title: FACS sorted epicardium-derived cells (CD31-tdTomato+PDPN-), Technical replicate 1, Biological replicate sample 2, E13.5

first: Quang

middle: Minh

last: Dang

state: Please select region, state or province

address: IDRM, Old Road Campus, Roosevelt Drive

department: Institute of Developmental and Regenerative Medicine (IDRM)

description: Library name: EPDC_E135_Sample2_r1

library_source: genomic

data_processing:
The ATAC-seq NF-core Nextflow pipeline (version 2.0) was used to pre-process ATAC-seq sequencing data, consisting of the following steps: quality control, adapter trimming, alignment to the UCSC mm10 genome, filtering unwanted reads, and merging across biological replicates. Filtering removed: reads aligning to mitochondrial DNA and blacklisted regions. PCR duplicates, multi-mapped reads, and reads that have an insert size > 2kb and contain > 4 mismatches.
Alignment files are converted to bed files using the randsample function of MACS2 (version 2.2.9.1) with 100% of tags kept (-p 100).  Peak-calling was performed with MACS2 using the following parameters: -f BEDPE -g mm -q 0.01 --nomodel --shift -73 --extsize 146 --call-summits --cutoff-analysis --keep-dup all.   The resulting peak summits were then extended by 250 bp to both sides to a fixed width of 501 bp. Peaks that extend beyond chromosome ends were filtered. The remaining peaks went through an iterative removal process to filter out less significant peaks that overlap with more significant ones.
The bigWig files for the epicardium and EPDC bulk ATAC-seq were normalised using the trimmed mean of M values normalisation method to account for differences in the peak landscape (signal-to-noise ratio) between samples. We used FeatureCounts to extract read counts for peaks and create a region-by-sample matrix. We then used this matrix to calculate a scale factor for each sample using EdgeR, which was then used to scale bigWig files accordingly using the –scaleFactor parameter of the bamCoverage tool.
Assembly: mm10
Supplementary files format and content: bigWig (.bw); BigWig files were generated using bamCoverage
Supplementary files format and content: Peak files called using MACS2

molecule: genomic DNA

source_name: Heart

extract_protocol:
Whole embryonic hearts were enzymatically dissociated using the Neonatal Heart Dissociation Kit (Miltenyi Biotec) following the manufacturer’s instructions and as previously described. Biological replicate samples are indipendent samples generated from pooled hearts.E11.5, E13.5, and E17.5  hearts (Rosa26tdTomato; Wt1CreERT2/+) from littermate embryos were pooled prior to dissociation (E11.5: 6 hearts/sample; E13.5: 4-13  Hearts/sample; E17.5: 4 Hearts/sample) to maximise cell numbers for FACS and corresponding FMO controls, and achieve a target sort of 50,000 epicardial cells/sample for the downstream ATAC-seq protocol. Single-cell suspensions in cell staining buffer (Biolegend) were pre-treated for 5 minutes on ice with TruStain FcX antibody, followed by surface staining with BV421 anti-CD31 and APC/Cy7 anti-Podoplanin (PDPN) antibody for 30 minutes on ice, then washed with PBS before being incubated with SYTOX Green Dead Cell Stain for 5 minutes on ice. After PBS washes, cells were resuspended in sorting buffer containing 2% FBS in PBS. BD FACSAria III was used to sort 40,000-50,000 live cells negative for SYTOX Green and CD31, and positive for tdTomato and PDPN, into 0.5% BSA in PBS. Live epicardial cells (CD31-tdTomato+PDPN+) from E11.5 and E17.5 hearts and live epicardiium-derived cells (EPDCs) (CD31-tdTomato+PDPN-) from E12.5 and E13.5 hearts were isolated by FACS were subjected to the ATAC-seq protocol as previously described.
ATAC-seq DNA libraries were generated as previously described, with minor modifications. Reactions were purified using the MinElute Reaction Cleanup Kit (Qiagen) following the manufacturer’s instructions. Pre-amplification of transposed fragments (5 cycles) was performed using NEBNext Ultra II Q5 Master Mix (NEB) and Nextera i7 index adapters (IDT). The number of additional amplification cycles (typically 4) was determined using the qPCR method. Final PCR products were purified using a double-sided bead purification method with SPRIselect beads (0.5X volume followed by 1.3X volume of SPRI beads). Final cleanup was performed with the MinElute Reaction Cleanup Kit (Qiagen). Libraries were assessed for quality using an Agilent TapeStation with a D1000 DNA ScreenTape assay, and quantified with the KAPA Library Quantification Kit. Next-generation sequencing (NGS) was conducted on equimolar pooled libraries using the NextSeq 500/550 High Output v2.5 kit (75 cycles) (Illumina), with paired-end reads (40 bp x 2) and 8 bp single index reads.

value: Heart

value: Epicardial cells


title: RNASeq6_T2_sgEIF4G2

status: Public on Apr 13 2026

type: SRA

city: New York

first: Chritine

last: Chio

state: NY

department: ICG

country: USA

institute: Columbia Unievristy

description: Library name: RNASeq6

library_source: transcriptomic

data_processing:
After sequencing, samples were processed with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next 3' adapters were trimmed from reads using Cutadapt (v3.2). Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome hg38 using STAR (v2.7.7a), during the alignment multimapping reads were not retained. The exclusion of multimapping reads reduces false positive differential and pausing calls. The removal of multimapping reads may lead to underestimates of counts for genes with high rates of pseudogenization or duplication events. PCR duplicates were removed using UMI-tools (v1.1.1). Gene coverage was calculated using Eclipsebio's proprietary feature counting algorithm and ribosome occupancy was calculated by dividing coverage in the ribosome protected footprint (RPF) library by the RNA-Seq library. Differentially expressed and occupied genes were identified using DESeq2. For transcriptome analyses, genomic aligned reads were aligned to the transcriptome with mudskipper (v0.1.0). Transcriptome aligned reads were processed with riboWaltz and custom analysis programs developed by Eclipsebio to determine codon usage, stall sites, 5' UTR loading, and 3' read through. ORF detection was performed on genome alignments using ribotricer (v1.3.3).
Assembly: hg38
Supplementary files format and content: tsv , Files conatin Ribosome occupancy (RO), Ribosome footprints(RPF) and RNA seq differentially expressed genes

molecule: total RNA

organism: Mus musculus

source_name: Cell Line

growth_protocol: Monolayer KPC primary pancreatic cancer cells were generated from tumors derived from Trp53+/LSL-R172H, Kras+/LSL-G12D, Pdx1-Cre (KPC) mice (44). HEK293T cell line was from ATCC (Cat# CRL-3216, RRID:CVCL_0063). All cells were cultured in DMEM (Gibco Cat#11995073) supplemented with 10% fetal bovine serum (FBS) (Corning Cat# 35-010-cv) and 1% PS unless stated otherwise.  All cells were cultured at 37 °C with 5% CO2.

extract_protocol:
For each starting sample, cells were lysed and 1 µg of total RNA was isolated for RNA-Seq while 9 µg of total RNA was digested with RNase I to isolate ribosome protected RNA footprints (RPFs). Both sample types were taken through rRNA depletion and RNA-seq samples were heat fragmented. Both sample types then underwent adapter ligation.
Ligated RNA was reverse transcribed, libraries were generated via PCR, and then sequenced on a NextSeq 2000.

tag: tissue

value: Cell Line

tag: cell line

tag: cell type

value: PDA

tag: genotype


title: FACS sorted epicardium-derived cells (CD31-tdTomato+PDPN-), Biological replicate sample 1, E13.5

city: Oxford

country: United Kingdom

institute: University of Oxford

description: Library name: EPDC_E135_Sample1

tag: treatment


title: iN-Exp-42-POM1

city: La Jolla

first: Daniel

last: Ojeda-Juarez

state: CA

address: 9500 Gilman Dr. MC 0612

institute: UC San Diego

description:
Library name: Sample 12
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.42.POM1

data_processing:
Fastqs were processed by the Center for RNA Technologies and Therapeutics at UC San Diego using the nf-core RNA-seq pipeline (3.13.2) [https://doi.org/10.5281/zenodo.1400710].
Differential expression analysis was performed with DESeq2 v1.32.0 on the raw counts matrix.
Assembly: reads were adapter trimmed with cutadapt (3.4), mapped using STAR (2.7.9a), and quantified with Salmon (1.10.1) using annotations derived from Gencode V40.
Supplementary files format and content: tsv file includes transcripts per million for each sample

growth_protocol: Human iPSCs from the wild-type genetic background (WTC11; male, Asian) line containing a Tet-ON 3G-controlled Ngn2 transgene (Wang et al., 2017) were cultured in DMEM/F-12 (HAM) with Essential 8 Supplement (Life Technology, A1517001) and split at a 1:6 dilution when confluent using StemPro Accutase (Gibco, A11105) for dissociation. iPSCs from passages 12 to 19 were used for pre-differentiation. iNs were differentiated with a two-step protocol (pre-differentiation and maturation) as previously described (Wang et al., 2017). Briefly, for pre-differentiation, iPSCs were plated in six-well plates coated with Matrigel, and incubated in knockout Dulbecco’s modified Eagle’s medium (KO-DMEM)/F12 medium containing N2 supplement, non-essential amino acids (1X NEAA; Life Technologies™), mouse laminin (1 μg/mL; Life Technologies™), brain-derived neurotrophic factor (BDNF, 10 ng/mL; Peprotech), neurotrophin-3 (NT3,10 ng/mL; Peprotech), and doxycycline (2 μg/mL; Sigma) for 3 days. Day 1 media only was supplemented with Y-27632 (10 µM; Cayman). The medium was changed daily. For maturation (Day 4), pre-differentiated iN precursor cells were dissociated, counted, and plated at 650,000 cells/well in six-well plates coated with poly-L-lysine (PLL) in maturation medium containing 50% DMEM/F12, 50% Neurobasal-A medium, 0.5X B27 supplement, 0.5X N2 supplement, 1X GlutaMax, 1X NEAA, doxycycline (2 μg/mL), mouse laminin (1 μg/mL), BDNF (10 ng/mL), and NT3 (10 ng/mL). Half the medium was changed weekly. Cells were handled in a sterile tissue culture hood, stored in a cell culture incubator with 5% CO2 at 37 °C, and checked for bacterial contamination. Four passages of iPSC were tested for mycoplasma contamination with the LookOut Mycoplasma PCR Detection kit (Sigma-Aldrich).

