title: mES-HSC-mixed-5hmC

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
The SPEED datasets in this study were generated in paired-end format. Read 1 contains one segment of barcode in the 5’terminal (barcode 1) and following genomic DNA fragment. Read 2 carries three barcode segments from the 5’terminal sequentially (barcode 3/ barcode 2/ barcode 1). The data processing pipeline was modified from previous study14.
1). Data pre-processing. Sequencing quality of raw read was examined by FastQC (v0.11.9). Raw SPEED data reads were subjected to FastQC (v0.11.9) for checking sequencing quality and trimmed adaptors by Trimmomatic (v 0.38) under PE mode (-phred33 ILLUMINACLIP: TruSeq3-PE-2. fa: 2:30:10 TRAILING:3 SLIDINGWINDOW: 4:20 MINLEN:50).
2). Barcode identification and removal. Each full-length barcode was composed of 3 segments (barcode 1/ barcode 2/ barcode 3). To ensure the completeness, both read 1 and read 2 were used in barcode identification by BarcodeIdentification_v1.2.0.jar with the default parameters 2 and the barcode was added behind the read name. Finally, reads contain all the three barcode segments were filter for following analyses. In generally, around 75% reads were labeled by full-length barcode. To prevent the inclusion of extra barcode sequences at the 3' end of read 1, the second-round barcode-removing was performed by cutadapt (v 1.18) with parameters ‘-j 15 -m 50 -a "file: Split-Pool-jx_3barcode_rev. fa"’.
3). Mapping to genome and PCR duplicates removal. For mESC, mouse cerebral and cerebellar cortex SPEED data, read 1 in each SPEED library underwent two round barcode-removing (described above) were mapped on mm10 reference genome using Bowtie2 (v 2.3.5), and parameter ‘--trim5 11’ was set to remove barcodes on 5’terminal. Uniquely mapped reads were filtered and sorted by genome coordinates using samtools (v 1.9). The barcode strings on read names were stored in bam file tag ‘CB: Z:’. PCR duplicates were marked by the same start/end position and the same barcode and were removed in the following analysis. In analysis of mESC and hSC mixed library, reads were simultaneously mapped to both hg38 and mm10, and the aforementioned analyses were repeated. Subsequently, reads mapped to hg38 and mm10 were counted separately from deduplicated BAM files for each barcode to verify the single-nuclei labeling validity of SPEED library.
4).5hmC peak calling. The 5hmC-enriched regions in each sample were identified as peaks via MACS2 (v 2.1.2) with parameters ‘-f BAM -g mm -q 0.01 --nomodel --extsize 400 --max-gap 500 --keep-dup all’. The peaks in mouse brain and cerebellum are combined for DHMR analyses. The peaks were annotated by ‘annotatePeaks.pl’ in HOMER (v 4.10) with the default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mES and Human cord blood

extract_protocol:
1) Nuclei isolation or extraction Cells or purified nuclei were crosslinked with formaldehyde and lysised with lysis buffer.
2) DNA fragmentation SDS and Triton X-100 were used to isolate and permeabilize nuclei. DNA fragmentation was performed by HpyCH4V in 0.1% Triton, 0.2% Tween-20, 0.2% NP-40, and PBS in to get the DNA fragment size range with 200-500bp.
3) DNA End-repair The dA-tailing process was initiated by adding dA tailing buffer to the nuclei, composed of nuclease-free H2O, dA-tail reaction buffer, and Klenow fragment.
4) Barcode in nuclei ligation The isolated nuclei, DPM barcoded tag and ligation mix ( 2 × Instant Sticky-end Ligase Master Mix, 5 × Quick Ligase Buffer, and 1,2-propanediol) were loaded into each well of a 96-well plate. The 96 well plate was subjected to meticulous mixing at 20 °C, allowing the ligation reaction to progress over a duration of 2 hour. After incubation, the in-nuclei DNA ligation was stopped. The contents of each well were transferred into new tube and washed.The nuclei were next performed second and third rounds of ODD and TERMINAL barcode ligation.
5) DNA reverse crosslinking The ligated-nuclei were reverse crosslinked  with 5 × Proteinase K Buffer and Proteinase K. Then, ligated-DNA was purified by DNA clean & concentrator kit.
6) 5hmC labeling and library construction 5hmC labeling and enrichment procedures follow the published protocols13, 14. Following the reaction, DNA substrates were purified by using the DNA Clean & Concentrator Kit and subsequently reconstituted in H2O.
Library construction was performed according to manufacturer’s recommendations for NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: mES and Human cord blood

value: E14g2a and HSPC (hematopoitic stem and projenitor cell)


title: T17_Humanized CJ HCC- ZT18

status: Public on Jan 01 2025

type: SRA

city: Houston

first: Loning

last: Fu

state: Texas

address: One Baylor Plaza

department: Medicine

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

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 hg38 and mm10 using STAR aligner with parameter ( --outSAMattributes NM).
FeatureCounts implemented in Subread package was used to count the sequencing reads from mapped BAM files.The number of reads falling in the exons of this meta-transcript were counted
Differential gene expression was evaluated using the R package EdgeR and expression was further normalized using the R package RUVr
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text files include raw read count for each annoted gene

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: Humanized CJ HCC

extract_protocol:
Liver or HCC were removed, flash frozen in liquid nitrogen, RNA was processed using PureLinkTM RNA Minikit (Cat#12183018A), and extracted RNAs were used for the construction of RNA libraries using Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)

tag: tissue

value: h-HCC

tag: genotype


title: 2nd exp Unstim dup2

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: 2nd exp Unstim dup2

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.0.11
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Assembly: mm10/GRCm38
Supplementary files format and content: Gene expression in text format, content include gene name, symbol, chromosome, length of transcripts, raw reads, and normalized reads per kilobase per million (RPKM)

organism: Mus musculus

source_name: spleen

growth_protocol: Murine CD8+ T cells were isolated from the spleens of 6- to 8-week-old C57BL/6 mice through negative selection and magnetic separation (Stem Cell Technologies Cat# 19853). Purified murine CD8+ T cells were pre-activated with plate-bound anti-mouse CD3 (2 µg/mL; clone 145-2C11, BioXCell Cat# BE0001-1) and soluble anti-mouse CD28 (1 µg/mL; clone 37.51, BioXCell Cat# BE0015-1) and cultured in complete RPMI media for 48 hours at 37°C.

extract_protocol:
Cells were then lysed in TRIzol reagent (Invitrogen Cat# 15596026), RNA was isolated using Direct-zol RNA MiniPrep Kit (Zymo Research Cat# R2052)
RNA-Sequencing libraries were prepared  using KAPA mRNA HyperPrep Kit (Roche Cat# KK8440), after quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina NovaSeq system.

treatment_protocol: Cells were rested overnight and restimulated with mIL-21 or 21h10 at 100 pM, 1 nM, 10 nM, and 100 nM concentrations for 24 hours in complete RPMI media at 37°C.

value: spleen

tag: cell type

value: CD8+ T cells

value: wild-type

tag: treatment

value: pre-activated


title: SKI3 RNAi mock R3

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

description: Library name: Sample6

library_source: other

data_processing:
Following sequencing, small RNA sequencing adapters were removed using cutadapt (v2.10). Sequences matching ribosomal or transfer RNA were filtered out using bowtie (v1.3.1). Reads of 21 and 22 nucleotides were mapped on the Mt5.0  genome (Pecrix et al., 2018) with ShortStack (v3.8.5) under strict no-mismatch conditions (--mismatches 0), keeping all primary multi-mapping (--bowtie_m all) and correcting for multi-mapped reads based on uniquely mapped reads (--mmap u). The read accumulation of 21/22nt for each gene annotation was quantified using ShortStack (Axtell, 2013). To assess miRNA abundance, the count of sequences corresponding to each mature miRNA in Medicago miRBase (v22) was used (Kozomara and Griffiths-Jones, 2014). Differential 21/22nt sRNA accumulation and log2 fold changes between conditions were computed using DESeq2 (v1.34.0) (Love et al., 2014). FDR correction of the p-value was used.
Assembly: MtrunA17r5.0-ANR
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: other

organism: Medicago truncatula

source_name: Roots

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher Scientific),
Small RNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s instructions, starting with 500 ng of Total RNA extracted with Trizol. Briefly,  3′ and 5’ adaptors were ligated to the ends of the single-stranded RNA. After ligation of the adaptors, the small RNAs were used as a template for the synthesis of one complementary strand of DNA. Reverse transcribed molecules that contain both adaptor sequences were then amplified by PCR. Libraries were characterized using gel electrophoresis and the amplified libraries were isolated.

value: Roots

tag: cell line

value: SKI3 RNAi

value: Root cells

value: WT

value: mock


title: A549 cells, shControl, 3 days after ionizing radiation1

city: Beijing

first: Li

last: Xinyan

address: No.17, Panjiayuan Nanli, Chaoyang District, Beijing

country: China

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
DESeq2 R package (1.20.0)
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample

organism: Homo sapiens

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used was used for the construction of sequencing libraries
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magneticbeads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activitiesAfter adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization.In order to select cDNA fragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-FidelityDNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products werepurified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: non-small cell lung cancer cell lines

value: ionizing radiation


title: 2nd exp Unstim dup1

description: 2nd exp Unstim dup1


title: GC3

city: Xiamen

first: Jichen

last: Chen

state: None Selected

address: Fujian province xiamen city

institute: Xiamen University

data_processing:
The sequenced data (raw data) was filtered by SOAPnuke (v1.4.0) (Yuxin Chen et al., 2018) and clean data was obtained. Then the clean data was assembled via Trinity (v2.0.6) and quality assessed via BUSCO (Grabherr et al., 2011). After that, the clean data was mapped to the assembled unique gene by Bowtie 2 (v2.2.5) (Langmead & Salzberg, 2012) and its expression level was calculated with RSEM (v1.2.8) (Parrish et al., 2014). The coding sequences of unigenes were identified and aligned to SwissProt by the software Transdecoder (v3.0.1) (Kim et al., 2015) and Basic Local Alignment Search Tool (Blast), respectively. Hmmscan were took out for the identified of homologous and coding sequences. Then, MISA (v1.0) (Thiel et al., 2003) and Primer3 (v2.2.2) (Untergasser et al., 2012) were used for the detection of unigenes and the designment of primer for SSR detection.
The differential genes within and between group were performed using DESeq and PossionDis. The differential expressed genes were identified with |Fold change| ≥ 1.5 and Q_value ≤ 0.05. The expression heatmap were performed via TBtools-II (v2.007) software (C. Chen et al., 2020).
Assembly: The assembled unigenes were annotated with multiple functional databases Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/), Gene Ontology (GO, https://www.geneontology.org/), Non-Redundant Protein Sequence Database (NR, ftp://ftp.ncbi.nlm.nih.gov/blast/db), Nucleotide Sequence Database (NT, ftp://ftp.ncbi.nlm.nih.gov/blast/db), Swiss-Prot (https://www.expasy.org/resources/uniprotkb-swiss-prot), Protein family (Pfam, http://pfam.xfam.org/), and Clusters of orthologous groups for eukaryotic complete genomes (KOG, ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kyva).

