title: PC3, MN, Rep2

description: Library name: 10277-AF-17

value: prostate tumor


title: PC3, MN, Rep1

status: Public on Jul 20 2026

type: SRA

city: Houston

first: Abigail

last: Fabiano

state: TX

address: 6100 Main St

department: Bioengineering

country: USA

institute: Rice University

description: Library name: 10277-AF-16

library_source: transcriptomic

data_processing:
Psuedoalignment was completed using Kallisto and data was processed using DESeq2 in R.
Used tximport to import and transform the data, genes with counts < or =10 were removed.
Transformed count data on the log2 scale via variance stabilizing transform.
Significant genes are denoted as those with a -log10(Padj) > 2.
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: Counts.csv files contain raw counts for each sample, as well as TPM abundance and transcript length.

molecule: total RNA

organism: Homo sapiens

source_name: prostate tumor

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 1% penstrep, 10 mM HEPES, and 1 mM sodium pyruvate. PC3 cells were maintained in RPMI supplemented with 10% heat-inactivated FBS, 1% penstrep, and 10 mM HEPES. Cells were incubated in humidified conditions at 37C and 5% CO2.

extract_protocol:
RNA was harvested using the Rneasy kit from QIAGEN, with a DNA digestion.
Libraries were constructed by the VANTAGE NGS core at Vanderbilt University Medical Center.

treatment_protocol: MR cells were treated with 10-20 pulses of 3950 dyn/cm2 of high-intensity (HI) FSS every time the cells were passaged, up to ~50-60 passages. MN condition was a static control (same as the parental), simply at a higher passage. MR* (unsheared) condition is the MR cells sheared ~50-60 passages, and then passaged 10 times with no HI FSS treatment. MR-young cells were exposed to HI FSS for ~20 passages.

tag: tissue

tag: cell line

tag: cell type

value: immortalized prostate cancer (bone-met)

tag: genotype

value: MN

tag: treatment

value: High passage control


title: LF-16F Stool sRNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: LF-16F

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings.
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix tables with the raw mature miRNA read counts for each sample

source_name: Stool

extract_protocol:
Stool samples were collected in a collection tube containing a nucleic acid stabilizing solution (Norgen Biotek) for subsequent nucleic acid isolation. The returned samples were stored at -80°C. RNA was extracted from 200 µL aliquots using the stool total RNA purification kit (Norgen Biotek Corp.) according to the manufacturer’s protocol. RNA quality and quantity were verified in accordance with the MIQE guidelines (http://miqe.gene-quantification.info/). RNA concentration was quantified using the Qubit microRNA assay kit (Invitrogen) on a Qubit fluorimeter (Invitrogen).
Small RNA-seq libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep for Illumina® (New England Biolabs, Inc.) kit used to convert small RNA transcripts into barcoded cDNA libraries. For each library, 200 ng of RNA were processed as starting material. Each library was prepared with a unique indexed primer. Multiplex adapter ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the manufacturer's protocol. After PCR amplification, the cDNA constructs were purified with the QIAQuick® PCR Purification Kit (QIAGEN), following the modifications suggested by the NEBNext® Multiplex Small RNA Library Prep for Illumina® protocol. Final libraries were loaded on the Bioanalyzer® 2100 (Agilent Technologies) using the DNA High Sensitivity Kit (Agilent Technologies) according to the manufacturer's protocol. Libraries were pooled together (34-plex) and further purified with a gel size selection. A final Bioanalyzer® 2100 run with the High Sensitivity DNA Kit (Agilent Technologies) allowed the assessment of DNA libraries quality regarding size, purity, and concentration. The obtained libraries were subjected to the Illumina sequencing pipeline on Illumina NextSeq500 sequencers (75 cycles, Illumina Inc., USA).

value: Stool

tag: campania region

value: LF


title: LF-14F Stool sRNA-Seq

description: Library name: LF-14F


title: LF-18M Stool sRNA-Seq

description: Library name: LF-18M


title: LF-19M Stool sRNA-Seq

description: Library name: LF-19M


title: PC3, Parental, Rep2

description: Library name: 10277-AF-14

value: Parental

value: Control


title: LF-20M Stool sRNA-Seq

description: Library name: LF-20M


title: LF-15F Stool sRNA-Seq

description: Library name: LF-15F


title: PC3, Parental, Rep3

description: Library name: 10277-AF-15


title: LF-17M Stool sRNA-Seq

description: Library name: LF-17M


title: SZN-043 70d, replicate 2, hep enriched, scRNAseq

city: South San Francisco

first: Russell

last: Fletcher

state: CA

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

description:
Library name: RFSZ-10X-3F
10x Genomics v3 3'

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 8.0.0
Data exploration, normalization, dimension reduction, clustering, DE, and GSEA analyses were done in R (version 4.3.2)
Data from the same animal replicate derived from the hepatocyte-enrichment workflow and from the non-hepatocyte enrichment workflow were combined at the beginning of the analysis.
From the full data set, hepatocytes and non-hepatocytes were subsetted and analyzed separately.
Assembly: GRCm39
Supplementary files format and content: aggregated cellular barcodes from Cellranger output
Supplementary files format and content: feature/genes from Cellranger output
Supplementary files format and content: aggregated UMI matrix from Cellranger output
Supplementary files format and content: log2 of scran + RUVg normalized counts matrix of hepatocytes as tab delimited text file
Supplementary files format and content: hepatocyte QC, batch and experimental condition metadata in tab delimited text file
Supplementary files format and content: log2 of scran + RUVg normalized counts matrix of non-hepatocytes as tab delimited text file
Supplementary files format and content: non-hepatocyte QC, batch, experimental condition, and cell type metadata in tab delimited text file

organism: Mus musculus

source_name: liver

growth_protocol: Mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). All animal experimentation was in accordance with the ‘‘Guide for the Care and Use of Laboratory Animals’’ prepared by the National Academy of Sciences. Protocols for animal experimentation were approved by the Surrozen Institutional Animal Care and Use Committee. 7-week-old C57Bl/6J female mice were acclimatized 4-5 per cage a minimum of two days prior to the experiment. Mice were kept 12/12-hour light/dark cycle in a 30% to 70% humidity environment and room temperature ranging from 20°C to 26°C.

extract_protocol:
At 24h, 14d, or 70d of the experiment, livers were perfused with a collagenase solution to dissociate the cells, and live cells were then purified by FACS.
Standard 10x Genomics Chromium 3’ v3 scRNA-seq reagents were used. Approximately 2000-4000 cells were loaded per channel. Cells from one animal replicate were captured per channel, and a cell fraction enriched for hepatocytes or for non-hepatocytes from each animal replicate were captured per channel. Standard 10x Genomics Chromium 3’ v3 scRNA-seq RT, cDNA amplification, and sequencing library preparation protocols were followed. Multiplexed sequencing libraries were sequenced on Illumina Hi Seq 4000 S1 lanes, averaging about 50,000 reads per cell.

treatment_protocol: Mice were dosed intraperitoneally once with either 10 mg/kg of an Anti-GFP antibody or with 10 mg/kg of SZN-043 and mice livers were collected at 24-hours, 14-days, 70-days.

value: liver

value: liver cells

tag: strain

tag: age

value: 6-8 weeks old

tag: batch

value: SZN-043 70d, hep enriched, replicate 2


title: SZN-043 70d, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-3E
10x Genomics v3 3'

value: SZN-043 70d, hep enriched, replicate 1


title: Donor 8 RARAF 0 Gy

city: Kingston

first: Michael

last: Antosh

state: RI

address: 2 Lippitt Rd

institute: University of Rhode Island

description: Library name: Sample 71

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

source_name: Whole blood

growth_protocol: Sampled from donors under IRB protocol IRB-AAAS5693 at Columbia University.

extract_protocol:
Blood samples preserved in PAXgene RNA stabilization reagent were sent to Azenta, where total RNA was extracted followed by globin reduction.
QIAGEN Fast Select rRNA HMR and Globin Kit, plus NEGNext Ultra II RNA Library preparation kit.  Note: sequencer model number listed may be incorrect.

treatment_protocol: Each sample was irradiated with 42% photons and 58% neutrons, at either the RINSC source or the RARAF source.

value: Whole blood

tag: irradiation site

value: RARAF

tag: radiation dose_(gy)

tag: Sex

value: Male


title: PC3, Parental, Rep1

description: Library name: 10277-AF-13


title: LF-10F Stool sRNA-Seq

description: Library name: LF-10F


title: mature DCs, 48h, control, rep2

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: Ctrl24_2

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42) human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 38)
Supplementary files format and content: Text file including the normalized counts for each sample.

growth_protocol: THP-1 human monocytic cells were maintained in 100-mm tissue culture dishes in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 µM 2-mercaptoethanol, and 10% heat-inactivated fetal bovine serum (FBS), hereafter referred to as cell culture medium. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ and maintained according to the ATCC recommendations (TIB-202), being passaged twice weekly and reseeded at a density of 2–4×10⁵ viable cells/mL to maintain exponential growth. For differentiation, THP-1 cells were seeded at a density of 1x10^5 cells/mL in T-35 tissue culture flasks and cultured for five days in cell culture medium supplemented with rhIL-4 (1500 U/mL) and GM-CSF (1500 U/mL) to induce differentiation into immature dendritic cells (iDCs).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and total RNA was purified using RNeasy spin columns including on-column DNase digestion. RNA was eluted in RNase-free water and stored at −80 °C until use. RNA concentration and purity were assessed by measuring absorbance at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The A260/A280 and A260/A230 ratios were used to evaluate RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra RNA Library Preparation kit.

treatment_protocol: On day five of differentiation, iDCs were seeded at a density of 1×10⁶ cells/mL in 12-well plates containing complete treatment medium and exposed for 24 h to PFOA (10 µg/mL), PFOS (10 µg/mL), or vehicle control (0.1% DMSO, v/v). Following the initial 24-h exposure, a maturation cocktail consisting of rhIL-4 (3,000 IU/mL), rhGM-CSF (1,500 IU/mL), rhTNF-α (2,000 IU/mL), and ionomycin (200 ng/mL) was added to induce maturation into mature dendritic cells (mDCs). PFAS and control compounds remained present throughout the maturation period. Cells were harvested after 24 or 72 h of maturation, corresponding to total exposure times of 48 and 96 h, respectively.

