line Hep3B and the normal human hepatocyte line L02 were purchased from the Shanghai Institute of Cell Biology, Chinese Academy of Sciences (Shanghai, China). All cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were maintained at 37℃ in a humidified atmosphere containing 5% CO₂.

extract_protocol:
The protocol involved the extraction of total RNA from cultured L02 and Hep3B cell lines using TRIzol Reagent, followed by quality control of the RNA using a Bioanalyzer and NanoDrop spectrophotometer. Subsequently, sequencing libraries were constructed from the qualified RNA with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions, which included mRNA enrichment, fragmentation, cDNA synthesis, and adapter ligation. The final prepared libraries were then sequenced on an Illumina NovaSeq 6000 platform to generate paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal human hepatocyte cell line


title: EndoC-βH1, treated with Hu1060 ctrl-EVs

description: Library name: Ctrl_EV_1060


title: hep3b-2 [small RNA]

description:
Library name: SAMPLE11
Hep3B_2

value: human hepatocellular carcinoma cell line


title: EndoC-βH1, treated with Hu1060 cyto-EVs

description: Library name: Cryo_EV_1060


title: hep3b-3 [small RNA]

description:
Library name: SAMPLE12
Hep3B_3


title: l02-2 [small RNA]

description:
Library name: SAMPLE8
L02_2


title: l02-1 [small RNA]

description:
Library name: SAMPLE7
L02_1


title: hep3b-1 [small RNA]

description:
Library name: SAMPLE10
Hep3B_1


title: FRSK_Met-ENK


title: hep3b-3 [long RNA]

description:
Library name: SAMPLE6
Hep3B_3


title: hep3b-1 [long RNA]

description:
Library name: SAMPLE4
Hep3B_1


title: hep3b-2 [long RNA]

description:
Library name: SAMPLE5
Hep3B_2


title: l02-1 [long RNA]

description:
Library name: SAMPLE1
L02_1


title: BMMSC-2D-EV-3

city: Tallahassee

first: li

last: sun

state: FL

address: 1115 West Call st.

institute: FSU College of Medicine

description: Library name: Sample 3

data_processing:
Raw data for miR-seq were submitted to OASIS online miR analysis tool to identify small RNAs on Human reference genome hg38. Differential expressed miRs were analyzed by both OASIS and miRNet using default settings. RNA-seq data was analyzed by NetworkAnalyst 3.0. Genes with counts less than 10, variance less than 10% and unannotated were filtered and normalized by Log2-counts per million. Differentially expressed genes (DEGs) were identified by DEseq2. Heatmap of globe differential expressed genes and gene enriched pathways were also visualized by the same online tool.
Assembly: hg38
Supplementary files format and content: Excel worksheet file (.xlsx) of raw counts for all samples

source_name: Bone marrow

growth_protocol: Frozen hMSCs from passage 0 to 2 were acquired from Tulane Centre for Gene Therapy. The hMSCs were isolated from the bone marrow of multiple healthy donors with age 19–49 years old. hMSCs were thawed, expanded, and maintained in complete culture media (CCM) containing α-MEM with 10% FBS and 1% Penicillin/Streptomycin in a standard incubator at 37°C with 5% CO2 and 20% O2. hMSCs at passage 4 to 7 were suspended in CCM and 1.0 × 105 hMSCs in 2 mL CCM were seeded in each well of ultra-low attachment (ULA) six-well plates. The ULA plates were placed on a rocking base of a WAVE Bioreactor in a standard humidified incubator (37°C, 5% CO2) under controlled rocking angles (i.e., 8°) and rocking speeds (i.e., 20 rockings/min, or rpm) for 18 to 72 h. The rocking conditions generate wave motion of media under defined shear stress that supports spontaneous aggregation of hMSCs (100-300 μm in diameter). For 3D-hMSC-EV collection, the CCM was replaced by the media that contain EV-depleted FBS (i.e., FBS was ultracentrifuged at 100,000 g for 18 h to remove particle and EVs) and cultured for 2 days before media collection. The parallel 2D hMSC culture was used as a control condition, and the conditioned media were collected after 2-day culture for 2D-hMSC-EV isolation.

extract_protocol:
EV samples were treated with RNase to final concentration of 50 ng/mL, at room temperature for 30 mins. RNase inhibitor and PCR grade water were added to EV samples to make a total volume of 200 μL. miRs were isolated by adding 600 μL Trizol LS according to manufacturer’s instruction. To increase the yield of small RNAs, three volumes of 100% ethanol and linear acrylamide were used instead of isopropyl alcohol and incubation time was also increased to overnight at -20°C. The isolated RNAs were quantified by Qubit microRNA assay kit.
Small RNA libraries (using equal RNA mass) were generated with NEBNext Multiplex Small RNA Library Prep Set for Illumina. To increase yield and prevent primer/adaptor dimer, 3’ SR primer was diluted to 1:5 and ligation time was increased to overnight at 16°C.

