title: Flavopiridol_treated_PAF1_Cut&Run_replicate_2

description: Library name: Flavopiridol_treated_PAF1_Cut_Run_replicate_2


title: Flavopiridol_treated_No_Halo_Control_Cut&Run_replicate_2

status: Public on Jun 10 2026

type: SRA

city: New York

first: Feiyue

last: Lu

state: NY

department: Institute for Systems Genetics

country: USA

institute: NYU School of Medicine

description: Library name: Flavopiridol_treated_No_Halo_Control_Cut_Run_replicate_2

library_source: genomic

data_processing:
Paired-end CUT&RUN sequencing reads were assessed with FastQC (Babraham Bioinformatics - FastQC A Qu...) using default criteria, then adapter and quality trimming were performed using Trim Galore (Trim Galore: A wrapper tool around Cu...) in paired-end mode. Trimmed reads were aligned with Bowtie2 (Langmead and Salzberg 2012)(local, very-sensitive-local) to an E. coli reference genome to quantify spike-in reads and to a custom Drosophila melanogaster genome: starting from the dm6 assembly, we swapped the histone locus repeats for a single instance of the consensus sequence of the ~ 5kb repeated unit, followed by a stretch of unspecified bases to retain the register of Chr. 2L regions downstream of the histone locus with the dm6 assembly. This procedure prevents the undesirable exclusion of histone locus reads that do not map unambiguously to a unique repeat. As a result, reads from the ~110 histone repeats pile up on a single unit, ensuring ample read depth and providing an average profile of the repeat unit. Alignments were processed with SAMtools (Danecek et al. 2021), including sorting/indexing and filtering by a minimum mapping quality, and reads mapping to the mitochondrial genome were removed. Spike-in normalization was applied by computing a per-sample scaling factor from the number of mapped E. coli reads, and scaled genome-wide coverage tracks were generated using deepTools (Ramírez et al. 2016) bamCoverage. Replicates were then averaged to generate a mean bigWig track, and background-corrected bigWigs were produced by subtracting from each coverage track the coverage track obtained from non-Halo-expressing negative-control ovaries submitted to the same biological treatment and processed identically. Signal around transcription start sites was summarized with deepTools computeMatrix and visualized using plotHeatmap and plotProfile.  For gene-level quantification, CUT&RUN signal was first summarized per gene and per sample as a single numeric value (summed signal across the gene), and these values were then aggregated across all samples for the genes of interest. For each gene, background signal was estimated separately for each treatment using the matched negative-control samples and averaged across replicates, then subtracted from the corresponding experimental samples to obtain background-corrected gene signals. To calculate the summary matrix used for plotting, the background-corrected control condition for each comparison was scaled to 1 by dividing both the control and treatment background-corrected signals by the mean background-corrected control signal computed across replicates for that gene. Results were then visualized as replicate-level points with the mean indicated for each condition.
Assembly: dm6
Supplementary files format and content: .bw
Library strategy: CUT&Run

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: adult ovaries

extract_protocol:
CUT&RUN libraries were prepared using the CUTANA™ CUT&RUN Kit (EpiCypher, Cat. No. 14-1048) following the manufacturer’s instructions with minor modifications. In brief, ovaries were harvested from 0-6 hr old adult females fattened with yeast paste for 8-10 hrs to reach development Stage 10. Four pairs of ovaries were collected per replicate, with two to four replicates prepared per genotype per condition. For drug-treated conditions, ovaries were incubated in growth media containing either 500 μM TRI or 500 nM FP for 35 min. To allow for antibody binding in situ, cells were permeabilized in buffer containing 0.05% digitonin. The ovaries were incubated with rabbit polyclonal Halotag antibody (Promega G9281; 1:100) at 4°C overnight. The w1118 line, lacking HaloTag expression, served as a negative control. Following antibody incubation, pAG-MNase (EpiCypher, Cat. No. 15-1016) was added to bind the antibody-labeled chromatin. Targeted digestion was activated by the addition of 100 mM CaCl2. To normalize read counts across conditions, 0.1 ng of E. coli Spike-in DNA (EpiCypher, Cat. No. 18-1401) was added to each reaction within the Stop Buffer master mix used to halt MNase activity.
CUT&RUN-enriched DNA was isolated from the supernatant and purified using 1.66x SPRIselect beads (Beckman Coulter, Cat. No. 21-1405). Purified DNA was quantified via Qubit fluorometer. Sequencing libraries were generated using universal i5 and uniquely barcoded i7 primers with 14 PCR cycles. All subsequent library purifications were performed using 1.66x SPRIselect beads to eliminate residual primers and concentrate the samples. Final library quality and fragment distribution—targeting a peak at ~300 bp representing mononucleosomes plus sequencing adapters—were confirmed via Bioanalyzer prior to paired-end sequencing on an Illumina NextSeq 550.

tag: tissue

value: adult ovaries

tag: genotype

tag: treatment

value: Flavopiridol


title: Triptolide_treated_PAF1_Cut&Run_replicate_2

description: Library name: Triptolide_treated_PAF1_Cut_Run_replicate_2

value: Triptolide


title: Triptolide_treated_No_Halo_Control_Cut&Run_replicate_2

description: Library name: Triptolide_treated_No_Halo_Control_Cut_Run_replicate_2


title: Nontreated_Control_Pol2_Cut&Run_replicate_4

description: Library name: Nontreated_Control_Pol2_Cut_Run_replicate_4

value: DMSO


title: DMSO_treated_PAF1_Cut&Run_replicate_2

description: Library name: DMSO_treated_PAF1_Cut_Run_replicate_2


title: DMSO_treated_No_Halo_Control_Cut&Run_replicate_2

description: Library name: DMSO_treated_No_Halo_Control_Cut_Run_replicate_2


title: Flavopiridol_treated_PAF1_Cut&Run_replicate_1

description: Library name: Flavopiridol_treated_PAF1_Cut_Run_replicate_1


title: Flavopiridol_treated_Pol2_Cut&Run_replicate_3

description: Library name: Flavopiridol_treated_Pol2_Cut_Run_replicate_3


title: PAG029_Inf_E2

status: Public on Jun 11 2026

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

library_source: transcriptomic

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: TPM

molecule: total RNA

organism: Homo sapiens

source_name: PAG029 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

value: Blood

tag: visit

value: Malaria Symptomatic stage


title: In vitro, Reactive culture, rep 2

city: Alcalá de Henares

first: Sergio

last: Gascón

state: Madrid

address: Avenida de León, 1

department: Department of Molecular and Cellular Neuroscience

country: Spain

institute: Cajal Neuroscience Center - CSIC

description:
Library name: RNA14
In vitro reactive culture (RC) generated from lesion cores dissected 1 day after cortical stab-wound injury (A/P -1.6 mm to -2.5 mm, M/L ±1.5 mm to ±2.5 mm, and D/V 0.5 mm) and cultured for 6 days. Whole culture collected for RNA-seq (CD171+, ACSA-2+) .

data_processing:
Raw paired-end reads were aligned to the reference genome using HISAT2.
Assembly: GRCm39
Supplementary files format and content: Comma-delimited csv file contains raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
RNA was extracted using the ReliaPrep™ RNA Miniprep System (Promega).
RNA libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042).

treatment_protocol: Based on Bregma coordinates, surgical lancet injuries were performed creating a grid in the following coordinates: A/P -1.6 mm to -2.5 mm, M/L ±1.5 mm to ±2.5 mm, and D/V 0.5 mm. One day after the injury, the lesion core was dissected and dissociated with the Papain Dissociation System (Worthington), and subjected to a FACS sorting protocol (previously described). For in vitro samples, after 1 day, the core of the lesion was dissected and cultured in vitro for 6 days in DMEM/F12 medium supplemented with glucose (45%, 1:100), penicillin/streptomycin (1:100), B27 (1:200), 10% fetal bovine serum (FBS), and GlutaMax, at 37ºC in 8% CO₂ . The whole resulting cell culture was included in the analysis.

value: cortex

value: WT

value: reactive culture (injured cortex cultured 6 days in vitro)

tag: strain

tag: age

value: 2-3 months old


title: Flavopiridol_treated_No_Halo_Control_Cut&Run_replicate_1

description: Library name: Flavopiridol_treated_No_Halo_Control_Cut_Run_replicate_1


title: RAW-POPC-Chol2

city: La Jolla

first: Antonio

last: De Maio

state: CA

address: 9500 Gilman dr

institute: UC San Diego

description: Library name: sample 8

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using the STAR v2.5.1a aligner.
Read quantification was performed with RSEM v1.3.0 and GENCODE annotation (Mus_musculus.GRCm38.68.gtf). The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.
Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing corrections using a moderated t-statistic in Limma.
Functional enrichment of the differentially expressed genes was performed using the Bioconductor GSVA package for implementing GSEA, Signaling Pathway Impact Analysis with the Bioconductor package SPIA and overrepresentation analysis in WebGestalt.
Assembly: mm10
Supplementary files format and content: tab-delimited CSV file include FPKM values for each sample

extract_protocol:
Total RNA isolation was performed using RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA sequencing libraries were then generated from 1 µg of RNA using the TruSeq® Stranded Total RNA Library Prep Gold Sample Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW26.7 macrophages were incubated with POPC liposomes for 1 hour containing or not free cholesterol (n=3). Control cells were treated with vehicle (PBS) in the same conditions (n-3).

tag: cell line

tag: cell type

value: Macrophages

value: POPC liposomes-Chol


title: iNKs and reference samples sub-library 3

city: Stevenage

first: Marina

last: Tarunina

state: Hertfordshire

address: Plasticell Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road

country: United Kingdom

institute: Plasticell Ltd.