organism: Skeletonema costatum

source_name: cells

growth_protocol: 12:12 light dark cycle

extract_protocol:
About 10 million cells of alga sample in 100th days were collected and frozen in liquid nitrogen. Each group included three replicates. After that, the frozen alga samples were sent to BGI Genomic Center (Shenzhen, China) for the extraction, purification, and check of RNA.
The RNA samples were isolated via denatured and mRNA was enriched by oligo (dT) -attached magnetic beads. Then, the mRNA was fragmented at the suitable temperature. The cDNA was synthesis via the method of sequencing by synthesis (SBS). Furthermore, the double-stranded cDNA fragments are subjected to end-repair, adding poly A, ligating the adaptor and enrichment(Peredo & Cardon, 2020). After the construction of cDNA libraries, it was tested via Agilent 2100 Bioanalyzer and then sequenced via the Illumina HiSeq™ 4000 platform (Rädecker et al., 2021).

value: cells

value: wild type

value: GC


title: SKI3 RNAi mock R2

description: Library name: Sample5


title: A549 cells, shControl, sham irradiation3

value: sham irradiation


title: 1st exp h10.100pM.24h dup2

description: 1st exp h10.100pM.24h dup2


title: T7-5_Humanized CJ HCC- ZT10

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)


title: T13-3_Humanized CJ HCC- ZT18

value: h-HCC


title: T12_Humanized CJ HCC- ZT10


title: A549 cells, shControl, sham irradiation2


title: 1st exp h10.100pM.24h dup1

description: 1st exp h10.100pM.24h dup1

value: spleen


title: T11_Humanized CJ HCC- ZT10


title: 1st exp h10.1nM.24h dup2

description: 1st exp h10.1nM.24h dup2

value: CD8+ T cells


title: GUS RNAi mock R2

description: Library name: Sample2

value: GUS RNAi


title: GUS RNAi mock R3

description: Library name: Sample3


title: A549 cells, shControl, 3 days after ionizing radiation2


title: 1st exp h10.1nM.24h dup1

description: 1st exp h10.1nM.24h dup1

value: wild-type

value: pre-activated


title: GUS RNAi mock R1

description: Library name: Sample1

value: Roots


title: T10_Humanized CJ HCC- ZT10


title: 1st exp WT.100pM.24h dup2

description: 1st exp WT.100pM.24h dup2


title: T7_Humanized CJ HCC- ZT10


title: HUVEC, 30 min TNFa, H3K27ac, replicate 2

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

library_source: genomic

data_processing:
Raw read files were aligned to the human reference genome (hg38) using Bowtie2. The ShortRead package was used to convert these into genome-wide coverage files. Peak calling was performed as previously described (Stadhouders et al. 2015, https://github.com/supatt-lab/rChIPSeqTools). Peaks with ≥20 read counts at each peak summit and FDR ≤ 0.001 (using nonspecific, IgG, ChIP-seq data as background) were selected.
Assembly: hg38
Supplementary files format and content: bigWig, bed file of peaks

molecule: genomic DNA

source_name: Umbilical vein endothelial cells

growth_protocol: HUVECs from pooled donors (Lonza, cat. #00191027) were cultured in endothelial basal medium (EBM-2) with supplements (Lonza, cat. #CC-3162) and 5% FBS. Cells were starved for 16-18 h in EBM + 0.5% FBS prior to treatment.

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
15–30 million cells were crosslinked (10 min, 20°C) in 1% paraformaldehyde (Electron Microscopy Science). Nuclei were isolated, and chromatin was prepared, fragmented, and collected using the ChIP-It High Sensitivity kit (Active Motif). Immunoprecipitation was performed on aliquots of ∼25 µg chromatin using antisera targeting acetylated lysine 27 of histone H3 (Abcam; ab4729), the H3K27ac ChIP-seq grade Antibody (Diagenode, C15210016), or IgG controls (Active Motif; 53017). DNA was purified using a DNA clean-up kit (Zymo Research) and used as template for high throughput DNA sequencing on an Illumina HiSeq 2000 platform.

treatment_protocol: HUVECs were treated with 10 ng/mL human TNFα (PeproTech, cat. #300-01A) for 30 min.

value: Umbilical vein endothelial cells

value: 30 min TNFa

tag: chip antibody

value: Diagenode, C15210016


title: HUVEC, 30 min TNFa, H3K27ac, replicate 1

value: Abcam, ab4729


title: T1-5_Humanized CJ HCC- ZT2


title: 1st exp WT.100pM.24h dup1

description: 1st exp WT.100pM.24h dup1


title: ZDP-3Flag;zdp-1ape2-2

city: Shanghai

first: wenjie

last: liang

address: Guoquan North Road

institute: Fudan university

description: Arabidopsis thaliana seedlings WGBS Raw sequence reads

data_processing:
methylpy version 1.3
Assembly: TAIR10
Supplementary files format and content: bigWig file

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
The total DNA of the genome was extracted by DNeasy plant mini kit (QIAGEN) after the plant material was grown on the petri dish for 14 days
BGI used Bisulfite processing to construct the library

value: seedlings

value: APE2 knockout


title: zdp-1ape2-2fpg-2MMS

value: ZDP and APE2 and FPG knockout


title: 1st exp WT.1nM.24h dup2

description: 1st exp WT.1nM.24h dup2


title: T7-4_Humanized CJ HCC- ZT10


title: Ribo footprints pTRIPZ RACK1, mutant RACK1 Replicate 2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
For the ribosome profiling analysis, we used hg19/GRCh37 for  the genome assembly and Gencode v.24 for the transcriptome reference.
Reads aligning to rRNAs and contaminants were filtered out using Bowtie v1.1.2, and all remaining reads were aligned to the custom transcriptome described above with Tophat v.2.1.1 (Kim et al., 2013) using --b2-very-sensitive --transcriptome-only --no-novel-juncs --max-multihits=64 flags.  These alignments were assigned a specific P-site nucleotide using a 12-nt offset from the 3' end of reads.  Read counting and gene expression (RPKM) calculations for both ribosome profiling and RNA-seq are performed in Python 2.7 using Plastid (Dunn and Weissman, 2016) and differential expression analysis was done by DESeq2 (Love et al., 2014).  Translation efficiency was calculated as ribosome profiling RPKM/RNA-seq RPKM.
Assembly: hg19
Supplementary files format and content: Counts, RPKMs
Library strategy: Ribo-seq

source_name: OVCAR3 cells

growth_protocol: OVCAR3 cells were cultured in RPMI media containing 10% FBS, 1% Pencillin-streptavidin, 1% Glutamax. RACK1 expressing OVCAR3 cells were cultured in 0.5 ug/mL and 250 µg/mL G418. The selection antibiotics were not added when the cells were plated for the experiments.

extract_protocol:
For performing ribosome profiling (Ribo-seq), ribosome-protected footprints were prepared for sequencing as described in a recently updated protocol of ribosome profiling (Chen et al., 2020; McGlincy and Ingolia, 2017).  Briefly, the cells were plated, grown, and subjected to the various treatments and experimental conditions indicated as described above.  They were the rapidly harvested and lysed.  Clarified cell lysates were treated with RNase I (Invitrogen) to digest RNA not protected by ribosomes.  The 80S ribosomes were isolated by centrifuging lysates through a 34% sucrose cushion at 100,000 x g for 1 hour at 4°C.  The RNA was purified from the ribosome pellet using the Direct-zol RNA kit (Zymo Research).  It was then resolved by electrophoresis through a denaturing gel, and the fragments corresponding to 28 to 34 bp were extracted from the gel.
The 3' ends of the ribosome footprint RNA fragments were treated with T4 polynucleotide kinase (New England Biolabs, M0201) to allow ligation of a pre-adenylated DNA linker with T4 Rnl2(tr) K227Q (New England Biolabs, M0351S).  The DNA linker used incorporates sample barcodes to enable library multiplexing, as well as unique molecular identifiers (UMIs) to enable removal of duplicated sequences.  To separate ligated RNA fragments from unligated DNA linkers, 5'-deadenylase (Epicentre, DA11101K) was used to deadenylate the pre-adenylated linkers, which were then degraded by the 5'-3' ssDNA exonuclease RecJ (NEB, M0264S).  After rRNA reduction using the riboPOOL rRNA depletion kit (siTOOLs Biotech, H. sapiens pool), the RNA-DNA hybrid was used as a template for reverse transcription, followed by circularization with CircLigase (Epicentre, CL4111K). Finally, PCR of the cDNA circles was used to attach suitable adapters and indices for Illumina sequencing.

treatment_protocol: For RACK1 expressing cells, OVCAR3 cells were plated in 15 cm plates. Next day the cells were treated with 1 ug/mL doxycycline. For TARG1 knockdown,  OVCAR3 cells cultured in 15 cm plates were transfected with 30 nM siRNA targeting OARD1 (TARG1) or a control siRNA. Forty eight hours after the dox treatment or siRNA transfection, the cells were harvested rapidly for ribosome profiling.