extract_protocol:
Samples were lysed in RLT buffer and RNA isolated using the RNeasy Micro kit (Cat# 74004; Qiagen) following the manufacturer’s protocol.
samples with an RNA Integrity Number (RIN) greater than 8.5 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). Samples were processed following the manufacturer's instructions.

treatment_protocol: For RNA-seq, 6 - 8 week-old iNs were treated with PBS, POM1 (33 nM), or IgG (33 nM) for 2 hours.

value: iPSC-derived neurons from WTC11 cells


title: KO1_Colon tissue

city: Shanghai

first: Ming

last: Feng

address: 280 S. Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: KO1_lib
KO1_FPKM

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke.
Trimmed seaence reads were mapped to mm39 using Hisat2.
Read count extraction and normalization were performed using RSEM.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Samples

source_name: Colon

extract_protocol:
Total RNA was isolated using Trizol reagent.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads; following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature, after which the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter, and the products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Colon

tag: strain

tag: Sex

value: female

value: ChREBP knockout

value: AOM/DSS

tag: time


title: iN-Exp-42-PBS

description:
Library name: Sample 11
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.42.PBS

value: PBS


title: FACS sorted epicardium-derived cells (CD31-tdTomato+PDPN-), Technical replicate 2, Biological replicate sample 2, E13.5

description: Library name: EPDC_E135_Sample2_r2


title: YZ791

city: Chongqing

first: Xinyu

last: Zhou

address: 1 Youyi Road, Yuzhong District

department: Department of Psychiatry

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Raw reads were first cleaned by removing reads containing the adapter by using Trimmomatic. FastQC (version0.10.1) was used to assess the quality of raw reads. Clean reads were then aligned to the human reference genome GRCh38 using HISAT2. FeatureCounts was used to count reads mapped to individual genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
For each enrolled participant, 2mL fasting venous blood samples were collected in PAXgene Blood RNA Tubes. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN) and isolated from peripheral blood using TRIzol® Reagent according to the manufacturer's protocol.
RNA purification, reverse transcription, library construction, and sequencing were done at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) (Illumina, San Diego, CA). A library of RNA-seq transcripts was made with 1μg of total RNA and the Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA). Messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. The resulting double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). The synthesized cDNA was then subjected to end-repair, phosphorylation, and 'A' base addition as per Illumina's library construction protocol. The libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose, and then PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After measuring with Qubit 4.0, the Nova Seq 6000 sequencer was used to read the paired-end RNA-seq library (2 × 150bp read length).

value: peripheral blood

tag: disease state

value: Major depressive disorder (MDD)

value: Without Drug therapy


title: CTL1_Colon tissue

description:
Library name: CTL1_lib
CTL1_FPKM

value: WT


title: YZ809

value: Drug therapy


title: iN-Exp-41-PBS

description:
Library name: Sample 8
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.41.PBS


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 2, E11.5

description: Library name: ATAC_E115_EPI2


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 1, E11.5

description: Library name: ATAC_E115_EPI1


title: YZ796


title: PPP-ctrl-rep3

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description: Library name: PPP-ctrl-rep3

data_processing:
Reads were mapped to the mm10 reference genome via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Read counts per gene were calculated by featureCounts (Subread v1.5.0-p1) with parameters "-s2 -Sfr -p".
Signal tracks were generated by STAR v2.5 with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.
Supplementary files format and content: Normalized signal tracks in bigWig format.

source_name: testis

extract_protocol:
RNA was extracted using the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems, KIT0204)
250 ng of RNA were used for  libraries preparation using the TruSeq Stranded mRNA Library Prep protocol (Illumina, #20020594).

value: testis

tag: developmental stage

value: Ppp1r3c f/f


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 2, E17.5

description: Library name: ATAC_E175_EPI2

value: Heart


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 3, E17.5

description: Library name: ATAC_E175_EPI3

value: Epicardial cells


title: macrophages present in the steady state, rep 2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Library name: Ctrl_R2

data_processing:
FastQ files were preprocessed first by inspecting raw short-reads for quality with FastQC (Babraham Bioinformatics) and then were quality-filtered and adapter-trimmed with Fastp version 0.23.2 (Chen et al., 2018) (--length_required 50).
Filtered reads were subsequently aligned against mouse genome (Mus_musculus.GRCm39, primary assembly) with RNA-STAR version 2.7.11a (Dobin et al., 2013) (--alignIntronMin 20 --alignIntronMax 100000). Alignment files were first indexed with Samtools version 1.10 (Li et al., 2009).
Aligned reads were then assigned to genes, using the annotation file Mus_musculus.GRCm39.109.gtf, with the function featureCounts of Subread version 2.0.6 (Liao et al., 2013) (-t exon -g gene_id -M --primary -s 2).
Differentially expressed genes (DEGs) were determined with DESEq2 version 1.40.2 (Love et al., 2014) using default parameters.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: peritoneal fluid

growth_protocol: Tim4+ resMØs were isolated by FACS from peritoneal cell suspensions from control mice, and from mice at day 12 after MTO injection, after immunofluorescent staining with PECy7-conjugated anti-CD11b (eBioscience), APC-conjugated anti-MHCII (eBioscience) and Brilliant Violet 421-conjugated 14 anti-Tim4 (BD Biosciences); propidium iodide (Sigma) was added for viability staining before sorting. Cells were sorted using a BD FACSAria™ II sorter (BD Biosciences) with a 85 μm nozzle, at the Flow Cytometry Facility of the Centro de Biología Molecular Severo Ochoa (CBMSO, Madrid). FACS-sorted resMØ preparations had a purity > 97%. Sorted cells were subsequently spun at 400g, resuspended in 100 μl of Lysis solution (Invitrogen) and stored at -80ºC until RNA extraction.

extract_protocol:
Total RNA was extracted, from 3 biological replicates per condition, using the RNAqueous-Micro Kit (Invitrogen), according to the manufacturer’s instructions. RNA samples were quantified and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies).
30 ng of total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher). Libraries were sequenced at a final concentration of 650 pM using a P2 flow cell in a NextSeq 2000 sequencer (Illumina) to generate 100pb single reads.

value: peritoneal fluid

value: macrophage


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 3, E11.5

description: Library name: ATAC_E115_EPI3


title: YZ688


title: YZ680


title: NC1

city: Fuzhou

first: xiaochai

last: lv

address: Xin-quan Road

institute: Fujian Medical University Union Hospital

description: Library name: Sample 1

data_processing:
Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. Differentially expressed miRNA between two groups were filtered by Fold Change and P-value.
miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Assembly: rn6
Supplementary files format and content: miRNA_Expression.xlsx The table contains the number of miRNA raw counts identified and normalized counts.

organism: Rattus

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent
The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were successively ligated to RNA samples. Then, the adaptor-ligated RNA was reversely transcribed into cDNA, followed by PCR amplification. After amplification, the cDNA libraries were size-selected for miRNA fractions before sequencing and then sequenced in platform.

value: Hippocampus

value: Sprague-Dawley

tag: batch


title: YZ687


title: CTL3_Colon tissue

description:
Library name: CTL3_lib
CTL3_FPKM

value: Colon

value: female


title: FACS sorted epicardium-derived cells (CD31-tdTomato+PDPN-), Biological replicate sample 1, E12.5

description: Library name: EPDC_E125_Sample1


title: PPP-KO-rep2

description: Library name: PPP-KO-rep2

value: Sf1-Cre Ppp1r3c f/f


title: iN-Exp-40-POM1

description:
Library name: Sample 6
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.40.POM1

value: iPSC-derived neurons from WTC11 cells


title: PPP-ctrl-rep2

description: Library name: PPP-ctrl-rep2


title: iN-Exp-41-IgG

description:
Library name: Sample 7
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.41.IgG

value: IgG


title: YZ686

value: peripheral blood

value: Major depressive disorder (MDD)


title: PPP-ctrl-rep1

description: Library name: PPP-ctrl-rep1


title: iN-Exp-42-IgG

description:
Library name: Sample 10
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.42.IgG


title: Infected mice lung, 15 days, bio rep1

city: Shenzhen

first: feng

last: chun

institute: SUSTech

description: Library name: Treatment 1

data_processing:
Quality control of the sequencing data was performed using FastQC, followed by adapter trimming and removal of low-quality reads with Trim Galore. Paired-end alignment was conducted using STAR v2.7.11b, and output files were converted with SAMtools. Read counting was performed using featureCounts, focusing on reads mapped to exonic regions and excluding multi-mapped reads.
Assembly: GCF_000149245.1
Supplementary files format and content: A comma-separated values file containing raw counts, with genes in rows and samples in columns.

source_name: Lung

extract_protocol:
RNA was harvested using GoldHi Plasmid Mini Kit.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Lung

value: Infected


title: YZ692

value: Without Drug therapy


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, Mock infected control, rep3

first: Jeffrey

middle: Y

last: Lee

address: Dorothy Hodgkin Road

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed and adapter trimmed.
Reads were aligned to GRCh38 and HIV-1 NL4-3 reference sequence (AF324493.2) using STAR.
Crosslink position and counts were extracted using Bedtools and converted to BigWig files.
Significant RNA binding sites of PURA and PURB were determined using the R package DEW-seq.
Assembly: GRCh38, AF324493.2
Supplementary files format and content: BigWig file of crosslinked nucelotide positions (counts)
Library strategy: iCLIP-seq

source_name: Jurkat Flp-In T-Rex PURB-eGFP

growth_protocol: Jurkat Flp-In T-REx PURA-eGFP and PURB-eGFP cells were induced with 1 µg/ml of doxycycline overnight.

extract_protocol:
Cells were washed twice in PBS 1X, resuspended in 3 ml of PBS 1X, crosslinked with two rounds of 0.15 J/cm2 UV light irradiation at 254 nm, washed with PBS 1X and lysed in 1 ml RIPA buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% wt/vol Na deoxycholate and 0.2 mM AEBSF).
Libraries were constructed using iCLIP2 procotol (https://doi.org/10.1016/j.ymeth.2019.10.003)

treatment_protocol: Cells were infected with 1 MOI or mock infected of VSV-G-pseudotyped HIV-1-R-E-mCherry-Nef for 48 h.

value: Jurkat Flp-In T-Rex PURB-eGFP

tag: infection

value: Mock infection


title: PPP-KO-rep3

description: Library name: PPP-KO-rep3

value: testis


title: CTL2_Colon tissue

description:
Library name: CTL2_lib
CTL2_FPKM

value: WT

value: AOM/DSS


title: Infected mice lung, 15 days, bio rep2

description: Library name: Treatment 2


title: YZ679

value: Drug therapy


title: YZ792


title: iN-Exp-41-POM1

description:
Library name: Sample 9
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.41.POM1