value: 0.1% DMSO


title: LF-08F Stool sRNA-Seq

description: Library name: LF-08F


title: LNCaP, MR* (Unsheared), Rep3

description: Library name: 8063-AF-15

value: prostate tumor

value: LNCaP

value: immortalized prostate cancer (epithelial-like)

value: MR* (Unsheared)

value: x60 FSS, x10 passages no FSS


title: LF-09F Stool sRNA-Seq

description: Library name: LF-09F

value: Stool

value: LF


title: Anti-GFP 70d, replicate 2, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-3B
10x Genomics v3 3'

value: Anti-GFP 70d, hep enriched, replicate 2


title: LNCaP, MR* (Unsheared), Rep2

description: Library name: 8063-AF-14


title: LF-13M Stool sRNA-Seq

description: Library name: LF-13M


title: SZN-043 14d, replicate 2, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-2H
10x Genomics v3 3'

value: liver

value: SZN-043 14d, nonhep enriched, replicate 2


title: LNCaP, MR, Rep3

description: Library name: 8063-AF-12

value: MR

value: x60 FSS


title: LF-04F Stool sRNA-Seq

description: Library name: LF-04F


title: LF-03M Stool sRNA-Seq

description: Library name: LF-03M


title: LF-02M Stool sRNA-Seq

description: Library name: LF-02M


title: LF-12M Stool sRNA-Seq

description: Library name: LF-12M


title: Anti-GFP 70d, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-3C
10x Genomics v3 3'

value: liver cells

value: 6-8 weeks old

value: Anti-GFP 70d, nonhep enriched, replicate 1


title: Anti-GFP 70d, replicate 2, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-3D
10x Genomics v3 3'

value: Anti-GFP 70d, nonhep enriched, replicate 2


title: LF-11M Stool sRNA-Seq

description: Library name: LF-11M


title: SZN-043 14d, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-2G
10x Genomics v3 3'

value: SZN-043 14d, nonhep enriched, replicate 1


title: LF-07M Stool sRNA-Seq

description: Library name: LF-07M


title: Anti-GFP 70d, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-3A
10x Genomics v3 3'

value: Anti-GFP 70d, hep enriched, replicate 1


title: LNCaP, MR, Rep2

description: Library name: 8063-AF-11

value: prostate tumor

value: LNCaP


title: Human Chronic Wound sample HCWSD2

city: Atlanta

first: Paul

last: Briaud

state: GA

address: 311 Fesrt Dr

institute: Georgia Institute of Technology

description: Library name: MW73_HCWSD2

data_processing:
FASTQ files generated at this stage were used as input for trimming. Adapter trimming was performed using Trim Galore (v0.6.x), which internally uses Cutadapt for adapter removal. Trimming was applied separately to single-end and paired-end libraries using eight CPU cores per sample. Adapter sequences were automatically detected based on standard Illumina adapters. Reads shorter than 22 nucleotides after trimming were discarded. For paired-end libraries, trimming was performed in paired mode, and read pairs   were retained only if both mates passed trimming and length filtering. No additional manual quality-score thresholds were applied beyond Trim Galore’s default behavior. Trimmed reads were retained as FASTQ files and used for all downstream analyses. Following successful trimming, raw FASTQ files produced by fasterq-dump were removed to reduce disk space usage. To remove residual ribosomal RNA (rRNA) reads, trimmed reads were aligned against an rRNA reference database using Bowtie2. Alignments were performed separately for single-end and paired-end libraries with multithreading enabled. Reads mapping to rRNA sequences were discarded, while unmapped reads were retained and carried forward for subsequent analyses. This step reduced rRNA-derived signal prior to genomic alignment and quantification. Following rRNA filtering, reads were aligned to a decoy reference genome using Bowtie2 to eliminate non-target or contaminant reads. Reads mapping to the decoy reference were discarded, while unmapped reads were retained for downstream analysis. Reads that did not align to either the rRNA or decoy references were aligned to a Staphylococcus aureus pangenome reference using Bowtie2. Alignments were streamed directly to SAMtools for on-the-fly conversion to BAM format, sorting, and indexing, minimizing the generation of intermediate files. Single-end and paired-end libraries were aligned using the appropriate Bowtie2 modes. Gene-level quantification was performed using a gene-only GFF3 annotation of the S. aureus pangenome. Prior to read counting, annotation files were preprocessed to ensure consistent formatting and unique feature identifiers compatible with downstream quantification tools. Strand specificity was inferred independently for each sample prior to final quantification. For this purpose, a subset of up to 200,000 aligned reads was extracted from each BAM file. FeatureCounts (Subread package) was run on this subset in both forward-stranded (-s 1) and reverse-stranded (-s 2) modes. The proportion of reads assigned in each orientation was calculated, and strand specificity was assigned if ≥80% of reads mapped consistently to one strand. Samples that did not meet this threshold were treated as unstranded (-s 0). Final gene-level read counts were generated using featureCounts with the inferred strand setting for each sample. For paired-end libraries, fragments were counted, whereas for single-end libraries, individual reads were counted. Quantification was performed on the full, sorted BAM files. Output count tables were generated for downstream statistical analyses.
Assembly: S. aureus pangenome
Supplementary files format and content: tab delimited text file that includes gene raw counts for each samples

source_name: Superficial debridement from human chronic wound

extract_protocol:
Human chronic wound samples were processed as previously described (23). Samples were after collection and immediately preserved in RNAlater, and stored at 4°C overnight prior to storage at −80°C. Samples were thawed on ice, centrifuged at 10,000 × g for 30 min at 4°C to remove RNAlater, and transferred to bead-beating tubes containing a mixture of 2-mm zirconia and 0.1-mm zirconia–silica beads. Samples were resuspended in RNase- and DNase-free TE buffer and enzymatically lysed with lysozyme (1 mg/ml final concentration) and lysostaphin (0.17 mg/ml final concentration) at 37°C for 30 min. Mechanical lysis was performed by bead beating three times for 30 s with cooling on ice between cycles. Total RNA was extracted using RNA-Stat 60 followed by chloroform phase separation (200 μl chloroform per 1 ml RNA-Stat 60) and centrifugation at 12,000 × g for 15 min at 4°C. The aqueous phase was precipitated with isopropanol (0.5 ml per 1 ml RNA-Bee) in the presence of 20 μg linear acrylamide and incubated at −80°C overnight. RNA pellets were recovered by centrifugation at 12,000 × g for 30 min at 4°C, washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA concentration was determined using a NanoDrop spectrophotometer and quality was confirmed by Bioanalyzer
Ribosomal RNA was depleted using the RiboZero Gold bacterial kit for in vitro samples and the RiboZero Gold epidemiology kit for human samples, followed by ethanol precipitation. Depleted RNA was fragmented for 2 min using the NEBNext Magnesium RNA Fragmentation Module, and cDNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Kit according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq500 platform using 75-bp single-end reads.


title: Human Chronic Wound sample HCWDD2

description: Library name: MW67_HCWDD2

source_name: Deep Debridement from Human chronic wound.


title: LF-05F Stool sRNA-Seq

description: Library name: LF-05F


title: Epithelial cells 1

city: East Lansing

first: Axel

middle: Dizan

last: Schmitter-Sanchez

state: MI

address: 775 Woodlot Dr

department: Medicine

institute: Michigan State University

description: Library name: KTC_1

data_processing:
Reads were aligned to the Ensembl Mouse GRCm39 genome using STAR Aligner. DESeq2 was used to normalize raw counts and determine the differential expression of chemokine receptor genes among the epithelial and Langerhans cell samples.
Assembly: Ensembl Mouse GRCm39
Supplementary files format and content: A tab-delimited text matrix containing raw read counts per gene for each sample.

molecule: polyA RNA

source_name: Ear epidermis

extract_protocol:
Single cell suspension was collected from four huLangerin-CreER; Rosa-stop-tdTomato; Cx3cr1-GFP; K14-H2B-Cerulean mice during homeostasis. Ears were incubated epidermis side up in 2.5% Trypsin solution at 37°C for 90 min, and the epidermis was removed from the dermis. Single cell suspension was achieved by mincing, cutting, and running the sample through a 70 µm filter. LCs and epithelial cells were sorted using fluorescence-activated cell sorting (FACS) based on their red (LCs) and blue (epithelial cells) fluorescence.
Libraries were prepared using the KAPA mRNA HyperPrep Kit with dUTP-based strand specificity. Libraries were normalized to 10 nM, then loaded onto an Illumina NovaSeq flow cell. The sequencing was performed using 100 bp paired-end sequencing on an Illumina HiSeq NovaSeq.

value: Ear epidermis

value: Epithelial cells

value: 8 weeks


title: SZN-043 14d, replicate 2, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-2F
10x Genomics v3 3'

value: SZN-043 14d, hep enriched, replicate 2


title: LNCaP, MR* (Unsheared), Rep1

description: Library name: 8063-AF-13

value: immortalized prostate cancer (epithelial-like)

value: MR* (Unsheared)

value: x60 FSS, x10 passages no FSS


title: Human Chronic Wound sample HCWDD7

description: Library name: MW69_HCWDD7

value: Deep Debridement from Human chronic wound.


title: Human Chronic Wound sample HCWDB2

description: Library name: MW67_HCWDB2

source_name: Chronic Wound

value: Chronic Wound


title: LNCaP, MR, Rep1

description: Library name: 8063-AF-10

value: MR

value: x60 FSS


title: Human Chronic Wound sample HLC27

description: Library name: MW36_HLC27


title: SZN-043 14d, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-2E
10x Genomics v3 3'

value: liver

value: liver cells

value: 6-8 weeks old

value: SZN-043 14d, hep enriched, replicate 1


title: LNCaP, MN, Rep3

description: Library name: 8063-AF-09

value: prostate tumor

value: MN

value: High passage control


title: Covid skin 8

city: São Paulo

first: Maria

middle: Notomi

last: Sato

state: São Paulo

address: Av. Dr. Eneas de Carvalho Aguia, 470

department: Dermatology

country: Brazil

institute: University of São Paulo

description: Library name: Sample 13

data_processing:
Differentially expressed genes were identified using the DESeq2 package from R/Bioconductor, with statistical significance determined at an adjusted p-value ≤ 0.05 (Benjamini-Hochberg correction).
sequencing reads QA
adapters removal
Reads base correction and filtering
Reads mapping and counting
Sample outliers removal
Normalization
Differential expression calculation
Assembly: GRCh38 release-104
Supplementary files format and content: A tab-separated values (TSV) file containing normalized gene counts, with genes in rows and samples in columns.

source_name: Skin

extract_protocol:
Total RNA was extracted from autopsy-derived skin specimens using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Tissue homogenization was performed with a TissueRuptor (Qiagen). RNA integrity was assessed using the TapeStation system
Transcriptomic profiling was carried out using the Illumina TruSeq Stranded mRNA Library Prep Kit at the Large-Scale Sequencing Laboratory (SELA). Sequencing adapters were removed, and quality control of raw reads was performed using FastQC.  Reads were aligned to the reference human genome using the SUBREAD package  and quantified with FEATURECOUNTS

value: Skin


title: Covid skin 5

description: Library name: Sample 10


title: Covid skin 7

description: Library name: Sample 12


title: Anti-GFP 14d, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-2C
10x Genomics v3 3'

value: Anti-GFP 14d, nonhep enriched, replicate 1


title: LNCaP, MN, Rep1

description: Library name: 8063-AF-07

value: LNCaP


title: Covid skin 6

description: Library name: Sample 11


title: LNCaP, MN, Rep2

description: Library name: 8063-AF-08

value: immortalized prostate cancer (epithelial-like)


title: Covid skin 4

description: Library name: Sample 9


title: Anti-GFP 14d, replicate 2, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-2D
10x Genomics v3 3'

value: Anti-GFP 14d, nonhep enriched, replicate 2


title: Anti-GFP 14d, replicate 2, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-2B
10x Genomics v3 3'

value: Anti-GFP 14d, hep enriched, replicate 2


title: Covid skin 3

description: Library name: Sample 8


title: LNCaP, MR-young, Rep3

description: Library name: 8063-AF-06

value: MR-young

value: x20 FSS


title: Anti-GFP 14d, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-2A
10x Genomics v3 3'

value: Anti-GFP 14d, hep enriched, replicate 1


title: Covid skin 2

description: Library name: Sample 7


title: Covid skin 1

description: Library name: Sample 6


title: Health control 5

description: Library name: Sample 5


title: SZN-043 24h, replicate 2, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-1H
10x Genomics v3 3'

value: SZN-043 24h, nonhep enriched, replicate 2


title: Health control 4

description: Library name: Sample 4


title: Health control 3

description: Library name: Sample 3


title: SZN-043 24h, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-1G
10x Genomics v3 3'

value: liver

value: SZN-043 24h, nonhep enriched, replicate 1


title: Health control 2

description: Library name: Sample 2


title: LNCaP, Parental, Rep3

description: Library name: 8063-AF-03

value: Parental

value: Control


title: LNCaP, MR-young, Rep1

description: Library name: 8063-AF-04

value: prostate tumor


title: Health control 1

description: Library name: Sample1


title: Anti-GFP 24h, replicate 2, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-1F
10x Genomics v3 3'

value: liver cells

value: 6-8 weeks old

value: Anti-GFP 24h, nonhep enriched, replicate 2


title: LNCaP, Parental, Rep2

description: Library name: 8063-AF-02


title: SFC cells,CTRL,T0,ctrl,rep2

city: Bozen/Bolzano

first: Christian

middle: X

last: Weichenberger

state: BZ

address: Drususallee/Viale Druso 1

department: Institute for Biomedicine

institute: Eurac Research

data_processing:
The preprocessing of the reads has been performed with the DriverMap scoring software (HGVv2_1a). This program demultiplexes and scores DriverMap sequencing data from the Illumina NextSeq platform.
Transcripts were aligned with STAR (v 2.7.10a) to the human transcriptome GRCh38 (Ensembl v100) and quantified with featureCounts (package Rsubread v2.10.4).
Differential expression analysis was performed with DESeq2 package (v 1.28.1) using the Wald test for significance testing. Genes were considered differentially expressed with adjusted p value <0.05 and | log2FoldChange | >1.
Assembly: GRCh38 (Ensembl 100)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample in tab-separated format. The first column is not named and contains the NCBI Gene/EntrezGene IDs specifying the gene in the respecitve rows.