treatment_protocol: Extracellular vesicles were isolated from the conditioned media by polyethylene glycol (PEG) precipitation and ultracentrifugation according to previous publications. Briefly, cells were cultured in CCM with 10% EV-depleted FBS, and the conditioned media were collected every 48 h. The conditioned media were differential centrifuged (500 g for 5 min; 2,000 g for 10 min; 10,000 g for 30 min) to remove larger debris, apoptotic body and microvesicles. Supernatants then were mixed with PEG solution (16% wt./vol. PEG-6000, 1.0 M NaCl) at a 1:1 volume and incubated at 4°C overnight. The next day, the mixed solutions were centrifuged at 3,214 g for 1 h to obtain crude EVs. The pellets were resuspended in PBS and then ultracentrifuged at 100,000 g for 70 min using the SW-28 swing-bucket rotor in an Optima XL-100K ultracentrifuge (k factor-15). The concentrated vesicle suspension was centrifuged again in 1 mL polypropylene tubes in an Optima MAX-E tabletop ultracentrifuge using a TLA120.2 rotor to purify the vesicles and facilitate re-suspension of the pellet in a small volume of particle-free PBS in 100 μL. Purified EVs were stored in −80°C for further use.

value: Bone marrow

value: mesenchymal stem/stromal cells

value: WT

value: 2D culture


title: BMMSC-3D-EV-3

description: Library name: Sample 6

value: 3D culture


title: l02-3 [long RNA]

description:
Library name: SAMPLE3
L02_3


title: BMMSC-3D-EV-1

description: Library name: Sample 4


title: l02-2 [long RNA]

description:
Library name: SAMPLE2
L02_2


title: BMMSC-2D-EV-1

description: Library name: Sample 1


title: MHCC-97H cells treated with PBS for 24h

city: Tianjin

first: YUTONG

last: LI

address: Weijin Road No.94

department: Nankai University School of Medicine

institute: Nankai University

description:
Library name: Sample 1
raw counts_allSamples.txt：PBS control
PBS

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Liver

growth_protocol: MHCC-97H human hepatocellular carcinoma cells were cultured in high-glucose (4.5g/L) or low-glucose (0.45g/L) DMEM medium supplemented with 10% fetal bovine serum, in a humidified atmosphere at 37°C with 5% CO₂ under normoxic (21% O₂) or hypoxic (5%, 1%, 0.1% O₂) conditions as required for migrasome generation.

extract_protocol:
Total RNA was extracted from treated MHCC-97H cells using TRIzol reagent (or equivalent) according to the manufacturer‘s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: MHCC-97H cells were treated for 24 hours with: (1) PBS (control); (2) 2 𝜇g of migrasomes derived from MHCC-97H cells cultured under normoxia (Normo-Migs); (3) 2 𝜇g of migrasomes derived from MHCC-97H cells cultured under hypoxia (Hypo-Migs); or (4) 2 𝜇g of migrasomes derived from CD147 knockout MHCC-97H cells cultured under hypoxia (CD147KO-Migs).

value: Liver

value: hepatocellular carcinoma cells

value: PBS control

tag: batch


title: MHCC-97H cells treated with Hypo-Migs for 24h

description:
Library name: Sample 3
raw counts_allSamples.txt：Migrasomes from hypoxia-cultured MHCC-97H cells
Hypo_Mig


title: MHCC-97H cells treated with CD147KO-Migs for 24h

description:
Library name: Sample 4
raw counts_allSamples.txt：Migrasomes from hypoxia-cultured CD147-KO MHCC-97H cells
CD147_KO_Mig


title: BMMSC-3D-EV-2

description: Library name: Sample 5


title: DU145, Poly GC7 1

city: Nice

first: Michel

last: KAHI

address: 151 Route Saint Antoine

country: France

institute: INSERM U1065

description:
Library name: Sample 16
Column name in raw_count:Poly GC7 1

library_source: other

data_processing:
RNA-seq Preprocessing: Raw sequencing reads were aligned on the human genome (GRCh38) using STAR (v2.7.8a), with the annotation of known genes from gencode v37. Gene expression levels were then quantified using Salmon (1.4.0) and the annotation of protein coding genes from gencode v37.
Assembly: the human genome (GRCh38) using STAR (v2.7.8a)
Supplementary files format and content: excel files containing processed data

molecule: other

source_name: Prostate

growth_protocol: DU145 prostate cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
DU145 Cells were seeded at 106 cells/10cm dish, treated with 40µM CG7 48h later (D0) during 24h. At the end of this treatment, cells were treated 10min with emetin (Sigma-Aldrich) 25µg/ml, washed twice with PBS, and harvested by trypsination. Cytoplasmic lysates were prepared by incubation of cells 10min in hypotonic buffer (10mM Tris-HCl pH 7.4, 0.5mM MgCl2, 10mM KCl, 1X CompleteTM EDTA free protease inhibitor (Roche) and 10U/mL RNAseOutTM (Invitrogen). Cells are disrupted by shaking in presence of ceramic beads (10sec at 4500rpm in a Precellys Evolution homogenizer). Nuclei were pelleted by centrifugation at 750 g for 5min at 4°C, and mitochondria were pelleted by centrifugation at 12,000 g for 10min at 4°C. The protein content of the cytosolic extract was measured by Bradford assay and samples containing 2mg protein were loaded on top of 15–50% sucrose gradients poured using the Gradient Master (Serlabo Technologies). After ultracentrifugation at 250 000g during 105min at 4°C on a SW41 Beckman rotor, fractions of 700µl each were collected from each gradient while 254nm absorbance profiles were generated using an ISCO UA-6 detector.
the human genome (GRCh38) using STAR (v2.7.8a)

