title: Adult-4_scATAC-seq

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

description: Library name: Adult-4_ATAC

data_processing:
Multiome data were processed with CellRanger-ARC v2.0.2 using the D. melanogaster BDGP6.88 genome, beginning with FASTQ file generation via cellranger-arc mkfastq.
RNA-based cell calling from CellRanger v7 was used due to high ATAC background, followed by stringent filtering on gene/peak counts, mitochondrial/ribosomal RNA content, ATAC quality metrics, and doublet removal with demuxlet.
Cells were classified using supervised neural network models trained on a prior atlas and unsupervised WNN clustering, yielding refined P48 subclusters that served as a new reference for label transfer across stages.
Assembly: ENSEMBL-release-88-BDGP6
Supplementary files format and content:
Multiome.rds: A merged Seurat object (.rds format) containing each stage includes raw, normalized and scaled expression values for each cell in addition to the identities determined using different methods, as detailed in the paper.
RNAmarkers.csv: Table of neuron-enriched RNA markers identified across P24, P48, and Adult datasets. Each row corresponds to a gene with significantly enriched expression (adjusted p < 0.05, log2FC > 0.5), with metadata on statistical results and developmental stage.
ATACmarkers.csv: Table of neuron-enriched ATAC peaks identified across P24, P48, and Adult datasets. Each row corresponds to a genomic region with significantly enriched accessibility (adjusted p < 0.05, log2FC > 0.5), with metadata on statistical results and developmental stage.
atac_fragments.tsv.gz: Tab-separated file containing ATAC-seq fragment information (chromosome, start, end, cell barcode, and fragment count) for all profiled cells. This file is used to generate accessibility profiles across the genome.
atac_fragments.tsv.gz.tbi: Index file accompanyingatac_fragments.tsv.gz, generated to allow efficient querying of genomic intervals.
Links.xlsx: Excel table containing Seurat/Signac LinkPeaks outputs across all stages (Adult, P48, P24, and P0), individual stages, P0 OPC progenitor, and P0 OPC neuronal clusters.

source_name: Adult optic lobe

growth_protocol: Standard Drosophila rearing protocols

extract_protocol:
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits (10x Genomics)
Performed following the manufacturer's instructions: The nuclei were subjected to Tn5 transposition for 1 hour at 37°C and were then immediately loaded into a Chip J for generation of nanoliter-scale gel bead-in-emulsions (GEMs) using Chromium Controller. Following reverse-transcription, cleanup and pre-amplification PCR, the samples were split into two for the ATAC library PCR (9 cycles) and for cDNA amplification (7 cycles) followed by fragmentation, adaptor ligation and sample index PCR for the RNA library (11 cycles). We used 20 µl of the amplified cDNA for RNA library preparation (even though 10 µl is normally recommended), and the final resuspension of the ATAC libraries was done using 40 µl of EB buffer, even though 20 µl is normally recommended. We produced 5 different multiomic libraries (technical replicates) for the P48 stage, and 4 libraries for other stages (P0, P24 and Adult), aiming for ~20,000 cells per library (Detailed in Methods).