source_name: SFC

growth_protocol: Human iPSCs were cultured under feeder-free conditions on Matrigel matrix (Corning) in StemMACS iPS-Brew XF (Miltenyi Biotech) with 1% penicillin-streptomycin (Thermo Fisher Scientific). Cells were maintained in a saturated humidified atmosphere at 37°C and 5% CO2, and medium was changed every day.

extract_protocol:
Cells were recovered from the beads at days 10, 20 and 35 of differentiation, and total RNA was isolated using the Direct-zol RNA Miniprep Kit (#R2052, Zymo research).
The targeted RNA-seq libraries were produced using the DriverMapT Human Genome-Wide Expression Profiling Kit, V2 (Cellecta, Inc.), that measures all 19,000 human protein-coding genes. All samples were sequenced in 38 paired-end reads on the Illumina NextSeq500 platform.

treatment_protocol: For the encapsulation, 106 hiPSCs were gently mixed with 1 ml 1% w/v Alg solution with Fn. Alg beads were formed by slowly dripping the prepared Alg-cell suspension in 0.1 M CaCl2 with a 19-gauge needle, beads were then incubated for 20 min in the CaCl2 solution and washed 3 times with 1X PBS pH 7.4 (Thermo Fisher Scientific). The differentiation with both the 2D and 3D methods was based on the floor-plate-based neural induction protocol established by Kriks et al., with minor modifications (Kriks et. 2011; Zanon et. al 2017).

tag: culture condition

value: CTRL

value: SFC

value: ctrl

tag: time


title: SFC cells,CTRL,T0,ctrl,rep3


title: Anti-GFP 24h, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-1E
10x Genomics v3 3'

value: Anti-GFP 24h, nonhep enriched, replicate 1


title: B125 cells,CTRL,T0,mut,rep3

value: mut


title: LNCaP, Parental, Rep1

description: Library name: 8063-AF-01

value: LNCaP

value: immortalized prostate cancer (epithelial-like)


title: B125 cells,CTRL,T0,mut,rep2


title: SFC cells,CTRL,T0,ctrl,rep1


title: SZN-043 24h, replicate 2, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-1D
10x Genomics v3 3'

value: SZN-043 24h, hep enriched, replicate 2


title: PDO OKG146P, shControl and shZFP36L2 pooled together, IGFF, hash tag

city: New York

first: Qingwen

last: Jiang

state: NY

address: 417 East 68th Street, 1725

institute: memorial sloan kettering cancer center

description:
Library name: OKG146P_IGFF_HTO
10x Genomics

library_source: other

data_processing:
Raw sequencing data were quantified with Cell Ranger. CellBender (v.0.1.0), an unsupervised method for removing ambient RNA from scRNA-seq data, was used to generate a denoised (i.e., ambient-RNA-corrected) count matrix. CellBender-corrected counts were used in all downstream analysis. Doublets were identified and excluded using DoubletDetection (v3.0).
Cells were designated as outliers if they satisfied at least two of the following five conditions: 1) their log1p(total counts) were either more than 3 median absolute deviations (MADs) below or 5 MADs above the median of their organoid line; 2) their log1p(number of genes expressed) was either more than 3 MADs below or 5MADs above the median; 3) their percent of genes expressed in the top 20% of most highly expressed genes was more than 5 MADs below or above the median; 4) their feature-count distance (the difference between the value of log1p(number of genes expressed) observed, and the value predicted from the regression of log1p(number of genes expressed) on log1p(total counts)) was more than 5 MADs below or above the median; 5) their percentage of mitochondrial counts was both more than 2.5 MADs above the median and above the absolute threshold of 8%. Outliers and any remaining cells with fewer than 500 total counts, fewer than 400 detected genes, or greater than 20% mitochondrial content were excluded.
Assembly: GRCh38
Supplementary files format and content: H5AD file containing cells passing QC, deconvolved sample labels, and raw and CellBender-corrected counts.

molecule: protein

growth_protocol: Patient-derived organoids were cultured and expanded in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). Cells are embedded and plated in 40 μL domes of 3:1 Matrigel (Corning) :HISC medium mixture in suspension culture plates. After Matrigel domes solidified at 37 °C for 30 minutes, HISC medium supplemented with Y-27632 (MedChemExpress) was added to the well. Medium was refreshed every two days.

extract_protocol:
Organoids were dissociated into single cells and incubated with TotalSeq hashtag antibodies (BioLegend, #B0251, #B0252, #B0253) for 30 minutes on ice. Viable (DAPI-negative) cells were sorted using a 130 μm nozzle on a SH800S cell sorter (Sony) into DPBS containing 0.04% BSA. Equal numbers of hashtag-labelled shZFP36L2 and shCtrl cells were pooled per condition and resuspended at 700–1,300 cells/μL for library preparation. Cell viability exceeded 90% as determined by Trypan Blue exclusion.
Single-cell suspensions were loaded onto the Chromium Single Cell 3′ v3.1 platform (10x Genomics) according to the manufacturer's protocol, targeting up to 10,000 cells per sample for droplet-based encapsulation and barcoding. Following reverse transcription, emulsions were broken and cDNA was purified using Dynabeads MyOne SILANE, followed by PCR amplification. Libraries were sequenced on an Illumina NovaSeq platform with the following read configuration: Read 1, 28 cycles; i7 index, 8 cycles; Read 2, 90 cycles.

treatment_protocol: OKG146P patient-derived primary colorectal cancer organoids expressing doxycycline-inducible shZFP36L2 or shCtrl were cultured in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). All conditions were supplemented with 2 μg/mL doxycycline throughout. Medium was refreshed every two days. Organoids were cultured in HISC medium for 7 days (HISC condition), or in HISC medium for 7 days followed by intestinal growth factor-free (IGFF) medium — containing all base media components but lacking EGF, Noggin, A8301, FGF2, and IGF-I — for 7 days (differentiation condition), or in HISC for 7 days, IGFF for 7 days, then HISC for a further 7 days (dedifferentiation condition).

value: CRC PDO

value: shControl and shZFP36L2 pooled by hash tags

value: IGFF

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0251 anti-human Hashtag 1 (shControl), TotalSeq-B0252 anti-human Hashtag 2 (shZFP36L2), TotalSeq-B0253 anti-human Hashtag 3 (sample excluded from downstream analysis)


title: B125 cells,CTRL,T0,mut,rep1


title: SZN-043 24h, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-1C
10x Genomics v3 3'

value: liver

value: SZN-043 24h, hep enriched, replicate 1


title: 802 cells,CTRL,T0,ctrl,rep3


title: PDO OKG146P, shControl and shZFP36L2 pooled together, HISC, hash tag

description:
Library name: OKG146P_HISC_HTO
10x Genomics

value: HISC


title: 802 cells,CTRL,T0,ctrl,rep2


title: Anti-GFP 24h, replicate 2, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-1B
10x Genomics v3 3'

value: liver cells

value: 6-8 weeks old

value: Anti-GFP 24h, hep enriched, replicate 2


title: 802 cells,CTRL,T0,ctrl,rep1

value: CTRL

value: ctrl


title: PDO OKG146P, shControl and shZFP36L2 pooled together, IGFF, mRNA

description:
Library name: OKG146P_IGFF_mRNA
10x Genomics

value: mRNA


title: Anti-GFP 24h, replicate 1, hep enriched, scRNAseq

description:
Library name: RFSZ-10X-1A
10x Genomics v3 3'

value: Anti-GFP 24h, hep enriched, replicate 1


title: 2011 cells,CTRL,T0,mut,rep3

value: mut


title: 2011 cells,CTRL,T0,mut,rep2


title: 2011 cells,CTRL,T0,mut,rep1


title: SFC cells,3D,D35,ctrl,rep3

value: SFC


title: SFC cells,3D,D35,ctrl,rep2


title: PDO OKG146P, shControl and shZFP36L2 pooled together, HISC, mRNA

description:
Library name: OKG146P_HISC_mRNA
10x Genomics

value: CRC PDO


title: OKG146Li, frameshift ZFP36L2-ADAR, replicate3

description:
Library name: OKG146Li_fsZFP36L2_ADAR_3
OKG146LI_hypertribe.csv

data_processing:
Adapter trimming: Raw sequencing reads were trimmed for adapters and low-quality bases using Cutadapt (v4.8).
Alignment: Trimmed reads were aligned to the hg38 reference genome and construct sequences using STAR (v2.7.11b).
Editing site identification: RNA editing sites were identified using GATK HaplotypeCaller (v3.8.1.0), retaining only A-to-G substitutions on the forward strand and U-to-C substitutions on the reverse strand. Known genomic variants annotated in dbSNP (human_9606_b144_GRCh38p2) were excluded.
Statistical testing: Editing frequency at each site was assessed using a Beta-binomial test with Benjamini–Hochberg multiple testing correction.
Assembly: GRCh38
Supplementary files format and content: CSV file containing per-site RNA editing analysis results for all detected sites in indicated PDO lines, comparing wild-type ZFP36L2 (test) to frameshift mutant ZFP36L2 (fs-ZFP36L2, ctrl). Columns include Ensembl gene ID, gene symbol, genomic feature (exon/intron/utr3/utr5), editing site ID (chromosome:position_substitution), number of editing events in the gene, editing frequency difference (wt ZFP36L2 minus fs-ZFP36L2), mean editing frequency in fs-ZFP36L2 and wt ZFP36L2 conditions, nominal p-value (Beta-binomial test), and Benjamini-Hochberg adjusted p-value.

growth_protocol: Patient-derived CRC organoids were cultured and expanded in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). NGS-Wnt (0.5 M, ImmunePrecise N001) and R-spondin (10ng/mL, MBL-J2-004) were additianolly added to HISC media for normal colon organoid culture. Cells are embedded and plated in 40 μL domes of 3:1 Matrigel (Corning) :HISC medium mixture in suspension culture plates. After Matrigel domes solidified at 37 °C for 30 minutes, HISC medium supplemented with Y-27632 (MedChemExpress) was added to the well. Medium was refreshed every two days.

extract_protocol:
Total RNA was extracted from organoids using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was measured using the RiboGreen assay, and RNA quality was assessed using an Agilent Bioanalyzer.
300 ng of total RNA with RIN values of 9.8-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: ZFP36L2-ADAR or fsZFP36L2-ADAR induced by doxycycline at day5 organoid culture for 48hours.