value: KD of endogenous RACK1 and re-expression of mutant RACK1


title: T1-4_Humanized CJ HCC- ZT2


title: SKI3 RNAi mock R1

description: Library name: Sample4

value: SKI3 RNAi

value: Root cells

value: WT

value: mock


title: zdp-1ape2-2fpg-2


title: Ribo footprints pTRIPZ RACK1, mutant RACK1 Replicate 1


title: A549 cells, shControl, sham irradiation1

value: non-small cell lung cancer cell lines

value: sham irradiation


title: 1st exp WT.1nM.24h dup1

description: 1st exp WT.1nM.24h dup1

value: spleen

value: CD8+ T cells

value: wild-type


title: T5_Humanized CJ HCC- ZT2

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)

value: h-HCC


title: 1st exp Unstim dup2

description: 1st exp Unstim dup2

value: pre-activated


title: zdp-1ape2-2nrpd-3MMS

value: ZDP and APE2 and NRPD1 knockout


title: HUVEC, 30 min TNFa, Input

value: Umbilical vein endothelial cells

value: 30 min TNFa


title: T4_Humanized CJ HCC- ZT2


title: zdp-1ape2-2nrpd-3

value: seedlings


title: 1st exp Unstim dup1

description: 1st exp Unstim dup1


title: Ribo footprints pTRIPZ RACK1, wildtype RACK1 Replicate 1

value: KD of endogenous RACK1 and re-expression of WT RACK1


title: T3_Humanized CJ HCC- ZT2


title: zdp-1ape2-2sog1

value: ZDP and APE2 and SOG1 knockout


title: Ribo footprints siRNA TARG1 Replicate 2

value: TARG1 KD


title: T6_Humanized CJ HCC- ZT2


title: Subj_60,liver,HFD33w_bFKB1-Ab12w

city: Leiden

first: Martine

middle: C

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: Liver (lobus sinister lateralis hepatis)

extract_protocol:
RNA was extracted from ~10 mg snap-frozen liver tissue using a total-RNA isolation kit (RNA-Bee, Bio-connect, Huissen, the Netherlands). RNA concentrations were determined using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-40 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

tag: mouse id


title: T16_Humanized control HCC- ZT18

source_name: Humanized HCC


title: rdd-2MMS

value: DML1 and DML2 and ROS1 knockout


title: Subj_59,liver,HFD33w_bFKB1-Ab12w

value: Liver (lobus sinister lateralis hepatis)


title: rdd-2


title: Ribo footprints siRNA TARG1 Replicate 1


title: fpg-1MMS

value: FPG knockout


title: Ribo footprints siRNA Control Replicate 1

value: control


title: T13-2_Humanized control HCC- ZT18


title: Subj_58,liver,HFD33w_bFKB1-Ab12w


title: Ribo footprints siRNA Control Replicate 2


title: Subj_57,liver,HFD33w_bFKB1-Ab12w


title: T15_Humanized control HCC- ZT18


title: fpg-1


title: Input pTRIPZ RACK1, mutant RACK1 Replicate 2

data_processing:
For the RNA-seq analysis, we used hg19/GRCh37 for  the genome assembly and Gencode v.24 for the transcriptome reference.
For RNA-seq analysis the reads aligned to rRNAs and contaminants were filtered out using using Bowtie v1.1.2, and all remaining reads were aligned to the custom transcriptome with Tophat v.2.1.1 (Kim et al., 2013) using --b2-very-sensitive --transcriptome-only --no-novel-juncs --max-multihits=64 flags. Read counting and gene expression (RPKM) calculations are performed in Python 2.7 using Plastid (Dunn and Weissman, 2016) and differential expression analysis was done by DESeq2
Assembly: hg19
Supplementary files format and content: Counts, RPKMs

source_name: OVCAR3 Cells

extract_protocol:
For performing RNA-seq, input lysates from the samples subjected to Ribo-Seq was used.  Briefly, the cells were plated, grown, and subjected to the various treatments and experimental conditions indicated as described above.  They were the rapidly harvested and lysed.  Clarified cell lysates was used for RNA-seq library preparation.
Total RNA was isolated using the Direct-zol RNA kit (Zymo Research) according to the manufacturer's protocol.  After rRNA reduction using the riboPOOL rRNA depletion kit (siTOOLs Biotech, H. sapiens pool), the RNA was then used to generate strand-specific RNA-seq libraries TrueSeq Stranded Total RNA Library Prep (Illumina, 20020596).  The RNA-seq libraries were subjected to QC analyses (final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2000.
rRNA depleted-RNA-seq

value: KD of endogenous RACK1 and re-expression of mutant RACK1


title: Ribo footprints pTRIPZ RACK1, wildtype RACK1 Replicate 2


title: Subj_56,liver,HFD33w_bFKB1-Ab12w


title: zdp-1ape2-2MMS

value: ZDP and APE2 knockout


title: Input pTRIPZ RACK1, mutant RACK1 Replicate 1


title: Subj_55,liver,HFD33w_bFKB1-Ab12w


title: Subj_54,liver,HFD33w_bFKB1-Ab12w


title: Col-0MMS

value: WT


title: Subj_52,liver,HFD33w_bFKB1-Ab12w


title: zdp-1ape2-2_C

description: Arabidopsis thaliana seedlings RNA_seq Raw sequence reads

data_processing:
STAR
Assembly: TAIR10
Supplementary files format and content: raw_counts.txt

molecule: polyA RNA

extract_protocol:
After the plant material was grown on a petri dish for 14 days, total RNA was extracted using QIAGEN's RNeasy plant mini kit
PolyA RNA-seq library preparation by BGI


title: T7-3_Humanized control HCC- ZT10

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)


title: T9_Humanized control HCC- ZT10

value: h-HCC


title: zdp-1ape2-2_B


title: T8_Humanized control HCC- ZT10


title: Subj_50,liver,HFD33w_bFKB1-Ab12w


title: Input siRNA TARG1 Replicate 1


title: Input pTRIPZ RACK1, wildtype RACK1 Replicate 2


title: Input siRNA TARG1 Replicate 2


title: zdp-1ape2-2_A


title: Input pTRIPZ RACK1, wildtype RACK1 Replicate 1


title: Col-0_C


title: Subj_48,liver,HFD33w_bFKB1-Ab12w


title: Input siRNA Control Replicate 2


title: Subj_49,liver,HFD33w_bFKB1-Ab12w


title: T1-2_Humanized control HCC- ZT2


title: T1-3_Humanized control HCC- ZT2


title: T2_Humanized control HCC- ZT2


title: T13_Humanized control HCC- ZT18


title: Col-0_B


title: Col-0_A


title: A498 Sunitinib-resistant Dur treated replicate 3 [42Dur3]

city: Rockville

first: Alexis

middle: L

last: Norris

address: 7500 Standish Place

institute: US FDA

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

growth_protocol: Two human advanced renal cell carcinoma cell lines A498 and 786-O were purchased from ATCC. They were cultured in DMEM growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated foetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Sunitinib (SU11248) malate was purchased from Selleckchem. For the development of sunitinib-resistant cells, parental cells were exposed to increasing concentrations of sunitinib. In brief, the RCC cell lines were treated with varying concentrations of sunitinib (0, 1, 2, 3, 4, 5, 7, 10, 20, and 50μM). With the passage of time of every four days, it has been observed that A498 cells showed stable growth and eventually became confluent at a concentration of 2µM, while 798-O cells showed stable growth to confluence at a concentration of 4µM. It can be assumed that cells that grew to confluence had developed stable sunitinib-resistance after a period of four months or >20 passages. The cells were constantly in sunitinib containing medium throughout the selection process.

extract_protocol:
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.

treatment_protocol: Cells were treated with either Atezolizumab (AT), Avelumab (Av), or Durvalumab (Dur), at a concentration of 10mg/mL for 24 hours.

value: advanced clear cell renal cell carcinoma (ccRCC)

tag: drug resistance

value: Sunitinib

value: Durvalumab

tag: batch


title: T7-2_Humanized control HCC- ZT10


title: Input siRNA Control Replicate 1


title: Subj_45,liver,HFD33w_Ctr-Ab12w


title: 99_Without_Bacillus_S8

city: Jerusalem

first: Moshe

last: Alon

state: Israel

address: Gelber

country: Israel

institute: Hebrew University of Jerusalem

description:
Library name: 99_Without_Bacillus_S8
count_file_uninfected_plant.csv

data_processing:
Rsubread package 46. The featureCounts function was used to count reads that mapped to each one of the nuclear protein-coding genes. Based on principle component analysis, one outlier sample was removed from each treatment. DESeq2 was provided to identify genes that are differentially expressed between different conditions or groups.
Assembly: GCF_000001735.4_TAIR10.1_genomic.gtf
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: leaves

growth_protocol: Arabidopsis thaliana seeds (ecotype Columbia; Col-0) were surface sterilized with a cleaning solution (10% bleach and 0.1% Tween-20), shaken for 15 minutes at 1000 rpm, followed by five rinses with sterile distilled water. Seeds were stratified at 4 °C for 24-48 hours in the dark. After stratification, seeds were transferred to square plates containing Murashige Skoog medium (MS) supplemented with 0.8 agar and 1% sucrose. Plates were kept in a vertical position for seven days in a growth chamber under a 16-hour light/8-hour dark regime at 21o C day/18o C night. On the eighth day, the resulting seedlings were transferred to magenta boxes containing 250 ml soil sterilized three times at 25 Kilo-Grays of gamma radiation. This soil was watered with 30 ml MS medium.

extract_protocol:
Three replicate samples were collected from the shoots of each treatment after 24 hours of infection. The samples were washed with sterile water to remove soil particles, placed in 2 ml Eppendorf tubes with three sterile glass beads, and flash-frozen in liquid nitrogen. Tubes were stored at -80˚ C until processing. RNA was purified from plant tissue using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and stored at -80˚ C.
Illumina-based RNA-Seq libraries were prepared from two μg RNA. mRNA was purified from total RNA using Sera-mag oligo (dT) magnetic beads (GE Healthcare Life Sciences) and then fragmented in the presence of divalent cations (Mg2+) at 94 °C for six min. The resulting fragmented mRNA was used for first-strand cDNA synthesis using random hexamers and reverse transcriptase, followed by second-strand cDNA synthesis using HiFi DNA polymerase I and RNaseH. The DNA fragments were then adenylated to allow the ligation of Illumina KAPA adapters. Following library preparation, quality control, and quantification were performed using an Agilent 2100 Bioanalyzer- nano chip, and library quantity and pooling were measured by Qubit (dsDNA HS). Libraries were sequenced using NextSeq 500 high output kit V2 75 cycles to generate 30 million single-end reads per sample.Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC .Trim galore was used to remove the first 10-12 bases from the 5' end of the reads. The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using the

treatment_protocol: One week before each experiment, bacteria were inoculated from 50% glycerol stocks at -80 °C into 500 μl LB medium in a 96-deep-well plate. Bacterial cultures were grown at 28 °C, shaking at 250 rpm. After 4 days of growth, cultures were inoculated into fresh medium and returned to the incubator for an additional 48 hours, resulting in two copies of each culture (6 days old and 48 hours old). This method was chosen to account for the varied growth rates of the bacterial strains and to ensure that the inoculum included nonstationary cells from each strain. The optical density of each one of the individual cultures was measured at 600 nm (OD600) using an Infinite 200 Pro plate reader (TECAN). Bacterial cells were combined based on the optical density measurements into single tubes according to phylum. Then, the optical density of the new tubes was measured at 600 nm (OD600). All cultures were pooled while normalizing each culture to OD600 =0.1 and resuspended with liquid MS medium to remove the spent medium. Then, the bacteria were added according to the treatments in each experiment.