description:
Library name: LIB_3
Parse Biosciences Evercode WT v2

library_source: transcriptomic single cell

data_processing:
Read and barcode demultiplexing and quantification were run using the Parse Biosciences split-pipe pipeline v. 1.2.0.
Assembly: Ensembl GRCh38 reference genome release 108
Supplementary files format and content: count matrix

source_name: human iPSC, iNKs, PB-CD34+ cells, UCB-CD34+ cells, PBMC and PBMC-NK cells

extract_protocol:
iPSCs were thawed and recovered for one passage before fixation. PB-CD34+ cells were thawed and recovered overnight before fixation. UCB-CD34+ cells were thawed and recovered overnight before fixation. Donor PBMCs were thawed and recovered overnight before fixation. PBMC-NK were isolated from thawed and recovered donor PBMCs using NK cell Isolation Kit, human (Miltenyi Biotec), according to manufacturer’s protocol. iNKs were collected from differentiation experiment for fixation. All cells were fixed using EvercodeTM Cell Fixation v2 (Parse Biosciences), according to manufacturer’s protocol V2.1.2.
Libraries for single cell RNA sequencing (scRNA-seq) were prepared from fixed cells using EvercodeTM WT v2 (Parse Biosciences), according to manufacturer’s protocol V2.2.2. Number of fixed cells used for sample preparation was calculated using Parse Biosciences EvercodeTM WT Sample Loading Table v2 (Parse Biosciences), with targeted 2750 barcoded cells for each control sample (i.e. iPSC, PB-CD34+, UCB-CD34+, PBMC and PBMC-NK samples) and targeted 4125 barcoded cells for each iNK sample.


title: Triptolide_treated_No_Halo_Control_Cut&Run_replicate_1

description: Library name: Triptolide_treated_No_Halo_Control_Cut_Run_replicate_1


title: Triptolide_treated_PAF1_Cut&Run_replicate_1

description: Library name: Triptolide_treated_PAF1_Cut_Run_replicate_1


title: DMSO_treated_PAF1_Cut&Run_replicate_1

description: Library name: DMSO_treated_PAF1_Cut_Run_replicate_1


title: Nontreated_Control_Pol2_Cut&Run_replicate_3

description: Library name: Nontreated_Control_Pol2_Cut_Run_replicate_3


title: RAW-POPC-Chol1

description: Library name: sample 7


title: DMSO_treated_No_Halo_Control_Cut&Run_replicate_1

description: Library name: DMSO_treated_No_Halo_Control_Cut_Run_replicate_1


title: Nontreated_No_Halo_Control_Cut&Run_replicate_2

description: Library name: Nontreated_No_Halo_Control_Cut_Run_replicate_2


title: DMSO_treated_Pol2_Cut&Run_replicate_2

description: Library name: DMSO_treated_Pol2_Cut_Run_replicate_2

value: Nontreated


title: Degos_3_CSF_PostRuxo_Wk_0_TCR

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: CSF

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. Peripheral blood mononuclear cells (PBMCs) from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell capturing. cDNA was generated using 5' 10X kit and subsequenctly used for gene expression library and single cell TCR library preparation.
Single cell TCR library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: CSF


title: Flavopiridol_treated_Pol2_Cut&Run_replicate_2

description: Library name: Flavopiridol_treated_Pol2_Cut_Run_replicate_2


title: Triptolide_treated_Pol2_Cut&Run_replicate_2

description: Library name: Triptolide_treated_Pol2_Cut_Run_replicate_2


title: Flavopiridol_treated_Pol2_Cut&Run_replicate_1

description: Library name: Flavopiridol_treated_Pol2_Cut_Run_replicate_1


title: Degos_3_CSF_PostRuxo_Wk_12_Rep2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).


title: DMSO_treated_Pol2_Cut&Run_replicate_1

description: Library name: DMSO_treated_Pol2_Cut_Run_replicate_1


title: Nontreated_No_Halo_Control_Cut&Run_replicate_1

description: Library name: Nontreated_No_Halo_Control_Cut_Run_replicate_1


title: Triptolide_treated_Pol2_Cut&Run_replicate_1

description: Library name: Triptolide_treated_Pol2_Cut_Run_replicate_1


title: Nontreated_Control_Pol2_Cut&Run_replicate_2

description: Library name: Nontreated_Control_Pol2_Cut_Run_replicate_2


title: Nontreated_Control_Pol2_Cut&Run_replicate_1

description: Library name: Nontreated_Control_Pol2_Cut_Run_replicate_1


title: KOLF_KO_rep2

city: San Francisco

first: Elena

last: Turkalj

institute: UCSF

description: Library name: KOLF_KO_rep2

data_processing:
Raw FASTQ files were processed using PIPseeker v3.3. Cellular barcodes and intrinsic molecular identifiers (IMIs) were extracted and appended to read headers, and adapter and poly-A sequences were trimmed. Reads were aligned to the human reference genome (GRCh38.p13, GENCODE v40) using STAR v2.7.11a. Gene expression matrices were generated by collapsing IMIs and assigning reads to genes. Quality control filtering excluded cells with fewer than 300 or greater than 6,500 detected genes, or greater than 12% mitochondrial gene expression. Data were normalized using SCTransform and integrated across samples using Harmony for batch correction. Dimensionality reduction was performed using principal component analysis, and cells were visualized using UMAP. Clustering was performed using a shared nearest neighbor graph and the Louvain algorithm. Cell type annotation was performed using ScType and manual curation based on canonical marker genes. Differential expression analysis was conducted using pseudobulk aggregation and edgeR (glmLRT), with significance defined as FDR < 0.05 and log2 fold change > 1.
Assembly: hg38
Supplementary files format and content: cell barcodes after filtering of control rep 1, ct1_barcodes.tsv.gz
Supplementary files format and content: cell barcodes after filtering of control rep 2, ct2_barcodes.tsv.gz
Supplementary files format and content: cell barcodes after filtering of control rep 3,  ct3_barcodes.tsv.gz
Supplementary files format and content: cell barcodes after filtering of METTL5 KO rep 1, ko1_barcodes.tsv.gz
Supplementary files format and content: cell barcodes after filtering of METTL5 KO rep 2,  ko2_barcodes.tsv.gz
Supplementary files format and content: cell barcodes after filtering of METTL5 KO rep 3, ko3_barcodes.tsv.gz
Supplementary files format and content: features after filtering of control rep 1, ct1_features.tsv.gz
Supplementary files format and content: features after filtering of control rep 2, ct2_features.tsv.gz
Supplementary files format and content: features after filtering of control rep 3, ct3_features.tsv.gz
Supplementary files format and content: features after filtering of METTL5 KO rep 1, ko1_features.tsv.gz
Supplementary files format and content: features after filtering of METTL5 KO rep 2, ko2_features.tsv.gz
Supplementary files format and content: features after filtering of METTL5 KO rep 3, ko3_features.tsv.gz
Supplementary files format and content: matrix after filtering of control rep 1, ct1_matrix.mtx.gz
Supplementary files format and content: matrix after filtering of control rep 2, ct2_matrix.mtx.gz
Supplementary files format and content: matrix after filtering of control rep 3, ct3_matrix.mtx.gz
Supplementary files format and content: matrix after filtering of METTL5 KO rep 1, ko1_matrix.mtx.gz
Supplementary files format and content: matrix after filtering of METTL5 KO rep 2, ko2_matrix.mtx.gz
Supplementary files format and content: matrix after filtering of METTL5 KO rep 3, ko3_matrix.mtx.gz
Supplementary files format and content: DE analysis of METTL5-KO vs Ctrl Day 75 organoids, ctrl_vs_M5KO_DE.csv
Supplementary files format and content: GSEA and GO analysis of uregulated genes for METTL5 KO day 75 organoids, GSEA_GO_upreg_M5KO.csv
Supplementary files format and content: GSEA and GO analysis of uregulated genes for Control day 75 organoids, GSEA_GO_upreg_Ctrl.csv

source_name: Dorsal cortical forebrain organoids

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were maintained under feeder-free conditions and dissociated using Accutase. For organoid formation, 10,000 cells per well were seeded into low-attachment 96-well plates in iPSC medium supplemented with ROCK inhibitor (Day 0). From Days 3-6, organoids were cultured in neural induction (NI) medium supplemented with inhibitors of TGF-β (SB431542), BMP (LDN-193189), and Wnt signaling (IWR-1-endo), with ROCK inhibitor included initially and removed after Day 6. From Days 9-25, organoids were maintained in neural maintenance medium (MM1) consisting of a 1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2 and B27 minus vitamin A, along with EGF and FGF to support neural progenitor expansion. Organoids were transferred to an orbital shaker at approximately Day 18 to improve nutrient distribution. From Days 26-35, organoids were maintained in MM1 without growth factors. From Days 35-55, organoids were cultured in MM2 (MM1 supplemented with B27 containing vitamin A and ascorbic acid) to promote neuronal differentiation. From Days 56-62, MM2 was supplemented with LIF, followed by supplementation with BDNF and NT-3 from Days 63-70 to support neuronal maturation. After Day 70, organoids were maintained in MM2 until collection. Organoids were harvested at Day 75 of differentiation for single-cell RNA sequencing.