title: Pancreatic tumor and TME cells, Serpinb2 KO

first: Chiara

last: Falcomatà

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Siania

description:
Library name: Sample_2
10x Genomics

data_processing:
Raw FASTQ files were aligned to the reference genome Gex-mm10-2020-A using CellRanger v5.0.1 (10x Genomics). Feature barcode matrix files generated by CellRanger were utilized for downstream analyses.
Assembly: Gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic tumor

extract_protocol:
Fresh PDAC samples were minced and enzymatically digested with the tumor dissociation kit (Miltenyi, catalog no. 130-096-730) for 40 minutes at 37 °C with agitation. The cell suspension was strained through a 70 µm strainer, spun down and resuspended in flow cytometry buffer (PBS, 2% bovine serum albumin, 5 mM EDTA). Cells were centrifuged at 350 g for 5 minutes at 4°C and then pellets were resuspended with ACK lysis buffer (Life Technologies) to lyse red blood cells at room temperature for 10 min and washed with cold flow buffer. Samples were then resuspended in PBS.
scRNA-Seq was conducted using the Chromium platform (10x Genomics) with the 5’ Gene Expression (5’ GEX) V2 kit, with a targeted recovery of 8,000 cells. Gel-Bead in Emulsions (GEMs) were generated on the sample chip K using the Chromium X (10x Genomics). Barcoded cDNA was extracted from GEMs through Post-GEM RT cleanup and amplified via 13 PCR cycles. Amplified cDNA was fragmented, end-repaired, poly A-tailed, adapter-ligated, and sample-indexed according to the manufacturer’s instructions. Libraries were quantified using TapeStation (Agilent) and QuBit (ThermoFisher) and sequenced in paired-end mode on an Illumina NovaSeq 6000 instrument, with a target depth of 25,000 reads per cell.

value: Pancreatic tumor

value: KPC FC1245 orthotopically injected

value: tumor cells, immune and stromal compartments


title: SFC cells,3D,D35,ctrl,rep1


title: OKG146Li, frameshift ZFP36L2-ADAR, replicate2

description:
Library name: OKG146Li_fsZFP36L2_ADAR_2
OKG146LI_hypertribe.csv


title: SFC cells,3D,D20,ctrl,rep3


title: Pancreatic tumor and TME cells, control KO

description:
Library name: Sample_1
10x Genomics


title: Pancreatic tumor and TME cells, Serpine1 KO

description:
Library name: Sample_3
10x Genomics


title: SFC cells,3D,D20,ctrl,rep2


title: OKG146Li, frameshift ZFP36L2-ADAR, replicate1

description:
Library name: OKG146Li_fsZFP36L2_ADAR_1
OKG146LI_hypertribe.csv


title: SFC cells,3D,D20,ctrl,rep1


title: spawning, male, headkidney #10

city: PULLMAN

last: Phelps

state: WA

address: 1815 Ferdinand's Lane, VBRB 160

department: Animal Sciences

institute: Washington State University

description:
Library name: P10H
ctm_male.csv

data_processing:
Raw reads (FASTQ) were filtered by sample, adapters were trimmed, and low-quality reads were removed using the default setting of TrimGalore package (version 0.6.4)
Cleaned reads were annotated and quantified against the transcriptome generated from O. gorbuscha reference transcriptome (OgorEven_v1.0) using the Salmon 1.8.0 package.
Using the salmon quant function and the validateMapping parameter, pair-end reads were quantified against the decoy-aware index to generate quantifications of captured mRNA for each sample.
Using R (v4.3.3) and the Rstudio (v 2023.12.0) package tximport (v1.30.0), transcript abundance was calculated, then normalized using the vst function on the transcript-level estimates to correct for transcript length differences before compiled into a count matrix of 40,756 genes.
Assembly: GCF_021184085.1
Supplementary files format and content: ctm_ files present raw gene counts, by sex, for muscle/headkidney/gonads across major migration timepoints, ocean, river, and spawn.

organism: Oncorhynchus gorbuscha

source_name: headkidney

extract_protocol:
Samples were treated with RNALater, then RNA was isolated using trizol method.
Proprietary polyA enrichment library preparation done by Novogene.

value: headkidney

value: male

value: spawning


title: SFC cells,3D,D10,ctrl,rep3


title: SFC cells,3D,D10,ctrl,rep2


title: OKG146Li, Wildtype ZFP36L2-ADAR, replicate3

description:
Library name: OKG146Li_ZFP36L2_ADAR_3
OKG146LI_hypertribe.csv


title: spawning, male, gonads #10

description:
Library name: P10G
ctm_male.csv

source_name: gonads

value: gonads


title: OKG146Li, Wildtype ZFP36L2-ADAR, replicate2

description:
Library name: OKG146Li_ZFP36L2_ADAR_2
OKG146LI_hypertribe.csv


title: B125 cells,3D,D35,mut,rep3


title: spawning, male, muscle #9

description:
Library name: P9M
ctm_male.csv

source_name: muscle

value: muscle


title: B125 cells,3D,D35,mut,rep2


title: SFC cells,3D,D10,ctrl,rep1


title: B125 cells,3D,D35,mut,rep1


title: spawning, male, headkidney #9

description:
Library name: P9H
ctm_male.csv


title: B125 cells,3D,D20,mut,rep3


title: OKG146Li, Wildtype ZFP36L2-ADAR, replicate1

description:
Library name: OKG146Li_ZFP36L2_ADAR_1
OKG146LI_hypertribe.csv


title: OKG146P, frameshift ZFP36L2-ADAR, replicate3

description:
Library name: OKG146P_fsZFP36L2_ADAR_3
OKG146P_hypertribe.csv


title: B125 cells,3D,D20,mut,rep2


title: B125 cells,3D,D20,mut,rep1


title: spawning, male, gonads #9

description:
Library name: P9G
ctm_male.csv


title: B125 cells,3D,D10,mut,rep3


title: OKG146P, frameshift ZFP36L2-ADAR, replicate2

description:
Library name: OKG146P_fsZFP36L2_ADAR_2
OKG146P_hypertribe.csv


title: spawning, male, muscle #8

description:
Library name: P8M
ctm_male.csv


title: B125 cells,3D,D10,mut,rep2


title: B125 cells,3D,D10,mut,rep1


title: OKG146P, frameshift ZFP36L2-ADAR, replicate1

description:
Library name: OKG146P_fsZFP36L2_ADAR_1
OKG146P_hypertribe.csv


title: spawning, male, gonads #8

description:
Library name: P8G
ctm_male.csv


title: 802 cells,3D,D35,ctrl,rep3


title: 802 cells,3D,D35,ctrl,rep2


title: OKG146P, Wildtype ZFP36L2-ADAR, replicate3

description:
Library name: OKG146P_ZFP36L2_ADAR_3
OKG146P_hypertribe.csv


title: spawning, male, muscle #7

description:
Library name: P7M
ctm_male.csv


title: 802 cells,3D,D35,ctrl,rep1


title: OKG146P, Wildtype ZFP36L2-ADAR, replicate2

description:
Library name: OKG146P_ZFP36L2_ADAR_2
OKG146P_hypertribe.csv


title: 802 cells,3D,D20,ctrl,rep3


title: 802 cells,3D,D20,ctrl,rep2


title: 802 cells,3D,D20,ctrl,rep1


title: OKG146P, Wildtype ZFP36L2-ADAR, replicate1

description:
Library name: OKG146P_ZFP36L2_ADAR_1
OKG146P_hypertribe.csv


title: spawning, male, headkidney #7

description:
Library name: P7H
ctm_male.csv


title: spawning, male, gonads #7

description:
Library name: P7G
ctm_male.csv


title: 802 cells,3D,D10,ctrl,rep3


title: MSK107Li, frameshift ZFP36L2-ADAR, replicate3

description:
Library name: MSK107Li_fsZFP36L2_ADAR_3
MSK107LI_hypertribe.csv


title: 802 cells,3D,D10,ctrl,rep2


title: 802 cells,3D,D10,ctrl,rep1


title: spawning, male, headkidney #6

description:
Library name: P6H
ctm_male.csv


title: MSK107Li, frameshift ZFP36L2-ADAR, replicate2

description:
Library name: MSK107Li_fsZFP36L2_ADAR_2
MSK107LI_hypertribe.csv


title: 2011 cells,3D,D35,mut,rep3


title: spawning, male, gonads #6

description:
Library name: P6G
ctm_male.csv


title: 2011 cells,3D,D35,mut,rep2


title: spawning, female, muscle #5

description:
Library name: P5M
ctm_female.csv

value: female


title: MSK107Li, Wildtype ZFP36L2-ADAR, replicate3

description:
Library name: MSK107Li_ZFP36L2_ADAR_2
MSK107LI_hypertribe.csv


title: MSK107Li, frameshift ZFP36L2-ADAR, replicate1

description:
Library name: MSK107Li_fsZFP36L2_ADAR_1
MSK107LI_hypertribe.csv


title: 2011 cells,3D,D35,mut,rep1


title: 2011 cells,3D,D20,mut,rep3


title: 2011 cells,3D,D20,mut,rep2


title: spawning, female, headkidney #5

description:
Library name: P5H
ctm_female.csv


title: 2011 cells,3D,D20,mut,rep1


title: MSK107Li, Wildtype ZFP36L2-ADAR, replicate1

description:
Library name: MSK107Li_ZFP36L2_ADAR_1
MSK107LI_hypertribe.csv


title: 2011 cells,3D,D10,mut,rep3


title: spawning, female, gonads #5

description:
Library name: P5G
ctm_female.csv


title: 2011 cells,3D,D10,mut,rep2


title: OKG146Li PDO cells, shZFP36L2, 5h ActD, replicate3

description:
Library name: OKG146Li_shZFP36L2_5hr_3
decay_OKG146LI_all.csv

data_processing:
Adapter trimming and quality filtering: Raw sequencing reads were trimmed for adapters and low-quality bases using Cutadapt (v4.8).
Alignment and quantification: Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b). Gene-level read counts were quantified using HTSeq (v2.0.5).
Within-condition decay rate estimation: Differential expression analysis was performed using DESeq2 (v1.42.0) comparing ActD-treated (5 h) versus untreated samples separately for shCtrl and shZFP36L2 to capture per-condition mRNA decay rates.
ZFP36L2-dependent decay rate calculation: Gene-level read counts were normalized globally across all four conditions (shCtrl ± ActD, shZFP36L2 ± ActD). The ZFP36L2 dependency score for each gene was calculated as the log₂ ratio of the treated/untreated fold-change in shZFP36L2 cells over the treated/untreated fold-change in shCtrl cells.
Assembly: GRCh38
Supplementary files format and content: CSV file containing per-gene RNA half-life differences between shZFP36L2 and shCtrl organoids in MSK107LI, with Ensembl gene ID, gene symbol, decay difference (shZFP36L2 minus shCtrl half-life), and associated p-value and adjusted p-value.
Supplementary files format and content: CSV file containing per-gene RNA half-life differences between shZFP36L2 and shCtrl organoids in OKG146LI, with Ensembl gene ID, gene symbol, decay difference (shZFP36L2 minus shCtrl half-life), and associated p-value and adjusted p-value.

treatment_protocol: PDO OKG146Li expressing shCtrl or shZFP36L2 were cultured in ENAFI medium supplemented with 2 μg/mL doxycycline. On day 5, organoids were treated with or without 5 μg/mL Actinomycin D for 5 hours and harvested for bulk RNA-seq profiling.