treatment_protocol: No treatments

value: Adult optic lobe

value: Canton S x DGRP hybrid

value: < 1 day old

tag: Sex

value: female

tag: library type

value: ATAC


title: A549 cell, Wide type, WT_IgG_rep1

status: Public on Jul 15 2026

type: SRA

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

description: Library name: WT, IgG CUT_Tag-1

library_source: genomic

data_processing:
Raw reads were trimmed using fastp (v0.23.2) in paired-end mode.Trimmed reads were aligned to human hg38 genome using Bowtie (v.2.4.2) with the parameters '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10-X 700'. For spike-in normalization, the reads were also aligned to the E. coli genome by Bowtie (v.2.4.2) with the options ‘--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700’. Duplicated reads were then filtered using SAMtools (v.1.9). Reads adjusted to total reads were aligned to E. coli genome using bedtools(v2.30.0). Peak identification was performed using SEACR(v1.3). Adjusted reads were then converted to strand-specific bigwig files with the bamCoverage command from deepTools(v3.5.2). The coverage heatmaps were created using plotHeatmap from deepTools (v.3.5.2)
Assembly: GRCh38
Supplementary files format and content: bigwig, bed
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: A549 cells  were maintained in RPMI 1640 supplemented with 10% (v/v) fetal bovine serum (FBS) and 1%penicillin/streptomycin at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
For each CUT&Tag reaction, 2 × 10⁵ EDTA-free A549 cells were immobilized on Protein A magnetic beads (Cat. No. N259-YH01-01S) and incubated with 1 μg primary antibody overnight at 4 °C without agitation. On the following day, a secondary antibody (10 μg/mL) was added to amplify the signal. Subsequently, 1 μL ChiTag® pAG-Transposome (Cat. No. N2) was added and activated, and tagmented DNA was enriched using Tagment DNA Extract Beads (Cat. No. N240). Five nanograms of DNA were then used for sequencing library preparation with the NovoNGS® DNA Library FlashPrep Kit for Illumina® (Cat. No. N231).
Five nanograms of DNA were then used for sequencing library preparation with the NovoNGS® DNA Library FlashPrep Kit for Illumina® (Cat. No. N231).

tag: cell line

tag: cell type

value: Human Lung Cancer Cell Line

tag: genotype

value: WT

tag: cut&tag antibody

value: IgG （CST, #2729）


title: stimulated microglia replicate 2

city: Halle

first: Martin

middle: Sebastian

last: Staege

address: Ernst-Grube-Str. 40

department: Paediatrics I

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
Library name: treated 2
column name in raw_counts_All_Samples.txt: T2

library_source: transcriptomic

data_processing:
reads were mapped to murine genome mm39 using HISAT2
mapped reads were quantified using featureCounts
data processing was performed on the galaxy server (https://usegalaxy.org/)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw fragment counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

molecule: total RNA

organism: Mus musculus

source_name: brain

growth_protocol: Cells were seeded in complete DMEM/F12 in a 75 cm2 cell culture flask coated with 0.1% poly-L-ornithine. Flasks were washed with complete DMEM/F12 after overnight incubation and stimulated with 20% L-929 conditioned medium in complete DMEM/F12 on day 8, 13, 21 and 29 after isolation. Microglia were collected by shaking the flasks for 5.5 h at 70 rpm and subsequently aspirating the cell suspension.

extract_protocol:
Total RNA was isolated from cell pellets or lysates using the Nucleospin RNA XS isolation kit (Machery-Nagel).
RNA libraries were constructed by BMKGENE, Berlin, Germany using standard protocolls.

treatment_protocol: For stimulation, microglia were cultured in the presence of 100ng/mL human TGFbeta, 100 ng/mL human IL34 and 100 ng/mLCX3CL1.

tag: strain

tag: tissue

value: brain

value: microglia

tag: age

value: 1-3 days

tag: treatment

value: stimulated with TGFbeta, IL34 and CX3CL1


title: lean-mock_487

city: Kongens Lyngby

first: Betina Lyngfeldt

last: Henriksen

address: Anker Engelunds Vej 101

country: Denmark

institute: Technical University of Denmark

description: Library name: LowerT487

data_processing:
Dr Tom, BGI Genomics
Trimmed sequencing reads were quality- and adapter-filtered by BGI
Reads were mapped to the Sus scrofa reference genome (Sscrofa11.1) using Hisat2
Read counts per gene were extracted and normalized to TPM values.
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: Raw read counts for each sample can be found trachea_readcounts.xlsx
Supplementary files format and content: TPM for each samples can be found in trachea_TPM.xlsx

organism: Sus scrofa

source_name: Trachea

extract_protocol:
Total RNA was extracted using a gentleMACS Dissociator (Miltenyi Biotec) for homogenization and miRNeasy Kit (Qiagen) for extraction.
RNA libraries were constructed using the BGI stranded mRNA library construction protocol. Briefly, mRNA was enriched using oligo-dT beads, fragmented, and reverse-transcribed to generate first- and second-strand cDNA. The cDNA was end-repaired, 3’ adenylated, and ligated to sequencing adapters. Libraries were then PCR-amplified and converted into DNA nanoballs prior to sequencing on the DNBSEQ platform.