extract_protocol:
Day 75 control and METTL5-KO cerebral organoids were dissociated into single-cell suspensions using papain-based enzymatic digestion. Organoids were incubated in activated papain supplemented with DNase I at 37 °C, gently triturated, and further digested until a uniform single-cell suspension was obtained. Digestion was stopped with ovomucoid inhibitor, and cells were collected by centrifugation, resuspended in 0.04% BSA/HBSS, and passed through a 37 μm cell strainer. Cell viability was confirmed by trypan blue staining before downstream single-cell RNA-seq library preparation.
Single-cell RNA-seq libraries were generated from single-cell suspensions prepared from day 75 control and METTL5-KO cerebral organoids using the PIPseq-V T10 kit (Fluent BioSciences) according to the manufacturer’s protocol. Cellular barcodes and intrinsic molecular identifiers were incorporated during library preparation to enable single-cell transcriptome profiling. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 150 bp sequencing.

value: Dorsal cortical forebrain organoids

value: Cerebral organoid cells

value: METTL5 KO


title: PAG006_Inf_E2

source_name: PAG006 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: KOLF_KO_rep3

description: Library name: KOLF_KO_rep3


title: Treg WT [GZ_06]

type: genomic

city: Berlin

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz1

country: Germany

institute: Berlin Institute of Health Center for Regenerative Therapies

hyb_protocol: After bisulfite conversion, the gDNA, was fragmented, hybridized, and stained as per the guidelines of the Infinium HD protocol.

scan_protocol: Bead arrays were scanned using the iScan.

data_processing:
The raw intensity data files (IDAT) were preprocessed using minfi version 1.42.0 by quantile normalization. Probes were filtered based on not meeting the detection p-value threshold against the background (p<0.01), being reported as cross-reactive, revisions of Illumina's manifest (Infinium MethylationEPIC v1.0 13.03.2020), or being at a SNP, using the minfi function dropLociWithSnps.
Quantile normalized, filtered based on p-value and croos-reactivity. Beta values, between 0-1.

label: Cy3 and Cy5

source_name: Treg WT

label_protocol: Infinium HD Methylation Assay Reference Guide.

extract_protocol: genomic DNA was extracted using Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) following instructions provided by the manufacturer. Isolated genomic DNA was subjected to bisulfite conversion using Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) according to manufacturer's instructions.

value: Treg WT

tag: donor

tag: Sex

value: male


title: KOLF_KO_rep1

description: Library name: KOLF_KO_rep1


title: KOLF_CT_rep2

description: Library name: KOLF_CT_rep2

value: Wildtype/Control


title: KOLF_CT_rep3

description: Library name: KOLF_CT_rep3


title: Degos_3_Skin_Inflam_PostRuxo_Wk_12

description: 10x Genomics

source_name: Skin

value: Skin


title: MACR_FAB_3

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: sanple 9

data_processing:
demultiplexed fasq reads from Novogene Inc., were aligned and analyzed using the Alpine high performance computing resource at the University of Colorado Boulder (University of Colorado Boulder Research Computing. 2023. Alpine. University of Colorado Boulder. https://doi.org/10.25811/k3w6-pk81).
Fastq files were filtered for quality and adapters removed using fastp v0.23.2, then aligned with human genome assembly GRCh38.p14 and annotated with Ensmble version 114 using STAR v 2.7.10b. differential expression analysis computed using Deseq
Assembly: GRCh38.p14
Supplementary files format and content: raw counts csv file
Supplementary files format and content: normalized counts csv file

source_name: cells

growth_protocol: human THP-1 cells were grown in DMEM plus 10 percent FBS with essential and non essential amino acids, glutamine and PenStrep

extract_protocol:
Cells were collected in RNA lysis buffer (350 μL/sample) and frozen at −80 °C until RNA isolation was performed.
RNA was extracted from frozen samples using the RNeasy kit (Qiagen Germantown, MD) according to manufacturer's instructions and sent to Novogene Corporation Inc. (Sacramento, CA) for RNA sequencing. RNA quality was determined by bioanalyzer (Agilent Technologies, Santa Clara, CA) to have RIN (RNA integrity number) of over 9.0 for all samples. mRNA was enriched using oligo (dT) beads, followed by cDNA library generation using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA).

treatment_protocol: cells were plated at 100,000 cells per well in culture media with IL-1β and TNF-α at 20 ng/mL. Plates were then sandwiched with germanium embedded fabricBAF on top and bottom of wells without cell contact and placed in 37 °C in a 5 % CO2 incubator for 18 hour

value: cells

value: immortalized human monocyte


title: KOLF_CT_rep1

description: Library name: KOLF_CT_rep1


title: MACR_STIM_2

description: Library name: sanple 11


title: MACR_FAB_2

description: Library name: sanple 8


title: MACR_STIM_3

description: Library name: sanple 12


title: MACR_STIM_1

description: Library name: sanple 10


title: MACR_FAB_1

description: Library name: sanple 7


title: MACR_CTRL_3

description: Library name: sanple 6


title: MACR_CTRL_2

description: Library name: sanple 5


title: MACR_CTRL_1

description: Library name: sanple 4


title: MACR_BWR_3

description: Library name: sanple 3


title: MACR_BWR_2

description: Library name: sanple 2


title: CTRL 12

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Library name: R129

data_processing:
High-quality reads were aligned to the human reference genome GRCh38 using STAR (v2.7.9a). Gene-level transcript abundance was quantified using RSEM (v1.3.1).
Gene expression levels were reported as transcripts per million (TPM).
Assembly: GRCh38
Supplementary files format and content: Gene-level expression estimates reported as TPM values for each sample.

source_name: NonTumor liver

extract_protocol:
Total RNA was extracted from liver tissue samples using TRIzol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using a LabChip GX system.
cDNA libraries were prepared from total RNA using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit (Yeasen) following the manufacturer's protocol. Libraries were subjected to paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq 6000 platform.

value: NonTumor liver

tag: group

value: CTRL


title: MACR_BWR_1

description: Library name: sanple 1


title: CTRL 11

description: Library name: R128


title: CTRL 9

description: Library name: R126


title: CTRL 8

description: Library name: R125


title: CTRL 7

description: Library name: R124


title: CTRL 6

description: Library name: R123


title: CTRL 5

description: Library name: R122


title: CTRL 4

description: Library name: R121


title: CTRL 10

description: Library name: R127


title: CTRL 3

description: Library name: R120


title: MASLD 12

description: Library name: R118

value: MASLD


title: MASLD 13

description: Library name: R119


title: MASLD 11

description: Library name: R117


title: MASLD 10

description: Library name: R116


title: MASLD 8

description: Library name: R113


title: MASLD 9

description: Library name: R114


title: MASLD 3

description: Library name: R108


title: MASLD 2

description: Library name: R107


title: MASLD 4

description: Library name: R109


title: MASLD 6

description: Library name: R111


title: MASLD 1

description: Library name: R106


title: MASLD 5

description: Library name: R110


title: CTRL 1

description: Library name: R105


title: MASLD-HCC 95

description: Library name: R104

value: MASLD-HCC


title: MASLD-HCC 94

description: Library name: R103

source_name: Tumor liver

value: Tumor liver


title: MASLD-HCC 93

description: Library name: R102


title: MASLD-HCC 92

description: Library name: R101


title: MASLD-HCC 91

description: Library name: R99


title: MASLD-HCC 88

description: Library name: R96


title: MASLD-HCC 87

description: Library name: R95


title: MASLD-HCC 85

description: Library name: R93


title: MASLD-HCC 83

description: Library name: R90


title: MASLD-HCC 86

description: Library name: R94


title: MASLD-HCC 84

description: Library name: R92


title: MASLD-HCC 82

description: Library name: R89


title: MASLD-HCC 81

description: Library name: R87


title: MASLD-HCC 80

description: Library name: R86


title: MASLD-HCC 79

description: Library name: R84


title: MASLD-HCC 78

description: Library name: R83


title: MASLD-HCC 77

description: Library name: R82


title: MASLD-HCC 76

description: Library name: R81


title: MASLD-HCC 75

description: Library name: R80


title: MASLD-HCC 74

description: Library name: R79


title: MASLD-HCC 73

description: Library name: R78


title: MASLD-HCC 71

description: Library name: R76


title: MASLD-HCC 72

description: Library name: R77


title: MASLD-HCC 69

description: Library name: R74


title: MASLD-HCC 67

description: Library name: R72


title: MASLD-HCC 66

description: Library name: R71


title: MASLD-HCC 65

description: Library name: R70


title: MASLD-HCC 64

description: Library name: R69


title: MASLD-HCC 63

description: Library name: R68


title: MASLD-HCC 62

description: Library name: R67


title: MASLD-HCC 61

description: Library name: R66


title: MASLD-HCC 60

description: Library name: R65


title: MASLD-HCC 59

description: Library name: R64


title: MASLD-HCC 56

description: Library name: R61


title: MASLD-HCC 57

description: Library name: R62


title: MASLD-HCC 54

description: Library name: R59


title: MASLD-HCC 55

description: Library name: R60


title: MASLD-HCC 53

description: Library name: R58


title: MASLD-HCC 52

description: Library name: R57


title: MASLD-HCC 51

description: Library name: R56


title: MASLD-HCC 50

description: Library name: R55


title: MASLD 7

description: Library name: R112


title: CTRL 2

description: Library name: R115


title: MASLD-HCC 47

description: Library name: R52


title: MASLD-HCC 48

description: Library name: R53


title: MASLD-HCC 45

description: Library name: R48


title: MASLD-HCC 49

description: Library name: R54


title: MASLD-HCC 46

description: Library name: R49


title: 3-months-rep2

city: Cambridge

first: Yuancheng Ryan

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: 2-3m-b2

data_processing:
ATAC-seq data was aligned to the mm10 genome using bowtie2, and duplicate reads were removed using Picard MarkDuplicates. Aligned data was processed using samtools and converted to fragments files with bedtools bamtobed.
Assembly: mm10
Supplementary files format and content: ATAC-seq fragments files (.fastq.gz) : Tab-delimited files with 5 columns corresponding to the chromosome, start, end, sample name, and duplicate count for each paired-end fragment.