treatment_protocol: Cells were treated with GC7 (N¹-guanyl-1,7-diaminheptane) at the indicated concentration for 24 h, Control samples (Ctl) were treated with vehicle only.

value: Prostate

value: metastatic prostate carcinoma


title: DU145, Poly Ctl 1

description:
Library name: Sample 13
Column name in raw_count:Poly Ctl 1

value: Ctl


title: DU145, Poly GC7 2

description:
Library name: Sample 17
Column name in raw_count:Poly GC7 2


title: DU145, Cyto GC7 3

description:
Library name: Sample 12
Column name in raw_count:Cyto GC7 3

molecule: cytoplasmic RNA


title: DU145, Poly Ctl 3

description:
Library name: Sample 15
Column name in raw_count:Poly Ctl 3


title: BMMSC-2D-EV-2

description: Library name: Sample 2


title: DU145, Cyto Ctl 2

description:
Library name: Sample 8
Column name in raw_count:Cyto Ctl 2


title: DU145, Cyto GC7 1

description:
Library name: Sample 10
Column name in raw_count:Cyto GC7 1


title: DU145, Poly Ctl 2

description:
Library name: Sample 14
Column name in raw_count:Poly Ctl 2


title: DU145, Poly GC7 3

description:
Library name: Sample 18
Column name in raw_count:Poly GC7 3


title: DU145, Cyto GC7 2

description:
Library name: Sample 11
Column name in raw_count:Cyto GC7 2


title: DU145, Cyto Ctl 3

description:
Library name: Sample 9
Column name in raw_count:Cyto Ctl 3


title: primary GBM patient 94

city: Seongnam-si

first: Jaejoon

last: Lim

address: 59 Yatap-ro, Bundang-gu

department: College of Medicine

institute: CHA University

description:
Library name: Sample 37
CHA-GBM-115

data_processing:
At first, reads for each sample were mapped to the reference genome(Mouse mm10) by Tophat(v2.0.13) . The aligned results were added to Cuffdiff(v2.2.1)  to report differentially expressed genes. For library normalization and dispersion estimation, geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods  were applied.
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality
The cleaned reads were aligned to the Homo sapiens (hg38) using HISAT v2.1.0, based on the HISAT implementations
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million)
Statistical analyses of differential gene expression were performed by DESeq2 v 1.38.3 (Love. et al. 2014) using raw counts as input
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count, FPKM and TPM for each sample

source_name: Brain tissue

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy Mini Kit following the manufacturer’s instruction
A library was independently prepared with 0.5ug of total RNA for each sample by Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., San Diego, CA, USA, #20020599)

value: Brain tissue

value: IDH1 wild type


title: primary GBM patient 93

description:
Library name: Sample 36
CHA-GBM-114


title: DU145, Cyto Ctl 1

description:
Library name: Sample 7
Column name in raw_count:Cyto Ctl 1


title: primary GBM patient 84

description:
Library name: Sample 27
CHA-GBM-103


title: primary GBM patient 92

description:
Library name: Sample 35
CHA-GBM-113


title: primary GBM patient 90

description:
Library name: Sample 33
CHA-GBM-111


title: primary GBM patient 83

description:
Library name: Sample 26
CHA-GBM-102


title: primary GBM patient 81

description:
Library name: Sample 24
CHA-GBM-100


title: primary GBM patient 82

description:
Library name: Sample 25
CHA-GBM-101


title: MHCC-97H cells treated with Normo-Migs for 24h

description:
Library name: Sample 2
raw counts_allSamples.txt：Migrasomes from normoxia-cultured MHCC-97H cells
Normo_Mig