value: 5h ActD


title: 2011 cells,3D,D10,mut,rep1


title: spawning, female, muscle #4

description:
Library name: P4M
ctm_female.csv


title: SFC cells,2D,D35,ctrl,rep3


title: OKG146Li PDO cells, shZFP36L2, 5h ActD, replicate2

description:
Library name: OKG146Li_shZFP36L2_5hr_2
decay_OKG146LI_all.csv


title: SFC cells,2D,D35,ctrl,rep2


title: SFC cells,2D,D35,ctrl,rep1


title: spawning, female, headkidney #4

description:
Library name: P4H
ctm_female.csv


title: OKG146Li PDO cells, shZFP36L2, 5h ActD, replicate1

description:
Library name: OKG146Li_shZFP36L2_5hr_1
decay_OKG146LI_all.csv


title: SFC cells,2D,D20,ctrl,rep3


title: spawning, female, gonads #4

description:
Library name: P4G
ctm_female.csv


title: OKG146Li PDO cells, shZFP36L2, no ActD, replicate3

description:
Library name: OKG146Li_shZFP36L2_0hr_3
decay_OKG146LI_all.csv

value: no ActD


title: SFC cells,2D,D20,ctrl,rep1

value: ctrl


title: SFC cells,2D,D20,ctrl,rep2


title: spawning, female, muscle #3

description:
Library name: P3M
ctm_female.csv


title: SFC cells,2D,D10,ctrl,rep3


title: OKG146Li PDO cells, shZFP36L2, no ActD, replicate2

description:
Library name: OKG146Li_shZFP36L2_0hr_2
decay_OKG146LI_all.csv


title: SFC cells,2D,D10,ctrl,rep2


title: SFC cells,2D,D10,ctrl,rep1


title: OKG146Li PDO cells, shZFP36L2, no ActD, replicate1

description:
Library name: OKG146Li_shZFP36L2_0hr_1
decay_OKG146LI_all.csv


title: B125 cells,2D,D35,mut,rep3


title: spawning, female, muscle #2

description:
Library name: P2M
ctm_female.csv


title: B125 cells,2D,D35,mut,rep1


title: spawning, female, headkidney #2

description:
Library name: P2H
ctm_female.csv


title: OKG146Li PDO cells, shCtrl, 5h ActD, replicate3

description:
Library name: OKG146Li_shCtrl_5hr_3
decay_OKG146LI_all.csv

value: shCtrl


title: B125 cells,2D,D20,mut,rep3


title: B125 cells,2D,D35,mut,rep2


title: OKG146Li PDO cells, shCtrl, 5h ActD, replicate2

description:
Library name: OKG146Li_shCtrl_5hr_2
decay_OKG146LI_all.csv


title: B125 cells,2D,D20,mut,rep2


title: spawning, female, gonads #2

description:
Library name: P2G
ctm_female.csv


title: B125 cells,2D,D20,mut,rep1


title: spawning, female, gonads #3

description:
Library name: P3G
ctm_female.csv


title: B125 cells,2D,D10,mut,rep3


title: spawning, female, headkidney #1

description:
Library name: P1H
ctm_female.csv


title: B125 cells,2D,D10,mut,rep2


title: OKG146Li PDO cells, shCtrl, 5h ActD, replicate1

description:
Library name: OKG146Li_shCtrl_5hr_1
decay_OKG146LI_all.csv


title: OKG146Li PDO cells, shCtrl, no ActD, replicate3

description:
Library name: OKG146Li_shCtrl_0hr_3
decay_OKG146LI_all.csv


title: B125 cells,2D,D10,mut,rep1


title: spawning, female, gonads #1

description:
Library name: P1G
ctm_female.csv


title: 802 cells,2D,D35,ctrl,rep3


title: OKG146Li PDO cells, shCtrl, no ActD, replicate2

description:
Library name: OKG146Li_shCtrl_0hr_2
decay_OKG146LI_all.csv


title: 802 cells,2D,D35,ctrl,rep2


title: river, female, muscle #9

description:
Library name: O9M
ctm_female.csv

value: river


title: 802 cells,2D,D35,ctrl,rep1


title: OKG146Li PDO cells, shCtrl, no ActD, replicate1

description:
Library name: OKG146Li_shCtrl_0hr_1
decay_OKG146LI_all.csv


title: 802 cells,2D,D20,ctrl,rep3


title: 802 cells,2D,D20,ctrl,rep2


title: MSK107Li PDO cells, shZFP36L2, 5h ActD, replicate3

description:
Library name: MSK107Li_shZFP36L2_5h_3
decay_MSK107LI_all.csv


title: river, female, headkidney #9

description:
Library name: O9H
ctm_female.csv


title: river, female, gonads #9

description:
Library name: O9G
ctm_female.csv


title: MSK107Li PDO cells, shZFP36L2, 5h ActD, replicate2

description:
Library name: MSK107Li_shZFP36L2_5h_2
decay_MSK107LI_all.csv


title: 802 cells,2D,D10,ctrl,rep3


title: 802 cells,2D,D20,ctrl,rep1


title: 802 cells,2D,D10,ctrl,rep1


title: 802 cells,2D,D10,ctrl,rep2


title: MSK107Li PDO cells, shZFP36L2, 5h ActD, replicate1

description:
Library name: MSK107Li_shZFP36L2_5h_1
decay_MSK107LI_all.csv


title: LNCaP, MR-young, Rep2

description: Library name: 8063-AF-05

value: prostate tumor

value: LNCaP

value: immortalized prostate cancer (epithelial-like)

value: MR-young

value: x20 FSS


title: river, female, headkidney #8

description:
Library name: O8H
ctm_female.csv


title: 2011 cells,2D,D35,mut,rep2

value: mut


title: MSK107Li PDO cells, shZFP36L2, no ActD, replicate3

description:
Library name: MSK107Li_shZFP36L2_0h_3
decay_MSK107LI_all.csv

value: CRC PDO


title: 2011 cells,2D,D35,mut,rep3


title: river, female, gonads #8

description:
Library name: O8G
ctm_female.csv


title: 2011 cells,2D,D35,mut,rep1


title: MSK107Li PDO cells, shZFP36L2, no ActD, replicate2

description:
Library name: MSK107Li_shZFP36L2_0h_2
decay_MSK107LI_all.csv


title: 2011 cells,2D,D20,mut,rep3


title: river, female, muscle #7

description:
Library name: O7M
ctm_female.csv


title: 2011 cells,2D,D20,mut,rep2


title: MSK107Li PDO cells, shZFP36L2, no ActD, replicate1

description:
Library name: MSK107Li_shZFP36L2_0h_1
decay_MSK107LI_all.csv


title: 2011 cells,2D,D20,mut,rep1


title: 2011 cells,2D,D10,mut,rep3


title: river, female, headkidney #7

description:
Library name: O7H
ctm_female.csv

value: headkidney


title: 2011 cells,2D,D10,mut,rep2


title: MSK107Li PDO cells, shCtrl, 5h ActD, replicate3

description:
Library name: MSK107Li_shCtrl_5h_3
decay_MSK107LI_all.csv


title: 2011 cells,2D,D10,mut,rep1


title: river, female, gonads #7

description:
Library name: O7G
ctm_female.csv


title: MSK107Li PDO cells, shCtrl, 5h ActD, replicate2

description:
Library name: MSK107Li_shCtrl_5h_2
decay_MSK107LI_all.csv


title: MSK107Li PDO cells, shCtrl, 5h ActD, replicate1

description:
Library name: MSK107Li_shCtrl_5h_1
decay_MSK107LI_all.csv


title: human EV_2

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Next Gen Sequencing was performed on Illumina NextSeq with SE75 (Single-end, 75 bp) at an approximate depth of 10-15 million reads per sample.
Sequence alignment was performed using Bowtie2 (v2.5.1; Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.) local mode alignment with default parameters.  The fastq files were mapped to the human reference genome using the Ensembl GRCh38 cDNA and non-coding RNA combined reference. Normalized read counts and differential expression were calculated for each transcript by DESeq2  (v1.16.1; Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 2014, 15:550).
Assembly: GRCh38
Supplementary files format and content: excel file includes raw counts for each sample

source_name: human platelet derived extracellular vesicles (EV)

growth_protocol: Day 1 human platelets were pelleted by low spin centrifugation and pellets frozen at -80oC. Platelet derived extracellular vesicles (EV) were aliquoted and stored at -80oC. Some vials of PEV were lyophilized and the dried powder was resuspended in water and the PEVs were used for RNA extraction.

extract_protocol:
Total EVs or platelet pellets were lysed and crude RNA extracted using SBI’s spin column based RNA Purification Kit. RNA quality and quantity were checked on Bioanalyzer (Agilent) using the RNA Pico kit and assessed for presence of small RNA.
Total RNA population, starting with as little as 1 ng of total RNA, was entered into small RNA library prep using Qiagen small RNA library prep kit. Successful libraries were purified by gel extraction to ensure the correct size was isolated. Libraries were amplified by qPCR and assessed for viability by the concentration (>1 nM) to be moved on to sequencing.


title: human EV_1

value: human platelet derived extracellular vesicles (EV)


title: human EV_2_frozen

source_name: frozen human platelet derived extracellular vesicles (EV_frozen)


title: river, male, muscle #6

description:
Library name: O6M
ctm_male.csv

value: male


title: river, male, headkidney #6

description:
Library name: O6H
ctm_male.csv


title: wild type, expansion, replicate 3

first: James

middle: J

last: Bieker

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

description: Library name: W3A

data_processing:
Mouse RNA-seq reads were mapped to the mouse genes (Ensembl v75) using Bowtie (v0.12.8) (Langmead et al., 2009) allowing up to 2-mismatches and a maximum of 200 multiple hits. The gene expected read counts and transcripts per million (TPMs) were estimated by RSEM (v1.2.3) (Li and Dewey, 2011).
TPMs were median-by-ratio normalized, and replicates were merged via calculating average normalized TPMs.
Differentially expressed genes (DEGs): The EBSeq package (Leng et al., 2013) was used to assess the probability of gene expression (mRNAs) being differentially expressed between any two given conditions. We required that DEGs should have FDR<5% via EBSeq and >2 fold-change of “normalized read counts+1”.
Gene ontology (GO) enrichment analysis was performed using the R package (“allez”) (Newton et al., 2007). The enrichment p-values were further adjusted by Benjamini–Hochberg (BH) multiple test correction.
Assembly: EnsDb.Mmusculus.v75
Supplementary files format and content: TABLE S1, normalized TPM, xls file, all samples

source_name: fetal liver

growth_protocol: Extensively self-renewing erythroblasts from Klf1+/+ and Klf1-/- E12.5 fetal livers were expanded and terminally differentiated using protocols as described previously (England et al., 2011; Gnanapragasam et al., 2016). These cells from each embryo provided a biological replicate for analysis. Embryos were from 4-6 week old heterozygous Klf1+/- females obtained after mating with heterozygous Klf1+/- males (Perkins et al., 1995). All are in C57Bl6 background. Animal experiments were approved by the IACUC committee at Mount Sinai, protocol 2019-0042.

extract_protocol:
RNA isolation was performed as previously described using Tri reagent (Sigma) (Elagooz et al., 2022).
Poly A library was prepared and HiSeq 100nt Single read sequencing was performed to obtain greater than 40 million reads per sample at the Institute for Genomics and Multiscale Biology at the Icahn School of Medicine at Mount Sinai.