source_name: Ear Fibroblasts

extract_protocol:
Cells were incubated with custom-loaded Tn5 transposase in high-salt transposition buffer for 30 minutes at 37 °C with agitation. Transposed DNA was purified using the Zymo DNA Clean & Concentrator kit.
Libraries were pre-amplified for 5 cycles, then subjected to qPCR to determine the additional number of cycles needed, minimizing amplification bias. Final libraries were purified, quality-checked by gel electrophoresis, and quantified. Sequencing was performed on an Illumina platform using paired-end reads, targeting ~20 million reads per sample.

value: Ear Fibroblasts


title: COPA_siRNA_repeat_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample 6
Cells were transfected with COPA siRNA and harvested 72 hours later - replicate 3

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit (Qiagen) following the manufacturer’s instructions
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: WT

value: COPA siRNA transfection


title: MASLD-HCC 44

description: Library name: R45


title: MASLD-HCC 43

description: Library name: R44


title: MASLD-HCC 42

description: Library name: R43


title: MASLD-HCC 90

description: Library name: R98


title: MASLD-HCC 41

description: Library name: R42


title: MASLD-HCC 40

description: Library name: R41


title: MASLD-HCC 38

description: Library name: R39


title: MASLD-HCC 37

description: Library name: R38


title: MASLD-HCC 36

description: Library name: R37


title: MASLD-HCC 39

description: Library name: R40


title: MASLD-HCC 35

description: Library name: R36


title: MASLD-HCC 89

description: Library name: R97


title: MASLD-HCC 34

description: Library name: R35


title: MASLD-HCC 33

description: Library name: R34


title: MASLD-HCC 32

description: Library name: R33


title: MASLD-HCC 31

description: Library name: R32


title: MASLD-HCC 30

description: Library name: R31


title: MASLD-HCC 29

description: Library name: R30


title: MASLD-HCC 27

description: Library name: R28


title: MASLD-HCC 25

description: Library name: R26


title: MASLD-HCC 28

description: Library name: R29


title: MASLD-HCC 26

description: Library name: R27


title: MASLD-HCC 22

description: Library name: R23


title: MASLD-HCC 21

description: Library name: R22


title: MASLD-HCC 23

description: Library name: R24


title: MASLD-HCC 24

description: Library name: R25


title: MASLD-HCC 20

description: Library name: R21


title: MASLD-HCC 19

description: Library name: R20


title: MASLD-HCC 18

description: Library name: R19


title: MASLD-HCC 17

description: Library name: R18


title: MASLD-HCC 70

description: Library name: R75


title: MASLD-HCC 16

description: Library name: R17


title: MASLD-HCC 68

description: Library name: R73


title: MASLD-HCC 14

description: Library name: R15


title: MASLD-HCC 13

description: Library name: R14


title: MASLD-HCC 12

description: Library name: R13


title: MASLD-HCC 11

description: Library name: R12


title: MASLD-HCC 15

description: Library name: R16


title: MASLD-HCC 10

description: Library name: R11


title: MASLD-HCC 9

description: Library name: R10


title: MASLD-HCC 8

description: Library name: R9


title: MASLD-HCC 7

description: Library name: R7


title: MASLD-HCC 6

description: Library name: R6


title: MASLD-HCC 4

description: Library name: R4


title: MASLD-HCC 5

description: Library name: R5


title: MASLD-HCC 3

description: Library name: R3


title: MASLD-HCC 2

description: Library name: R2


title: MASLD-HCC 1

description: Library name: R1


title: MASLD-HCC 58

description: Library name: R63


title: HAECs, Ctrl miRNA, rep3

city: Xi'an

first: Chen

last: Wang

address: Yanta West Road No.277

country: China

institute: The First Affiliated Hospital of Xi’an Jiaotong University

description: Library name: NC_3

data_processing:
HISAT2 (https://ccb.jhu.edu/software/hisat2)
Assembly: GRCh38
Supplementary files format and content: FPKM and raw counts for each sample

source_name: HAECs

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. 1.0ug of total RNA was used for the construction of sequencing libraries
The RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: HAECs

value: human aortic endothelial cells

value: HAECs transfected with control miRNA


title: HAECs, Ctrl miRNA, rep1

description: Library name: NC_1


title: HAECs, miR-30e-5p mimic, rep3

description: Library name: M_3

value: miR-30e-5p overexpression

value: HAECs transfected with miR-30e-5p


title: HAECs, Ctrl miRNA, rep2

description: Library name: NC_2


title: HAECs, miR-30e-5p mimic, rep2

description: Library name: M_2


title: HAECs, miR-30e-5p mimic, rep1

description: Library name: M_1


title: Normal Donor 2

city: Warminster

first: Maksim

middle: Alexandrovich

last: Shestov

state: Pennsylvania

address: 675 E Street Rd

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

description: Library name: Normal BM 2

data_processing:
Raw base call files were demultiplexed to FASTQ files, and FASTQs were processed using the 10x Genomics Cell Ranger pipeline for read alignment, barcode processing, UMI counting, and generation of gene-by-cell count matrices.
Assembly: GRCh38
Supplementary files format and content: Processed data are provided as Cell Ranger gene-barcode count matrices containing UMI counts per gene for each detected cell barcode.

source_name: Bone marrow

extract_protocol:
Bone marrow aspirates were collected from relapsed AML patients prior to lymphodepleting chemotherapy. Mononuclear cells were isolated, and viable single-cell suspensions were prepared for single-cell RNA-seq library generation.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium platform according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

value: Bone marrow

value: Normal Donor


title: Normal Donor 1

description: Library name: Normal BM 1


title: Normal Donor 3

description: Library name: Normal BM 3


title: Relapsed AML Patient 7

description: Library name: Relapsed AML 7

value: Relapsed AML Patient


title: Relapsed AML Patient 5

description: Library name: Relapsed AML 5


title: Relapsed AML Patient 6

description: Library name: Relapsed AML 6


title: Relapsed AML Patient 4

description: Library name: Relapsed AML 4


title: Relapsed AML Patient 2

description: Library name: Relapsed AML 2


title: Relapsed AML Patient 3

description: Library name: Relapsed AML 3


title: Relapsed AML Patient 1

description: Library name: Relapsed AML 1


title: before extracellular vesicle treatment, S01055

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

description: Library name: S01055

data_processing:
The raw fastq data were trimmed for adapter sequences using Cutadapt (v0.6.7) and subjected to quality control using FastQC (v0.11.9). The trimmed sequences were then mapped to the GRCh38.p13 genome using STAR (v2.7.9a), and feature Counts (v2.0.3) was used to count the reads mapped to each gene, resulting in a count matrix.
Assembly: GRCh38.p13
Supplementary files format and content: raw counts for each samples

source_name: blood

extract_protocol:
RNA was extracted from samples by Trizol reagent
Reverse transcription was conducted by reverse transcriptase, double strand cDNA was conducted using mRNA second strand synthesis kit, double strand DNA was cleaned with beads, sequencing library was constructed with Library preparation kit

value: blood

value: before


title: after extracellular vesicle treatment, S010542

description: Library name: S010542

value: after


title: before extracellular vesicle treatment, S010541

description: Library name: S010541


title: after extracellular vesicle treatment, S01048

description: Library name: S01048


title: after extracellular vesicle treatment, S01050

description: Library name: S01050


title: after extracellular vesicle treatment, S01047

description: Library name: S01047


title: after extracellular vesicle treatment, S01045

description: Library name: S01045


title: after extracellular vesicle treatment, S01044

description: Library name: S01044


title: after extracellular vesicle treatment, S01041

description: Library name: S01041


title: after extracellular vesicle treatment, S01043

description: Library name: S01043


title: after extracellular vesicle treatment, S01039

description: Library name: S01039


title: after extracellular vesicle treatment, S01040

description: Library name: S01040


title: after extracellular vesicle treatment, S01036

description: Library name: S01036


title: after extracellular vesicle treatment, S01034

description: Library name: S01034


title: after extracellular vesicle treatment, S01032

description: Library name: S01032


title: after extracellular vesicle treatment, S01028

description: Library name: S01028


title: after extracellular vesicle treatment, S01027

description: Library name: S01027


title: after extracellular vesicle treatment, S01029

description: Library name: S01029


title: after extracellular vesicle treatment, S01026

description: Library name: S01026


title: after extracellular vesicle treatment, S01024

description: Library name: S01024


title: after extracellular vesicle treatment, S01023

description: Library name: S01023


title: after extracellular vesicle treatment, S01021

description: Library name: S01021


title: after extracellular vesicle treatment, S01017

description: Library name: S01017


title: after extracellular vesicle treatment, S01019

description: Library name: S01019


title: after extracellular vesicle treatment, S01015

description: Library name: S01015


title: after extracellular vesicle treatment, S01013

description: Library name: S01013


title: before extracellular vesicle treatment, S01007

description: Library name: S01007


title: before extracellular vesicle treatment, S01005

description: Library name: S01005


title: before extracellular vesicle treatment, S01003

description: Library name: S01003


title: CP1806

city: fuzhou

first: 豪博

last: 黄

address: 本人（申请人）

institute: 福建医科大学附属协和医院

description: Library name: Sample 6

data_processing:
Raw reads were processed using trimadap to remove adapters, seqtk trimfq v1.0 to remove low-quality bases, and lengthsort.pl to filter short fragments. Ribosomal RNA was depleted using Bowtie2 v2.2.6. Clean reads were aligned to the Homo sapiens reference genome (GRCh38.p14) using HISAT2 v2.0.4. Aligned BAM files were processed with Samtools v1.9 and Sambamba v0.6.4. Gene-level expression was quantified using StringTie v1.3.3b.
Assembly: Homo sapiens (GRCh38.p14)
Supplementary files format and content: This submission includes only raw FASTQ sequence files for all samples; no processed expression matrices or derived data files are provided.