value: leaves


title: A498 Sunitinib-resistant Dur treated replicate 2 [42Dur2]


title: Subj_43,liver,HFD33w_Ctr-Ab12w


title: Q12_Humanized NASH CJ liver- ZT18

source_name: Humanized NASH CJ liver

value: h-Liver


title: 98_Without_Bacillus_S7

description:
Library name: 98_Without_Bacillus_S7
count_file_uninfected_plant.csv


title: Subj_42,liver,HFD33w_Ctr-Ab12w


title: Q11_Humanized NASH CJ liver- ZT18


title: A498 Sunitinib-resistant Av treated replicate 3 [42Av3]

value: Avelumab


title: A498 Sunitinib-resistant Dur treated replicate 1 [42Dur1]


title: Subj_41,liver,HFD33w_Ctr-Ab12w


title: Q10_Humanized NASH CJ liver- ZT18


title: 97_Without_Bacillus_S6

description:
Library name: 97_Without_Bacillus_S6
count_file_uninfected_plant.csv


title: A498 Sunitinib-resistant Av treated replicate 2 [42Av2]


title: Subj_46,liver,HFD33w_bFKB1-Ab12w


title: 92_Full_SynCom_S2

description:
Library name: 92_Full_SynCom_S2
count_file_uninfected_plant.csv


title: Q9_Humanized NASH CJ liver- ZT18


title: A498 Sunitinib-resistant Av treated replicate 1 [42Av1]


title: Q8_Humanized NASH CJ liver- ZT10


title: 91_Full_SynCom_S1

description:
Library name: 91_Full_SynCom_S1
count_file_uninfected_plant.csv


title: Subj_40,liver,HFD33w_Ctr-Ab12w


title: A498 Sunitinib-resistant At treated replicate 3 [42At3]

value: Atezolizumab


title: 114_without_Firmicutes_uninfected

description:
Library name: 114_without_Firmicutes_uninfected
count_file_uninfected_plant.csv


title: Subj_37,liver,HFD33w_Ctr-Ab12w


title: Q7_Humanized NASH CJ liver- ZT10


title: Subj_36,liver,HFD33w_Ctr-Ab12w


title: T1_Humanized control HCC- ZT2


title: A498 Sunitinib-resistant At treated replicate 2 [42At2]


title: Q6_Humanized NASH CJ liver- ZT10


title: 113_without_Firmicutes_uninfected

description:
Library name: 113_without_Firmicutes_uninfected
count_file_uninfected_plant.csv


title: A498 Sunitinib-resistant At treated replicate 1 [42At1]


title: Subj_35,liver,HFD33w_Ctr-Ab12w


title: Q5_Humanized NASH CJ liver- ZT10


title: 93_Full_SynCom_S3

description:
Library name: 93_Full_SynCom_S3
count_file_uninfected_plant.csv


title: 111_without_Firmicutes_uninfected

description:
Library name: 111_without_Firmicutes_uninfected
count_file_uninfected_plant.csv


title: Subj_34,liver,HFD33w_Ctr-Ab12w


title: 54_without_Firmicutes_infected24h

description:
Library name: 54_without_Firmicutes_infected24h
count_file_infected_plant.csv


title: Subj_33,liver,HFD33w_Ctr-Ab12w


title: 9.0_pcw_M_F0374_A14

city: Marseille

first: Heather

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

description: Library name: A14

library_source: transcriptomic single cell

data_processing:
All libraries were sequenced on a Nextseq 500 (Illumina). The sequenced snRNAseq libraries were processed and aligned to the human reference genome (GRCh38-2020-A) using Cell Ranger software v.3.1.0 (10x Genomics), with unique molecular identifiers (UMI) counted for each barcode.
Three datasets of snRNAseq from euploid hearts sequenced on different runs (HEF_DN_F0000530, 8.6 pcw, female; HEF_DN_F0000374, 9.0 pcw, male; HEF_DN_F0000467, 10.7 pcw, male) were analyzed using default parameters in the Seurat 4.1.1 pipeline and 40 PCA dimensions (Hao et al., 2021; Stuart et al., 2019). The pipeline included QC and data filtration, identification of highly variable genes, dimensional reduction, graph-based clustering, and differential expression analysis for the identification of cluster markers. Each dataset was preprocessed and analyzed separately, and later integrated with anchor-based batch correction.
After standard quality control, reads were aligned to the human reference genome (GRCh38-2020-A) with SpaceRanger v2.0.1 to generate a UMI count matrix per spot. Spots overlaid by tissue were designated from the H&E scans using the manual alignment tool from Loupe Browser v6.4.1 (10X Genomics) to retain only tissue-associated barcodes. Two poorly adherent tissue slices of the 8.4 pcw heart were excluded from further analyses. Two (A90-A91) and four slices (A17-A20) of the younger and older hearts were retained for further analysis and respectively had >3000 median UMI counts per spot under tissue.
Spatial transcriptomic data were first explored by individual section using the provided Loupe software v8.0 (10X Genomics) and in further depth with Seurat v5.0.3 (Hao et al., 2024), using the first 30 dimensions. The *.cloupe files are within the respective *_spatial.zip folders. The number of clusters (communities based on a shared nearest-neighbor modularity optimization-based algorithm) was obtained by applying resolutions of 0.45 for section A17, 0.65 for section A18, 0.35 for section A19, 0.20 for section A20, 0.30 for section A90 and 0.35 for section A91. The R package ‘scTransform’ was used for normalization and variance stabilization (Hafemeister and Satija, 2019). After individual slices were examined and compared, data were integrated using Seurat v5.0.3, spots re-clustered by applying resolutions of 0.47, and clusters manually annotated based on prior knowledge of DEGs and anatomy.
Assembly: hg38
Supplementary files format and content: tab-separated or comma-separated values files and matrix files
Supplementary files format and content: image files in JPEG or PNG format
Supplementary files format and content: hypertext markup language summary files
Supplementary files format and content: Loupe Browser *.cloupe format files
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene identifiers
Supplementary files format and content: matrix.mtx.gz: Gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: Aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: Image of tissues overlain by spots
Supplementary files format and content: scalefactors_json.json: Scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: High resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: Low resolution image of tissue
Supplementary files format and content: tissue_positions.csv: List of spatial barcodes and coordinates specifying spots
Supplementary files format and content: web_summary.html: html file summarizing alignment and tissue/expression data under spot coordinates per section
Supplementary files format and content: cloupe.cloupe: Annotated *.cloupe files compatible with Loupe Browser 7.0 and higher (free software from 10X Genomics)
Supplementary files format and content: snRNAseq_integ3h_UMAPproj10X.csv: UMAP coordinates of A14, A94 and A95 integrated nuclear transcriptomes, used in De Bono et al. 2025

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Terminations of pregnancy were induced using a standard combined mifepristone and misoprostol protocol, followed by aspiration. Gestational age was initially determined by ultrasound, refined by measurement of foot length (Evtouchenko et al., 1996; Hern, 1984; O’Rahilly and Müller, 1987; O’Rahilly and Müller, 2010), and confirmed through comparison and contribution of high-resolution photographs of our samples to a staged morphometric and histological cardiac atlas hosted at the Human Developmental Biology Resource (Gerrelli et al., 2015) (https://hdbratlas.org/organ-systems/cardiovascular-system/heart/dissections/gallery.html). Intact hearts were recovered from aspiration detritus under a Zeiss binocular microscope, rinsed in ice-cold phosphate-buffered saline (PBS) and maintained on ice in Hank’s buffered saline solution until further processing. For snRNAseq, intact hearts were dissociated for single-nucleus incorporation into the GEMs of the 10X Chromium platform. Dissociation was begun by an initial crush in liquid nitrogen, continued with 10-20 strokes in a Dounce homogenizer over ice, and nuclei further separated from debris over a discontinuous density gradient at 30-35% iodixanol as per a community protocol ("Son of Frankenstein" protocol, https://dx.doi.org/10.17504/protocols.io.bsxhnfj6 ). For Visium sections, hearts were flash-frozen in Leica Frozen Section Compound (FSC)22 in polypropylene molds floated over isopentane cooled by liquid nitrogen. Blocks were wrapped in aluminum and stored at -80°C pending quality control (staging, sexing and euploidy). One male heart at 8.4 pcw (HEF_DN_F0000476) and a female heart at 9.7 pcw (HEF_DN_F0000298) were chosen for spatial transcriptomic library generation. Blocks were trimmed to a 6.5 x 6.5 mm square, sectioned at 10 µm and slices melted onto one of: a 10X Genomics Tissue Optimization Slide to determine optimal time for protease digestion (18 minutes); Superfrost Plus (Menzel Gläser) slides for subsequent validation; or a Visium v1 Spatial Gene Expression slide (10X Genomics, one individual heart per slide). All were stored with desiccant at -20°C until further processing. As per the Visium v1 Gene Expression protocol, sections were stained in hematoxylin/eosin (H&E), coverslipped in a glycerol-based solution, imaged at 10X on an AxioScan 7 (Zeiss), then barcoded mRNA content was captured to generate DNA libraries.
Single-nucleus libraries were prepared by the Genomics and Bioinformatics facility (GBiM) of the U1251 / Marseille Medical Genetics lab using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (PN-1000269) with Dual Index Kit TT Set A (PN-1000215, 10X Genomics), according to manufacturer’s instructions.
Spatial transcriptomic library generation followed the Visium v1 Gene Expression protocol, where sections were stained in hematoxylin/eosin (H&E), coverslipped in a glycerol-based solution, imaged at 10X on an AxioScan 7 (Zeiss), then barcoded mRNA content was captured to generate DNA libraries.

value: Heart

value: XY


title: Subj_38,liver,HFD33w_Ctr-Ab12w

value: Liver (lobus sinister lateralis hepatis)


title: 8.6_pcw_F_F0530_A94

description: Library name: A94

value: XX


title: 52_without_Firmicutes_infected24h

description:
Library name: 52_without_Firmicutes_infected24h
count_file_infected_plant.csv


title: Q2_Humanized NASH CJ liver- ZT2


title: Q3_Humanized NASH CJ liver- ZT2


title: 51_without_Firmicutes_infected24h

description:
Library name: 51_without_Firmicutes_infected24h
count_file_infected_plant.csv


title: Q1_Humanized NASH CJ liver- ZT2


title: gallbladder, 6weeks, exposed

first: wentao

last: shao

address: 150, jimo road

department: Shanghai East Hospital

institute: Tongji University School of Medicine

data_processing:
Cell Ranger software (v6.1.1) was used to perform sample de-multiplexing by function mkfastq. Then the Fastq files were run with function count using default settings, including alignment (GRCm38 mouse reference genomes), filtering, and UMI counting.
Assembly: mm10
Supplementary files format and content: barcodes.tsv :cell barcode files (-1 for control group, -2 for 3 weeks group, -3 for 6 weeks group)
Supplementary files format and content: features.tsv :gene files
Supplementary files format and content: matrix.mtx :gene-barcode counts

source_name: gallbladder

extract_protocol:
After the mice were sacrificed, gallbladder was removed. A total of 10 gallbladders per group were washed with D-Hanks solution, and cut into small pieces. One mL 0.25% Trypsin (Gibco, China) were added, and the mixture was shaken for 20 min at 37C. The mixture was passed through a 40 μm cell strainer to collect the filtrate. The gallbladder pieces were re-digested for another two times. All filtrates were centrifuged at 1500 rpm for 5 minutes, and the supernatants were removed. The cell pellets were then suspended in DMEM containing 10% FBS. The living single cells were transferred to cold scRNA-seq lysis buffer.
The cells were re-suspended on concentration of 700~1,200 cell/μL and loaded on a Chromium Single Cell Instrument (10X Genomics, United States) to generate single cell gel beads in emulsion. GEMs were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined. The final library pool was sequenced on the Illumina Novaseq6000 instrument using 150-base-pair paired-end reads.