value: fetal liver

tag: developmental stage

value: embryonic day 12.5

value: erythroid

value: WT


title: wild type, expansion, replicate 2

description: Library name: W2A

tag: tissue


title: MSK107Li PDO cells, shCtrl, no ActD, replicate3

description:
Library name: MSK107Li_shCtrl_0h_3
decay_MSK107LI_all.csv

tag: cell line

value: no ActD


title: wild type, expansion, replicate 1

description: Library name: W1A

tag: cell type


title: river, male, gonads #6

description:
Library name: O6G
ctm_male.csv

value: gonads


title: MSK107Li PDO cells, shCtrl, no ActD, replicate2

description:
Library name: MSK107Li_shCtrl_0h_2
decay_MSK107LI_all.csv

tag: genotype

value: shCtrl


title: knockout, expansion, replicate 2

description: Library name: K2A


title: knockout, expansion, replicate 3

description: Library name: K3A


title: river, male, muscle #5

description:
Library name: O5M
ctm_male.csv

value: muscle

tag: treatment

value: river


title: knockout, expansion, replicate 1

description: Library name: K1A


title: wild type, differentiation d2, replicate 3

description: Library name: W3D


title: wild type, differentiation d2, replicate 2

description: Library name: W2D


title: MSK107Li PDO cells, shCtrl, no ActD, replicate1

description:
Library name: MSK107Li_shCtrl_0h_1
decay_MSK107LI_all.csv


title: river, male, headkidney #5

description:
Library name: O5H
ctm_male.csv


title: wild type, differentiation d2, replicate 1

description: Library name: W1D


title: Pro_S03 Small BPH prostate scRNA-seq

city: Guangzhou

first: Ning

state: Guangdong

address: 253 Middle Industrial Road

country: China

institute: Southern Medical University

description:
Library name: Pro_S03
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue

data_processing:
Raw FASTQ files were generated by the sequencing provider.
The sequencing provider performed standard CellRanger count processing (cellranger-9.0.0) to generate per-sample filtered feature-barcode matrices. The CellRanger web summaries report chemistry as Single Cell 3' v3 (polyA), with intronic reads included (include-introns=true), and transcriptome/reference as GRCh38-2020-A / refdata-gex-GRCh38-2020-A.
Downstream quality control, filtering, integration, clustering, annotation, and endothelial-focused analyses were performed by the authors using Seurat/Harmony and project scripts.
Processed matrices submitted with this metadata are sequencing-provider CellRanger filtered MEX files only; downstream author analyses are not included as provider analysis output.
Assembly: Homo sapiens GRCh38; CellRanger reference refdata-gex-GRCh38-2020-A (reported as GRCh38-2020-A in provider CellRanger web summaries).
Supplementary files format and content: Per-sample CellRanger filtered feature-barcode matrices in MEX format: sample-prefixed barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

source_name: prostate

growth_protocol: Prostate tissue specimens were obtained from patients undergoing surgery for benign prostatic hyperplasia under institutional ethics approval (approval no. Liwan Central 2025015).

extract_protocol:
Fresh prostate tissue was dissociated into single-cell suspensions for 10x Genomics single-cell RNA-seq library preparation.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' Gene Expression platform by the sequencing provider. The CellRanger web summaries report chemistry as Single Cell 3' v3 (polyA); the provider report describes Chromium Single Cell 3' Gene Expression Dual Index libraries and Illumina NovaSeq PE150 sequencing.

treatment_protocol: No experimental treatment was applied to the tissue specimens before single-cell library preparation.

value: prostate

tag: disease state

value: benign prostatic hyperplasia

tag: size group

value: Small BPH

tag: prostate weight_(g)

tag: age (years)

tag: surgery

value: Transurethral prostate surgery


title: river, male, gonads #5

description:
Library name: O5G
ctm_male.csv


title: knockout, differentiation d2, replicate 3

description: Library name: K3D


title: knockout, differentiation d2, replicate 2

description: Library name: K2D


title: river, male, muscle #4

description:
Library name: O4M
ctm_male.csv


title: knockout, differentiation d2, replicate 1

description: Library name: K1D


title: Pro_S02 Small BPH prostate scRNA-seq

description:
Library name: Pro_S02
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue


title: Pro_S01 Small BPH prostate scRNA-seq

description:
Library name: Pro_S01
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue


title: C794, scRNA-seq

city: Bunkyo-ku

first: Akiyasu

last: Iwase

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description:
Fluidigm C1
C794

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: mm10
Supplementary files format and content: Fluidigm_raw_counts.txt. Tab-separated matrix files include raw counts for each single-cell
Supplementary files format and content: Fluidigm_SCT_counts.txt. Tab-separated matrix files include normalized counts by SCTransform from Seurat for each single-cell

source_name: heart

extract_protocol:
Cardiac NCCs labeled by Wnt1-Cre; R26-EYFP mice at E11.5, 12.5, 14.5 and 17.5 around sub-region of aorticopulmonary septum were dissociated by using 0.25 w/v% trypsin / 1 mmol/L EDTA・4Na solution (Wako) at 37 °C, 15 minutes. Enzymes were neutralized with equal volume of DMEM (Wako) with 10% fetal bovine serum (FBS) (SIGMA). Cell suspensions were filtered through a 35 μm nylon mesh cell strainer（FALCON 352235.  Cells were kept on ice until cell sorting. Cell sorting was performed in a fluorescence-activated cell sorting (FACS) AriaⅡcell sorter (BD Biosciences).
EYFP-positive single cells were captured on the Fluidigm C1 Medium-cell (10-17 μm cell diameter) integrated fluidic circuit (IFC) for single cell cDNA libraries for mRNA sequencing. EYFP-positive cells were loaded on the IFC chips at concentration of 300 cells per μL. All captured cells were photographed to check whether cells were truly EYFP-positive and were dissociated for single cells by using KEYENCE BZ-X710. Single cell cDNAs were prepared on Fluidigm C1 system by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System (Clontech). Only single cell cDNAs confirmed by imaging data were performed quality check (QC) by using Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina HiSeq 2500.

value: heart

value: Wnt1-Cre; R26-EYFP


title: C790, scRNA-seq

description:
Fluidigm C1
C790


title: C792, scRNA-seq

description:
Fluidigm C1
C792


title: river, male, muscle #3

description:
Library name: O3M
ctm_male.csv


title: C788, scRNA-seq

description:
Fluidigm C1
C788


title: Pro_L03 Large BPH prostate scRNA-seq

description:
Library name: Pro_L03
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue

value: Large BPH


title: Pro_L02 Large BPH prostate scRNA-seq

description:
Library name: Pro_L02
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue


title: C784, scRNA-seq

description:
Fluidigm C1
C784


title: river, male, headkidney #3

description:
Library name: O3H
ctm_male.csv

value: headkidney

value: male


title: C781, scRNA-seq

description:
Fluidigm C1
C781


title: Pro_L01 Large BPH prostate scRNA-seq

description:
Library name: Pro_L01
10x Genomics single-cell RNA-seq of de-identified benign prostatic hyperplasia prostate tissue


title: C780, scRNA-seq

description:
Fluidigm C1
C780


title: river, male, gonads #3

description:
Library name: O3G
ctm_male.csv


title: C775, scRNA-seq

description:
Fluidigm C1
C775


title: C773, scRNA-seq

description:
Fluidigm C1
C773


title: river, male, muscle #2

description:
Library name: O2M
ctm_male.csv


title: C772, scRNA-seq

description:
Fluidigm C1
C772


title: AML PDX TUH96_P2 Ribo-seq

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

description:
Library name: TUH96_P2
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model TUH96 at passage P2. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.

data_processing:
Raw Ribo-seq reads were processed for quality control and periodicity assessment using RiboSeQC. Reads were used for downstream analysis of ribosome occupancy and translational regulation.
Assembly: GRCh38
Supplementary files format and content: RiboSeq_counts_matrix_GEO.tsv
Library strategy: Ribo-Seq

source_name: xenografted human AML cells

growth_protocol: AML patient-derived xenograft cells were expanded in vivo through serial transplantation in NSG mice. Leukemic cells were harvested at defined passages and FACS-purified as viable human AML blasts (hCD45+ hCD33+).

extract_protocol:
Cells (1 × 107) were lysed in polysome buffer containing cycloheximide. Lysates were subjected to sucrose gradient ultracentrifugation (10–50% sucrose), and 80S monosome fractions were collected. Ribosome-protected RNA fragments were generated by RNase I digestion and size-selected (25–34 nucleotides).
Ribosome-protected fragments were ligated to adapters, reverse-transcribed, circularized, and PCR-indexed to generate Ribo-seq libraries. Libraries were sequenced as single-end reads (1 × 100 bp) on a NovaSeq 6000 platform.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: xenografted human AML cells

value: hCD45+ hCD33+ AML blasts


title: AML PDX TUH96_P1 Ribo-seq

description:
Library name: TUH96_P1
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model TUH96 at passage P1. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C770, scRNA-seq

description:
Fluidigm C1
C770


title: river, male, headkidney #2

description:
Library name: O2H
ctm_male.csv


title: AML PDX TUH84_P2 Ribo-seq

description:
Library name: TUH84_P2
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model TUH84 at passage P2. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C766, scRNA-seq

description:
Fluidigm C1
C766


title: C769, scRNA-seq

description:
Fluidigm C1
C769


title: river, male, gonads #2

description:
Library name: O2G
ctm_male.csv


title: AML PDX TUH83_P2 Ribo-seq

description:
Library name: TUH83_P2
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model TUH83 at passage P2. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C762, scRNA-seq

description:
Fluidigm C1
C762


title: C763, scRNA-seq

description:
Fluidigm C1
C763


title: AML PDX TUH83_P1 Ribo-seq

description:
Library name: TUH83_P1
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model TUH83 at passage P1. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C755, scRNA-seq

description:
Fluidigm C1
C755


title: river, female, headkidney #1

description:
Library name: O1H
ctm_female.csv

value: female


title: C757, scRNA-seq

description:
Fluidigm C1
C757


title: C753, scRNA-seq

description:
Fluidigm C1
C753


title: AML PDX PAR27_P2 Ribo-seq

description:
Library name: PAR27_P2
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model PAR27 at passage P2. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C752, scRNA-seq

description:
Fluidigm C1
C752


title: C744, scRNA-seq

description:
Fluidigm C1
C744


title: river, female, gonads #1

description:
Library name: O1G
ctm_female.csv


title: AML PDX PAR27_P1 Ribo-seq

description:
Library name: PAR27_P1
FACS-purified human AML blasts (hCD45+ hCD33+) from PDX model PAR27 at passage P1. Ribosome-protected fragments (25–34 nt) generated after polysome fractionation and RNase I digestion.


title: C743, scRNA-seq

description:
Fluidigm C1
C743


title: TUH109 P0 scRNAseq

description: Library name: TUH109_P0_scRNA

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) to generate gene-barcode matrices.
Reads were aligned to the human reference genome (GRCh38) and gene expression matrices were generated.
Cell barcodes and unique molecular identifiers (UMIs) were used to quantify gene expression per cell.
Filtered gene-barcode matrices were generated after removal of low-quality cells and empty droplets.
Assembly: GRCh38
Supplementary files format and content: Processed data include filtered gene-barcode matrices generated by Cell Ranger, consisting of matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz files for each sample.

source_name: AML primary TUH109 at P0 (human AML cells)

growth_protocol: Patient-derived xenograft (PDX) AML cells were expanded in immunodeficient mice and harvested from bone marrow at defined transplantation stages (P0, P1, P2).

extract_protocol:
Single-cell suspensions were prepared from peripheral blood or bone marrow samples. Cells were filtered, counted, and viability assessed prior to library preparation.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium platform following the manufacturer's protocol (Chromium Single Cell 3' kit). Cells were partitioned into nanoliter-scale droplets and barcoded for downstream analysis.

treatment_protocol: No treatment was applied. Samples correspond to untreated AML PDX cells collected at different transplantation stages.