source_name: plasma

extract_protocol:
Total RNA was extracted from 1 mL of plasma using a plasma/serum miRNA ex-traction kit (Bio You). The concentration of the extracted total RNA was assessed using a Qubit RNA assay (Life Technologies).
A total RNA library (>50 nt) was prepared using a SMARTer Stranded Total RNA-Seq Kit v2. Following the kit protocol, reverse transcription, addition of sequencing adapters and barcodes, construction and purification of cDNA libraries, depletion of ribosomal RNA (rRNA), PCR amplification of cDNA libraries, and additional purification steps were performed. Purified cDNA libraries were sequenced using an Illumina Nova-Seq6000 platform.

value: plasma

value: non-pCR

value: untreated


title: CP1788

institute: 福建医科大学附属协和医院

description: Library name: Sample 4


title: before extracellular vesicle treatment, S01001

description: Library name: S01001


title: CP1537

institute: 福建医科大学附属协和医院

description: Library name: Sample 2

value: pCR


title: CP1620

institute: 福建医科大学附属协和医院

description: Library name: Sample 3


title: CP1531

institute: 福建医科大学附属协和医院

description: Library name: Sample 1


title: 8-day TGF-β

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description:
Library name: D810
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1
Assembly: GRCh38-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoid

growth_protocol: Human iPSCs were maintained on Matrigel-coated plates in mTeSR1 medium under feeder-free conditions at 37°C and 5% CO₂. Colonies were passaged every 4–5 days using EDTA when cultures reached ~70–80% confluency. Human iPSC-derived skin organoids were generated following a previously established Nature protocol. Mature organoids were maintained in N2B27 medium consisting of DMEM/F12 and Neurobasal medium.

extract_protocol:
Skin organoids were digested and dissociated into single cell suspension. Cells were stained with 7AAD (BD catalog#559925). 7AAD- viable cells were flow sorted using BD FACSAria flow cytometer.
Sorted single cell suspensions of 4 samples,10x GEM-X OCM 3' Gel Bead v4 (10xGenomics PN 2001126), and partitioning oil (10xGenomics PN 2001213) were loaded into 10x Genomics GEM-X 3' OCM Chip (PN 2001099) to capture single cells in nanoliter-scale oil droplets by 10xChromiumX  instrument and generate Gel Beads-In-EMulsions (GEMs), and each sample was loaded with one set of beads with unique list of barcodes. Four samples were barcoded separately but multiplexed in the same GEMs. About 60% loaded cells can be captured in oil droplets, each with a gel bead containing oligoes bearing a bead-unique barcode and a 3’ end poly T sequence.  individual cells were lysed in droplets, the released mRNA bind to barcoded Poly T, and full length of single strand cDNA from each single nucleus are synthesized by “template switch” mechanism. GEMs containing single cell barcoded-cDNA were broken and all single cell cDNA libraries were pooled together. Pooled cDNA were cleaned up by DynaBeads MyOne™ Silane beads (10xGenomics PN 2000048) and then preamplified by PCR to generate sufficient mass for sequencing library construction. The sequencing libraries were constructed as 3’-biased whole transcriptome libraries by following steps of cDNA fragmentation, end repair & A-tailing adaptor ligation, and sample index PCR amplification.

treatment_protocol: Organoids were treated with TGF-β (10 ng/mL) for 8 or 14 days, with medium changed every other day, prior to transcriptomic analysis.

value: organoid

value: iPSC

value: wt

value: TGF-β


title: Control

description:
Library name: Control
10X Genomics


title: F05650303-2

description: Library name: Jin_F8

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw paired-end FASTQ files were quality- and adapter-trimmed using Trimmomatic v0.36 in paired-end mode with parameters: PE -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Paired trimmed reads were retained for downstream analysis.
Trimmed paired-end reads were aligned to the human hg38 reference genome using STAR v2.7.3a with parameters: --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts --limitBAMsortRAM 64000000000.
Gene-level read counts were generated from STAR coordinate-sorted BAM files using htseq-count with the hg38 refGene GTF annotation file and parameters: -f bam -r pos -s reverse -t exon -i gene_id -m union -a 10.
Count tables were used for downstream differential gene expression analysis.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

source_name: primary skin fibroblast

growth_protocol: Immortalized human skin fibroblasts or primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells were maintained by replacing the medium every 2–3 days and subcultured before reaching full confluence to preserve normal morphology and proliferative capacity.

extract_protocol:
Total RNA was extracted from cultured fibroblasts using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and samples were stored at –80°C until further use
Using the NEBNext Ultra II RNA Library Prep Kit for Illumina with poly(A) selection, we begin with high-quality total RNA and enrich mRNA using oligo-dT magnetic beads to capture polyadenylated transcripts, followed by washing and elution; we then fragment the purified mRNA under heat and prime it for reverse transcription to generate first-strand cDNA, after which we perform second-strand synthesis to produce double-stranded cDNA (optionally incorporating strand specificity), and subsequently carry out end repair and dA-tailing to create adapter-compatible ends; we ligate sequencing adapters, purify the library using magnetic beads (with optional size selection), and amplify it by PCR with indexed primers to enrich adapter-ligated fragments, and finally we assess library size distribution and concentration before pooling and sequencing on an Illumina platform.

treatment_protocol: Cells were treated either with or without TGF‑β or with compoound F05650303 for 48 hours.

value: primary skin fibroblast

value: fibroblast


title: TGF-β+ F05650303-2

description: Library name: Jin_F6


title: TGF-β+ F05650303-1

description: Library name: Jin_F5


title: TGF-β-1

description: Library name: Jin_F3


title: Control-2

description: Library name: Jin_F2


title: Control-1

description: Library name: Jin_F1


title: shRUNX2-3+TGF-β

description: Library name: Jin_E12

source_name: immortalized skin fibroblast

value: immortalized skin fibroblast


title: shRUNX2-1+TGF-β

description: Library name: Jin_E10


title: shControl-3+TGF-β

description: Library name: Jin_E9


title: shControl-2+TGF-β

description: Library name: Jin_E8


title: shControl-1+TGF-β

description: Library name: Jin_E7


title: shRUNX2-2

description: Library name: Jin_E5


title: shRUNX2-1

description: Library name: Jin_E4


title: shControl-3

description: Library name: Jin_E3


title: shControl-2

description: Library name: Jin_E2


title: shControl-1

description: Library name: Jin_E1


title: Primary human skin fibroblast + TGF-β replicate 2

description: Library name: LJ8

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
CUT-RUNTools-2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) was used to trim, align, and call peaks. Used default settings, EXCEPT set "frag_120" to "FALSE".
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --binSize 10
Assembly: Gencode GRCh38 p14 Release 47
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Run

source_name: Primary skin fibroblast

growth_protocol: Primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Medium was refreshed as needed, and cells were subcultured before reaching full confluence to maintain normal morphology and proliferative capacity.

extract_protocol:
Detach fibroblasts (passages 2–5) using 0.05–0.25% trypsin-EDTA until cells are in suspension.Neutralize trypsin with complete growth medium and collect cells by centrifugation (300 × g, 5 min). Wash cells with PBS.
Cells were permeabilized and incubated with an anti-RUNX2 antibody, followed by protein A–MNase to cleave DNA at RUNX2-bound sites. Released DNA fragments were purified and used to prepare sequencing libraries via end repair, A-tailing, adapter ligation, and limited-cycle PCR amplification, followed by size selection for ~150–400 bp fragments. Libraries were quality-checked and quantified prior to sequencing.

treatment_protocol: Cells were treated with or without TGF‑β, for 48 hours.

value: Primary skin fibroblast


title: Primary human skin fibroblast + TGF-β replicate1

description: Library name: LJ7


title: Primary human skin fibroblast replicate 1

description: Library name: LJ5


title: KO_Clone2_5h_rep3

city: Berkeley

first: Pooja

last: Mukherjee

state: California

address: 2151 Berkeley Way

institute: University of California, Berkeley

description:
Library name: S18
Knockout Clone2 Jurkat T cells, activated (5h), biological replicate 3

data_processing:
Data integrity verified by MD5 checksums; quality assessed with FastQC v0.12.1.
Adapter and low-quality base trimming performed with cutadapt using Illumina TruSeq adapter sequences and Phred quality cutoff Q20.
Transcript quantification performed with kallisto using Ensembl GRCh38 cDNA reference (Homo_sapiens.GRCh38.cdna.all.fa.gz) with 100 bootstrap samples.
Differential expression analyzed with sleuth in R at transcript level using design ~genotype with WT as reference; Wald test used for log2FC and FDR-adjusted q-values.
Assembly: GRCh38
Supplementary files format and content: Per-sample transcript-level estimated counts and TPM in TSV format (kallisto abundance.tsv output).

source_name: Jurkat

growth_protocol: Human Jurkat Clone E6-1 (ATCC TIB-152) was obtained from the Berkeley Cell Culture Facility. Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS and 0.01% Penicillin-Streptomycin (10,000 U/mL) at 1×10⁵ to 1×10⁶ cells/mL. Cells were routinely tested for mycoplasma contamination.