title: primary GBM patient 89

description:
Library name: Sample 32
CHA-GBM-109


title: primary GBM patient 85

description:
Library name: Sample 28
CHA-GBM-104


title: primary GBM patient 74

description:
Library name: Sample 16
CHA-GBM-93


title: primary GBM patient 88

description:
Library name: Sample 31
CHA-GBM-107


title: primary GBM patient 86

description:
Library name: Sample 29
CHA-GBM-105


title: primary GBM patient 71

description:
Library name: Sample 13
CHA-GBM-90


title: primary GBM patient 70 subventricular zone

description:
Library name: Sample 11
CHA-GBM-89_1


title: primary GBM patient 87

description:
Library name: Sample 30
CHA-GBM-106


title: primary GBM patient 69 subventricular zone_1

description:
Library name: Sample 9
CHA-GBM-88_1


title: primary GBM patient 70 tumor core region

description:
Library name: Sample 12
CHA-GBM-89_2


title: primary GBM patient 80

description:
Library name: Sample 23
CHA-GBM-99


title: primary GBM patient 79 peripheral region

description:
Library name: Sample 22
CHA-GBM-98_2


title: primary GBM patient 69 tumor core region

description:
Library name: Sample 10
CHA-GBM-88_3


title: primary GBM patient 78

description:
Library name: Sample 20
CHA-GBM-97


title: primary GBM patient 91

description:
Library name: Sample 34
CHA-GBM-112


title: primary GBM patient 72

description:
Library name: Sample 14
CHA-GBM-91


title: primary GBM patient 67 subventricular zone

description:
Library name: Sample 4
CHA-GBM-86_1


title: primary GBM patient 76

description:
Library name: Sample 18
CHA-GBM-95


title: primary GBM patient 77

description:
Library name: Sample 19
CHA-GBM-96


title: primary GBM patient 68 tumor core region

description:
Library name: Sample 7
CHA-GBM-87_1


title: primary GBM patient 67 tumor normal region

description:
Library name: Sample 5
CHA-GBM-86_2


title: primary GBM patient 65

description:
Library name: Sample 2
CHA-GBM-84


title: primary GBM patient 75

description:
Library name: Sample 17
CHA-GBM-94


title: primary GBM patient 73

description:
Library name: Sample 15
CHA-GBM-92


title: primary GBM patient 68 tumor normal region

description:
Library name: Sample 8
CHA-GBM-87_2


title: primary GBM patient 79 tumor core region

description:
Library name: Sample 21
CHA-GBM-98_1


title: primary GBM patient 66

description:
Library name: Sample 3
CHA-GBM-85


title: iMg_PFF_4h_29

first: Jina

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

description: Library name: Sample 21

data_processing:
Raw sequencing data quality was assessed with FastQC (v0.11.9)
Trim Galore (v 0.6.4_dev) was employed to remove adapters from paired-end sequencing reads
Clean reads were aligned to the human reference genome (GRCh38) using STAR aligner (v2.7.5c).
Transcript abundance was quantified with RSEM (v1.3.3)
Normalization was performed using the TMM method, followed by log2 transformation.
Assembly: GRCh38
Supplementary files format and content: Processed RNA expression data,csv format

source_name: Stem cell

extract_protocol:
Total RNA was extracted from iMicroglia using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Illumina NovaSeq 6000

value: Stem cell

value: Human induced pluripotent stem cells (iPSCs)-derived microglia

value: microglia

value: a-synuclein preformed fibrils


title: iMg_KO_4h_27

description: Library name: Sample 19

value: kinetically stable a-synuclein oligomers


title: iMg_sPFF_4h_34

description: Library name: Sample 26

value: sonicated a-synuclein preformed fibrils


title: primary GBM patient 67 tumor core region

description:
Library name: Sample 6
CHA-GBM-86_3


title: iMg_KO_4h_28

description: Library name: Sample 20


title: iMg_PFF_4h_30

description: Library name: Sample 22


title: iMg_EO_4h_19

description: Library name: Sample 11

value: EGCG stabilized a-synuclein oligomers


title: primary GBM patient 64

description:
Library name: Sample 1
CHA-GBM-83


title: iMg_EO_4h_20

description: Library name: Sample 12


title: iMg_EO_4h_17

description: Library name: Sample 9


title: iMg_DO_4h_23

description: Library name: Sample 7

value: dopamine stabilized a-synuclein oligomers


title: iMg_sPFF_4h_35

description: Library name: Sample 27


title: iMg_sPFF_4h_36

description: Library name: Sample 28


title: iMg_PFF_4h_32

description: Library name: Sample 24


title: iMg_sPFF_4h_33

description: Library name: Sample 25


title: iMg_DO_4h_21

description: Library name: Sample 5


title: iMg_con_4h_4

description: Library name: Sample 4

value: Control


title: iMg_PFF_4h_31

description: Library name: Sample 23


title: iMg_KO_4h_26

description: Library name: Sample 18


title: iMg_con_4h_3

description: Library name: Sample 3


title: iMg_KO_4h_25

description: Library name: Sample 17


title: iMg_con_4h_2

description: Library name: Sample 2


title: iMg_Fib_4h_15

description: Library name: Sample 15

value: matured a-synuclein fibrils


title: iMg_con_4h_RNA_1

description: Library name: Sample 1


title: iMg_Fib_4h_16

description: Library name: Sample 16


title: iMg_Fib_4h_14

description: Library name: Sample 14


title: iMg_EO_4h_18

description: Library name: Sample 10


title: A549 cells, KRT19-OVE, RNA-Seq rep2

city: Zhengzhou

first: Yue

last: Du

address: No. 1, Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

department: Department of Clinical Laboratory

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: A549_KRT19-OVE_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