value: gallbladder

tag: Sex

value: male

value: treated with nanoplastics by oral gavage for 6 weeks


title: Subj_32,liver,HFD33w_Ctr-Ab12w


title: 38_without_Bacillus_infected24h

description:
Library name: 38_without_Bacillus_infected24h
count_file_infected_plant.csv


title: P12_Humanized NASH control liver- ZT18

source_name: Humanized NASH liver


title: gallbladder, 3weeks, exposed

value: treated with nanoplastics by oral gavage for 3 weeks


title: 8.4_pcw_M_F0476_D_A91

description: Library name: A91

data_processing:
All libraries were sequenced on a Nextseq 500 (Illumina). The sequenced snRNAseq libraries were processed and aligned to the human reference genome (GRCh38-2020-A) using Cell Ranger software v.3.1.0 (10x Genomics), with unique molecular identifiers (UMI) counted for each barcode.
Three datasets of snRNAseq from euploid hearts sequenced on different runs (HEF_DN_F0000530, 8.6 pcw, female; HEF_DN_F0000374, 9.0 pcw, male; HEF_DN_F0000467, 10.7 pcw, male) were analyzed using default parameters in the Seurat 4.1.1 pipeline and 40 PCA dimensions (Hao et al., 2021; Stuart et al., 2019). The pipeline included QC and data filtration, identification of highly variable genes, dimensional reduction, graph-based clustering, and differential expression analysis for the identification of cluster markers. Each dataset was preprocessed and analyzed separately, and later integrated with anchor-based batch correction.
After standard quality control, reads were aligned to the human reference genome (GRCh38-2020-A) with SpaceRanger v2.0.1 to generate a UMI count matrix per spot. Spots overlaid by tissue were designated from the H&E scans using the manual alignment tool from Loupe Browser v6.4.1 (10X Genomics) to retain only tissue-associated barcodes. Two poorly adherent tissue slices of the 8.4 pcw heart were excluded from further analyses. Two (A90-A91) and four slices (A17-A20) of the younger and older hearts were retained for further analysis and respectively had >3000 median UMI counts per spot under tissue.
Spatial transcriptomic data were first explored by individual section using the provided Loupe software v8.0 (10X Genomics) and in further depth with Seurat v5.0.3 (Hao et al., 2024), using the first 30 dimensions. The *.cloupe files are within the respective *_spatial.zip folders. The number of clusters (communities based on a shared nearest-neighbor modularity optimization-based algorithm) was obtained by applying resolutions of 0.45 for section A17, 0.65 for section A18, 0.35 for section A19, 0.20 for section A20, 0.30 for section A90 and 0.35 for section A91. The R package ‘scTransform’ was used for normalization and variance stabilization (Hafemeister and Satija, 2019). After individual slices were examined and compared, data were integrated using Seurat v5.0.3, spots re-clustered by applying resolutions of 0.47, and clusters manually annotated based on prior knowledge of DEGs and anatomy.
Assembly: hg38
Supplementary files format and content: tab-separated or comma-separated values files and matrix files
Supplementary files format and content: image files in JPEG or PNG format
Supplementary files format and content: hypertext markup language summary files
Supplementary files format and content: Loupe Browser *.cloupe format files
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene identifiers
Supplementary files format and content: matrix.mtx.gz: Gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: Aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: Image of tissues overlain by spots
Supplementary files format and content: scalefactors_json.json: Scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: High resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: Low resolution image of tissue
Supplementary files format and content: tissue_positions.csv: List of spatial barcodes and coordinates specifying spots
Supplementary files format and content: web_summary.html: html file summarizing alignment and tissue/expression data under spot coordinates per section
Supplementary files format and content: cloupe.cloupe: Annotated *.cloupe files compatible with Loupe Browser 7.0 and higher (free software from 10X Genomics)
Supplementary files format and content: snRNAseq_integ3h_UMAPproj10X.csv: UMAP coordinates of A14, A94 and A95 integrated nuclear transcriptomes, used in De Bono et al. 2025
Library strategy: Spatial transcriptomics


title: 9.7_pcw_F_F0298_A_A17

description: Library name: A17-A18-A19-A20


title: 37_without_Bacillus_infected24h

description:
Library name: 37_without_Bacillus_infected24h
count_file_infected_plant.csv


title: 8.4_pcw_M_F0476_B_A90

description: Library name: A90


title: 36_without_Bacillus_infected24h

description:
Library name: 36_without_Bacillus_infected24h
count_file_infected_plant.csv


title: gallbladder, control

value: treated with vehicle by oral gavage for 6 weeks


title: P10_Humanized NASH control liver- ZT18

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)


title: Home caged cerebral single cell RNASeq 4

data_processing:
barcedeed processing,gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebral cortex

extract_protocol:
1).Contextual fear conditioning  Prior to fear conditioning, mice underwent a 3-day handling regimen, involving 5-minute sessions in the holding room where they were housed. Subsequently, the mice explored fear-conditioning boxes scented with 1% acetic acid (CleverSys, Inc) for 3 minutes, followed by exposure to four bursts of foot shocks (0.55 mA, 2 seconds each) at 1-minute intervals. Post-shock exposure, mice remained in the behavior chamber for an additional 2 minutes before being returned to their home cages.
2).Nuclei isolation from the mouse brain For nuclei isolation from the mouse forebrain and cerebellum, an adapted protocol22 was employed. The adult mouse brains were extracted and sectioned. Next, the cortices of the forebrain and cerebellum were dissected and homogenized. Then, the homogenized tissue was filtered transferred to a 50-mL tube, and layered over a 5-mL sucrose cushion. Finally, the crude nuclei were then pelleted and resuspended in NWR Buffer.
Library construction was performed according to manufacturer’s recommendations for Chromium Next GEM Single Cell 5’ Reagent Kits v2 from 10 × Genomics.

value: cerebral cortex

value: cells of cerebral  cortex

value: WT

value: home caged


title: 10.7_pcw_M_F0467_A95

description: Library name: A95


title: Q4_Humanized NASH CJ liver- ZT2

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 hg38 and mm10 using STAR aligner with parameter ( --outSAMattributes NM).
FeatureCounts implemented in Subread package was used to count the sequencing reads from mapped BAM files.The number of reads falling in the exons of this meta-transcript were counted
Differential gene expression was evaluated using the R package EdgeR and expression was further normalized using the R package RUVr
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text files include raw read count for each annoted gene

value: h-Liver


title: 34_Full_SynCom_infected24h

description:
Library name: 34_Full_SynCom_infected24h
count_file_infected_plant.csv

value: leaves


title: hepatocellular carcinoma tissue of HCC patient 3

city: Nantong

first: Jie

last: Yuan

address: 20# Xisi Road

institute: Affiliated Hospital of Nantong University

data_processing:
Raw sequencing data generated form Illumina NextSeq 500 that pass the Illumina chastity filter are used to the following analysis. Trimmed reads (trimmed 5', 3'-adaptor bases)are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Assembly: tRNA sequences of eytoplasmic were downloaded from GtRNAdb. tRNA sequences of mitochondrial were predicted with tRNAscan-SE software.
Supplementary files format and content: A total XLSX file contains information about each sample and the raw counts.
Supplementary files format and content: Column A: tRF_ID, The ID of tRF & tiRNA; Column B: tRF_Seq, The sequence of tRF & tiRNA; Column C: Type, The type of tRF & tiRNA; Column D: Length, The length of sequence; Column E: AlignInfo, Alignment information, format (tRNA_id,tRNA_Seq,aminoacid-anticodon,start); Column F~K: Count, The counts of reads; Column L~Q: CPM, The counts of per million mapped reads

source_name: hepatocellular carcinoma tissue

extract_protocol:
High quality samples are most important for small RNA sequencing projects. The recommended purified total RNA amount is 1~2ug. Alternatively, we offer to isolate RNA from your sample sources, including cultured cells, tissues, serum or plasma. Before the sequencing experiment, we check the integrity and quantity of each RNA sample using agarose gel electrophoresis and NanodropTM instrument. The RNA QC results are included in the service report. tRNA derived fragments (tRF & tiRNA) are heavily decorated by RNA modifications that interfere with small RNA-seq library construction. We do the following treatments before library preparation for total RNA samples: 3'-aminoacyl (charged) deacylation to 3'-OH for 3' adaptor ligation, 3' -cP (2' ,3' -cyclic phosphate) removal to 3' -OH for 3' adaptor ligation, 5' -OH (hydroxyl group) phosphorylation to 5' -P for 5' -adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50bp singleread.