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research).
mRNA libraries were prepared by Novogene using poly-A enrichment and sequenced on Illumina NovaSeq PE150.

treatment_protocol: Jurkat cells were activated with plate-bound anti-CD3 and soluble anti-CD28 antibodies for 5 hours. Unactivated samples (0h) were left untreated.

value: Jurkat

value: T cell lymphocyte

value: 5 hour activation


title: KO_Clone2_5h_rep2

description:
Library name: S17
Knockout Clone2 Jurkat T cells, activated (5h), biological replicate 2


title: KO_Clone2_5h_rep1

description:
Library name: S16
Knockout Clone2 Jurkat T cells, activated (5h), biological replicate 1


title: KO_Clone1_5h_rep3

description:
Library name: S15
Knockout Clone1 Jurkat T cells, activated (5h), biological replicate 3


title: KO_Clone1_5h_rep2

description:
Library name: S14
Knockout Clone1 Jurkat T cells, activated (5h), biological replicate 2


title: KO_Clone1_5h_rep1

description:
Library name: S13
Knockout Clone1 Jurkat T cells, activated (5h), biological replicate 1


title: WT_5h_rep3

description:
Library name: S12
Wild-type Jurkat T cells, activated (5h), biological replicate 3

value: WT


title: WT_5h_rep1

description:
Library name: S10
Wild-type Jurkat T cells, activated (5h), biological replicate 1


title: KO_Clone2_0h_rep1

description:
Library name: S7
Knockout Clone2 Jurkat T cells, unactivated (0h), biological replicate 1

value: Unactivated


title: WT sample 1 brain

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression between rag2 mutant and WT fish was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: Brain

growth_protocol: Fish were grown at 28°C in a central filtration recirculating system with a 12 h light/dark cycle at the Hebrew University of Jerusalem (Aquazone ltd, Israel). Fish were fed with live Artemia until the age of 2 weeks (#109448, Primo), and starting week 3, fish were fed three times a day on weekdays (and once a day on weekends), with GEMMA Micro 500 Fish Diet (Skretting Zebrafish, USA), supplemented with Artemia once a day.

extract_protocol:
Brain and liver were isolated as described in (Astre et al. 2022)
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS,Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS,5067-5584). Libraries were sequenced by NextSeq 2000 P2, 100 cycle,75 bp single-end (Illumina, 20024906) with ~40 million reads per sample.

value: Brain

value: 2 months

value: Male


title: KO_Clone1_0h_rep2

description:
Library name: S5
Knockout Clone1 Jurkat T cells, unactivated (0h), biological replicate 2


title: KO_Clone1_0h_rep1

description:
Library name: S4
Knockout Clone1 Jurkat T cells, unactivated (0h), biological replicate 1


title: Vehicle_rep3

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 3

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 and hg19 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

source_name: Hippocampus

growth_protocol: Pregnant mice were randomly divided and intranasally administered the PM on days 9, 12, and 15 of pregnancy. The mice delivered pups on day 21 of pregnancy. Hippocampal tissues were collected from the pups at 14–18 weeks of age.

extract_protocol:
Total RNA was extracted from frozen hippocampus tissue of mice using the PureLink RNA Mini kit according to the manufacturer’s instructions (Thermo Fisher Scientific). The concentration and quality of RNA were assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies, CA). Ribosomal RNA was removed from 1 ug of total RNAs with more than RIN value 8.0 and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, NEB#E7775) and 100bp paired-end sequencing was done with a NovaSeq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: Hippocampus

value: normal saline (Veh)


title: Vehicle_rep2

description: Library name: Sample 2


title: WT_0h_rep3

description:
Library name: S3
Wild-type Jurkat T cells, unactivated (0h), biological replicate 3


title: WT_5h_rep2

description:
Library name: S11
Wild-type Jurkat T cells, activated (5h), biological replicate 2


title: WT_0h_rep2

description:
Library name: S2
Wild-type Jurkat T cells, unactivated (0h), biological replicate 2


title: KO_Clone2_0h_rep3

description:
Library name: S9
Knockout Clone2 Jurkat T cells, unactivated (0h), biological replicate 3


title: WT_0h_rep1

description:
Library name: S1
Wild-type Jurkat T cells, unactivated (0h), biological replicate 1


title: KO_Clone2_0h_rep2

description:
Library name: S8
Knockout Clone2 Jurkat T cells, unactivated (0h), biological replicate 2


title: ADT_Enza_3

first: Jun

last: Jiang

address: Changle No.169

institute: Air Force Medical University

description: Library name: Sample9

data_processing:
RNA-seq was performed on an Illumina NovaSeq 6000 system
This step involved removing adapter sequences, low-quality bases (Phred score < 20), and reads that became too short after trimming
reads were aligned to the reference genome (GRCh38) using HISAT2
A splice-aware aligner was used to correctly map reads that span exon-exon junctions
Assembly: Ensembl GRCh38
Supplementary files format and content: xlsx files include gene expression matrix

source_name: Prostate tumor

growth_protocol: Primary human prostate cancer CAFs were cultured in DMEM/F12 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA was synthesized using SuperScript II Reverse Transcriptase according to the manufacturer’s instructions.

treatment_protocol: Cells were divided into three groups: treated with Vehicle (DMSO control), treated with Androgen Deprivation Therapy (ADT) alone (5% charcoal-stripped serum (CSS)), and treated with a combination of ADT and Enzalutamide (5% charcoal-stripped serum (CSS) and 25µM ENZ).

value: Prostate tumor

value: Primary Cancer-Associated Fibroblast

value: css+Enza


title: ADT_Enza_2

description: Library name: Sample8


title: ADT_Enza_1

description: Library name: Sample7


title: after extracellular vesicle treatment, S01049

description: Library name: S01049

value: blood

value: after


title: ADT_2

description: Library name: Sample5

value: css


title: ADT_1

description: Library name: Sample4


title: Vehicle_3

description: Library name: Sample3


title: after extracellular vesicle treatment, S01042

description: Library name: S01042


title: PAG175_Inf_E2

city: Abu dhabi

first: Youssef

last: Idaghdour

address: Saadiyat Marina District

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: PAG175 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

value: Blood

value: Malaria Symptomatic stage


title: Vehicle_2

description: Library name: Sample2


title: after extracellular vesicle treatment, S01046

description: Library name: S01046


title: ADT_3

description: Library name: Sample6


title: after extracellular vesicle treatment, S01035

description: Library name: S01035


title: KO_Clone1_0h_rep3

description:
Library name: S6
Knockout Clone1 Jurkat T cells, unactivated (0h), biological replicate 3

value: Jurkat

value: T cell lymphocyte


title: after extracellular vesicle treatment, S01033

description: Library name: S01033


title: 2600007_JWH005-Molm13_D5_NT_Ctrl_rep2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description:
Library name: sample 3
RNA.STRANDED_RSEM_gene_count.tsv
RNA.STRANDED_RSEM_gene_TPM.tsv

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina).
Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’ Filtered reads were then mapped to the Homo sapiens reference genome GRC38(hg38) using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1)on the Gencode annotation v31 with ERCC92.
To identify the differentially expressed genes, normalization factors are first estimated using the trimmed mean of M values (TMM) and genes with CPM < 1 in all samples were removed. Next, the TMM normalization factors and raw counts were then used for the Limma-voom analysis using the “voom”, “lmFit” and “eBayes” functtions from the limma R package.
Assembly: hg38
Supplementary files format and content: gene-based raw counts tsv file
Supplementary files format and content: gene-based TPM tsv file

source_name: Blood

growth_protocol: MOLM13 leukemia cell lines were cultured in RPMI-1640 medium (Corning) containing 10% fetal bovine serum (Hyclone), two mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific) in an incubator at 37°C, 5% CO2, and 95% humidity.

extract_protocol:
MOLM13 targeted by sgNT or sgMBNL1-CDS were collected at day 3 and day 5 after infection.
About 200 ng of total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, followed by conversion into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR). After the end repair procedure, dA-tailing, and adapter ligation, each cDNA library was purified and enriched by 11 cycles of PCR amplification. We performed the paired-end 101-cycle sequencing on the NovaSeq 6000 sequencer (Illumina).

treatment_protocol: High-titer viruses of Lenti-sgRNA-Puro-IRES-CFP, Lenti-Cas9-Blast, and Lenti-dCas9-KRAB-blast were generated by co-transfection of helper plasmids (VSVG, RTR2, and GAGPOL) in 293T cells, which were cultured in DMEM (Thermo Fisher Scientific) with 10% heat-inactivated fetal bovine serum (Hyclone) and two mM L-glutamine (Sigma) at 37 °C in 5% CO2. MOLM13 eukemia cells were transduced with  Lenti-Cas9-Blast and Lenti-sgMBNL1-CDS-Puro-IRES-CFP and selected for stable transduction by blasticidin and puromycin.