growth_protocol: RPMI-1640, 10% fetal bovine serum, 2mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.Cells were cultured in a humidiﬁed 5% CO2 incubator at 37℃.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human non-small cell lung cancer


title: iMg_DO_4h_24

description: Library name: Sample 8


title: A549 cells, KRT19-OVE, RNA-Seq rep1

description: Library name: A549_KRT19-OVE_rep1


title: iMg_Fib_4h_13

description: Library name: Sample 13


title: A549 cells, EV, RNA-Seq rep2

description: Library name: A549_EV_rep2

value: EV


title: iMg_DO_4h_22

description: Library name: Sample 6


title: S28Tumor

city: Ulsan

first: YOU

last: SEONGJUN

institute: Ulsan National Institute of Science and Technology

description: Library name: SAMPLE7

data_processing:
For RNA sequencing data processing, adapter sequences were removed using Cutadapt(v2.9), reads were quality filtered using Trimmomatic (v0.39), which scanned reads from the 5’ end and discarded those shorter than 36 bases. The filtered reads in fastQ files were then aligned to the human reference genome (hg38) with Ensembl v103 annotations using STAR (v2.6.1). Gene quantification was performed using RSEM (v1.3.1) in conjunction with STAR, both operating with default parameters._Human
For RNA sequencing data processing, adapter sequences were removed using Cutadapt(v2.9), reads were quality filtered using Trimmomatic (v0.39), which scanned reads from the 5’ end and discarded those shorter than 36 bases. The filtered reads in fastQ files were then aligned to the mouse reference genome (M26) with Ensembl v103 annotations using STAR (v2.6.1). Gene quantification was performed using RSEM (v1.3.1) in conjunction with STAR, both operating with default parameters._Mouse
Assembly: human reference genome (hg38)
Assembly: mouse reference genome (M26)
Supplementary files format and content: length, effective length, expected count, TPM, FPKM

source_name: Primary colorectal cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)_Human. For RNA extraction from mouse tissue, we followed the manufacturer's portocol using Trizol reagent(Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines. RNA quantity was measured using the Qubit HS RNA assay (Thermo Fisher Scientific)_Mouse
mRNA library preparation (poly A enrichment) , the kit we used was Fast RNA-seq Lib Prep Kit V2 (RK20306). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection._Human.Library preparation was performed using the MGIEasy RNA Directional Library Prep Kit (MGI, Shenzhen, China), and paired-end sequencing (150 bp) was conducted on a DNBSEQ-T7 platform, following the manufacturer’s protocol._Mouse

value: Primary colorectal cancer


title: A549 cells, EV, RNA-Seq rep3

description: Library name: A549_EV_rep3


title: S44NT

description: Library name: SAMPLE2

source_name: Normal

value: Normal


title: S14NT

description: Library name: SAMPLE4


title: S20NT

description: Library name: SAMPLE6


title: S14Tumor

description: Library name: SAMPLE3


title: A549 cells, KRT19-OVE, RNA-Seq rep3

description: Library name: A549_KRT19-OVE_rep3


title: A549 cells, EV, RNA-Seq rep4

description: Library name: A549_EV_rep4


title: A549 cells, EV, RNA-Seq rep1

description: Library name: A549_EV_rep1


title: KT-47 resistance 2_2

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: Library name: AF1008

data_processing:
The raw reads were firs trimmed (Trim-Galore v0.6.3) and human specific reads were kept by BBSPlit (BBMap v38.94) and mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation Human Release 31(GRCh38.p12).
Assembly: hg38
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM text files

source_name: kidney tumor

growth_protocol: KT-47 was heterotopically engrafted into the flanks of C.B-17 scid (C.B-Igh-1b/IcrTac-Prkdcscid) mice (6–8 weeks old; Taconic Farms, Hudson, NY, USA) without cell culture intermediates.

extract_protocol:
Total RNA extraction was performed in triplicate from biologically independent snap frozen samples of WTPDX tumors at each of the chemotherapy resistance phenotypes / timepoints (Pre-treatment [KT-47PT], Pre-resistance, KT-47 Resistance 1 [KT-47R1], KT-47 Resistance 2 [KT-47R2]) using the Qiagen RNeasy Mini Plus Kit (Qiagen, Hilden, Germany) and confirmed using the Thermo Scientific NanoDrop™ One Microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts).
RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.  Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: Tumor-bearing mice were treated with actinomycin-D (0.30 mg/kg intraperitoneal q21 days x 3; Baxter Oncology, Lebanon, NJ), vincristine (1 mg/kg intraperitoneal q7 days x 8; Hospira, Lake Forest, IL), and doxorubicin (4 mg/kg IV q7 days x 8; Pfizer, New York, NY, USA). Three timepoints were selected as experimental groups during this treatment schema for further inquiry: pre-treatment (no VAD chemotherapy exposure in WTPDX model), pre-resistance (VAD chemotherapy exposure without evidence of complete chemoresistance), and resistance (VAD chemotherapy exposure with complete chemotherapy resistance documented). The resistance timepoint was separated into resistance clone 1 and resistance clone 2 (KT-47R1, KT-47R2) which were originally derived from two different mice.