value: hepatocellular carcinoma tissue


title: Home caged cerebral single cell RNASeq 3


title: 32_Full_SynCom_infected24h

description:
Library name: 32_Full_SynCom_infected24h
count_file_infected_plant.csv


title: P9_Humanized NASH control liver- ZT18

extract_protocol:
Liver or HCC were removed, flash frozen in liquid nitrogen, RNA was processed using PureLinkTM RNA Minikit (Cat#12183018A), and extracted RNAs were used for the construction of RNA libraries using Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: paraneoplastic tissue of HCC patient 2

source_name: paraneoplastic tissue

value: paraneoplastic tissue


title: Home caged cerebral single cell RNASeq 2


title: hepatocellular carcinoma tissue of HCC patient 2


title: P8_Humanized NASH control liver- ZT10


title: Home caged cerebral single cell RNASeq 1


title: P7_Humanized NASH control liver- ZT10


title: 31_Full_SynCom_infected24h

description:
Library name: 31_Full_SynCom_infected24h
count_file_infected_plant.csv


title: P11_Humanized NASH control liver- ZT18


title: hepatocellular carcinoma tissue of HCC patient 1


title: paraneoplastic tissue of HCC patient 1


title: P5_Humanized NASH control liver- ZT10


title: Home caged cerebellar single cell RNASeq 4

source_name: cerebellar cortex

value: cerebellar cortex

value: cells of cerebellar cortex


title: P6_Humanized NASH control liver- ZT10


title: paraneoplastic tissue of HCC patient 3


title: M.2

city: Bronx

first: Rachel

last: Hazan

state: Bronx

address: 1300 Morris Park Ave

department: Pathology

institute: Albert Einstein College of Medicine

data_processing:
Adaptor sequences were first trimmed from the RNA sequencing reads using Trimgalore v0.3.7 and sequence quality was assessed using fastqc v.0.11.4.
Trimmed reads were then aligned against human genome hg38 using STAR v2.5.1.
Gene counts were also calculated with STAR. Pairwise differential analysis was performed on raw gene counts to compare gene expression profiles between samples with different conditions using R package DESeq2 v1.28.
Differential genes were considered significant if the fold change was more than 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: MDA-MB-468 cells were maintained in 10%FBS/RPMI and 1% Penstrep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using a tissue/cell total RNA mini kit from EZ BioResearch following the manufacturer's protocol.
Purified total RNA was used to prepare Libraries following the protocol usingQIAseq Stranded RNA Lib Kit with UDIand QIAseq FastSelect -rRNA HMR Kit (Qiagen INC.)for Illumina sequencing

treatment_protocol: MDA-MB-468 cells were stained with CD104-PE, and CD44-APC antibodies and sorted.

value: triple-negative breast cancer cell line

tag: cell subtype

value: Sorted CD104-/CD44+ cells


title: Home caged cerebellar single cell RNASeq 3


title: P4_Humanized NASH control liver- ZT2


title: M.1


title: Home caged cerebellar single cell RNASeq 2


title: P3_Humanized NASH control liver- ZT2


title: rtgill.car.1.B08

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.car.1.B08
Cell lysate
car.counts.txt
car.lib16_S1.B08.expression.values

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Oncorhynchus mykiss

source_name: RTgill-W1 car rep 1 conc 7

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

value: Rainbow trout gill


title: rtgill.car.1.D08

description:
Library name: rtgill.car.1.D08
Cell lysate
car.counts.txt
car.lib16_S1.D08.expression.values

source_name: RTgill-W1 car rep 1 conc 5


title: rtgill.car.1.E08

description:
Library name: rtgill.car.1.E08
Cell lysate
car.counts.txt
car.lib16_S1.E08.expression.values

source_name: RTgill-W1 car rep 1 conc 4


title: rtgill.car.1.C08

description:
Library name: rtgill.car.1.C08
Cell lysate
car.counts.txt
car.lib16_S1.C08.expression.values

source_name: RTgill-W1 car rep 1 conc 6


title: rtgill.car.1.A08

description:
Library name: rtgill.car.1.A08
Cell lysate
car.counts.txt
car.lib16_S1.A08.expression.values

source_name: RTgill-W1 car rep 1 conc 8


title: E/M.2

value: Sorted CD104+/CD44+ cells


title: P2_Humanized NASH control liver- ZT2


title: rtgill.smet.3.H07

description:
Library name: rtgill.smet.3.H07
Cell lysate
smet.counts.txt
smet.lib24_S1.H07.expression.values

source_name: RTgill-W1 smet rep 3 conc 1


title: Home caged cerebellar single cell RNASeq 5

first: Xu

last: Chu

institute: Fudan University Shanghai Cancer Center


title: Bulk.2

value: Unsorted


title: Fear conditioned cerebral single cell RNASeq 4

value: fear conditioned


title: L7-2_Humanized control liver- ZT18

first: Loning

last: Fu

institute: Baylor College of Medicine

source_name: Humanized liver

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)


title: rtgill.smet.3.G07

description:
Library name: rtgill.smet.3.G07
Cell lysate
smet.counts.txt
smet.lib24_S1.G07.expression.values

source_name: RTgill-W1 smet rep 3 conc 2


title: P1_Humanized NASH control liver- ZT2


title: Fear conditioned cerebral single cell RNASeq 5

value: cerebral cortex


title: Bulk.1


title: rtgill.smet.3.F07

description:
Library name: rtgill.smet.3.F07
Cell lysate
smet.counts.txt
smet.lib24_S1.F07.expression.values

source_name: RTgill-W1 smet rep 3 conc 3


title: rtgill.smet.3.E07

description:
Library name: rtgill.smet.3.E07
Cell lysate
smet.counts.txt
smet.lib24_S1.E07.expression.values

source_name: RTgill-W1 smet rep 3 conc 4


title: Exosome_U2OS

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

data_processing:
Alignment and count step with the QIAGEN RNA-seq Analysis Portal
Supervised analysis with DESeq2 from UMI count
Assembly: Ensembl GRCh38
Supplementary files format and content: count data, tsv format

source_name: osteosarcoma

growth_protocol: cells were grown in RPMI or DMEM +10% exosome depleted SVF

extract_protocol:
miRNeasy kit (Qiagen)
Libraries were prepared according to the Qiaseq miRNa library prep kit protocol. Libraries were sequenced on the NextSeq 500 5illumina) following the manufacturer's protocols.

treatment_protocol: small EV were isolated from supernatant by ultracentrifugation

value: osteosarcoma

value: small extracellular vesicle

tag: disease


title: Fear conditioned cerebral single cell RNASeq 3

city: shanghai

address: Dong'an Road

value: cells of cerebral  cortex

value: WT


title: Fear conditioned cerebral single cell RNASeq 2


title: L18_Humanized control liver- ZT18

city: Houston

address: One Baylor Plaza

value: h-Liver


title: rtgill.smet.3.D07

description:
Library name: rtgill.smet.3.D07
Cell lysate
smet.counts.txt
smet.lib24_S1.D07.expression.values

source_name: RTgill-W1 smet rep 3 conc 5


title: Exosome_Ramos

source_name: leukemia

value: leukemia

value: Ramos


title: L17_Humanized control liver-ZT18


title: Fear conditioned cerebral single cell RNASeq 1

source_name: cerebral cortex


title: L16_Humanized control liver- ZT18


title: Home caged cerebellar single cell RNASeq 1

value: cerebellar cortex

value: home caged


title: rtgill.smet.3.C07

description:
Library name: rtgill.smet.3.C07
Cell lysate
smet.counts.txt
smet.lib24_S1.C07.expression.values

source_name: RTgill-W1 smet rep 3 conc 6


title: E/M.1

value: triple-negative breast cancer cell line


title: Exosome_Raji

value: Raji


title: rtgill.smet.3.B07

description:
Library name: rtgill.smet.3.B07
Cell lysate
smet.counts.txt
smet.lib24_S1.B07.expression.values

source_name: RTgill-W1 smet rep 3 conc 7

value: Rainbow trout gill


title: Fear conditioned cerebellar single cell RNASeq 4

description: FC-cerebellar.tar.gz

source_name: cerebellar cortex

value: cells of cerebellar cortex


title: Fear conditioned cerebellar single cell RNASeq 3

description: FC-cerebellar.tar.gz


title: Exosome_MG63


title: rtgill.smet.3.A07

description:
Library name: rtgill.smet.3.A07
Cell lysate
smet.counts.txt
smet.lib24_S1.A07.expression.values

source_name: RTgill-W1 smet rep 3 conc 8


title: L13-2_Humanized control liver- ZT10


title: Exosome_Meso173

source_name: mesothelioma

value: mesothelioma


title: Exosome_Meso163


title: rtgill.smet.2.H07

description:
Library name: rtgill.smet.2.H07
Cell lysate
smet.counts.txt
smet.lib20_S1.H07.expression.values

source_name: RTgill-W1 smet rep 2 conc 1


title: L8_Humanized control liver- ZT10


title: Fear conditioned cerebellar single cell RNASeq 1

description: FC-cerebellar.tar.gz

value: fear conditioned


title: L7_Humanized control liver- ZT10

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)


title: rtgill.smet.2.G07

description:
Library name: rtgill.smet.2.G07
Cell lysate
smet.counts.txt
smet.lib20_S1.G07.expression.values

source_name: RTgill-W1 smet rep 2 conc 2


title: Exosome_Meso34


title: scCITE-seq of Mus musculus: control tumor

city: Seattle

first: Daniel

middle: Guorui

state: Washington

address: 1100 Fairview Ave N

department: Immunolog

institute: Fred Hutchinson Cancer Center

data_processing:
*library strategy: scCITE-seq
The constructed library was sequenced on Novaseq platform (Illumina) and processed via cellranger.
scCITE-seq data was normalized by log (ln) and library size (CPM + 1 for pseudo-count) normalization using Scanpy.
Assembly: mm10.
Supplementary files format and content: cellranger .h5 output file (filtered_feature_bc_matrix.h5) is provided with RNA and surface protein antibody counts.

source_name: tumor

extract_protocol:
Dissociated tumor tissue was sorted for transferred therapeutic T cells, sorted cells were assayed via 10X Genomics scCITE-seq protocol. Chromium Single Cell Kits (10x Genomics) were utilized to analyze the transcriptomic and surface protein levels simultaneously from the same cell. Experiments were performed according to manufacturer’s instructions.
Cells were stained with custom TotalSeq-B mouse antibodies (Biolegend) before loaded onto a Chromium Next GEM chip. Cells were lysed for reverse transcription and complementary DNA (cDNA) amplification in the Chromium Controller (10X Genomics). The polyadenylated transcripts were reverse-transcribed inside each gel bead-in-emulsion afterwards. Full-length cDNA along with cell barcode identifiers were PCR-amplified and sequencing libraries were prepared and normalized.