value: peripheral blood

value: Human AML cells

value: untreated


title: C740, scRNA-seq

description:
Fluidigm C1
C740


title: ocean, male, headkidney #9

description:
Library name: F9H
ctm_male.csv

value: ocean


title: ocean, male, muscle #9

description:
Library name: F9M
ctm_male.csv

value: muscle


title: C737, scRNA-seq

description:
Fluidigm C1
C737


title: C739, scRNA-seq

description:
Fluidigm C1
C739


title: Hippocampus, total RNA-Seq, 1078

city: Boston

first: Alexander

last: Knyshov

address: 72 E Concord St

institute: Boston University

description: Library name: 1078

data_processing:
Trimmomatic 0.39 was used to trim adaptors and low-quality reads
STAR 2.7.10b was used to align trimmed reads to the human reference genome (GRCh38)
RSEM 1.3.3 with Ensembl v108 annotation was used to calculate transcript-based gene expression
Circular RNAs were called using circexplorer3/CLEAR 1.0.1
Assembly: GRCh38
Supplementary files format and content: csv files include linear RNA TPM and circular RNA FPB values for each Sample

source_name: hippocampus

extract_protocol:
We used human brain samples with the age range of 54-110 years old. Frozen hippocampal tissues were collected from a coronal section of the caudal hippocampus at the level of the lateral geniculate nucleus at the Boston University Alzheimer’s disease Research Center (BU-ADRC). After RNA extraction, RNA was purified using RNeasy Mini Kits (Qiagen), and the RNA integrity number was calculated using an RNA 6000 Pico assay on a Bioanalyzer 2100 (Agilent Technologies).
Total RNA Seq Library Prep:  Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA is depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.  Samples are then fragmented using heat and magnesium.  1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated and the library is amplified.  Strands marked with dUTPs are not amplified, allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing. All libraries were prepared in a strand-specific manner. RNA Seq Library Prep for PolyA+ and PolyA- sequencing: Using the Kapa RNA HyperPrep Kit with RiboErase, rRNA is depleted starting from 500ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA. Following rRNA depletion, mRNA is selected by oligo-dT beads using the KAPA mRNA HyperPrep kit. After the first and second capture, the PolyA minus fraction is kept. After the PolyA captures, the minus fractions are concentrated using the Zymo RNA Clean and Concentrator Kit. Both the PolyA plus and minus fractions are fragmented using heat and magnesium. Following first-strand synthesis with random primers, second-strand synthesis, and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the Agilent Tapestation.

value: hippocampus

tag: rqn

tag: age

value: Male

tag: ad status

tag: batch


title: TUH102 P2 scRNAseq

description: Library name: TUH102_P2_scRNA

source_name: AML PDX TUH102 at P2 (human AML cells from mouse bone marrow)

value: mouse bone marrow


title: Hippocampus, total RNA-Seq, 1083

description: Library name: 1083

tag: Sex


title: C731, scRNA-seq

description:
Fluidigm C1
C731


title: ocean, male, gonads #9

description:
Library name: F9G
ctm_male.csv

value: gonads


title: TUH102 P1 scRNAseq

description: Library name: TUH102_P1_scRNA

source_name: AML PDX TUH102 at P1 (human AML cells from mouse bone marrow)


title: C728, scRNA-seq

description:
Fluidigm C1
C728

value: heart


title: ocean, male, muscle #8

description:
Library name: F8M
ctm_male.csv


title: C729, scRNA-seq

description:
Fluidigm C1
C729

value: Wnt1-Cre; R26-EYFP


title: ocean, male, headkidney #8

description:
Library name: F8H
ctm_male.csv


title: C726, scRNA-seq

description:
Fluidigm C1
C726


title: C727, scRNA-seq

description:
Fluidigm C1
C727


title: TUH84 P2 scRNAseq

description: Library name: TUH84_P2_scRNA

source_name: AML PDX TUH84 at P2 (human AML cells from mouse bone marrow)


title: C725, scRNA-seq

description:
Fluidigm C1
C725


title: ocean, male, gonads #8

description:
Library name: F8G
ctm_male.csv


title: C724, scRNA-seq

description:
Fluidigm C1
C724


title: TUH84 P1 scRNAseq

description: Library name: TUH84_P1_scRNA

source_name: AML PDX TUH84 at P1 (human AML cells from mouse bone marrow)


title: ocean, female, muscle #7

description:
Library name: F7M
ctm_female.csv


title: C722, scRNA-seq

description:
Fluidigm C1
C722


title: TUH84 P0 scRNAseq

description: Library name: TUH84_P0_scRNA

source_name: AML primary TUH84 at P0 (human AML cells)


title: ocean, female, headkidney #7

description:
Library name: F7H
ctm_female.csv


title: C721, scRNA-seq

description:
Fluidigm C1
C721


title: C716, scRNA-seq

description:
Fluidigm C1
C716


title: river, male, gonads #4

description:
Library name: O4G
ctm_male.csv

value: river


title: TUH76 P2 scRNAseq

description: Library name: TUH76_P2_scRNA

source_name: AML PDX TUH76 at P2 (human AML cells from mouse bone marrow)


title: C715, scRNA-seq

description:
Fluidigm C1
C715


title: ocean, female, gonads #7

description:
Library name: F7G
ctm_female.csv


title: TUH76 P0 scRNAseq

description: Library name: TUH76_P0_scRNA

source_name: AML primary TUH76 at P0 (human AML cells)


title: C736, scRNA-seq

description:
Fluidigm C1
C736


title: C712, scRNA-seq

description:
Fluidigm C1
C712


title: C711, scRNA-seq

description:
Fluidigm C1
C711


title: ocean, male, headkidney #6

description:
Library name: F6H
ctm_male.csv

source_name: headkidney

value: headkidney


title: C710, scRNA-seq

description:
Fluidigm C1
C710


title: TUH32 P0 scRNAseq

description: Library name: TUH32_P0_scRNA

source_name: AML primary TUH32 at P0 (human AML cells)


title: ocean, male, gonads #6

description:
Library name: F6G
ctm_male.csv

source_name: gonads

value: male


title: C708, scRNA-seq

description:
Fluidigm C1
C708


title: TUH07 P0 scRNAseq

description: Library name: TUH07_P0_scRNA

source_name: AML primary TUH07 at P0 (human AML cells)


title: ocean, female, muscle #5

description:
Library name: F5M
ctm_female.csv

source_name: muscle


title: C701, scRNA-seq

description:
Fluidigm C1
C701


title: river, female, muscle #1

description:
Library name: O1M
ctm_female.csv


title: C674, scRNA-seq

description:
Fluidigm C1
C674


title: TUH06 P2 scRNAseq

description: Library name: TUH06_P2_scRNA

source_name: AML PDX TUH06 at P2 (human AML cells from mouse bone marrow)


title: C672, scRNA-seq

description:
Fluidigm C1
C672

source_name: heart


title: C673, scRNA-seq

description:
Fluidigm C1
C673


title: ocean, female, gonads #5

description:
Library name: F5G
ctm_female.csv


title: TUH06 P1 scRNAseq

description: Library name: TUH06_P1_scRNA

source_name: AML PDX TUH06 at P1 (human AML cells from mouse bone marrow)


title: C709, scRNA-seq

description:
Fluidigm C1
C709


title: C670, scRNA-seq

description:
Fluidigm C1
C670


title: C668, scRNA-seq

description:
Fluidigm C1
C668


title: TUH06 P0 scRNAseq

description: Library name: TUH06_P0_scRNA

source_name: AML primary TUH06 at P0 (human AML cells)


title: ocean, female, muscle #4

description:
Library name: F4M
ctm_female.csv


title: C667, scRNA-seq

description:
Fluidigm C1
C667


title: AML PDX TUH102 P2 bulk RNA-seq

description:
Library name: TUH102_P2
Model TUH102 timepoint P2

data_processing:
Raw sequencing reads were quantified using Salmon. Transcript-level estimates were aggregated at the gene level to generate count and TPM matrices used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts for all samples.
Supplementary files format and content: Tab-delimited text files containing gene-level TPM values for all samples.

source_name: xenografted human AML cells

growth_protocol: AML patient-derived xenograft cells were expanded in vivo through serial transplantation in immunodeficient mice and collected at passages P0, P1, and P2.

extract_protocol:
Total RNA was extracted from AML patient-derived xenograft cells using standard RNA extraction procedures.
RNA-seq libraries were prepared using Illumina-compatible protocols for poly(A)-selected RNA sequencing.

value: xenografted human AML cells

value: AML cells


title: C666, scRNA-seq

description:
Fluidigm C1
C666


title: TUH102 P0 scRNAseq

description: Library name: TUH102_P0_scRNA

source_name: AML primary TUH102 at P0 (human AML cells)


title: C664, scRNA-seq

description:
Fluidigm C1
C664


title: ocean, female, headkidney #4

description:
Library name: F4H
ctm_female.csv

value: female


title: C662, scRNA-seq

description:
Fluidigm C1
C662


title: AML PDX TUH102 P1 bulk RNA-seq

description:
Library name: TUH102_P1
Model TUH102 timepoint P1


title: ocean, female, headkidney #5

description:
Library name: F5H
ctm_female.csv


title: ocean, female, gonads #4

description:
Library name: F4G
ctm_female.csv


title: C723, scRNA-seq

description:
Fluidigm C1
C723


title: AML PDX TUH102 P0 bulk RNA-seq

description:
Library name: TUH102_P0
Model TUH102 timepoint P0

source_name: peripheral blood

value: peripheral blood


title: C660, scRNA-seq

description:
Fluidigm C1
C660


title: ocean, male, muscle #3

description:
Library name: F3M
ctm_male.csv


title: C661, scRNA-seq

description:
Fluidigm C1
C661


title: C659, scRNA-seq

description:
Fluidigm C1
C659


title: AML PDX TUH96 P2 bulk RNA-seq

description:
Library name: TUH96_P2
Model TUH96 timepoint P2


title: C658, scRNA-seq

description:
Fluidigm C1
C658


title: C655, scRNA-seq

description:
Fluidigm C1
C655


title: ocean, male, gonads #3

description:
Library name: F3G
ctm_male.csv


title: AML PDX TUH96 P1 bulk RNA-seq

description:
Library name: TUH96_P1
Model TUH96 timepoint P1


title: C654, scRNA-seq

description:
Fluidigm C1
C654


title: C650, scRNA-seq

description:
Fluidigm C1
C650


title: ocean, female, muscle #2

description:
Library name: F2M
ctm_female.csv


title: C647, scRNA-seq

description:
Fluidigm C1
C647


title: AML PDX TUH96 P0 bulk RNA-seq

description:
Library name: TUH96_P0
Model TUH96 timepoint P0


title: C643, scRNA-seq

description:
Fluidigm C1
C643


title: ocean, female, headkidney #2

description:
Library name: F2H
ctm_female.csv


title: C713, scRNA-seq

description:
Fluidigm C1
C713


title: AML PDX TUH93 P2 bulk RNA-seq

description:
Library name: TUH93_P2
Model TUH93 timepoint P2


title: ocean, male, muscle #1

description:
Library name: F1M
ctm_male.csv


title: C635, scRNA-seq

description:
Fluidigm C1
C635


title: C630, scRNA-seq

description:
Fluidigm C1
C630


title: AML PDX TUH93 P0 bulk RNA-seq

description:
Library name: TUH93_P0
Model TUH93 timepoint P0


title: C627, scRNA-seq

description:
Fluidigm C1
C627


title: ocean, male, headkidney #1

description:
Library name: F1H
ctm_male.csv


title: C626, scRNA-seq

description:
Fluidigm C1
C626


title: AML PDX TUH84 P2 bulk RNA-seq

description:
Library name: TUH84_P2
Model TUH84 timepoint P2


title: ocean, male, gonads #1

description:
Library name: F1G
ctm_male.csv


title: C625, scRNA-seq

description:
Fluidigm C1
C625


title: C622, scRNA-seq

description:
Fluidigm C1
C622


title: TREM2KO, Myelin, rep 2

status: Public on Jul 21 2026

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Library name: HSA-000028206
TREM2 KO, Myelin