value: kidney tumor

value: Wilms tumor patient-derived xenograft

value: VAD


title: KT-47 preresistance_1

description: Library name: AF1004


title: KT-47 preresistance_3

description: Library name: AF1006


title: KT-47 pretreatment_3

description: Library name: AF1003


title: S26Tumor

description: Library name: SAMPLE9


title: S26NT

description: Library name: SAMPLE10


title: AML191 100 nM FHD-286 rep1

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description:
Library name: KBr_AML191_100_nM_FHD_1
KBr_AML191_100_nM_FHD_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: AML cells UCSD-AML1, AML191, and AML242 PDX cells were cultured in 20% FBS containing RPMI media and supplemented with 10 ng/mL of GMCSF.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with FHD-286 (100 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: lymphocyte

tag: disease state

value: Acute myeloid leukemia


title: S28NT

description: Library name: SAMPLE8


title: AML191 Control rep2

description:
Library name: KBr_AML191_0_nM_2_8slash8
KBr_AML191_0_nM_2_8slash8

value: DMSO Control


title: S20Tumor

description: Library name: SAMPLE5


title: UCSD-AML1 Control rep3

description:
Library name: KBr_UCSD_0_nM_3_8slash8
KBr_UCSD_0_nM_3_8slash8


title: S44Tumor

description: Library name: SAMPLE1


title: AML242 100 nM FHD-286 rep2

description:
Library name: KBr_AML242_100nM_FHD_2
KBr_AML242_100nM_FHD_2


title: A549 cells, KRT19-OVE, RNA-Seq rep4

description: Library name: A549_KRT19-OVE_rep4


title: KT-47 resistance 1_3

description: Library name: AF1012


title: KT-47 resistance 2_1

description: Library name: AF1007


title: KT-47 resistance1_1

description: Library name: AF1010


title: KT-47 resistance 2_3

description: Library name: AF1009


title: KT-47 preresistance_2

description: Library name: AF1005


title: AML242 Control rep1

description:
Library name: KBr_AML242_0nM_1
KBr_AML242_0nM_1


title: AML242 Control rep2

description:
Library name: KBr_AML242_0nM_2
KBr_AML242_0nM_2


title: KBc_AML242_100_FHD_BRG1 1/27/23

description:
Library name: KBc_AML242_FHD_BRG1
KBc_FHD_BRG1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

growth_protocol: Human EVI1 expressing AML242 PDX cells were cultured in 20% FBS containing RPMI-1640 media + 10 ng/mL GMCSF.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing for ChIP-Seq. DNA fragments were PCR amplified for 12-15 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: For ChIP-Seq analysis, 1 x 10^7 Human AML 242 cells were treated for 16 hours with DMSO, or 100 nM of FHD-286 for 16 hours. Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analyses.

tag: chip antibody

value: BRG1 Abcam:Ab110641


title: AML242 Control rep3

description:
Library name: KBr_AML242_0nM_3
KBr_AML242_0nM_3


title: AML242_100_FHD_H3K27Ac

description:
Library name: KBc_AML242_FHD_H3K27Ac
KBc_FHD_H3K27Ac

value: H3K27Ac Active Motif RRID:AB_2793305


title: KT-47 pretreatment_2

description: Library name: AF1002


title: AML242_Control_H3K27Ac

description:
Library name: KBc_AML242_Ctrl_H3K27Ac
KBc_Ctrl_H3K27Ac


title: AML191 100 nM FHD-286 Replicate 2

description:
Library name: KBa_AML191_100FHD_Rep_2
AML191 100 nM FHD-286 Replicate 2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

growth_protocol: UCSD-AML1 and AML191 cells were cultured in 20% FBS containing RPMI media supplemented with 10 ng/mL of GM-CSF.

extract_protocol:
Bulk ATAC-Seq analysis was performed following the protocol of Buenrostro et al 2015. Tn5 transposase-tagmented genomic DNA was utilized to make libraries for next generation sequencing.
Bulk ATAC Sequencing Libraries were constructed following standard Illumina protocols for paired-end sample indexing with I7 and I5 sequencing indices. Indexed libraries were amplified for 10-12 cycles of PCR.

treatment_protocol: AML cells were treated with 100 nM of FHD-286 for 16 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.