value: WT

value: day 5


title: Vehicle_1

description: Library name: Sample1


title: 2600004_JWH002-Molm13_D3_KO_Ctrl_rep1

description:
Library name: sample 2
RNA.STRANDED_RSEM_gene_count.tsv
RNA.STRANDED_RSEM_gene_TPM.tsv

value: KO

value: day 3


title: 2600008_JWH006-Molm13_D5_KO_Ctrl_rep2

description:
Library name: sample 4
RNA.STRANDED_RSEM_gene_count.tsv
RNA.STRANDED_RSEM_gene_TPM.tsv


title: si_ITGB4_3

city: Shijiazhuang

first: Yi

last: Si

state: Hebei

address: No. 89 Donggang Road

institute: The First Hospital of Hebei Medical University

description: Library name: SAMPLE6

data_processing:
RNA quality assessed, libraries prepared, sequenced on NovaSeq.
Raw reads trimmed, aligned to genome, expression quantified as FPKM.
Differential expression analyzed with DESeq2/edgeR using adjusted p-value.
GO, KEGG, GSEA enrichment performed via clusterProfiler and GSEA tool.
Additional analyses: SNP, AS, PPI, fusion, WGCNA, immune profiling.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colorectal cancer

extract_protocol:
Total RNA was extracted from cells using the RNA-Easy Kit (Vazyme Biotech Co., Ltd., Nanjing, China).
The library was constructed from total RNA using poly-T magnetic beads, M-MuLV Reverse Transcriptase, DNA Polymerase I, RNase H, AMPure XP, and Phusion High-Fidelity DNA polymerase.

value: colorectal cancer

value: cancer cell


title: si_ITGB4_2

description: Library name: SAMPLE5


title: 2600003_JWH001-Molm13_D3_NT_Ctrl_rep1

description:
Library name: sample 1
RNA.STRANDED_RSEM_gene_count.tsv
RNA.STRANDED_RSEM_gene_TPM.tsv


title: si_ITGB4_1

description: Library name: SAMPLE4


title: si_NC_2

description: Library name: SAMPLE2


title: si_NC_3

description: Library name: SAMPLE3


title: si_NC_1

description: Library name: SAMPLE1


title: T42_RESRT

city: Redwood City

first: Dmitry

last: Velmeshev

address: 3200 Bridge Parkway

department: Oncology

institute: Galvanize Therapeutics

description:
Library name: T42_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)

data_processing:
BDRhapsody pipeline+Seurat
Assembly: GRCh38
Supplementary files format and content: combined raw counts matrix (RNA)
Supplementary files format and content: gene names
Supplementary files format and content: cell names
Supplementary files format and content: combined raw counts matrix (AbSeq)
Supplementary files format and content: protein names
Supplementary files format and content: cell metadata

source_name: Lung

extract_protocol:
Single cell dissociation
BDRhapsody

value: Lung

tag: provider

value: Galvanize Therapeutics

tag: collection date

tag: collection location

value: Spain

value: Female

tag: study group

value: PEF Treatment

value: Ablation after diagnostic biopsy

tag: histologic subtype

value: Adenocarcinoma

tag: ethnicity

value: Hispanic or Latino

tag: race

value: White

tag: nsclc clinical_stage


title: T42_RESRU

description:
Library name: T42_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

tag: tissue

tag: treatment


title: T41_INXBX

description:
Library name: T41_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Male

value: Squamous cell carcinoma


title: T41_RESRT

description:
Library name: T41_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T35_RESRT

description:
Library name: T35_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Netherlands

value: Not Hispanic or Latino


title: T41_RESRU

description:
Library name: T41_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: before extracellular vesicle treatment, S01006

description: Library name: S01006

value: blood

value: before


title: CP1436

institute: 福建医科大学附属协和医院

description: Library name: Sample 5

value: plasma

tag: genotype

value: non-pCR

value: untreated


title: T33_RESRT

description:
Library name: T33_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Lung

tag: age

value: Galvanize Therapeutics

value: Mucinous adenocarcinoma


title: dPA_CloneF6_H3K4me3

city: London

first: James

middle: A.

last: Cain

address: Guy's Hospital, Great Maze Pond

department: Infectious Diseases

institute: King's College London

description: Library name: dPA Clone F6, H3K4me3

data_processing:
CUT&RUN fastq files were processed using the pipeline summarised in Figure 2.2. Adapters were trimmed from fastq reads using trim-galore. Fastq files were aligned using bowtie2 (Langmead and Salzberg, 2012) to a N-Masked mouse genome (mm39). The N-Masked genome file was generated using SNPSplit (Krueger and Andrews, 2016) that required B6/CAST SNP information (.vcf) and the mm39 fasta genome sequence file. Once aligned, the aligned reads are then split into B6 (maternal) and CAST (paternal) read files for processing into .bigWigs using deeptools (Ramírez et al., 2014). Reads upstream and downstream of Mcts2 were counted using featureCounts with a custom .saf file from the aligned and split .bam file. RPKM normalisation was performed on aligned reads mapping to chr2 to alleviate normalisation artefacts derived from other chromosomes.
Assembly: mm39
Supplementary files format and content: .bigWig files showing RPKM normalisation. bigWig files also provided for split alleles post-SNPsplit processing, either RPKM normalised to the whole genome or specificallly at chromosome 2.
Library strategy: CUT&Run

growth_protocol: Hybrid C57BL/6 / CAST/EiJ mouse NSCs were extracted from the subventricular zone and expanded as previously described (Ferrón et al., 2007). NSCs were cultured in N2B27 media + Fgf2 + Egf : DMEM/F12 [Gibco, 11320033]: Neurobasal [Gibco, 21103049] at a 1:1 ratio, N2 1X final [Millipore, SCM012], B27 0.5x final [Gibco, 17504- 044], L-Glutamine 1x final [Gibco, 25030-024] and 2-mercaptoethanol 0.1mM [Gibco, 31350-010]. FGF2 [Peprotech, 100-18B] and EGF [Peprotech, 315-09] were reconstituted at in PBS + 0.1% BSA and 1µl of each growth factor was added per 10ml of N2B27 media to a final concentration of 10ng/ml. Cell culture plates were coated with 1/100th diluted GeltrexTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix [Gibco, A1413201] in DMEM-F12 media prior to NSC plating. Cells were detached using Accutase [Millipore, SCR005] and passaged every 2-3 days when reaching 80% confluency. Cells being recovered from liquid nitrogen storage were cultured for one day in N2B27 + Fgf2 + Egf + RevitaCellTM Supplement 1X [ThermoFisher, A2644501].

extract_protocol:
CUT&RUN was performed on freshly detached NSCs following the protocol detailed in(Janssens and Henikoff, 2019) with some modifications detailed here. Activation buffer and Concanavalin A beads were purchased from Cell Signalling Technologies [#93569]. Digitonin concentration utilised was at 5% across all buffers and MNase digestion time was at 30mins on ice unless otherwise stated. Recovery of DNA fragments using each method was confirmed using Qubit dsDNA HS Assay [Invitrogen, Q32851]. 10ng of this DNA was utilised for generation of CUT&RUN libraries.
Libraries were generated using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® [E7645S] and index using NEBNext® Mtiplex Oligos for Illumina® (Index Primers Set 1) [E7335S]. 1µl of 3µM of NEBNext Adaptor was utilised to reduce adaptor dimers. Sera-Mag select beads [Cytiva, 29343052] were used for DNA clean-up and size selection. DNA Library size was measured using Agilent High Sensitivity D1000 ScreenTape [Agilent, 5067- 5585].

value: Brain

tag: cell line

value: Neural Stem Cells

value: deltaH13d poly(A)+/-

tag: batch


title: T33_RESRU

description:
Library name: T33_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

tag: donor

value: Spain

value: Female

value: PEF Treatment

value: Ablation after diagnostic biopsy

value: Hispanic or Latino


title: T33_INXBX

description:
Library name: T33_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)

tag: Sex

value: White


title: T35_RESRU

description:
Library name: T35_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Netherlands

value: Male

value: Squamous cell carcinoma

value: Not Hispanic or Latino


title: T31_RESRT

description:
Library name: T31_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T31_RESRI

description:
Library name: T31_RESRI
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T31_RESRU

description:
Library name: T31_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T31_INXBX

description:
Library name: T31_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T30_RESRU

description:
Library name: T30_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Adenocarcinoma


title: T30_INXBX

description:
Library name: T30_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Lung


title: T30_RESRT

description:
Library name: T30_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Galvanize Therapeutics


title: T29_RESRU

description:
Library name: T29_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T28_RESRT

description:
Library name: T28_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T28_RESRU

description:
Library name: T28_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T28_INXBX

description:
Library name: T28_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T25_RESRT

description:
Library name: T25_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T29_RESRT

description:
Library name: T29_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T25_INXBX

description:
Library name: T25_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T24_RESRU

description:
Library name: T24_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: IB


title: T24_INXBX

description:
Library name: T24_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T25_RESRU

description:
Library name: T25_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T24_RESRT

description:
Library name: T24_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T22_INXBX

description:
Library name: T22_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Mucinous adenocarcinoma


title: T22_RESRU

description:
Library name: T22_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T19_RESRT

description:
Library name: T19_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T19_RESRU

description:
Library name: T19_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T22_RESRT

description:
Library name: T22_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T19_INXBX

description:
Library name: T19_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T18_RESRI

description:
Library name: T18_RESRI
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T18_RESRT

description:
Library name: T18_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T18_INXBX

description:
Library name: T18_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T18_RESRU

description:
Library name: T18_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T17_RESRU

description:
Library name: T17_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T17_RESRT

description:
Library name: T17_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T16_RESRU

description:
Library name: T16_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T17_INXBX

description:
Library name: T17_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T16_RESRT

description:
Library name: T16_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T16_INXBX

description:
Library name: T16_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T15_RESRT

description:
Library name: T15_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T15_RESRU

description:
Library name: T15_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T14_RESRT