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, Mock infected control, rep2


title: iN-Exp-39-1-POM1

description:
Library name: Sample 3
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.39.1.POM1


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, Mock infected control, rep1


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP immunoprecipiated for PURB, Mock infected control, rep3


title: YZ673


title: iN-Exp-39-1-PBS

description:
Library name: Sample 2
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.39.1.PBS

value: PBS


title: FACS sorted epicardial cells (CD31-tdTomato+PDPN+), Biological replicate sample 1, E17.5

description: Library name: ATAC_E175_EPI1

value: Heart

value: Epicardial cells


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, Mock infected control, rep3

source_name: Jurkat Flp-In T-Rex PURA-eGFP

value: Jurkat Flp-In T-Rex PURA-eGFP


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP immunoprecipiated for PURB, Mock infected control, rep2


title: iN-Exp-40-PBS

description:
Library name: Sample 5
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.40.PBS

value: iPSC-derived neurons from WTC11 cells


title: iN-Exp-39-1-IgG

description:
Library name: Sample 1
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.39.1.IgG

value: IgG


title: YZ670

value: peripheral blood


title: RAW264.7 cells, shTrem2, rep3

city: Beijing

first: Jiayu

last: Wang

state: Beijing

address: Beijing Chao-Yang Hospital, 8 Gongren Tiyuchang Nanlu, Beijing, China

institute: Beijing Chao-Yang Hospital, Capital Medical University

description:
Library name: Sample6
shTrem2_B3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: xls files include FPKM values for each sample

growth_protocol: RAW264.7 cells were cultured in RAW264.7 cell-specific medium (Procell, CM-0190) under standard conditions (37 °C, 5% CO₂).

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥ 6.5, 28S:18S≥ 1.0, >1g) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

treatment_protocol: RAW264.7 cells were treated with 20 ng/ml IL-4 protein (MedChemExpress, HY-P70653) for 24 hours to induce polarization. After that, renal tubular epithelial cell debris was added for co-culture.

value: Trem2 knockdown (shTrem2)


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, Mock infected control, rep1


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, Mock infected control, rep3


title: RAW264.7 cells, shTrem2, rep2

description:
Library name: Sample5
shTrem2_B2


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, Mock infected control, rep1


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, Mock infected control, rep2


title: YZ664

value: Major depressive disorder (MDD)


title: RAW264.7 cells, shTrem2, rep1

description:
Library name: Sample4
shTrem2_B1


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, HIV-1 infected, rep3

value: HIV-1 infection (MOI 1)


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, HIV-1 infected, rep1


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP size-matched input for PURB, HIV-1 infected, rep2


title: YZ666


title: YZ667

value: Without Drug therapy


title: iN-Exp-40-IgG

description:
Library name: Sample 4
Collumn name in salmon.merged.transcript_tpm.tsv: iN.Exp.40.IgG


title: PPP-KO-rep1

description: Library name: PPP-KO-rep1

value: Sf1-Cre Ppp1r3c f/f


title: RAW264.7 cells, shNC, rep3

description:
Library name: Sample3
shNC_A3

value: Empty vector control (shNC)


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP immunoprecipiated for PURB, HIV-1 infected, rep3

value: Jurkat Flp-In T-Rex PURB-eGFP


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP immunoprecipiated for PURB, HIV-1 infected, rep1


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, HIV-1 infected, rep2


title: YZ652


title: YZ678


title: RNA-Seq, Ma10 cells, MTTP knockout 4

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

description: Library name: Q4

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCh37/hg19 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm39
Supplementary files format and content: Microsoft Excel Open XML Format Spreadsheet file includes raw counts for each sample

growth_protocol: MA10 cells from ATCC were cultured in DMEM/F12 medium supplemented with 15% horse serum and antibiotics in humidified chamber with 5% CO2 at 37ᴼC.

extract_protocol:
Total RNA was extracted from cells using Trizol method. RNA was further cleaned up by RNA clean up kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 48h cultures of MA10 cells were treated with 0.5 mM 8-BrcAMP in DMEM/F12 medium for 3h.

value: Leydig cells

value: Wildtype


title: YZ648


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, HIV-1 infected, rep1


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, HIV-1 infected, rep3


title: YZ647

value: Drug therapy


title: RNA-Seq, Ma10 cells, MTTP knockout 3

description: Library name: Q3


title: YZ646


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, HIV-1 infected, rep1


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP immunoprecipiated for PURA, HIV-1 infected, rep2


title: YZ645


title: RNA-Seq, Ma10 cells, MTTP knockout 1

description: Library name: Q1


title: YZ671


title: YZ642


title: RAW264.7 cells, shNC, rep2

description:
Library name: Sample2
shNC_A2


title: RAW264.7 cells, shNC, rep1

description:
Library name: Sample1
shNC_A1


title: MIA PaCa-2_MeTA#3+Tet_exp1

type: RNA

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in MIA PaCa-2_MeTA#3 cell line with tetracycline

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A: HPDE_MeTA#1, MIA PaCa-2_MeTA#3, and PK-9_MeTA#15 cells and G4112F: PK-1_MeTA#17 cells) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MIA PaCa-2_MeTA#3+Tet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Three cell lines derived from pancreatic cancer, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15, were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. A cell line derived from normal pancreatic ductal epithelial cell, HPDE_MeTA#1, was grown in HuMedia-KG2 (Kurabo, Osaka, Japan).

extract_protocol: The RNAs from HPDE_MeTA#1, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15 cells with (4 days tetracycline treatment) or without tetracycline were prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HPDE_MeTA#1, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15  cells were treated with or without 1 μg/ml tetracycline for 4 days.

value: MIA PaCa-2_MeTA#3

value: pancreatic cancer cell line

tag: tissue source

value: pancreas

tag: genotype/variation

value: with 1 μg/ml tetracycline for 4 days.


title: MIA PaCa-2_MeTA#3-Tet_exp1

description: Gene expression in MIA PaCa-2_MeTA#3 cell line without tetracycline

source_name: MIA PaCa-2_MeTA#3-Tet

value: none (no tetracycline)


title: YZ639


title: HPDE_MeTA#1+Tet_exp1

description: Gene expression in HPDE_MeTA#1 cell line with tetracycline

value: normal pancreatic ductal epitherial cell line


title: RNA-Seq, Ma10 cells, Wildtype 3

description: Library name: P3


title: YZ638

value: peripheral blood


title: RNA-Seq, Ma10 cells, Wildtype 4

description: Library name: P4


title: mut GBA-PD_2

city: Tübingen

first: Dina

last: Ivaniuk

address: Otfried Müller Str. 23

country: Germany

institute: DZNE

description: Gene expression data from day 55 iPS-derived neurons

hyb_protocol: Following fragmentation, 18-23 ug of cRNA were hybridized for 18-20 hr at 45C on Affymetrix GeneChip Human Gene 2.0 ST Array. Washing and staining was performed using the Affymetrix HWS Kit (Affymetrix P/N 900720) with a fluidics station (GeneChip Fluidics Station 450, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Robust Multi-array Analysis algorithm (RMA) did background correction, summarization and normalization with Affymetrix software Expression Console v1.* .Genes differentially expressed were selected based upon a 1.5-fold change cut-off and significant statistical difference (P<0.05).

label: biotin

source_name: Day 55 sorted neurons

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Induced pluripotent stem cells were differentiated into midbrain dopaminergic neurons according to Kriks et al, Nature 2011

extract_protocol: Total RNA was isolated from FACS sorted neurons using a PureLink RNA micro kit (Invitrogen) according to manufacturer’s instructions

treatment_protocol: At day 55 cells were subjected to FACS sorting. Sorted neurons were collected and used for microarray analysis

value: iPSC derived DA neurons

value: GBA-PD (N370S)

tag: age


title: RNA-Seq, Ma10 cells, Wildtype 2

description: Library name: P2


title: YZ634

value: Major depressive disorder (MDD)


title: mut GBA-PD_3


title: RNA-Seq, Ma10 cells, MTTP knockout 2

description: Library name: Q2


title: PK-9_MeTA#15-Tet_exp1

description: Gene expression in PK-9_MeTA#15 cell line without tetracycline


title: AML 124 Relapse 2 RNA seq

city: Charlottesville

first: Subhash

last: Prajapati

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Library name: AML_124_Rel2_riboM_RNAseq

data_processing:
Reads were aligned to the hg19 human genome using STAR aligner (version 2.3.0e). Aligned results were annotated using RefSeq gene model and HTSeq union mode.
Read counts were normalized to Transcripts per million reads (TPM) with normal bone marrow controls included in expression analysis for normal variance estimation as described in PMID 41608320.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab delimited file contains non-normalized raw read counts aligned to hg19

source_name: Bone Marrow

extract_protocol:
High quality RNA was isolated using phenol-chloroform/Trizol with subsequent purification using Qiagen Rneasy kit.
TruSeq RNA-Seq by ploy(A) enrichment

value: Bone Marrow


title: PK-9_MeTA#15+Tet_exp1

description: Gene expression in PK-9_MeTA#15 cell line with tetracycline


title: YZ633


title: YZ661


title: MA10 cells, MTTP knockout 2

description: Library name: KO2

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
8-BrcAMP-treated cells were frozen in 10% DMSO containing medium.
Nuclei are extracted from samples and tested for quality control (QC). After the QC, the nuclei pellets are resuspended in the Tn5 transposase reaction mix, which includes transposase and equimolar Adapter1 and Adapter 2. The mix of transposition reaction is incubated at 37°C for 30 min. PCR is then performed to amplify the library. Libraries were purified with the AMPure beads and library quality was assessed. After the construction of the library, the initial quantification was done with Tapestation 4150, and the library is diluted to 2-4ng/μl. Then the insertion size of the library is detected with NGS3K. If meeting the expectation, the accurate concentration of the library is quantified by Q-PCR (library effective concentration > 2nM) to ensure the accurate molar amount that will pooled for sequencing.

treatment_protocol: 48-h cultures of MA10 cells were treated with 0.5 mM 8-BrcAMP in DMEM/F12 medium for 3h.