value: tumor

value: therapeutic T cell

value: control


title: rtgill.smet.2.F07

description:
Library name: rtgill.smet.2.F07
Cell lysate
smet.counts.txt
smet.lib20_S1.F07.expression.values

source_name: RTgill-W1 smet rep 2 conc 3


title: L6_Humanized control liver- ZT2

source_name: Humanized liver


title: L5_Humanized control liver- ZT2


title: Exosome_Meso31

value: small extracellular vesicle


title: scCITE-seq of Mus musculus: D-Mannose treated tumor

value: D-mannose


title: rtgill.smet.2.E07

description:
Library name: rtgill.smet.2.E07
Cell lysate
smet.counts.txt
smet.lib20_S1.E07.expression.values

source_name: RTgill-W1 smet rep 2 conc 4


title: Exosome_Meso13


title: rtgill.smet.2.D07

description:
Library name: rtgill.smet.2.D07
Cell lysate
smet.counts.txt
smet.lib20_S1.D07.expression.values

source_name: RTgill-W1 smet rep 2 conc 5


title: Exosome_Meso11


title: L4_Humanized control liver- ZT2

value: h-Liver


title: L3_Humanized control liver- ZT2


title: rtgill.smet.2.C07

description:
Library name: rtgill.smet.2.C07
Cell lysate
smet.counts.txt
smet.lib20_S1.C07.expression.values

source_name: RTgill-W1 smet rep 2 conc 6


title: L9_Humanized control liver- ZT10


title: N3

city: xi'an

first: Qingan

last: Jia

state: Shaanxi

address: No. 127, Youyi West Road, Beilin District

institute: Northwestern Polytechnical University

data_processing:
Illumina Novaseq 6000
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Novaseq 6000
Read count extraction and normalization were performed using Illumina Novaseq 6000
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: whole blood

extract_protocol:
Total RNA was extracted from the cell using TRIzol® Reagent according the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

value: whole blood

value: lymphocyte

value: monocytes

value: burn wound healing-NC


title: N2


title: rtgill.smet.2.B07

description:
Library name: rtgill.smet.2.B07
Cell lysate
smet.counts.txt
smet.lib20_S1.B07.expression.values

source_name: RTgill-W1 smet rep 2 conc 7


title: Exosome_M88

source_name: melanoma

value: melanoma


title: p16M3

city: Nice

first: Francisco

last: Triana-Martinez

address: 30 avenue Voie Romaine - Batiment K

institute: Institute for Research on Cancer and Aging, Nice

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Bowtie v2.2.3 and single-end clean reads were aligned to the reference genome using TopHat v2.0.12
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: excel file cointaining FPKM count
Supplementary files format and content: Gene ID, Gene name, gene chromosome, gene star and end, gene strand, gene length, gene description

source_name: Peritoneal cavity

growth_protocol: Mice were housed 4 per cage in a temperature (20-220C) and humidity-controlled room, maintained on a 12-h light/dark cycle (07:00 to 19:00 light on), with standard food (A03, Scientific Animal Food and Engineering, U8200G10R) and water provided ad libitum and environmental enrichments.

extract_protocol:
After 12 months, animals were euthanized by cervical dislocation, and peritoneal cells were harvested by lavage with 10 ml of cold medium. RNA was isolated using RNeasy Mini Kit (Quiagen # 74104) according to the manufacturer’s protocol
In order to select cDNA fragments of preferentially 150 200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37  C for 15 min followed by 5 min at 95  C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Animales were mantained in the condicion previusly described during 12 months

value: Peritoneal cavity

value: F4/80+ cells

value: C57BL/6 p16-Cre/Rosa26-mtmg


title: Fear conditioned cerebellar single cell RNASeq 2

description: FC-cerebellar.tar.gz

value: cerebellar cortex

value: cells of cerebellar cortex

value: WT


title: Exosome_M193


title: N1


title: Exosome_M45


title: rtgill.smet.2.A07

description:
Library name: rtgill.smet.2.A07
Cell lysate
smet.counts.txt
smet.lib20_S1.A07.expression.values

source_name: RTgill-W1 smet rep 2 conc 8

value: Rainbow trout gill


title: M6

value: burn wound healing


title: p16M2


title: rtgill.smet.1.H07

description:
Library name: rtgill.smet.1.H07
Cell lysate
smet.counts.txt
smet.lib16_S1.H07.expression.values

source_name: RTgill-W1 smet rep 1 conc 1


title: Exosome_M18


title: cM3


title: p16M1


title: M4


title: rtgill.smet.1.G07

description:
Library name: rtgill.smet.1.G07
Cell lysate
smet.counts.txt
smet.lib16_S1.G07.expression.values

source_name: RTgill-W1 smet rep 1 conc 2


title: Exosome_M6


title: N4


title: M5


title: rtgill.smet.1.F07

description:
Library name: rtgill.smet.1.F07
Cell lysate
smet.counts.txt
smet.lib16_S1.F07.expression.values

source_name: RTgill-W1 smet rep 1 conc 3


title: Exosome_Jok

source_name: leukemia

value: leukemia

value: Jok


title: M3


title: cM1


title: Exosome_HOSMNNG

source_name: osteosarcoma

value: osteosarcoma

value: HOSMNNG

value: small extracellular vesicle


title: rtgill.smet.1.E07

description:
Library name: rtgill.smet.1.E07
Cell lysate
smet.counts.txt
smet.lib16_S1.E07.expression.values

source_name: RTgill-W1 smet rep 1 conc 4


title: rtgill.smet.1.D07

description:
Library name: rtgill.smet.1.D07
Cell lysate
smet.counts.txt
smet.lib16_S1.D07.expression.values

source_name: RTgill-W1 smet rep 1 conc 5


title: Exosome_H1650

source_name: NSCLC

value: NSCLC


title: B16F10 treated with PBS-3

city: ZhengZhou

first: Ming

last: Wang

address: jianshe Road

institute: ZhengZhou university

data_processing:
these libraries were sequenced on an Illumina sequencing platform, and 125-bp/150-bp paired-end reads were generated
Assembly: mm9
Supplementary files format and content: fastq.gz

extract_protocol:
the cells were collected in RNAiso Plus reagent for RNA isolation
RNA samples were then converted into libraries of cDNA fragments using the TruSeq Stranded mRNA LTSample Prep Kit

value: murine melanoma cell line


title: Exosome_H1437


title: B16F10 treated with PBS-2


title: rtgill.smet.1.C07

description:
Library name: rtgill.smet.1.C07
Cell lysate
smet.counts.txt
smet.lib16_S1.C07.expression.values

source_name: RTgill-W1 smet rep 1 conc 6


title: primary tumor, MM, rep5

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

institute: DKFZ (German Cancer Research Center)

description:
barcodes.tsv
counts.mtx
genes.tsv
metadata.tsv
normalised_counts.mtx

data_processing:
Merged FASTQ files were processed using cellranger v6.1.1 with default parameters and aligned to the mouse GRCm38 assembly. Subsequent analyses were conducted using Seurat v3.2.2 [Stuart et al., 2019]
To ensure data quality, we employed quantile-based thresholds for individual cell assessment. Cells exceeding the upper quantile threshold (90%) for the percentage of ribosomal and mitochondrial gene counts were considered potential outliers and excluded from downstream analyses. Moreover, we evaluated the number of detected features in each cell. Cells falling below the lower quantile threshold (2.5%) or exceeding the upper quantile threshold (97.5%) were categorized as low-quality or outlier cells, respectively, and were removed from further analyses.
For dimensionality reduction, we applied the RunUMAP function using the first 17 principal components for the entire dataset and the first 12 dimensions for the fibroblast subsetted dataset. Clustering was performed using the FindNeighbors function with the first 17 principal components and the FindClusters function with a resolution of 0.5. Marker genes for the identified clusters were determined using the FindAllMarkers function, with criteria set at >25% of cells expressing the markers in the given cluster and a log fold change of >0.25. To visualize gene expression levels projected onto UMAP plots, we utilized the cellcuratoR package [Voigt et al., 2020]. Cluster annotation was performed using known cell type markers to assign biological identities to the identified cell clusters.
To analyze the cell cycle phase for each cell, we followed the approach described by Tirosh et al. [2016]. Specifically, we assessed the relative expression of a set of 43 G1/S and 55 G2/M genes for each cell to generate a cell cycle score. Based on this score, we assigned cells to their corresponding cell cycle phase.
Assembly: mm10
Supplementary files format and content: Barcodes.tsv : cell barcodes
Supplementary files format and content: counts.mtx: raw counts matrix in matrix market format
Supplementary files format and content: normalized_counts.mtx: normalized counts matrix in matrix market format
Supplementary files format and content: genes.tsv: gene names corresponding to the counts matrix
Supplementary files format and content: metadata.tsv: tab-delimited file containing cell metadata

source_name: lung

extract_protocol:
Tissues of primary tumors (n=6), lung metastases (n=5) and unchallenged lungs (n=4) were mechanically dissociated followed by incubation for 45 min, rotating in the cold room, in 4 ml per 200 mg tissue of an enzyme mix containing LiberaseTM (#05401127007 Roche, Switzerland; 0.25 U/ml), Collagenase D (#11088866001 Roche, Switzerland; 0.6 U/ml), Dispase II (#17105-041 Gibco/ Thermo Fisher Scientific, USA; 4.5 U/ml) and DNaseI (Sigma Aldrich, USA; 50 U/ml). Remaining tissue fragments were further dissociated by passing the suspension through a syringe with an 18G cannula. The enzymatic reaction was stopped by adding DMEM containing 1 % BSA and 2.5 mM EDTA. After lysis of red blood cells (ACK buffer: 150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) cell suspensions were cryopreserved in 90 % FCS + 10 % DMSO until library preparation. The above described protocol for dissociation and cryopreservation was developed based on recommendations from 10x Genomics (CG00039 Rev D) and multiple protocols described in literature 38-41. Before library preparation, cells were rapidly thawed, washed in pre-warmed DMEM + 2 % BSA and FACsorted. Cells were either sorted for living tdTomato+ cells or for living tdTomato+ CD45-cells. For additional CD45+ cell depletion, cells were re-suspended in Fc-block (CD16/32; 1:100), incubated 10 min on ice in the dark. Next, CD45- APC/Cy7 antibody (30-F11, BioLegend 103115) was added to a final dilution of 1:100 and further incubated for 20 min on ice in the dark. After washing, the cell pellet was re-suspended in 500 µl FACS buffer. Immediately before the sort DAPI was added 1:1000 (DAPI stock 10 mg/ml). Cells were collected in DNA low binding tubes containing 200 µl PBS + 0.04 % BSA + 0.1 mM EDTA.
Library preparation was performed using the Chromium Next GEM single cell 3' GEM, Library and Gel Bead Kit v3.1 together with the Chromium Next GEM Chip G Single Cell Kit, following manufacturer's instructions. Sequencing of the libraries was performed by the next-generation sequencing (NGS) Core Facility at the German Cancer Research Centre on a NovaSeq 6000.