description:
Library name: T14_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T15_INXBX

description:
Library name: T15_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T13_RESRU

description:
Library name: T13_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T12_INXBX

description:
Library name: T12_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T12_RESRU

description:
Library name: T12_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T11_RESRT

description:
Library name: T11_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T11_RESRU

description:
Library name: T11_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T11_INXBX

description:
Library name: T11_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T09_RESRT

description:
Library name: T09_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T09_RESRU

description:
Library name: T09_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T09_INXBX

description:
Library name: T09_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T08_INXBX

description:
Library name: T08_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T08_RESRT

description:
Library name: T08_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T01_RESRT

description:
Library name: T01_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T02_RESRU

description:
Library name: T02_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T01_RESRU

description:
Library name: T01_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: T01_INXBX

description:
Library name: T01_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


title: RA-FLS, IL-17 + DMSO-treated, replicate 3

city: Seoul

first: Yong Joon

address: 50 Yonsei-ro, Seodaemun-gu

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: IL-17_DMSO_3
RNA sequencing of primary RA-FLS pretreated with DMSO for 1 h followed by IL-17 stimulation for 18 h

data_processing:
For quality control of raw sequencing data, FastQC v0.11.7 was used.
Sequence reads were trimmed to remove low-quality bases, adapters and contaminants using Trimmomatic 0.38.
Trimmed sequence reads were mapped to the human reference genome (GRCh38) using HISAT2 version 2.1.0.
Transcript assembly and quantification of gene expression from mapped reads were performed using StringTie version 2.1.3b.
Assembly: GRCh38
Supplementary files format and content: Gene-level read count matrix generated from RNA-seq analysis. Rows represent genes (Gene_Symbol) and columns correspond to samples including Control-1, Control-2, Control-3, IL-17-1, IL-17-2, IL-17-3, PA20-1, PA20-2, and PA20-3.
Supplementary files format and content: Comma-separated values (CSV) file containing gene expression read counts for each sample.

source_name: Synovium

growth_protocol: RA-FLS cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humid atmosphere with 5% CO2 at 37°C.

extract_protocol:
Extraction of cellular RNA was conducted with RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Polyadenylated mRNA was enriched using oligo-dT beads, fragmented, and reverse-transcribed into cDNA. Sequencing adapters were ligated to cDNA fragments followed by PCR amplification. Libraries were subjected to paired-end sequencing on an Illumina platform.

treatment_protocol: RA-FLS were divided into three groups: control (DMSO), IL-17 group (IL-17 + DMSO), and PA group (IL-17 + PA). Cells were pretreated with DMSO or Polygonum aviculare L. extract (PA, 20 µg/mL) for 1 h and subsequently stimulated with IL-17 for 18 h.

value: Synovium

tag: cell type

value: Fibroblast-like synoviocytes

tag: disease state

value: Rheumatoid arthritis

value: IL-17 + DMSO


title: RA-FLS, IL-17 + PA 20 μg/mL-treated, replicate 3

description:
Library name: IL-17_PA_3
RNA sequencing of primary RA-FLS pretreated with PA 20 μg/mL for 1 h followed by IL-17 stimulation for 18 h


title: RA-FLS, IL-17 + PA 20 μg/mL-treated, replicate 1

description:
Library name: IL-17_PA_1
RNA sequencing of primary RA-FLS pretreated with PA 20 μg/mL for 1 h followed by IL-17 stimulation for 18 h


title: RA-FLS, IL-17 + DMSO-treated, replicate 2

description:
Library name: IL-17_DMSO_2
RNA sequencing of primary RA-FLS pretreated with DMSO for 1 h followed by IL-17 stimulation for 18 h


title: RA-FLS, IL-17 + DMSO-treated, replicate 1

description:
Library name: IL-17_DMSO_1
RNA sequencing of primary RA-FLS pretreated with DMSO for 1 h followed by IL-17 stimulation for 18 h


title: RA-FLS, IL-17 + PA 20 μg/mL-treated, replicate 2

description:
Library name: IL-17_PA_2
RNA sequencing of primary RA-FLS pretreated with PA 20 μg/mL for 1 h followed by IL-17 stimulation for 18 h


title: RA-FLS, DMSO-treated, replicate 3

description:
Library name: DMSO_3
RNA sequencing of primary RA-FLS treated with DMSO

value: DMSO


title: RA-FLS, DMSO-treatedl, replicate 2

description:
Library name: DMSO_2
RNA sequencing of primary RA-FLS treated with DMSO


title: D140 Retinoshperes, SCR265, WIN treatment

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description: Library name: D140_WIN_RNA

data_processing:
Cellranger count was used to align RNA sequencing reads to the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrices generated from cellranger count are supplied for the control and WIN-treament samples as filtered_feature_bc_matrix.h5 files.

molecule: nuclear RNA

source_name: Retina

growth_protocol: Retinospheres (RS) were generated and cultured using approved BSL2 methods. As previously described, RS were maintained in low binding attachment plates in Retinal Differentiation Medium (RDM) in an incubator at 37 ºC with 5% CO2. RDM 5% + VitA: DMEM/DMEM/F12, supplemented with 5% fetal bovine serum (FBS), 2% B27, 1% NEAA and 1% Pen-Strep.

extract_protocol:
Briefly, RS (10 per conditions) were digested with Papain (Worthington) for 15-30 mins at 37°C on a nutator. Ovomucoid (Worthington) was added to stop the reaction. Dissociated cells were then centrifuged at 300g for 5 mins at 4°C. For each condition, cells were resuspended to a concentration of 1000 cells per ul.
Libraries constructions were carried out using the Chromium Next GEM single Cell 3’ Reagent kits v3.1 (Dual Index), following the manufacturer’s instructions.

treatment_protocol: WIN 18446 (R&DSystems, #4736, 1 uM)  were thawed and added to the experimental-condition media every other day for the duration of the experiment.

value: Retina

value: Retinal neurons and progenitors

value: D120 fetal tissue were cultured for 19 days with 1 uM WIN18446

value: Fetal day 120 + 20 days in culture


title: D140 Retinoshperes, SCR264, Control

description: Library name: D140_Control_RNA

value: D120 fetal tissue were cultured for 19 days with control media


title: Neuroblastoma tumor specimen, post-treatment, CASE2

city: Guangzhou

first: Xiya

last: Tan

state: None Selected

address: 51 Dongfeng Road East, Guangzhou 510060, P. R. China.

institute: Sun Yat-sen University Cancer Center

description: Library name: NB_post_CASE2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: ensembl112（GRCh38）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: tumor tissue

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

value: tumor tissue

value: after UCB NK cell infusion / anti-GD3 therapy


title: Huh7 cells  SR2

city: guanghzou

first: wancui

last: zhu

state: State...

address: zhongshan

institute: Sun Yat-sen University

description:
Library name: sample8
Huh7 sorafenib-resistant rep2

data_processing:
Raw reads in FASTQ format were first processed through fastp (version 0.20.0) to remove adapter-containing reads, reads containing N bases, and low-quality reads (Qphred ≤ 20 bases accounting for >50% of the read length).
Assembly: GRCh38 (Ensembl release 111)
Supplementary files format and content: FPKM_values.csv: CSV file containing FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each gene of each sample.

source_name: not

extract_protocol:
Total RNA was extracted with the Cell RNA Rapid Extraction Kit from GOONIE (400-100-100T) according to the manufacturer’s instructions.
RNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the manufacturer's protocols. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, and used for first-strand and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, the products were purified and PCR amplified to create the final library.

value: not

value: Hepatocellular carcinoma cells

value: SR

value: sorafenib


title: Huh7 cells  WT2

description:
Library name: sample6
Huh7 sensitive control rep2

value: WT

value: control


title: HepG2 cells  SR2

description:
Library name: sample4
HepG2 sorafenib-resistant rep2


title: Neuroblastoma tumor specimen, pre-treatment, CASE2

description: Library name: NB_before_CASE2

value: before UCB NK cell infusion / anti-GD2 therapy


title: HepG2 cells  SR1

description:
Library name: sample3
HepG2 sorafenib-resistant rep1


title: HepG2 cells  WT2

description:
Library name: sample2
HepG2 sensitive control rep2


title: HepG2 cells  WT1

description:
Library name: sample1
HepG2 sensitive control rep1


title: B4G12 cells, siNAMPT2

city: Beijing

first: Junyi

last: Wang

address: 69th Yongding Road

department: Ophthalmology

institute: The Third Medical Center, Chinese PLA General Hospital

description:
Library name: Sample5
siNAMPT2_FPKM

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomicbenchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38 using CLC genomic benchwork with default parameters
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: table-delimited text file include raw counts for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: human corneal endothelial cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyze (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
The purified Total RNA was subjected to a series of steps including mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3'-end adenylation, adapter ligation, and PCR enrichment to complete the construction of the sequencing sample library. The concentration of the constructed library was detected using a Qubit® 2.0 Fluorometer, and the library fragment size was verified by an Agilent 4200 TapeStation. Sequencing was performed on an Illumina NovaSeq 6000 platform with a PE150 (Paired-End 150 bp) sequencing mode.  Approximately 8 Gb of clean data per sample. The proportion of bases with a quality score higher than 20 (Q20) in each read direction shall be no less than 90%.

value: human corneal endothelial cells

value: corneal endothelial cells

value: NAMPT knockdown

value: siRNA treatment


title: B4G12 cells, siNAMPT3

description:
Library name: Sample6
siNAMPT3_FPKM


title: B4G12 cells, siControl2

description:
Library name: Sample2
siControl2_FPKM