value: MTPKO


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, Mock infected control, rep2

value: Jurkat Flp-In T-Rex PURA-eGFP

value: Mock infection


title: YZ631


title: Jurkat Flp-In T-Rex PURB-eGFP, iCLIP immunoprecipiated for PURB, HIV-1 infected, rep2

value: Jurkat Flp-In T-Rex PURB-eGFP

value: HIV-1 infection (MOI 1)


title: AML 130 Relapse 4 RNA seq

description: Library name: AML_130_Rel4_riboM_RNAseq

source_name: PBMCs

value: PBMCs


title: AML 124 Relapse 1 RNA seq

description: Library name: AML_124_Rel_riboM_RNAseq


title: MA10 cells, MTTP knockout 1

description: Library name: KO1

value: Leydig cells


title: AML 130 Relapse 3 RNA seq

description: Library name: AML_130_Rel3_riboM_RNAseq


title: AML 124 Diagnosis RNA seq

description: Library name: AML_124_Dx_riboM_RNAseq


title: RNA-Seq, Ma10 cells, Wildtype 1

description: Library name: P1

value: Wildtype


title: YZ630

value: Drug therapy


title: MA10 cells, Wildtype 2

description: Library name: WT2


title: Control_1

value: Control


title: mut GBA-PD_1


title: AML 130 Relapse 2 RNA seq

description: Library name: AML_130_Rel2_riboM_RNAseq


title: Control_2


title: HPDE_MeTA#1-Tet_exp1

description: Gene expression in HPDE_MeTA#1 cell line without tetracycline

value: pancreas

value: none (no tetracycline)


title: Control_3


title: YZ622

value: peripheral blood


title: AML 140 Relapse RNA seq

description: Library name: AML140_Rel


title: MA10 cells, Wildtype 1

description: Library name: WT1


title: AML 130 Diagnosis RNA seq

description: Library name: AML_130_Dx_riboM_RNAseq


title: AML 140 Diagnosis RNA seq

description: Library name: AML140_Dx


title: YZ621


title: YZ618


title: YZ619

value: Without Drug therapy


title: MVT1_ctc_single_m2

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

description:
Library name: Sample 15
10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were trimmed from the 3’ end until the final base had a quality score >30, utilizing Trimmomatic (v0.33). Quality assessment of RNA-seq data was performed using FastQC (v0.11.4). Trimmed reads were aligned to the appropriate reference genomes using STAR (v2.7.3a): the human genome (GRCh38) for LM2 samples and the mouse genome (GRCm39) for MVT1 samples. Gene-level expression counts were quantified with HTSeq (v2.0.5), using GENCODE gene annotations (release 44 for human, release M33 for mouse).
FASTQ files were demultiplexed and aligned using Cell Ranger (v6.0.0, 10x Genomics) with default parameters. Reads were aligned to species-specific reference genomes provided by 10x Genomics: refdata-gex-GRCh38-2020-A for human (LM2-NSG, BR16-NSG) samples and refdata-gex-mm10-2020-A for mouse (MVT1-FVB) samples. Doublet removal was performed using DoubletFinder (V2.0), following standard guidelines.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
For all cell types, viability assessment and fluorescence-based sorting were performed using a BD FACSAria Fusion cell sorter. Dead cells were excluded using SYTOX blue dead cell stain. Cancer cells were identified and sorted based on fluorescent markers: GFP for LM2 cells, RFP for BR16 cells, and CD90.2 for MVT1 cells, with the latter stained using Alexa Fluor 488 anti-mouse CD90.2 antibody.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3′ Gene Expression Kit v3. Briefly, viable single-cell suspensions were loaded onto Chromium Single Cell Chips, and libraries were constructed following the manufacturer’s protocol.


title: AML 139 Relapse RNA seq

description: Library name: AML139_Rel


title: MDCK cells, Mel56 (10 µM), N=1

city: Tokushima

first: Takashi

last: Kuzuhara

address: Yamashiro-cho

department: Faculty of Pharmaceutical Sciences

institute: Tokushima Bunri University

description:
Library name: PR8_Mel56 1
Colum name in raw_counts_All_Samples: PR8_Mel56_1

data_processing:
Trimmomatic v0.38, HISAT v2.1.0, SAMtools v1.9, StringTie v2.1.3b, and DESeq2 v1.38.3
Trimmomatic v0.38 was used to remove adapter sequences and trim poor-quality bases.
The cleaned reads were aligned to Canis lupus familiaris (CanFam3.1) using HISAT v2.1.0.
The aligned data (in SAM file format) were sorted and indexed using SAMtools v1.9.
The transcripts were assembled and quantified using StringTie v2.1.3b.
Gene-level and transcript-level quantifications were performed as raw read counts, Fragments Per Kilobase of transcript per million mapped reads, and TPM.
Statistical analyses of differential gene expression were performed using DESeq2 v1.38.3.
Assembly: Reference genome sequences and gene annotation data were downloaded from the NCBI Genome Assembly and RefSeq databases (Canis lupus familiaris [CanFam3.1]).
Supplementary files format and content: Text file includes raw counts, FPKM, and TPM for each sample.

organism: Canis lupus

source_name: kidney

growth_protocol: MDCK cells were cultured in growth medium (high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, and 4 mM L-glutamine). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cell lysates using an RNeasy Mini Kit (Qiagen, GmbH, Germany).
Total RNA concentration was calculated using Quant-IT RiboGreen (Thermo Fisher Scientific). To assess the integrity of total RNA, samples were run on a TapeStation RNA Screentape (Agilent Technologies, CA, USA). Only high-quality RNA preparations (RIN greater than 7.0) were used for RNA library construction. A library was independently prepared with 1 µg of total RNA for each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, CA, USA). The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T-attached magnetic beads. Following purification, mRNA was fragmented into small pieces using divalent cations at elevated temperatures. Cleaved RNA fragments were copied into first-strand cDNA using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) and random primers. This was followed by the synthesis of second-strand cDNA using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments underwent an end repair process, followed by the addition of a single ‘A’ base and ligation of the adapters. The products were purified and enriched using PCR to create a final cDNA library. Libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, MA, USA) and qualified using a TapeStation D1000 ScreenTape (Agilent Technologies).

treatment_protocol: MDCK cells were seeded in a 96-well plate (1 × 10⁴ cells/well). DMSO (0.1%) or Mel56 (10 μM) was mixed with or without A/PR/8/34 (MOI 0.01) virus in growth medium and incubated for 30 minutes at 37 °C with 5% CO₂, respectively. The resulting mixture was added to the cells for a 24-hour incubation at 37 °C with 5% CO2.

value: kidney

value: Madin-Darby canine kidney cells

value: Epitherial-like cell

value: WT

value: A/PR/8/34 at a MOI of 0.01 and treated with 10 µM Mel56

value: 24 hours


title: MVT1_primary_tumor_m2

description:
Library name: Sample 13
10X Genomics


title: AML 139 Diagnosis RNA seq

description: Library name: AML139_Dx

value: Bone Marrow


title: MVT1_ctc_cluster_m2

description:
Library name: Sample 16
10X Genomics


title: MVT1_lung_metastasis_m2

description:
Library name: Sample 14
10X Genomics


title: AML 130 Relapse 1 RNA seq

description: Library name: AML_130_Rel_riboM_RNAseq


title: MDCK cells, Mel56 (10 µM), N=3

description:
Library name: PR8_Mel56 3
Colum name in raw_counts_All_Samples: PR8_Mel56_3


title: MDCK cells, Mel56 (10 µM), N=2

description:
Library name: PR8_Mel56 2
Colum name in raw_counts_All_Samples: PR8_Mel56_2


title: AML 137 Relapse RNA seq

description: Library name: AML137_Rel


title: YZ616

value: Major depressive disorder (MDD)


title: YZ614


title: AML 137 Diagnosis RNA seq

description: Library name: AML137_Dx


title: MDCK cells, DMSO (0.1%), N=3

description:
Library name: PR8_DMSO 3
Colum name in raw_counts_All_Samples: PR8_DMSO_3

value: A/PR/8/34 at a MOI of 0.01 and treated with 0.1% DMSO


title: MDCK cells, DMSO (0.1%), N=2

description:
Library name: PR8_DMSO 2
Colum name in raw_counts_All_Samples: PR8_DMSO_2


title: MVT1_ctc_cluster_m1

description:
Library name: Sample 12
10X Genomics


title: AML 136 Relapse RNA seq

description: Library name: AML136_Rel


title: MVT1_ctc_single_m1

description:
Library name: Sample 11
10X Genomics


title: Jurkat Flp-In T-Rex PURA-eGFP, iCLIP size-matched input for PURA, HIV-1 infected, rep3

value: Jurkat Flp-In T-Rex PURA-eGFP

value: HIV-1 infection (MOI 1)


title: MDCK cells, DMSO (0.1%), N=1

description:
Library name: PR8_DMSO 1
Colum name in raw_counts_All_Samples: PR8_DMSO_1


title: YZ612

value: Drug therapy


title: AML 136 Diagnosis RNA seq

description: Library name: AML136_Dx


title: MVT1_lung_metastasis_m1

description:
Library name: Sample 10
10X Genomics


title: YZ610


title: DMDTC_DNMT3A_Mut4

type: genomic

city: Qingdao

first: liu

last: yanjun

state: shangdong

address: No. 1677 Wutaishan Road

department: Department of Pathology

institute: Qingdao University

description:
M6
Illumina Infinium MethylationEPIC v2.5 BeadChip data
DNMT3A_2606

hyb_protocol: Labeled DNA fragments were hybridized to the Illumina Infinium MethylationEPIC BeadChip at 48°C for 16–20 hours.

scan_protocol: The BeadChip was scanned using the Illumina iScan system to detect fluorescent signals.

data_processing:
Raw data (IDAT files) were processed using the minfi package in R. Background correction and normalization were performed. Probes with detection p-value > 0.05 were filtered out.
[processed value definition] Processed values represent methylation beta-values (range: 0 to 1), where 0 indicates fully unmethylated and 1 indicates fully methylated.

label: Cy3 and Cy5

label_protocol: Bisulfite-converted genomic DNA was amplified, fragmented, and labeled according to the standard Illumina Infinium Methylation Assay protocol.

extract_protocol: Genomic DNA was extracted from cultured cells using the TIANamp Genomic DNA Kit (TIANGEN, Cat. #CDP304-02) following the manufacturer's protocol. DNA was eluted in TE buffer, and purity was assessed by A260/A280 ratio (1.8-2.0) using a NanoDrop spectrophotometer. DNA concentration was quantified using Qubit dsDNA Quantification Assay Kit (Invitrogen, Cat. #Q32851). Only high-quality DNA samples (concentration ≥ 50 ng/µL, no degradation) were used for bisulfite conversion.