value: lung

value: melanoma primary tumor


title: B16F10 treated with PBS-1


title: Exosome_H358


title: rtgill.smet.1.B07

description:
Library name: rtgill.smet.1.B07
Cell lysate
smet.counts.txt
smet.lib16_S1.B07.expression.values

source_name: RTgill-W1 smet rep 1 conc 7


title: primary tumor, MM, rep4


title: B16F10 treated with rPPAA18C6@Dox-3


title: cM2

value: Peritoneal cavity


title: rtgill.smet.1.A07

description:
Library name: rtgill.smet.1.A07
Cell lysate
smet.counts.txt
smet.lib16_S1.A07.expression.values

source_name: RTgill-W1 smet rep 1 conc 8


title: Exosome_ADCA153


title: Exosome_Daudi

value: Daudi


title: primary tumor, TME, rep8


title: B16F10 treated with rPPAA18C6@Dox-2


title: rtgill.per.3.H06

description:
Library name: rtgill.per.3.H06
Cell lysate
per.counts.txt
per.lib23_S1.H06.expression.values

source_name: RTgill-W1 per rep 3 conc 1


title: B16F10 treated with rPPAA18C6@Dox-1


title: rtgill.per.3.G06

description:
Library name: rtgill.per.3.G06
Cell lysate
per.counts.txt
per.lib23_S1.G06.expression.values

source_name: RTgill-W1 per rep 3 conc 2


title: primary tumor, TME, rep6


title: M2

source_name: whole blood

value: whole blood

value: lymphocyte

value: monocytes


title: Exosome_A549


title: rtgill.per.3.F06

description:
Library name: rtgill.per.3.F06
Cell lysate
per.counts.txt
per.lib23_S1.F06.expression.values

source_name: RTgill-W1 per rep 3 conc 3


title: Exosome_M117

source_name: melanoma

value: melanoma


title: primary tumor, TME, rep5


title: M1


title: rtgill.per.3.E06

description:
Library name: rtgill.per.3.E06
Cell lysate
per.counts.txt
per.lib23_S1.E06.expression.values

source_name: RTgill-W1 per rep 3 conc 4

value: Rainbow trout gill


title: primary tumor, TME, rep4


title: Exosome_M113


title: rtgill.per.3.D06

description:
Library name: rtgill.per.3.D06
Cell lysate
per.counts.txt
per.lib23_S1.D06.expression.values

source_name: RTgill-W1 per rep 3 conc 5


title: rtgill.per.3.C06

description:
Library name: rtgill.per.3.C06
Cell lysate
per.counts.txt
per.lib23_S1.C06.expression.values

source_name: RTgill-W1 per rep 3 conc 6


title: primary tumor, TME, rep1-3


title: primary tumor, TME, rep7


title: metastasis, TME, rep1-3

value: melanoma lung metastasis


title: Exosome_M28


title: rtgill.per.3.B06

description:
Library name: rtgill.per.3.B06
Cell lysate
per.counts.txt
per.lib23_S1.B06.expression.values

source_name: RTgill-W1 per rep 3 conc 7


title: metastasis, MM, rep6


title: Primary freshly isolated BM-MSCs from donor MLDCryo04

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-separated raw count file of gene quantifications

source_name: Bone marrow

extract_protocol:
Total RNA was purified from sorted and ex-vivo expanded MSCs using the RNeasy Micro Kit (QIAGEN). DNase treatment was performed using RNase-free DNAse Set (QIAGEN), according to the manufacturer’s instructions. RNA was quantified with Nanodrop (Thermo Fisher) and its quality assessed by a 2100 Agilent Bioanalyser (Agilent Tech-nologies).
Minimum quality was defined as RNA integrity number (RIN) > 8. 300 ng of total RNA were used for library preparation with TruSeq Stranded mRNA (Illumina)

value: Bone marrow

value: Mesenchymal Stromal Cells

tag: condition

value: Primary

tag: donor


title: rtgill.per.3.A06

description:
Library name: rtgill.per.3.A06
Cell lysate
per.counts.txt
per.lib23_S1.A06.expression.values

source_name: RTgill-W1 per rep 3 conc 8


title: 11_5903

type: RNA

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

hyb_protocol: Hybridization was performed at 45°C for 16 h using 5 μg of biotinylated target with each GeneChip® Human Exon 1.0 ST array (HuEx-1_0-st-v2, Affymetrix). Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data were extracted from the scanned images and analyzed with the Expression Console software package (Affymetrix). Expression Console was used to compute separate gene-level and exon-level signal estimates for the Exon 1.0 ST Array data.

data_processing:
Exon-level estimates were derived using the PLIER (pm-gcbg) method after quantile sketch normalization. Probes sets (exons) were filtered for a ‘detected above background’ (DABG) P-value less than 0.05, resulting in 313 707 filtered exons that were considered in this study. Exon-level probe sets annotations were derived from the Affymetrix NetAffx file HuEx-1_0-st-v2 Probeset Annotations, CSV Format, Release 31. Gene-level estimates were derived using the IterPLIER (pm-gcbg) method after quantile sketch normalization. Only genes with core annotation (22 012 genes) were considered in this study. Transcript annotations were derived from the Affymetrix NetAffx file HuEx-1_0-st-v2 Transcript Cluster Annotations, CSV, Release 31.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na33.1.hg19.probeset.csv
Exon-level estimates were derived using the PLIER (pm-gcbg) method after quantile sketch normalization. Gene-level estimates were derived using the IterPLIER (pm-gcbg) method after quantile sketch normalization.

label: biotin

source_name: Typical Williams syndrome deletion, Female

label_protocol: Biotinylated target was prepared following the protocol described in Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling and Control Reagents (Affymetrix P/N 900652).

growth_protocol: The immortalized lymphoblastiod cells (LCLs) were grown in RMPI 1640 with 10% FBS, 5% pen/strep, 5% L-glutamine and 0.5% gentamycin.

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy Kit. Ribosomal RNA was removed from total RNA (1 μg per sample) using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen).

tag: disease state

value: Williams syndrome patient


title: Ex-vivo expanded BM-MSCs from donor MLDCryo04

value: Ex-vivo


title: Primary freshly isolated BM-MSCs from donor MLDCryo03


title: rtgill.per.2.H06

description:
Library name: rtgill.per.2.H06
Cell lysate
per.counts.txt
per.lib19_S1.H06.expression.values

source_name: RTgill-W1 per rep 2 conc 1


title: 12_5904

source_name: Typical Williams syndrome deletion, Male


title: metastasis, MM, rep4

source_name: lung


title: Ex-vivo expanded BM-MSCs from donor MLDCryo03


title: metastasis, TME, rep8


title: metastasis, MM, rep5


title: 54_5805


title: Exosome_LNCaP

source_name: prostate

value: prostate

value: LnCaP

value: small extracellular vesicle


title: rtgill.per.2.F06

description:
Library name: rtgill.per.2.F06
Cell lysate
per.counts.txt
per.lib19_S1.F06.expression.values

source_name: RTgill-W1 per rep 2 conc 3


title: Primary freshly isolated BM-MSCs from donor MLDCryo02


title: 52_5767


title: 50_5546


title: rtgill.per.2.E06

description:
Library name: rtgill.per.2.E06
Cell lysate
per.counts.txt
per.lib19_S1.E06.expression.values

source_name: RTgill-W1 per rep 2 conc 4


title: metastasis, TME, rep7

value: lung


title: 09_5682


title: metastasis, TME, rep6


title: Ex-vivo expanded BM-MSCs from donor MLDCryo02


title: Primary freshly isolated BM-MSCs from donor MLDCryo01


title: 49_5540


title: 53_5791


title: rtgill.per.2.C06

description:
Library name: rtgill.per.2.C06
Cell lysate
per.counts.txt
per.lib19_S1.C06.expression.values

source_name: RTgill-W1 per rep 2 conc 6


title: Ex-vivo expanded BM-MSCs from donor MLDCryo01


title: 51_5638


title: metastasis, TME, rep4


title: metastasis, TME, rep5


title: rtgill.per.2.B06

description:
Library name: rtgill.per.2.B06
Cell lysate
per.counts.txt
per.lib19_S1.B06.expression.values

source_name: RTgill-W1 per rep 2 conc 7


title: rtgill.per.2.G06

description:
Library name: rtgill.per.2.G06
Cell lysate
per.counts.txt
per.lib19_S1.G06.expression.values

source_name: RTgill-W1 per rep 2 conc 2


title: 47_5079


title: 44_5065


title: lung, unchallenged, rep6

description:
barcodes.tsv
counts.mtx
genes.tsv
metadata.tsv
normalised_counts.mtx

value: unchallenged


title: Primary freshly isolated BM-MSCs from donor HDPV5


title: lung, unchallenged, rep5


title: 43_5002


title: rtgill.per.2.A06

description:
Library name: rtgill.per.2.A06
Cell lysate
per.counts.txt
per.lib19_S1.A06.expression.values

source_name: RTgill-W1 per rep 2 conc 8


title: rtgill.per.1.H06

description:
Library name: rtgill.per.1.H06
Cell lysate
per.counts.txt
per.lib15_S1.H06.expression.values

source_name: RTgill-W1 per rep 1 conc 1


title: SC-EPCs, HTO-derived cDNA

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
Pre-processing of raw reads was performed using the 10x genomics Cell Ranger pipeline.
The reads were aligned to GRCh38 2020-A genome. cDNA reads were used to construct a count matrix, while HTO reads reads were used to count HTO tags using CITE-seq-Count-1.4.3 tool.
Further downstream analysis with integration was done using both Seurat and scanpy.
Assembly: GRCh38-2020A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Pancreatic endocrine progenitors

extract_protocol:
Early, late, polarized and unpolarized endocrin progenitors from 3 independent differentiation were purified by flow cytometry via NGN3-GFP and CD133. Purified cells were then barcoded with a unique Oligonucleotide Hash Tag. After Hash- and Cite-tagged cells were counted and checked for viability using a hematocytometer, 25,000 cells were loaded into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Pancreatic endocrine progenitors

value: human embryonic stem cell stem cell derived pancreatic endocrine progenitors

tag: library type

value: HTO

tag: antibodies/tags

value: NGN3-GFP+:early EP (A0259) and late EP (A0260); NGN3-GFP+/CD133+:Polarized EP (A0262); NGN3-GFP+/CD133-:Unpolarized EP (A0263)


title: rtgill.per.1.G06

description:
Library name: rtgill.per.1.G06
Cell lysate
per.counts.txt
per.lib15_S1.G06.expression.values

source_name: RTgill-W1 per rep 1 conc 2


title: rtgill.per.2.D06

description:
Library name: rtgill.per.2.D06
Cell lysate
per.counts.txt
per.lib19_S1.D06.expression.values

source_name: RTgill-W1 per rep 2 conc 5


title: lung, unchallenged, rep1

tag: tissue


title: SC-EPCs, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: 41_566


title: rtgill.per.1.F06

description:
Library name: rtgill.per.1.F06
Cell lysate
per.counts.txt
per.lib15_S1.F06.expression.values

source_name: RTgill-W1 per rep 1 conc 3

value: Rainbow trout gill