value: Trachea


title: A549 cell, Wide type, WT_antiARID1A_rep2

description: Library name: WT, ARID1A CUT_Tag-2


title: Adult-4_scRNA-seq

country: USA

description: Library name: Adult-4_GEX

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Drosophila melanogaster

value: mRNA


title: obese-IAV_486

description: Library name: LowerT486


title: microglia control replicate 2

description:
Library name: untreated 2
column name in raw_counts_All_Samples.txt: U2

value: control


title: A549 cell, Wide type, WT_antiARID1A_rep1

description: Library name: WT, ARID1A CUT_Tag-1


title: lean-mock_474

description: Library name: LowerT474


title: BMC06480-001 Healthy

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: BMC06480-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Library strategy: CITE-seq

source_name: Bone Marrow

extract_protocol:
BMMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca automatic cell counter.  Individual samples are hashtagged with unique oligo barcodes and stained with an antibody dependent tag (ADT) panel and pooled. Pools are stained with a viability dye (FSV510) and sorted for live cells using BD Aria Cell Sorter. Live cells are then collected and diluted to appropriate concentrations for 3' CITEseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Bone Marrow

value: BMMC

tag: subject id

value: Female

tag: race

value: Caucasian

tag: days since_first_visit

tag: visit

value: Healthy

tag: batch id

tag: sample bridging_control

value: FALSE


title: A549 cell, Wide type, WT_antiYTHDF1_rep2

description: Library name: WT, YTHDF1 CUT_Tag-2

value: YTHDF1 (Abacm, #ab220162)


title: Adult-3_scATAC-seq

description: Library name: Adult-3_ATAC

library_source: genomic single cell

value: Adult optic lobe

value: Canton S x DGRP hybrid

value: < 1 day old

value: female

value: ATAC


title: Adult-3_scRNA-seq

description: Library name: Adult-3_GEX


title: obese-IAV_466

description: Library name: LowerT466


title: Adult-2_scATAC-seq

description: Library name: Adult-2_ATAC


title: A549 cell, Wide type, WT_antiYTHDF1_rep1

description: Library name: WT, YTHDF1 CUT_Tag-1

value: Human Lung Cancer Cell Line

value: WT


title: stimulated microglia replicate 1

description:
Library name: treated 1
column name in raw_counts_All_Samples.txt: T1

value: brain

value: microglia

value: 1-3 days

value: stimulated with TGFbeta, IL34 and CX3CL1


title: microglia control replicate 1

description:
Library name: untreated 1
column name in raw_counts_All_Samples.txt: U1

value: control


title: HCC827 cells, Osimertinib-resistant, wildtype, rep2

city: Guangzhou

first: aochu

last: liu

state: Guangdong

address: No. 1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description:
Library name: Sample14
hcc827_AR_rep2

data_processing:
Raw reads were aligned to GRCh37 reference genome utilizing HISAT2 (version 2.2.1)and quantified with htseq-count program (version 2.0.8) under default setting. The raw read counts were then normalized using FPKM. Differentially expressed genes were determined through the DESeq2 package (version 1.42.1), applying a threshold of adjusted p-value < 0.05 and an absolute log2 fold-change (shRNA vs. control) greater than 0.5.
Assembly: hg19
Supplementary files format and content: combined FPKM tab file

growth_protocol: The HCC827 parent cell lines and HCC827AR (resistance) cell lines with or without shRNA-induced silencing of SMAD3, NR2F2 and ID3  were cultured in RPMI-1640 media, containing 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was extracted from HCC827 parental and HCC827AR (resistance) cells treated with AZD9291 (500 nM), using RNA RNeasy kit (Qiagen). 1 μg of total RNA was subjected to library synthesis using the  Accurate Biology RNA-Seq kit.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on MGIseq2000 platform (BGI-Shenzhen, China).

treatment_protocol: Osimertinib resistant cell lines, defined as HCC827AR, are estabolised by stepwise incubate the parental cell line HCC827 with increasing doses of AZD9291,from 10 nM to 500 nM. To maintained the resistance, 500 nM AZD9291 routinely supplemented in the culture medium.