treatment_protocol: Cells were transfected with plasmids encoding DNMT3A wild-type, DNMT3A mutants (c.891G>A, c.2312G>A, c.2595A>T, c.2606G>A), or empty vector control (pcDNA3.1(+)-Flag) using Lipofectamine™ 3000 reagent (Invitrogen, Cat. #L3000015) according to the manufacturer's instructions. Cells were harvested 48 hours post-transfection for genomic DNA extraction.

value: Papillary thyroid carcinoma cell line

value: Transfection with DNMT3A mutant c.2606G>A


title: SI_gd_Bcl6p_2

city: Hangzhou

first: Shiyuan

last: Xie

address: Shilongshan Street

institute: Westlake University

description:
Library name: SI_gd_Bcl6p_2
Sample from batch 2 mice
BCL6-RFP_gd_counts.txt

data_processing:
Low-quality reads and adaptor sequences were removed using Fastp (v0.23.4)
Clean reads were aligned to the mm10 genome by Bowtie2 (v2.5.3) with default parameters, and uniquely mapping reads were quantified using the featureCounts function in Subread (v2.0.6).
Bach effects in raw counts were corrected using the ComBat_seq function in sva (v3.50.0)
Differentially expressed genes (DEGs) were identified using DESeq2 (v1.42.0)
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

source_name: Small intestine

extract_protocol:
Total RNA from γδIELs or intestinal epithelial tissues was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
For RNA sequencing of γδIEL subsets from BCL6RFP reporter mice, CD160+ BCL6RFP+ and CD160– BCL6RFP– γδΙELs were FACS-sorted and sent to BGI Genomics for cDNA library preparation. For sequencing of target-genes-knockout (KO) γδIELs, CD160+ CD122– CD8αα γδΙΕLs from Bcl6ΔCd8a or Tcf7ΔCd8a mice and total CD8αα γδIELs from Prdm1ΔCd8a mice were FACS-sorted and sent to Novogene for cDNA library preparation. For sequencing of the epithelial cell layer, the entire large intestinal epithelium from S. Tm. (SL3261)-infected or uninfected mice was isolated and sent to Novogene for cDNA library preparation.

value: Small intestine

value: CD160+ BCL6-RFP+ gdIEL

value: Steady state


title: YZ613

value: peripheral blood


title: MVT1_primary_tumor_m1

description:
Library name: Sample 9
10X Genomics


title: SI_gd_Bcl6p_3

description:
Library name: SI_gd_Bcl6p_3
Sample from batch 3 mice
BCL6-RFP_gd_counts.txt


title: YZ608

value: Without Drug therapy


title: AML 135 Diagnosis RNA seq

description: Library name: AML135_Dx

value: PBMCs


title: DMDTC_DNMT3A_Mut3

description:
M5
Illumina Infinium MethylationEPIC v2.4 BeadChip data
DNMT3A_2595

value: Transfection with DNMT3A mutant c.2595A>T


title: YZ605


title: AML 133 Relapse RNA seq

description: Library name: AML133_Rel


title: YZ607


title: SI_gd_Bcl6n_3

description:
Library name: SI_gd_Bcl6n_3
Sample from batch 3 mice
BCL6-RFP_gd_counts.txt

value: CD160- BCL6-RFP0 gdIEL


title: SI_gd_Bcl6p_1

description:
Library name: SI_gd_Bcl6p_1
Sample from batch 1 mice
BCL6-RFP_gd_counts.txt


title: AML 135 Relapse RNA seq

description: Library name: AML135_Rel


title: DMDTC_DNMT3A_Mut2

description:
M4
Illumina Infinium MethylationEPIC v2.3 BeadChip data
DNMT3A_2312

value: Transfection with DNMT3A mutant c.2312G>A


title: SI_gd_Bcl6n_2

description:
Library name: SI_gd_Bcl6n_2
Sample from batch 2 mice
BCL6-RFP_gd_counts.txt

value: CD160- BCL6-RFP- gdIEL


title: AML 133 Diagnosis RNA seq

description: Library name: AML133_Dx


title: SI_gd_Bcl6n_1

description:
Library name: SI_gd_Bcl6n_1
Sample from batch 1 mice
BCL6-RFP_gd_counts.txt


title: DMDTC_DNMT3A_Mut1

description:
M3
Illumina Infinium MethylationEPIC v2.2 BeadChip data
DNMT3A_891

value: Transfection with DNMT3A mutant c.891G>A


title: DMDTC_DNMT3A_WT

description:
M2
Illumina Infinium MethylationEPIC v2.1 BeadChip data
DNMT3A_WT

value: DNMT3A wild-type

value: Transfection with DNMT3A wild-type


title: YZ596

value: Major depressive disorder (MDD)


title: AML 132 Relapse RNA seq

description: Library name: AML132_Rel


title: LI_gd_Bcl6p_2

description:
Library name: LI_gd_Bcl6p_2
Sample from batch 3 mice
LI_gdIEL_Bcl6p_b3
BCL6-RFP_gd_counts.txt

source_name: Large intestine

value: Large intestine


title: YZ593

value: Drug therapy


title: AML 129 Relapse RNA seq

description: Library name: AML129_Rel


title: YZ603


title: YZ592


title: AML 132 Diagnosis RNA seq

description: Library name: AML132_Dx

value: Bone Marrow


title: LI_gd_Bcl6p_1

description:
Library name: LI_gd_Bcl6p_1
A mixture of samples from batch 1-2 mice
LI_gdIEL_Bcl6p_b1-2
BCL6-RFP_gd_counts.txt


title: DMDTC_DNMT3A_Vector

description:
M1
Illumina Infinium MethylationEPIC v2.0 BeadChip data
DNMT3A_Flag

value: Papillary thyroid carcinoma cell line

value: Empty vector (pcDNA3.1(+)-Flag)

value: Transfection with empty vector pcDNA3.1(+)-Flag


title: AML 129 Diagnosis RNA seq

description: Library name: AML129_Dx


title: LI_gd_Bcl6n_3

description:
Library name: LI_gd_Bcl6n_3
A mixture of samples from batch 1-3 mice
LI_gdIEL_Bcl6n_b1-3
BCL6-RFP_gd_counts.txt

value: Steady state


title: Sheep Gall Bladder (predissociated cells) SFWT2011-1 #2 (WT term)

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: AH880

data_processing:
Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 genome using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: oviAri4
Supplementary files format and content: bigWig

organism: Ovis aries

source_name: Gall Bladder

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

value: Gall Bladder


title: YZ588

data_processing:
Raw reads were first cleaned by removing reads containing the adapter by using Trimmomatic. FastQC (version0.10.1) was used to assess the quality of raw reads. Clean reads were then aligned to the human reference genome GRCh38 using HISAT2. FeatureCounts was used to count reads mapped to individual genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

extract_protocol:
For each enrolled participant, 2mL fasting venous blood samples were collected in PAXgene Blood RNA Tubes. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN) and isolated from peripheral blood using TRIzol® Reagent according to the manufacturer's protocol.
RNA purification, reverse transcription, library construction, and sequencing were done at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) (Illumina, San Diego, CA). A library of RNA-seq transcripts was made with 1μg of total RNA and the Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA). Messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. The resulting double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). The synthesized cDNA was then subjected to end-repair, phosphorylation, and 'A' base addition as per Illumina's library construction protocol. The libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose, and then PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After measuring with Qubit 4.0, the Nova Seq 6000 sequencer was used to read the paired-end RNA-seq library (2 × 150bp read length).

value: peripheral blood


title: WT/WT_long2 biol rep 3

city: Newcastle upon Tyne

first: David

last: Lydall

address: Cookson Building, Medical School, Framlington Place

institute: Newcastle University

description: Library name: c58z5

data_processing:
Raw sequencing reads were processed using fastp to remove adapters and low-quality reads.
Clean reads were aligned to the Saccharomyces cerevisiae W303 reference genome (JRIU00000000) using HISAT2 (v2.2.1).
Transcript assembly was performed using StringTie (v2.2.3).
Gene-level read counts were obtained using featureCounts (v2.0.6).
FPKM values were calculated for exploratory analyses (PCA, heatmaps); differential expression analysis was performed using DESeq2 (v1.42.0). Genes with an adjusted p-value (padj) <= 0.05 were considered significantly differentially expressed.
Assembly: Saccharomyces cerevisiae W303 reference genome (JRIU00000000)
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for all samples.

organism: Saccharomyces cerevisiae

source_name: diploid yeast cells

growth_protocol: Yeast were cultured at 30 C on YEPD plates (1% yeast extract, 2% peptone, 2% dextrose) supplemented with adenine (75 mg/L). Haploid strains of opposite mating types were mated on YEPD plates to generate diploids. Zygotes were isolated using a tetrad dissection microscope and grown on YEPD plates for 3-5 days, followed by inoculation into liquid YEPD and growth overnight at 30 C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Strand-specific libraries were generated from poly(A)-selected mRNA using the New England Biolabs NEBNext Ultra Directional RNA Library Prep Kit.

treatment_protocol: No treatment was applied; samples represent different genotypes with varying telomere lengths.

value: diploid yeast cells

tag: telomere length

value: long


title: AML 128 Relapse RNA seq

description: Library name: AML128_Rel

value: PBMCs


title: WT/WT_long2 biol rep 2

description: Library name: c58z3


title: YZ590

first: Xinyu

last: Zhou

source_name: peripheral blood

value: Without Drug therapy


title: Sheep Gall Bladder (predissociated cells) SFWT2011-1 #1 (WT term)

description: Library name: AH879


title: AML 127 Relapse RNA seq

description: Library name: AML127_Rel


title: YZ587


title: Sheep Gall Bladder (predissociated cells) SFWT1730-2 #1 (WT term)

description: Library name: AH877


title: AML 128 Diagnosis RNA seq

description: Library name: AML128_Dx


title: WT/WT_long2 biol rep 1

description: Library name: c58z2


title: WT/WT_long1 biol rep 3

description: Library name: c57z3


title: Sheep pancreas organoid (173-1, WT term, p3, d5) #2

description: Library name: AH844

source_name: Pancreas organoid

value: Pancreas organoid


title: AML 125 Relapse RNA seq

description: Library name: AML125_Rel


title: YZ580


title: Sheep pancreas organoid (173-1, WT term, p3, d5) #1

description: Library name: AH843


title: Sheep Gall Bladder (predissociated cells) SFWT1730-2 #2 (WT term)

description: Library name: AH878


title: YZ576


title: WT/WT_long1 biol rep 2

description: Library name: c57z2


title: YZ574


title: AML 123 Relapse RNA seq

description: Library name: AML123_Rel


title: WT/WT_long1 biol rep 1

description: Library name: c57z1


title: AML 125 Diagnosis RNA seq

description: Library name: AML125_Dx


title: FB_S36303_5d_rep2

city: Hong Kong

first: Yan

last: Yan

address: HKUST, Clear Water Bay

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description:
Library name: S36303_5d_rep2
S36303_5d_2

data_processing:
Cleaned raw data reads were mapped to the reference genome (BDGP6) using STAR (2.5.4a).
Assembly: GCF_000001215.4
Supplementary files format and content: csv file includes raw reads for each Sample.