title: KT-47 pretreatment_1

description: Library name: AF1001


title: AML191 100 nM FHD-286 rep2

description:
Library name: KBr_AML191_100_nM_FHD_2
KBr_AML191_100_nM_FHD_2


title: UCSD-AML1 100 nM FHD-286 rep1

description:
Library name: KBr_UCSD_100_nM_FHD_1
KBr_UCSD_100_nM_FHD_1


title: AML242 100 nM FHD-286 rep1

description:
Library name: KBr_AML242_100nM_FHD_1
KBr_AML242_100nM_FHD_1


title: KT-47 resistance 1_2

description: Library name: AF1011


title: UCSD-AML1 100 nM FHD-286 rep3

description:
Library name: KBr_UCSD_100_nM_FHD_3
KBr_UCSD_100_nM_FHD_3


title: UCSD-AML1 Control rep1

description:
Library name: KBr_UCSD_0_nM_1_8slash8
KBr_UCSD_0_nM_1_8slash8


title: AML242 100 nM FHD-286 rep3

description:
Library name: KBr_AML242_100nM_FHD_3
KBr_AML242_100nM_FHD_3


title: AML191 Control rep1

description:
Library name: KBr_AML191_0_nM_1_8slash8
KBr_AML191_0_nM_1_8slash8


title: AML191 Control Replicate 2

description:
Library name: KBa_AML191_Ctrl_Rep_2
AML191 Control Replicate 2


title: AML191 100 nM FHD-286 Replicate 1

description:
Library name: KBa_AML191_100FHD_Rep_1
AML191 100 nM FHD-286 Replicate 1


title: MAW-2_rep3

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

description:
Library name: MAW-2_3
column name in raw counts All Samples.txt: MAW-2_rep3

data_processing:
NovaSeq Control Software v1.8.1
bcl2fastq2 v2.20
DRAGEN Bio-IT Platform v4.3.6
Assembly: GRCh38
Supplementary files format and content: csv files include read counts and TPM values of all samples.

source_name: Tumor generated by injection subcutaneously  immune-deficient mice.

growth_protocol: The human iPSCs were maintained on feeder layers of mitomycin C-treated embryonic mouse fibroblasts in primate embryonic stem cell medium (REPROCELL, Tokyo, Japan) supplemented with 4 ng/mL recombinant human fibroblast growth factor 2 (FUJIFILM, Tokyo, Japan). Differentiation of iPSC into cranial NCC (cNCC) was induced using a previously described protocol (PMID: 25464501). Cranial NCCs were cultured in Iscove’s modified Dulbecco’s medium (Thermo Fisher Scientific)/Ham’s F-12 (Thermo Fisher Scientific) 1:1 supplemented with 1x chemically defined lipid concentrate (GIBCO), 15 mg/ml apo-transferrin (Sigma), 450 mM monothioglycerol (Sigma), 5 mg/ml purified BSA (Sigma), 7 mg/ml Insulin (FUJIFILM) and 50 μg/mL penicillin/streptomycin (Sigma). 20 ng/ml EGF (R&D) and 20 ng/ml FGF2 (FUJIFILM) were used to maintain cNCCs. Cultures were maintained at 37ºC under 5% CO2 in air.

extract_protocol:
Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 8.
RNA libraries for RNA-seq were prepared using SMART-Seq mRNA kit (Takara Bio INC) following manufacturer's protocols.

treatment_protocol: In the preparation of the overexpression/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the plasmids (pCDH-CMV-MYCN-EF1a-puro, pCDH-SFFV-ALK(WT)-EF1a-bsd or pCDH-SFFV-ALK(F1174L)-EF1a-bsd) and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 10^5 cNCCs were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene. The infected cNCCs were cultured in medium containing 1 μg/ml puromycin for 3 d or 4 µg/mL blasticidin for 4 d, and were mixed with 0.3% agar dissolved in growth medium (CDMi + SB431542 + EGF + FGF2) and plated on top of a bottom layer of 0.5% agar dissolved in growth medium in a 35 mm dish. The transformed clones were isolated and injected subcutaneously immune-deficient mice.

value: Cranial neural crest cells from 414C2 hiPSC

value: Overexpression of MYCN and ALK

value: Injection subcutaneously  immune-deficient mice.


title: UCSD-AML1 100 nM FHD-286 Replicate 1

description:
Library name: KBa_UCSDAML1_100FHD_Rep_1
UCSD-AML1 100 nM FHD-286 Replicate 1


title: MAW-1_rep3

description:
Library name: MAW-1_3
column name in raw counts All Samples.txt: MAW-1_rep3

value: Tumor generated by injection subcutaneously  immune-deficient mice.


title: MAW-1_rep1

description:
Library name: MAW-1_1
column name in raw counts All Samples.txt: MAW-1_rep1


title: KBc_AML242_100_FHD_input

description:
Library name: KBc_AML242_FHD_input
KBc_FHD_input


title: AML191 Control Replicate 1

description:
Library name: KBa_AML191_Ctrl_Rep_1
AML191 Control Replicate 1


title: UCSD-AML1 Control Replicate 2

description:
Library name: KBa_UCSDAML1_Ctrl_Rep_2
UCSD-AML1 Control Replicate 2


title: UCSD-AML1 Control Replicate 1

description:
Library name: KBa_UCSDAML1_Ctrl_Rep_1
UCSD-AML1 Control Replicate 1


title: KBc_AML242_Ctrl_input

description:
Library name: KBc_AML242_Ctrl_input
KBc_Ctrl_input

value: Control


title: MAW-2_rep2

description:
Library name: MAW-2_2
column name in raw counts All Samples.txt: MAW-2_rep2