title: lean-IAV_465

description: Library name: LowerT465

value: Trachea


title: A549 cell, Wide type, antiS9.6

description: Library name: S9.6


title: Adult-2_scRNA-seq

description: Library name: Adult-2_GEX

value: mRNA


title: lean-IAV_461

description: Library name: LowerT461


title: HCC827 cells, Osimertinib-resistant, wildtype, rep1

description:
Library name: Sample13
hcc827_AR_rep1


title: Adult-1_scATAC-seq

description: Library name: Adult-1_ATAC


title: obese-IAV_460

description: Library name: LowerT460


title: HCC827 cells, wildtype, rep2

description:
Library name: Sample12
hcc827_rep2


title: A549 cell, YTHDF1 Kockdown, ARID1A siRNA, biol rep3

description: Library name: YTHDF1-KO.si-ARID1A-3

data_processing:
Raw reads were quality-trimmed and adapter-removed using TrimGalore (v0.6.6).
Cleaned reads were then aligned to the human reference genome GRCh38 (Ensembl release 97) using the STAR aligner (v2.7.0d) in two-pass mode.
Gene-level read counts were generated from the aligned BAM files using featureCounts (v2.0.1) with the Ensembl v97 annotation.
Differential expression analysis and Gene expression level(RPKM) were was performed on the count matrix using the edgeR (v3.32.1) package in R, applying TMM normalization and a generalized linear model.
Assembly: GRCh38
Supplementary files format and content: csv file includeGene-level read counts for each Sample

extract_protocol:
Total RNA was extracted and purified from 5×10⁵ cultured cells using the Quick-RNA™ MiniPrep Kit. 5 μg total RNA was used fot the construction of sequencung libraries
RNA-seq libraries were prepared using the Illumina TruSeq Stranded RNA Library Prep Kit following the manufacturer’s protocol

value: YTHDF1 knockout, ARID1A knockdown


title: Adult-1_scRNA-seq

description: Library name: Adult-1_GEX


title: lean-IAV_457

description: Library name: LowerT457


title: HCC827 cells, wildtype, rep1

description:
Library name: Sample11
hcc827_rep1


title: A549 cell, YTHDF1 Kockdown, ARID1A siRNA, biol rep2

description: Library name: YTHDF1-KO.si-ARID1A-2


title: A549 cell, Wide type, IgG

description: Library name: IgG


title: P48-7_scATAC-seq

description:
sex: females + male
Library name: P48-7_ATAC

source_name: P48 optic lobe

value: P48 optic lobe

value: pooled male and female


title: lean-IAV_454

description: Library name: LowerT454


title: HCC827 cells, Osimertinib-resistant, shSMAD3, rep2

description:
Library name: Sample10
HR_shSMAD3_rep2

value: SMAD3 knowndown


title: A549 cell, YTHDF1 Kockdown, ARID1A siRNA, biol rep1

description: Library name: YTHDF1-KO.si-ARID1A-1


title: P48-7_scRNA-seq

description:
sex: females + male
Library name: P48-7_GEX

value: Canton S x DGRP hybrid


title: obese-IAV_448

description: Library name: LowerT448


title: HCC827 cells, Osimertinib-resistant, shSMAD3, rep1

description:
Library name: Sample9
HR_shSMAD3_rep1


title: P48-6_scATAC-seq

description:
sex: females + male
Library name: P48-6_ATAC


title: A549 cell, ARID1A siRNA, biol rep3

description: Library name: si-ARID1A-3

value: ARID1A knockdown


title: obese-mock_435

description: Library name: LowerT435


title: HCC827 cells, Osimertinib-resistant, NC, rep2 (shSMAD3)

description:
Library name: Sample8
HR_PLKO_rep2

value: NC knockdown


title: A549 cell, ARID1A siRNA, biol rep2

description: Library name: si-ARID1A-2


title: P48-6_scRNA-seq

description:
sex: females + male
Library name: P48-6_GEX


title: lean-mock_432

description: Library name: LowerT432


title: A549 cell, ARID1A siRNA, biol rep1

description: Library name: si-ARID1A-1


title: P48-5_scATAC-seq

description:
sex: females + male
Library name: P48-5_ATAC

value: ATAC


title: HCC827 cells, Osimertinib-resistant, NC, rep1 (shSMAD3)