organism: Drosophila melanogaster

source_name: Fat body

extract_protocol:
Drosophila fat body were dissected and collected in iced cold 1X-DEPC-PBS buffer. Total RNA was extracted with the RNeasy Mini Kit (Qiagen).
cDNA libraries preparation and 150 bp paired-end sequencing were performed on Illumina HiSeq platform by Novogene.

value: Fat body

value: Adipocytes

tag: time point


title: FB_S36303_5d_rep4

description:
Library name: S36303_5d_rep4
S36303_5d_4

tag: tissue


title: WT/rif2delta biol rep 3

description: Library name: c56z3


title: AML 127 Diagnosis RNA seq

description: Library name: AML127_Dx


title: YZ581

city: Chongqing

address: 1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

value: Major depressive disorder (MDD)


title: YZ573


title: FB_S36303_5d_rep3

description:
Library name: S36303_5d_rep3
S36303_5d_3


title: AML 123 Diagnosis RNA seq

description: Library name: AML123_Dx


title: AML 121 Relapse RNA seq

description: Library name: AML121_Rel


title: FB_S36303_5d_rep1

description:
Library name: S36303_5d_rep1
S36303_5d_1


title: AML 121 Diagnosis RNA seq

description: Library name: AML121_Dx


title: YZ571


title: AML 120 Diagnosis RNA seq

description: Library name: AML120_Dx


title: YZ569


title: YZ570


title: WT/rif2delta biol rep 1

description:
Library name: c56z1
This replicate (c56z1) was identified as an outlier and excluded from primary analyses (see manuscript) but is included in the dataset.


title: FB_S36303_4d_rep2

description:
Library name: S36303_4d_rep2
S36303_4d_2


title: AML 120 Relapse RNA seq

description: Library name: AML120_Rel


title: FB_S36303_4d_rep3

description:
Library name: S36303_4d_rep3
S36303_4d_3


title: WT/WT biol rep 3

description: Library name: c55z3

value: WT/WT

value: normal


title: FB_S36303_4d_rep1

description:
Library name: S36303_4d_rep1
S36303_4d_1


title: YZ564


title: FB_S36303_4d_rep4

description:
Library name: S36303_4d_rep4
S36303_4d_4


title: YZ568

value: Drug therapy


title: YZ563


title: AML 119 Relapse RNA seq

description: Library name: AML119_Rel


title: AML 119 Diagnosis RNA seq

description: Library name: AML119_Dx

value: Bone Marrow


title: AH583 RNA-seq of CF sheep liver CF d50

description: Library name: AH583

data_processing:
Gallbladder RNA-seq: Raw reads were mapped to the Ovis Aries Oar_v4.0 (oviAri4) reference genome using STAR, version 2.7.9a. Aligned reads were quantified using Salmon, version 1.10.1 and annotation data from Oar_v4.0 was used to summarize data from transcript-level to gene-level. Data were filtered to exclude gene biotypes other than protein coding genes, which reduced the number of genes from 29285 to 20518. Next, genes were filtered for low expression, retaining only those with greater than 1 count per million (CPM) in multiple samples. This reduced the number of genes from 20518 to 17326. To identify differentially expressed genes (DEGs), counts were first corrected by estimating gene-wise dispersions using EdgeR. The count data were fitted to a gene-wise general linear model with group status as a coefficient, and contrasts were specified for comparisons of interest. The EdgeR quasi-likelihood F-test was used to determine whether there was differential expression (|logFC| > 0) after adjusting for gene-level posterior residual standard deviations. Significant DEGs were defined with minimum absolute fold change of 1.5 and a false-discovery rate (FDR) of 0.01. Results of DEG testing were visualized by volcano plots.
Liver RNA-seq: The Ovis aries genome (Oar_v4.0) and transcriptome were downloaded from NCBI (Genbank GCA_000298735.2, v4.0). We indexed the transcriptome for alignment with decoy sequences coming from the whole genome and aligned sheep liver RNAseq samples using Salmon (v.1.9.0). The tpm quantifications from salmon were quantile normalized with R package voom, and differential expression values were calculated with R package limma. The Likelihood Ratio Test (LRT) from R package DESeq2 was used to identify DEGs across different time points in WT and CFTR-/- separately, and between the genotypes at each time point.
Assembly: oviAri4
Supplementary files format and content: Tab-limited matrix of raw counts with genes in rows and samples in columns

source_name: Liver

extract_protocol:
50-100mg of sample was excised from frozen tissue and mixed with 1mL TRIzol Reagent and ceramic beads over ice. Tissue was homogenized and incubated at RT to dissociate the nucleoprotein complex. Solution was then mixed with 200uL chloroform, centrifuged, and the aqueous phase removed. RNA was precipitated with 100% isopropanol, washed with 75% ethanol, and solubilized in water.
RNA concentration and purity were measured by nanodrop and 1ug was used for library preperation.

value: Liver

value: CF

tag: donor number


title: WT/WT biol rep 2

description: Library name: c55z2

tag: cell type


title: WT/WT biol rep 1

description: Library name: c55z1

tag: genotype


title: YZ561

tag: treatment


title: WT/rif2delta biol rep 2

description: Library name: c56z2


title: FB_S35748_11d_rep4

description:
Library name: S35748_11d_rep4
S35748_11d_4


title: FB_S35748_11d_rep3

description:
Library name: S35748_11d_rep3
S35748_11d_3


title: AML 118 Relapse RNA seq

description: Library name: AML118_Rel


title: AH582 RNA-seq of CF sheep liver CF d50

description: Library name: AH582


title: AML 118 Diagnosis RNA seq

description: Library name: AML118_Dx


title: FB_S35748_11d_rep2

description:
Library name: S35748_11d_rep2
S35748_11d_2


title: AML 117 Relapse RNA seq

description: Library name: AML117_Rel


title: AH580 RNA-seq of CF sheep liver CF d65

description: Library name: AH580


title: AML 117 Diagnosis RNA seq

description: Library name: AML117_Dx


title: AH579 RNA-seq of CF sheep liver CF d80

description: Library name: AH579


title: FB_S35748_11d_rep1

description:
Library name: S35748_11d_rep1
S35748_11d_1


title: YZ550


title: YZ549


title: AH578 RNA-seq of CF sheep liver CF d80

description: Library name: AH578


title: YZ558


title: FB_S35748_8d_rep3

description:
Library name: S35748_8d_rep3
S35748_8d_3


title: AH577 RNA-seq of CF sheep liver CF d100

description: Library name: AH577


title: AML 116 Relapse RNA seq

description: Library name: AML116_Rel


title: YZ540


title: AH581 RNA-seq of CF sheep liver CF d65

description: Library name: AH581


title: AML 116 Diagnosis RNA seq

description: Library name: AML116_Dx


title: AML 113 Relapse RNA seq

description: Library name: AML113_Rel


title: AH576 RNA-seq of CF sheep liver CF d100

description: Library name: AH576


title: YZ552


title: YZ538


title: FB_S35748_8d_rep1

description:
Library name: S35748_8d_rep1
S35748_8d_1


title: FB_S35748_8d_rep4

description:
Library name: S35748_8d_rep4
S35748_8d_4


title: YZ537


title: FB_S35748_5d_rep4

description:
Library name: S35748_5d_rep4
S35748_5d_4


title: YZ536


title: AML 113 Diagnosis RNA seq

description: Library name: AML113_Dx


title: AH575 RNA-seq of CF sheep liver CF d120

description: Library name: AH575


title: FB_S35748_8d_rep2

description:
Library name: S35748_8d_rep2
S35748_8d_2


title: AML 111 Relapse RNA seq

description: Library name: AML111_Rel


title: AH574 RNA-seq of CF sheep liver CF d120

description: Library name: AH574


title: FB_S35748_5d_rep2

description:
Library name: S35748_5d_rep2
S35748_5d_2


title: FB_S35748_5d_rep3

description:
Library name: S35748_5d_rep3
S35748_5d_3


title: AH573 RNA-seq of CF sheep liver CF birth

description: Library name: AH573


title: AML 111 Diagnosis RNA seq

description: Library name: AML111_Dx


title: YZ533


title: YZ535


title: AML 109 Relapse RNA seq

description: Library name: AML109_Rel


title: FB_S35748_5d_rep1

description:
Library name: S35748_5d_rep1
S35748_5d_1


title: AH571 RNA-seq of WT sheep liver WT d50

description: Library name: AH571

value: WT


title: AH572 RNA-seq of CF sheep liver CF birth

description: Library name: AH572


title: AML 109 Diagnosis RNA seq

description: Library name: AML109_Dx


title: AH570 RNA-seq of WT sheep liver WT d50

description: Library name: AH570


title: YZ526


title: AML 108 Relapse RNA seq

description: Library name: AML108_Rel


title: AH569 RNA-seq of WT sheep liver WT d65

description: Library name: AH569


title: FB_S35748_4d_rep4

description:
Library name: S35748_4d_rep4
S35748_4d_4


title: FB_S35748_4d_rep3

description:
Library name: S35748_4d_rep3
S35748_4d_3


title: YZ525


title: YZ524


title: AML 108 Diagnosis RNA seq

description: Library name: AML108_Dx


title: FB_S35748_4d_rep2

description:
Library name: S35748_4d_rep2
S35748_4d_2


title: AH568 RNA-seq of WT sheep liver WT d65

description: Library name: AH568


title: YZ523


title: FB_S35748_4d_rep1

description:
Library name: S35748_4d_rep1
S35748_4d_1


title: AH567 RNA-seq of WT sheep liver WT d80

description: Library name: AH567


title: YZ517


title: CD8 T cell, WT_3

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

institute: zhejiang university

description:
Library name: Sample 6
Colume name in T4vsWT_deg.txt: WT_3

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: lymph nodes and spleen

extract_protocol:
RNA was extracted using Quick-RNA Miniprep kit(ZYMO RESEARCH).  1 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: lymph nodes and spleen