data_processing:
Raw data (FASTQ files) were processed using nf-core/rnaseq v3.11.2 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020) with GRCh38 genome sequences and gene annotations from Gencode version 42. To deduplicate unique molecular identifiers, the following umitools_bc_pattern was used: ^(?P.{6})(?P.{4}).*
To account for the fact that the QuantSeq 3' mRNA-Seq library protocol only captures a 3' tag from each transcript, the following custom argument was included in the nf-core/rnaseq workflow: extra_star_align_args: --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA.
The following custom arguments were passed to the salmon quantitation step of the workflow: extra_salmon_quant_args: --noLengthCorrection The nf-core/rnaseq workflow produces a SummarizedExperiment R object that is serialized to disk.
To generate the processed data file, this object was read into an R session, library sizes were estimated with the edgeR::normLibSizes function (version 4.4.2) using the TMM method and counts per million were returned with the edgeR::cpm function.
Assembly: GRCh38
Supplementary files format and content: Excel (XLSX) file with three worksheets: sample annotations, raw count matrix, normalized count matrix (CPM)

source_name: iPSC-derived microglia

growth_protocol: iPSC-derived microglia (iMG) were differentiated from a human, female iPSC line (Thermo Fisher Scientific, A18945, hereafter referred to as iPSC line 1) using a previously published and validated protocol66. iPSCs were maintained on matrigel-coated plates (Corning, CB356238) according to the manufacturer’s specifications in mTeSR-plus (STEMCELL Technologies, 100-0276). Culture medium was replenished every day with fresh medium. Cells were passaged every 5–7 days using Gentle cell dissociation (STEMCELL Technologies, 100-0485) or ReLeSR (STEMCELL Technologies, 100-0484) according to the manufacturer’s specifications. For all in vitro experiments, iPSCs were cultured in 5% O2, 5% CO2 at 37°C. At ~80% confluence hematopoietic differentiation was started. On Day 4 cells were sorted for marker CD235a and replated on matrigel coated plates into Hematopoietic Kit Medium B (STEMCELL Technologies, 05310) containing 10µM ROCK inhibitor (ATCC, Y27632) at 500,000 cells per well of a 6-well plate. From this point onward all steps from STEMCELL Technologies protocol were followed to generate highly pure HPCs.  Collected HPCs were confirmed to be >90% positive for marker CD43, seeded directly onto astrocyte feeder layers to generate iMG, and thereafter maintained in IMDM (Thermo Fisher Scientific, 31980030) supplemented with 10% FBS, 1X Penicillin/Strepyomycin, 20ng/mL hIL3 (Peprotech), 20ng/mL hGMCSF (Peprotech), and 20ng/mL hM-CSF (Peprotech).

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, 74034), and RNA quality was assessed using the TapeStation High Sensitivity RNA ScreenTape (Agilent, 5067-5579)
Library preparation was conducted in a 96-well PCR plate using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, A01173), incorporating the UMI second-strand synthesis module to identify and remove PCR duplicates, following the manufacturer’s protocol. Briefly, total RNA was used as input for oligo-dT priming during reverse transcription, followed by RNA removal. Unique Molecular Identifiers (UMIs) were introduced during second-strand synthesis, and cDNA was purified using magnetic beads, followed by 15 cycles of PCR with dual indexes and PCR purification with 0.8x magnetic beads. Library quantity and quality were assessed using TapeStation High Sensitivity D1000 ScreenTape (Agilent, 5067-5584). Libraries were pooled in equimolar ratios, and the sequencing pool underwent an additional 0.8x magnetic bead purification to remove residual adapter contamination. Sequencing was performed on an Illumina NextSeq 550 System High-Output Kit (SE, 75 bp, dual indexes) with a 5% PhiX spike-in by SeqMatic (Fremont, CA, USA).

treatment_protocol: gRNA sequences targeting AAVS1, GPR34, or TREM2 were identified using the IDT CRISPR-Cas9 guide RNA design checker, ordered from IDT, and re-suspended in TE buffer at 100uM. Guides were complexed with Alt-R Sp Cas9 (IDT, 1081059) and subsequent RNP was delivered into iMG by nucleofection using Lonza’s P3 Primary Cell 4D-Nucleofector X Kit (V4SP3960). iMG were maintained for 24-h in Deepwell Protein LoBind plates (Eppendorf, 951032107) and thereafter collected and centrifuged to remove dead cells. Cells were plated in relevant assay plates and maintained for 9 days with half medium changes every 2 days. WT, GPR34 KO, TREM2 KO, and GPR34/TREM2 KO induced microglia (iMG) cultured in microglia maintenance media were treated with either PBS or myelin (25 µg/mL) for 48 hours. For each sample, RNA was extracted from a pool of two replicate wells, each seeded with 25,000–30,000 cells.

value: iPSC-derived microglia

value: TREM2 KO

value: Myelin

tag: replicate


title: river, female, muscle #8

description:
Library name: O8M
ctm_female.csv

value: muscle


title: C619, scRNA-seq

description:
Fluidigm C1
C619


title: AML PDX TUH84 P0 bulk RNA-seq

description:
Library name: TUH84_P0
Model TUH84 timepoint P0


title: MKUC64_4

city: Bangkok

first: Apidet

last: Rakpenthai

state: Chatuchak

address: 50 Ngamwongwan Rd

country: Thailand

institute: Kasetsart University

description:
Library name: Sample 9
Biological replicate 3 of six-month-old leaf tissue from MKUC64-36-160.

data_processing:
Sequence read were trimmed by Trimmomatic
Trimmed read were mapped to ASM41409v2 genome by using HISAT2
Gene Expression Quantification and Profile were preform using StringTie
DEG analysis  were preform using DESeq2
Assembly: ASM41409v2 was used as a reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Manihot esculenta

source_name: CMV resistant line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Library Prep Kit and TruSeq Stranded mRNA Reference

value: CMV resistant line

value: CMV treatment


title: MKUC64_3

description:
Library name: Sample 8
Biological replicate 2 of six-month-old leaf tissue from MKUC64-36-160.


title: C617, scRNA-seq

description:
Fluidigm C1
C617


title: C611, scRNA-seq

description:
Fluidigm C1
C611


title: AML PDX TUH83 P2 bulk RNA-seq

description:
Library name: TUH83_P2
Model TUH83 timepoint P2


title: C603, scRNA-seq

description:
Fluidigm C1
C603


title: MKUC64_2

description:
Library name: Sample 7
Biological replicate 1 of six-month-old leaf tissue from MKUC64-36-160.


title: AML PDX TUH83 P1 bulk RNA-seq

description:
Library name: TUH83_P1
Model TUH83 timepoint P1


title: C602, scRNA-seq

description:
Fluidigm C1
C602


title: ITTI2_3

description:
Library name: Sample 6
Biological replicate 3 of six-month-old leaf tissue from TMS-IBA 980581.


title: C601, scRNA-seq

description:
Fluidigm C1
C601


title: AML PDX TUH83 P0 bulk RNA-seq

description:
Library name: TUH83_P0
Model TUH83 timepoint P0


title: C590, scRNA-seq

description:
Fluidigm C1
C590


title: ITTI2_2

description:
Library name: Sample 5
Biological replicate 2 of six-month-old leaf tissue from TMS-IBA 980581.


title: C580, scRNA-seq

description:
Fluidigm C1
C580


title: C577, scRNA-seq

description:
Fluidigm C1
C577


title: ITTI2_1

description:
Library name: Sample 4
Biological replicate 1 of six-month-old leaf tissue from TMS-IBA 980581.


title: C575, scRNA-seq

description:
Fluidigm C1
C575


title: AML PDX TUH76 P1 bulk RNA-seq

description:
Library name: TUH76_P1
Model TUH76 timepoint P1


title: C574, scRNA-seq

description:
Fluidigm C1
C574


title: C573, scRNA-seq

description:
Fluidigm C1
C573


title: HB100_4

description:
Library name: Sample 3
Biological replicate 3 of six-month-old leaf tissue from Huay Bong 100.

source_name: non-CMV resistant line

value: non-CMV resistant line


title: AML PDX TUH76 P0 bulk RNA-seq

description:
Library name: TUH76_P0
Model TUH76 timepoint P0


title: HB100_2

description:
Library name: Sample 2
Biological replicate 2 of six-month-old leaf tissue from Huay Bong 100.


title: C569, scRNA-seq

description:
Fluidigm C1
C569


title: C568, scRNA-seq

description:
Fluidigm C1
C568


title: AML PDX TUH10 P2 bulk RNA-seq

description:
Library name: TUH10_P2
Model TUH10 timepoint P2


title: C567, scRNA-seq

description:
Fluidigm C1
C567


title: HB100_1

description:
Library name: Sample 1
Biological replicate 1 of six-month-old leaf tissue from Huay Bong 100.


title: AML PDX TUH10 P1 bulk RNA-seq

description:
Library name: TUH10_P1
Model TUH10 timepoint P1


title: C564, scRNA-seq

description:
Fluidigm C1
C564


title: C562, scRNA-seq

description:
Fluidigm C1
C562


title: C560, scRNA-seq

description:
Fluidigm C1
C560


title: AML PDX TUH10 P0 bulk RNA-seq

description:
Library name: TUH10_P0
Model TUH10 timepoint P0


title: HEK293T, IFNg_24h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

first: JIANG

last: JIAYAO

address: 江苏省扬州市邗江区扬州大学文汇路校区

department: 扬州大学

institute: 扬州大学

description: Library name: 293T_IFNg_24h_2

data_processing:
Raw reads were trimmed with Trim Galore v0.6.5. Clean reads were aligned to the reference genome (GRCh38) using STAR v2.7.3. Obtaining gene-level read counts using the featureCount function from subread v2.0.0. Calculated TPM/FPKM value for each gene using RSEM v1.3.2. Differentially expressed genes were identified with FDR<0.05 and fold change>1 using DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited table, gene-level read counts

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, Nanjing, China).
RNA-seq libraries were construction by using DNBSEQ Eukaryotic Strand-specific mRNA library sample preparation kit (BGI), and sequenced as 150 bp paired-end reads with DNBSEQ platform (DNBSEQ Technology).

value: IFNg 24h


title: C558, scRNA-seq

description:
Fluidigm C1
C558

value: heart


title: HEK293T, IFNg_24h, RNA-seq, replicate 1

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_24h_1


title: C557, scRNA-seq

description:
Fluidigm C1
C557

value: Wnt1-Cre; R26-EYFP


title: C636, scRNA-seq

description:
Fluidigm C1
C636


title: AML PDX TUH06 P2 bulk RNA-seq

description:
Library name: TUH06_P2
Model TUH06 timepoint P2


title: C633, scRNA-seq

description:
Fluidigm C1
C633


title: AML PDX TUH93 P1 bulk RNA-seq

description:
Library name: TUH93_P1
Model TUH93 timepoint P1


title: HEK293T, IFNg_12h, RNA-seq, replicate 2

city: 江苏省 / 扬州市 / 邗江区

address: 江苏省扬州市邗江区扬州大学文汇路校区

description: Library name: 293T_IFNg_12h_2

value: IFNg 12h