description:
Library name: Sample7
HR_PLKO_rep1


title: NCOR2 00h Exp1 - Rep 1

city: San Francisco

first: Valerie

last: Weaver

state: CA

address: 513 Parnassus Avenue, HSE 560, Box 0456

department: Department of Surgery and Center for Bioengineering and Tissue Regeneration

institute: Johns Hopkins Univeristy

description:
Library name: NCOR2_00h.exp1.NCOR2.1_4_S212_L008.markdup.q30
Draw data to be made available on SRA

data_processing:
Reads were trimmed for adapters and low-quality bases (Phred <20).
Trimmed reads were aligned to mm39 using bowtie2 (MAPQ ≥30 retained).
Duplicate-marked BAM files were generated; proper paired reads used for analysis.
Peaks were called using MACS3 (FDR ≤1%) with IgG background subtraction.
Peak counts were generated; differential analysis performed using DESeq2 (adjusted p <0.05).
Assembly: Mouse genome build mm39.
Supplementary files format and content: Processed files include deduplicated BAM files, bigWig coverage tracks, and peak count matrices.
Supplementary files format and content: Peak files (BED/narrowPeak) and differential peak analysis results with adjusted p-values and log fold changes.
Library strategy: CUT&Tag

growth_protocol: 4T07 cells (NCOR2 knockdown or EGFP control) were plated (20,000 cells/well) and grown 24–48 h before CUT&Tag.

extract_protocol:
CUT&Tag performed in situ on adherent unfixed cells using NCOR2 antibody and pA-Tn5 tagmentation.
Tagmented DNA was PCR-amplified with indexed primers, pooled, purified, and sequenced (51 bp paired-end, NovaSeq X).

treatment_protocol: Cells were treated with IFNγ (6 hr timepoint) or vehicle control.

value: Malignant neoplasms of the mouse mammary gland

value: NCOR2 Knockdown


title: obese-mock_157

description: Library name: LowerT157


title: HCC827 cells, Osimertinib-resistant, NC, rep2 (shID3, shNR2F2)

description:
Library name: Sample6
HR_PLKO_rep2


title: A549 cell, YTHDF1 Kockdown, biol rep3

description: Library name: YTHDF1-KO-3

value: Human Lung Cancer Cell Line

value: YTHDF1 knockout


title: P48-5_scRNA-seq

description:
sex: females + male
Library name: P48-5_GEX


title: lean-IAV_156

description: Library name: LowerT156


title: HCC827 cells, Osimertinib-resistant, NC, rep1 (shID3, shNR2F2)

description:
Library name: Sample5
HR_PLKO_rep1


title: A549 cell, YTHDF1 Kockdown, biol rep2

description: Library name: YTHDF1-KO-2


title: P48-4_scATAC-seq

description:
sex: females + male
Library name: P48-4_ATAC


title: obese-IAV_149

description: Library name: LowerT149


title: HCC827 cells, Osimertinib-resistant, shNR2F2, rep2

description:
Library name: Sample4
HR_shNR2F2_rep2

value: NR2F2 knowndown


title: lean-IAV_148

description: Library name: LowerT148


title: A549 cell, YTHDF1 Kockdown, biol rep1

description: Library name: YTHDF1-KO-1


title: A549 cell, Wildtype, biol rep3

description: Library name: WT3

value: WT


title: HCC827 cells, Osimertinib-resistant, shNR2F2, rep1

description:
Library name: Sample3
HR_shNR2F2_rep1


title: P48-4_scRNA-seq

description:
sex: females + male
Library name: P48-4_GEX


title: P48-3_scATAC-seq

description:
sex: females + male
Library name: P48-3_ATAC


title: HCC827 cells, Osimertinib-resistant, shID3, rep2

description:
Library name: Sample2
HR_shID3_rep2

value: ID3 knowndown


title: obese-IAV_135

description: Library name: LowerT135

value: Trachea


title: A549 cell, Wildtype, biol rep2

description: Library name: WT2


title: P48-3_scRNA-seq

description:
sex: females + male
Library name: P48-3_GEX

value: mRNA


title: obese-mock_130

description: Library name: LowerT130


title: HCC827 cells, Osimertinib-resistant, shID3, rep1

description:
Library name: Sample1
HR_shID3_rep1


title: A549 cell, Wildtype, biol rep1

description: Library name: WT1


title: P24-4_scATAC-seq

description:
sex: females + males
Library name: P24-4_ATAC

source_name: P24 optic lobe

value: P24 optic lobe


title: PC9 cells, Osimertinib-resistant, H3K27ac (ChIP)