value: CD8 T cell

value: no treatment


title: YZ515

value: peripheral blood


title: AH566 RNA-seq of WT sheep liver WT d80

description: Library name: AH566


title: AML 107 Diagnosis RNA seq

description: Library name: AML107_Dx


title: AML 106 Relapse RNA seq

description: Library name: AML106_Rel


title: AML 106 Diagnosis RNA seq

description: Library name: AML106_Dx


title: CD8 T cell, WT_2

description:
Library name: Sample 5
Colume name in T4vsWT_deg.txt: WT_2


title: YZ508


title: AH564 RNA-seq of WT sheep liver WT d100

description: Library name: AH564


title: CD8 T cell, TCR4_3

description:
Library name: Sample 3
Colume name in T4vsWT_deg.txt: T4_3


title: AML 107 Relapse RNA seq

description: Library name: AML107_Rel


title: YZ509


title: CD8 T cell, WT_1

description:
Library name: Sample 4
Colume name in T4vsWT_deg.txt: WT_1


title: AH563 RNA-seq of WT sheep liver WT d120

description: Library name: AH563


title: YZ505


title: AML 105 Diagnosis RNA seq

description: Library name: AML105_Dx


title: AH562 RNA-seq of WT sheep liver WT d120

description: Library name: AH562


title: AML 104 Relapse RNA seq

description: Library name: AML104_Rel


title: CD8 T cell, TCR4_2

description:
Library name: Sample 2
Colume name in T4vsWT_deg.txt: T4_2


title: AML 105 Relapse RNA seq

description: Library name: AML105_Rel


title: AH565 RNA-seq of WT sheep liver WT d100

description: Library name: AH565


title: CD8 T cell, TCR4_1

description:
Library name: Sample 1
Colume name in T4vsWT_deg.txt: T4_1


title: AML 104 Diagnosis RNA seq

description: Library name: AML104_Dx


title: YZ504


title: 5xFAD_HM-EVs_3_HPC

city: Shanghai

first: Zhanping

last: Liang

state: Shanghai

address: zhennan Rd 500 tongji n=university

institute: Tongji Hospital Affiliated to Tongji University

description:
Library name: Sample18
Column name in FPKM_anno.xls: AD_EVs3_Hippo

data_processing:
150 bp paired-end beads were generated and raw reads of fastp format were processed using fastp. The clean reads were mapped to the reference using HISAT2.
FPKM of each gene was calculated and the read out of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: txt file includes FPKM values for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent (QIAGEN, Germany) according to the manufacture's instructions. RNA integrity was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
The libraries were constructed using VAHTS Universal V5 RNA Library Prep kit (Illumina) and sequenced on Illumina Novaseq 6000 platform.

treatment_protocol: male wildtype C57BL6J mice and 5xFAD mice intravenously injected with PBS, or 5xFAD mice intravenously injected with human breast milk-derived extracellular vesicles from 5-month-age to 6-month-age. Injections were conducted every 3 days for 10 times. After administration and behavioral tests, mice were anesthetized and perfused with ice-cold PBS.

value: Hippocampus

value: male

tag: strain

value: Human breast milk-derived extracellular vesicles, Intravenously/3 days for 10 times from 5-month-age


title: AH417 RNA-seq of WT sheep liver WT Term (male)

description: Library name: AH417


title: AH416 RNA-seq of WT sheep liver WT Term (female)

description: Library name: AH416


title: YZ507


title: YZ497


title: YZ502


title: AML 103 Diagnosis RNA seq

description: Library name: AML103_Dx


title: 5xFAD_HM-EVs_1_HPC

description:
Library name: Sample16
Column name in FPKM_anno.xls: AD_EVs1_Hippo

tag: Sex


title: AH561 RNA-seq of CF sheep gall bladder CF d120

description: Library name: AH561

source_name: Gallbladder

value: Gallbladder


title: YZ496


title: AML 103 Relapse RNA seq

description: Library name: AML103_Rel


title: AML 102 Relapse RNA seq

description: Library name: AML102_Rel


title: AML 102 Diagnosis RNA seq

description: Library name: AML102_Dx


title: 5xFAD_HM-EVs_2_HPC

description:
Library name: Sample17
Column name in FPKM_anno.xls: AD_EVs2_Hippo


title: 5xFAD_PBS_2_HPC

description:
Library name: Sample14
Column name in FPKM_anno.xls: AD_PBS2_Hippo

value: PBS, Intravenously/3 days for 10 times from 5-month-age


title: YZ494

value: Major depressive disorder (MDD)


title: AH559 RNA-seq of CF sheep gall bladder CF d100

description: Library name: AH559


title: AML 073 Relapse RNA seq

description: Library name: AML073_Rel

value: PBMCs


title: AML 073 Diagnosis RNA seq

description: Library name: AML073_Dx


title: YZ491

value: Without Drug therapy


title: AH560 RNA-seq of CF sheep gall bladder CF d120

description: Library name: AH560


title: AH557 RNA-seq of CF sheep gall bladder CF d80

description: Library name: AH557


title: Wildtype_PBS_2_HPC

description:
Library name: Sample11
Column name in FPKM_anno.xls: WT_PBS2_Hippo

value: wildtype


title: AH558 RNA-seq of CF sheep gall bladder CF d100

description: Library name: AH558


title: YZ487


title: YZ484

value: Drug therapy


title: AML 071 Relapse RNA seq

description: Library name: AML071_Rel

value: Bone Marrow


title: 5xFAD_PBS_1_HPC

description:
Library name: Sample13
Column name in FPKM_anno.xls: AD_PBS1_Hippo


title: 5xFAD_PBS_3_HPC

description:
Library name: Sample15
Column name in FPKM_anno.xls: AD_PBS3_Hippo


title: Wildtype_PBS_3_HPC

description:
Library name: Sample12
Column name in FPKM_anno.xls: WT_PBS3_Hippo


title: AH554 RNA-seq of WT sheep gall bladder WT birth

description: Library name: AH554


title: Wildtype_PBS_1_HPC

description:
Library name: Sample10
Column name in FPKM_anno.xls: WT_PBS1_Hippo


title: AH555 RNA-seq of WT sheep gall bladder WT birth

description: Library name: AH555


title: AML 067 Relapse RNA seq

description: Library name: AML067_Rel


title: AH556 RNA-seq of CF sheep gall bladder CF d80

description: Library name: AH556

value: CF


title: 5xFAD_HM-EVs_3_PFC

description:
Library name: Sample9
Column name in FPKM_anno.xls: AD_EVs3_PFC

source_name: Prefrontal cortex

value: Prefrontal cortex


title: YZ482


title: YZ490


title: AH553 RNA-seq of WT sheep gall bladder WT d120

description: Library name: AH553

value: WT


title: YZ481


title: AML 067 Diagnosis RNA seq

description: Library name: AML067_Dx


title: YZ478


title: 5xFAD_HM-EVs_2_PFC

description:
Library name: Sample8
Column name in FPKM_anno.xls: AD_EVs2_PFC


title: AML 065 Relapse RNA seq

description: Library name: AML065_Rel


title: 5xFAD_HM-EVs_1_PFC

description:
Library name: Sample7
Column name in FPKM_anno.xls: AD_EVs1_PFC


title: AH552 RNA-seq of WT sheep gall bladder WT d120

description: Library name: AH552


title: AH551 RNA-seq of WT sheep gall bladder WT d100

description: Library name: AH551


title: YZ475


title: 5xFAD_PBS_3_PFC

description:
Library name: Sample6
Column name in FPKM_anno.xls: AD_PBS3_PFC


title: YZ473


title: AML 064 Relapse RNA seq

description: Library name: AML064_Rel


title: AH550 RNA-seq of WT sheep gall bladder WT d100

description: Library name: AH550


title: AML 065 Diagnosis RNA seq

description: Library name: AML065_Dx


title: 5xFAD_PBS_2_PFC

description:
Library name: Sample5
Column name in FPKM_anno.xls: AD_PBS2_PFC


title: AML 071 Diagnosis RNA seq

description: Library name: AML071_Dx


title: YZ471


title: AML 064 Diagnosis RNA seq

description: Library name: AML064_Dx


title: YPD,72 h,bio rep5

first: feng

last: chun

description: Library name: Control 5

data_processing:
Quality control of the sequencing data was performed using FastQC, followed by adapter trimming and removal of low-quality reads with Trim Galore. Paired-end alignment was conducted using STAR v2.7.11b, and output files were converted with SAMtools. Read counting was performed using featureCounts, focusing on reads mapped to exonic regions and excluding multi-mapped reads.
Assembly: GCF_000149245.1
Supplementary files format and content: A comma-separated values file containing raw counts, with genes in rows and samples in columns.

organism: Cryptococcus neoformans

extract_protocol:
RNA was harvested using GoldHi Plasmid Mini Kit.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: cell line


title: YZ461

tag: disease state


title: Wildtype_PBS_3_PFC

description:
Library name: Sample3
Column name in FPKM_anno.xls: WT_PBS3_PFC


title: YZ456


title: Wildtype_PBS_2_PFC

description:
Library name: Sample2
Column name in FPKM_anno.xls: WT_PBS2_PFC


title: YPD,72 h,bio rep3

description: Library name: Control 3


title: AML 059 Diagnosis RNA seq

description: Library name: AML059_Dx


title: AML 059 Relapse RNA seq

description: Library name: AML059_Rel


title: YPD,72 h,bio rep4

description: Library name: Control 4


title: Wildtype_PBS_1_PFC

description:
Library name: Sample1
Column name in FPKM_anno.xls: WT_PBS1_PFC


title: AML 054 Relapse RNA seq

description: Library name: AML054_Rel


title: YZ452


title: YZ454


title: YPD,72 h,bio rep2

description: Library name: Control 2


title: YPD,72 h,bio rep1

description: Library name: Control 1


title: AML 054 Diagnosis RNA seq

description: Library name: AML054_Dx


title: 5xFAD_PBS_1_PFC

description:
Library name: Sample4
Column name in FPKM_anno.xls: AD_PBS1_PFC


title: AML 051 Relapse RNA seq

description: Library name: AML051_Rel


title: YZ450


title: Macrophage_BMEplus_rep2

city: Incheon

first: Dongjun

last: Yu

address: 100, Inha-ro, Michuhol-gu, Building 4, Room 105

department: Department of Biological Sciences and Bioengineering

country: South Korea

institute: Inha University

description:
Library name: BMEplus2
Column name in Read_counts_All_sample.csv: BMEplus_rep2