title: KBc_AML242_Ctrl_BRG1 1/27/23

description:
Library name: KBc_AML242_Ctrl_BRG1
KBc_Ctrl_BRG1


title: MAW-2_rep1

description:
Library name: MAW-2_1
column name in raw counts All Samples.txt: MAW-2_rep1


title: NP, EG, NR, rep3

city: Pontedera

first: Giada Graziana

last: Genchi

address: Viale Rinaldo Piaggio 34

country: Italy

institute: Istituto Italiano di Tecnologia

description:
Library name: Sample18
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

data_processing:
Analysis of RNA sequencing data was performed with a custom in-house written Nextflow Pipeline developed by Omiqa Bioinformatics. This pipeline includes the following steps.
FastQ Quality Control with FastQC (v.0.11.9)
Alignment with STAR to the hg38 reference genome provided by Gencode (v2.7.11b)
Reading Counting with featureCounts (v2.18.0) by setting multi-mapping read counts to true and strandness to reversed, based on an initial quality control step
MultiQC report generation using FastQC, Star and Feature count data (v.1.10.1)
Differential Gene Expression Analysis with DESeq2 (v1.44.0)
Gene Ontology Analysis with clusterProfiler (v4.12.0)
Volcano Plot Generation with EnhancedVolcano (v1.22.0)
Heatmap Generation with pheatmap (v1.0.12)
Assembly: hg38
Supplementary files format and content: data.rds: alignment summary and read counts per gene for all samples
Supplementary files format and content: dds.rds: DEseq dds object
Supplementary files format and content: res.dge.filtered.rds: results of differential gene expression analysis

growth_protocol: SH-SY5Y neuroblastoma cells were maintained in HEPES-buffered proliferative medium within bioreactors under passive thermal conditioning during upload to the International Space Station (ISS). Once on board the ISS, bioreactors were equally distributed between static and dynamic slots of the Kubik incubator, implying exposure to real microgravity with cosmic radiation and simulated Earth gravity with cosmic radiation, respectively. The experiment started when cells were administered with HEPES-buffered differentiative medium (either added or not with nanoparticles at a final concentration of 20 µg/ml) and they were incubated at +37°C. At 48 h from start of incubation in Kubik, the medium was refreshed (either added or not with nanoparticles). At 96 h from start of incubation in Kubik, the cell cultures were rinsed with saline solution, fixed and cold stowed at -80°C. On Earth, cell cultures were exposed to the same thermal profile registered during spaceflight, and they were equally distributed between static and dynamic conditions, implying exposure to Earth gravity without cosmic radiation and simulated microgravity (by rotation on random positioning machine) without cosmic radiation.

extract_protocol:
Total RNA extraction and purification was conducted with MirVana PARIS kit (Ambion) by following the manufacturer’s instructions.
A quantity of 300 ng of total RNA underwent Poly(A) mRNA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #7490). RNA library was built by using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760/E7765).

treatment_protocol: SH-SY5Y were allowed to proliferate in DMEM-F12 medium supplemented with 15 mM HEPES, 10% FBS and 100 U/mL penicillin - 100 μg/mL streptomycin. Differentiation was induced by administration of DMEM-F12 medium supplemented with 15 mM HEPES, 2% FBS, 10 µM retinoic acid, 100 U/mL penicillin - 100 μg/mL streptomycin, and either added or not with 20 µg/ml polydopamine nanoparticles.

value: Neuroblastoma Cell

value: WT

value: with nanoparticles, with Earth gravity, without cosmic radiation


title: NNP, SMG, NR, rep1

description:
Library name: Sample19
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with simulated microgravity, without cosmic radiation


title: MAW-1_rep2

description:
Library name: MAW-1_2
column name in raw counts All Samples.txt: MAW-1_rep2


title: NP, EG, NR, rep1

description:
Library name: Sample16
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: NNP, SEG, CR, rep2

description:
Library name: Sample8
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with simulated Earth gravity, with cosmic radiation


title: NNP, EG, NR, rep1

description:
Library name: Sample9
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with Earth gravity, without cosmic radiation


title: NNP, SEG, CR, rep1

description:
Library name: Sample7
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: NP, SMG, NR, rep3

description:
Library name: Sample24
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: with nanoparticles, with simulated microgravity, without cosmic radiation


title: NP, SMG, NR, rep1

description:
Library name: Sample22
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: NP, SMG, NR, rep2

description:
Library name: Sample23
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: UCSD-AML1 100 nM FHD-286 Replicate 2

description:
Library name: KBa_UCSDAML1_100FHD_Rep_2
UCSD-AML1 100 nM FHD-286 Replicate 2

value: lymphocyte


title: NNP, MG, CR, rep1

description:
Library name: Sample1
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with real microgravity, with cosmic radiation


title: NNP, SMG, NR, rep3

description:
Library name: Sample21
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: NNP, SMG, NR, rep2

description:
Library name: Sample20
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.