description: Library name: Sample6

library_source: other

data_processing:
Raw reads were first mapped to the hg19 reference genome using Bwa (version 0.7.17) with default parameters. High-quality mapped reads were then extracted and sorted using SAMtools (version 1.13) . PCR duplicates were removed with the Picard MarkDuplicates tool (version 1.136), and blacklist regions were filtered out using bedtools (version 2.30.0).
Peaks were called using MACS2 (Model-Based Analysis of ChIP-Seq, version 2.2.9.1) with the parameters “-q 0.01 -extsize=146 -nomodel -B”. Bigwig files were created using the deepTools bamCompare function (version 3.1.3) with the settings “-operation subtract -normalizeUsing CPM -extendReads 146 -binSize 20”.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: other

growth_protocol: The HCC827 parent cell lines, HCC827AR (resistance), PC9 parent cell lines, and PC9AR (resistance) cell lines were cultured in RPMI-1640 media, containing 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
ChIP uses the method we described before.
Library preparation is performed using MGIEasy Universal DNA Library Prep Set (MGI-Shenzhen, China). Firstly, A certain amount of purified ChIPed DNA sample is taken and converted into blunt-end DNA through end repair reaction. Then an adenosine is added to the 3′ ends of the end repaired DNA through A-tailing reaction. Later, library adaptors are connected through adaptor ligation process, Finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and SE50 bases reads are generated on MGI2000 platform (BGI-Shenzhen, China).

treatment_protocol: Osimertinib resistant cell lines, defined as HCC827AR and PC9AR, are estabolised by stepwise incubate the parental cell line HCC827 and PC9 with increasing doses of AZD9291,from 10 nM to 500 nM. To maintained the resistance, 500 nM AZD9291 routinely supplemented in the culture medium.

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: lean-mock_127

description: Library name: LowerT127


title: A549 cell, YTHDF1 KO, biol rep3

description: Library name: KO-3


title: obese-IAV_125

description: Library name: LowerT125


title: P24-4_scRNA-seq

description:
sex: females + males
Library name: P24-4_GEX

tag: Sex

value: pooled male and female


title: A549 cell, YTHDF1 KO, biol rep2

description: Library name: KO-2


title: P24-3_scATAC-seq

description:
sex: females + males
Library name: P24-3_ATAC

tag: library type


title: lean-IAV_124

description: Library name: LowerT124


title: PC9 cells, H3K27ac (ChIP)

description: Library name: Sample4

tag: cell line


title: A549 cell, YTHDF1 KO, biol rep1

description: Library name: KO-1

tag: cell type


title: P24-3_scRNA-seq

description:
sex: females + males
Library name: P24-3_GEX


title: PC9 cells (Input)

description: Library name: Sample5

tag: genotype


title: obese-mock_113

description: Library name: LowerT113


title: HCC827 cells, Osimertinib-resistant, H3K27ac (ChIP)

description: Library name: Sample3


title: A549 cell, Wide type, biol rep3

description: Library name: WT-3


title: P24-2_scATAC-seq

description:
sex: females + males
Library name: P24-2_ATAC


title: obese-IAV_111

description: Library name: LowerT111


title: HCC827 cells (Input)

description: Library name: Sample2


title: A549 cell, Wide type, biol rep2

description: Library name: WT-2


title: P24-2_scRNA-seq

description:
sex: females + males
Library name: P24-2_GEX


title: obese-IAV_108

description: Library name: LowerT108


title: HCC827 cells, H3K27ac (ChIP)

description: Library name: Sample1


title: A549 cell, Wide type, biol rep1

description: Library name: WT-1


title: P24-1_scATAC-seq

description:
sex: females + males
Library name: P24-1_ATAC


title: lean-IAV_104

description: Library name: LowerT104


title: P24-1_scRNA-seq

description:
sex: females + males
Library name: P24-1_GEX


title: Mixed, barcode-transduced EL4 and Jurkat Cells, In Vitro, barcode library

city: Denver

first: Kole

middle: R

last: DeGolier

state: Colorado

address: 1400 Jackson St

department: Immunology and Genomic Medicine

institute: National Jewish Health

description:
Library name: 2024.KRD008bc
10X Genomics with custom retroviral barcoding