data_processing:
Preprocessing: Low quality reads and adapter sequences were filtered using cutadapt tool (ver 2.8), parameter: quality-cutoff (20) and minimum-length (50).
Alignment: filtered reads were mapped to the reference genome related to the species. The parameters have been set based on ENCODE standard options. Reference data: species: mus_musculus, resouce: Ensembl, genome assembly: GRCm38.p6 (GCA_000001635.8), genemodel version: 99, using STAR tool (ver 2.7.1a) with following parameters: outFilterType (BySJout), outFilterMultimapNmax (20), alignSJoverhangMin (8), alignSJDBoverhangMin (1), outFilterMismatchNmax (999), outFilterMismatchNoverLmax (0.04), alignIntronMin (20), alignIntronMax (1000000), and alignMatesGapMax (1000000).
Data QC: data QC was performed to verify sequencing data and alignment data using FastQC (ver 0.11.9), PCAtools, and Gviz (ver 1.30.0).
Assembly: Reference data: species: mus_musculus, resouce: Ensembl, genome assembly: GRCm38.p6 (GCA_000001635.8), genemodel version: 99
Supplementary files format and content: Processed read count data with respective gene ID

source_name: Tumor

growth_protocol: E. coli (ATCC #25922) and S. aureus (ATCC #29213) were grown on LB medium for 12 h at 37°C, 200 rpm. The bacterial cell concentration was adjusted to optical density (OD) 600 of 0.7 and harvested by centrifugation (8,000 ×g, 5 min). The supernatant was discarded, the cell pellet was resuspended with 200 μg/mL lysozyme (#L4919, Sigma-Aldrich, St. Louis, MO, USA) (in 200 mM Tris-HCl, pH 8.0), and kept at room temperature for 10 min. The same volume of 10 μg/mL DNase I (#11284932001, Roche, Mannheim, Germany) (in 50 mM Tris-HCl, 2% Triton, pH 8.0) was added and incubated at 4°C for 30 min. The samples were centrifuged at 1,633 ×g for 5 min. The supernatant was collected and centrifuged at 22,967 ×g for 10 min. The pellet was resuspended in excess PBS and centrifuged at 22,967 ×g for 10 min. The supernatant was discarded, and the pellets were collected in the required volume of PBS. Centrifugation temperature was maintained at 4°C.

extract_protocol:
RNA was extracted using Universal RNA extraction kit (Bioneer, Korea).
RNA library was prepared using the SMARTer Stranded Total RNA-Seq kit v2–Pico input mammalian kit (Takara).

treatment_protocol: Subcutaneous CT-26 tumors were intratumorally injected with either PBS or BMEplus particles

value: Tumor

value: Macrophage

value: BMEplus


title: AML 051 Diagnosis RNA seq

description: Library name: AML051_Dx


title: YZ449

value: peripheral blood


title: Macrophage_BMEplus_rep1

description:
Library name: BMEplus1
Column name in Read_counts_All_sample.csv: BMEplus_rep1


title: YZ432


title: Macrophage_BMEplus_rep3

description:
Library name: BMEplus3
Column name in Read_counts_All_sample.csv: BMEplus_rep3


title: AML 049 Relapse RNA seq

description: Library name: AML049_Rel


title: Macrophage_PBS_rep2

description:
Library name: PBS2
Column name in Read_counts_All_sample.csv: PBS_rep2

value: PBS


title: FRA2KO MRTX-1133 (50nM) treat 2

city: Columbus

first: Gian Luca

last: Rampioni Vinciguerra

state: OH

address: 460W 12th Avenue

department: Cancer Biology and Genetics

institute: The Ohio State University

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Transcriptome analysis was conducted on two different samples per condition and was performed with Clariom™ S Assay, Human (ThermoFisher Scientific, USA). The analysis for Clariom™ S Human Affymetrix panel of >21K genes was carried out by Transcriptome Analysis Console software (TAC v4 - Thermo Fisher Scientific) and it consists of three main steps: 1) data quality control; 2) normalization (signal space transformation robust multiple-array average); 3) differentially expression analysis employing the eBayes method from limma R package included in TAC software.

source_name: FRA2KO MRTX-1133 (50nM) treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (GeneChip WT PLUS Reagent Kit, 2013, Affymetrix).

growth_protocol: AsPC-1 cells were cultured in RPMI completed medium at 37 degrees and 5% CO2

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: WT MRTX-1133 resistant AsPC-1 cells were obtained with continuous administration of escalating doses of MRTX-1133 from 1nM to 50nM for 30 days. FRA2KO AsPC-1 cells were treated with MRTX-1133 50nM for 48hours.

value: MRTX-1133 (50nM) treat


title: YZ435


title: AML 048 Relapse RNA seq

description: Library name: AML048_Rel

source_name: Bone Marrow


title: AML 049 Diagnosis RNA seq

description: Library name: AML049_Dx


title: YZ427


title: YZ425


title: Macrophage_PBS_rep3

description:
Library name: PBS3
Column name in Read_counts_All_sample.csv: PBS_rep3


title: Macrophage_PBS_rep1

description:
Library name: PBS1
Column name in Read_counts_All_sample.csv: PBS_rep1


title: AML 047 Relapse RNA seq

description: Library name: AML047_Rel


title: FRA2KO MRTX-1133 (50nM) treat 1


title: YZ420


title: AML 047 Diagnosis RNA seq

description: Library name: AML047_Dx

source_name: PBMCs


title: YZ419


title: AML 045 Relapse RNA seq

description: Library name: AML045_Rel


title: WT Day 4RC

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description:
Library name: SAMPLE 31
WT EBS Day R4C

data_processing:
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization was used to do Differential Expression transcriptional analysis. Through NASQAR, DEseq2 was used to perform pairwise differential expression comparisons between WT and KO mESCs and generate a Volcano plot, Distance heatmap and a PCA plot. GO analysis was also done on NASQAR to generate GO plots for Cellular Components and Molecular Functions. Heatmaps were generated in R (v4.3.0) using the pheatmap package to visualize the expression patterns of selected gene sets across wild-type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS) mESCs at Day 0. Raw gene expression matrices from bulk RNA-seq were first imported using the readr package. Gene sets related to specific biological functions (e.g., stemness, lineage commitment, extracellular matrix) were defined manually, and the corresponding expression values were extracted from the full dataset using the dplyr package. Replicates for each condition (WT_1–3, KO_1–3, NLS_1–3) were retained as individual columns or averaged using rowMeans() to create representative condition-specific profiles when required. Expression values were transformed into a numeric matrix. The matrix was then scaled row-wise (z-score) to allow for comparison of relative expression across samples. Heatmaps were plotted using pheatmap with hierarchical clustering applied to genes (rows), while preserving the experimental condition order for samples (columns). A custom diverging color palette (navy–white–firebrick3) was used to depict low to high expression.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Embryonic stem cells

growth_protocol: P60 culture dishes were coated with 3 mL of 0.1% gelatin solution and incubated at 37 °C for 15 min. Mouse embryonic stem cell (mESC) medium was pre-warmed to 37 °C. The gelatin solution was then replaced with 5 mL of mESC medium. A total of 5.0 × 10⁵ cells were seeded for each condition: wild type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS). Cultures were maintained at 37 °C and 5% CO₂ for 2 days after seeding. Once cultures reached 70–90% confluency, cells were processed for RNA extraction.

extract_protocol:
RNA was extracted using RNAzol RT (Molecular Research Center, Catalog #R4533), a reagent designed for the isolation of total and small RNA from human, animal, plant, bacterial, and viral samples. Cells were washed with calcium- and magnesium-free DPBS and dissociated with TrypLE for 1 min. TrypLE was aspirated, then 1 mL of mESC medium was added, and cells were gently pipetted to detach them from the culture dish. The cell suspension was transferred to a 15-mL conical tube and pelleted by centrifugation at 500 × g for 3 min. The supernatant was removed, and 500 µL of RNAzol RT was added directly to the pellet. The pellet was fully resuspended by pipetting to ensure complete lysis and homogenization, and the lysate was transferred to a 1.5- mL microcentrifuge tube. A total of 0.2 mL of RNase-free water was added to each tube. Samples were capped, shaken vigorously for 15 s, and incubated for 15 min at room temperature. The mixture was centrifuged at 12,000 × g for 15 min at 4 °C, producing a pellet containing DNA, proteins, and polysaccharides, while RNA remained in the upper phase. The supernatant was carefully transferred to a new tube without disturbing the pellet. An equal volume of 100% isopropanol was added to the supernatant to precipitate RNA. Samples were incubated for 10 min at room temperature and then centrifuged at 12,000 × g for 10 min, forming a white RNA pellet. RNA pellets were washed twice with 75% ethanol (0.4–0.6 mL per mL of initial supernatant). Each wash was followed by centrifugation at 8,000 × g for 3 min at room temperature, after which the ethanol was removed by pipetting. The final RNA pellet was resuspended in 20 µL of RNase-free water without air-drying. Samples were vortexed at room temperature for 2 min to ensure complete solubilization.
45 NEB Ultra II RNA, PolyA selected

value: Embryonic stem cells

value: mESC


title: NLS Day 4RC

description:
Library name: SAMPLE 33
NLS EBS Day R4C


title: KO Day 4RC

description:
Library name: SAMPLE 32
KO EBS Day R4C


title: YZ431

value: Major depressive disorder (MDD)


title: WT MRTX-1133 res 2

source_name: WT MRTX-1133 resistant

value: MRTX-1133 res


title: FRA2KO unt 2

source_name: FRA2KO untreated

value: untreated


title: FRA2KO unt 1


title: AML 048 Diagnosis RNA seq

description: Library name: AML048_Dx

data_processing:
Reads were aligned to the hg19 human genome using STAR aligner (version 2.3.0e). Aligned results were annotated using RefSeq gene model and HTSeq union mode.
Read counts were normalized to Transcripts per million reads (TPM) with normal bone marrow controls included in expression analysis for normal variance estimation as described in PMID 41608320.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab delimited file contains non-normalized raw read counts aligned to hg19

extract_protocol:
High quality RNA was isolated using phenol-chloroform/Trizol with subsequent purification using Qiagen Rneasy kit.
TruSeq RNA-Seq by ploy(A) enrichment

value: PBMCs


title: YZ407

value: Drug therapy


title: WT unt 1

source_name: WT untreated


title: NLS Day 4RB

description:
Library name: SAMPLE 30
NLS EBS Day R4B


title: AML 045 Diagnosis RNA seq

description: Library name: AML045_Dx