data_processing:
scATAC-seq files were demultiplexed using cellranger-atac mkfastq
Demultiplexed data was processed using the cellranger-atac pipeline.
Peaks were called and .bam files were generated using the ArchR pipeline (https://www.archrproject.com/bookdown/index.html).
Assembly: GRCmm10, GRChg38
Supplementary files format and content: .bam files containing peaksets called on single murine data experiment (2025.KRD012) or compiled human data experiments (KRD024, KRD029, KRD039, KRD040).

organism:
Homo sapiens
Mus musculus

source_name: Mixed Jurkat/EL4

growth_protocol:
In Vitro, Murine Cells: Mouse CAR T cells were cultured in cRPMI as described above. CD8+ T cells were isolated from 10-16 week old C57BL/6 mouse splenocytes using the MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend, Cat No. 480035). On day 0, T cells were activated with 1µg/mL anti-CD3 and 1µg/mL anti-CD28 overnight. Cells were transduced on day 1 by centrifugation at 2000xg for 90 minutes at 37°C with fresh gammaretrovirus and 10ug/mL polybrene, followed by removal of retrovirus and polybrene after the spin and replacement with fresh media containing the specified amount of IL-2, either 10IU/mL or 100IU/mL (National Cancer Institute). Transduction was repeated on the following day (day 2), and then cells were removed from anti-CD3/anti-CD28 stimulation and plated at 1x106 cells/mL in fresh media containing IL-2. On day 3 and 4, cells were replated at 1x106 cells/mL in fresh media containing IL-2. For the “swap” condition, IL-2 concentration was changed from 100IU/mL to 10IU/mL. Cells were FACS sorted (Lymphocytes > Singlets > Live > CD8+ > mThy1.1+) and captured for scATAC-seq on day 5, 16 hours after the IL-2 “swap” (or media replacement for the “high” and “low” IL-2 conditions).
In Vitro, Human Cells: CD3+ human T cells were cultured in Human T Cell Expansion Media (hTCEM), consisting of AIM-V (Gibco, Cat No 12055-091) supplemented with 5% FBS and 10mM HEPES (Gibco, 15630-080). On day 0, T cells were thawed and activated with Dynabeads Human T cell Expander CD3/CD28 (Gibco, Cat No. 11141D) at a 3:1 bead:cell ratio at 1x106 cells/mL, in hTCEM supplemented with 40IU/mL IL-2 and cultured for 48 hours. On day 2, T cells were counted and transduced at 2x106 cells per well in a 6 well plate, with 10µg/mL Protamine Sulfate (Millipore-Sigma, Cat No. P4020-1G), spinning at 1000xg for 2.5 hours at 32°C. On day 3, T cells were transduced again with fresh virus. On day 4, beads were removed, and cells were plated in fresh hTCEM supplemented with 100IU/mL IL-2 at 0.5x106 cells/mL. On day 6, cells were replated at 0.5x106 cells/mL with fresh hTCEM and 100IU/mL IL-2, and a small aliquot was taken to check transduction efficiency. On day 8, cells were counted with a small aliquot taken for FACS sorting (Lymphocytes > Singlets > Live > CD4+ or CD8+ > mThy1.1+) and scATAC-seq capture (‘Pretransfer’ timepoint), with the rest cryopreserved in Freeze Media as described above.

extract_protocol:
After sorting, cells were pooled, washed once in cold PBS and then lysed in Lysis Buffer (Nuclease-Free H2O with 10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin) for the following times: 5 mins (cell lines), 3 mins (in vitro primary cells), 3 mins 45 seconds (ex vivo primary cells). Cells were then resuspended in 1X Nuclei Buffer and analyzed for nuclei count and lysis efficiency via 0.4% Trypan Blue staining on the Countess 3 (ThermoFisher), with >95% lysis efficiency typical. Cells were then diluted to ≤2.4x106 cells/mL for capture of ~8000 nuclei in a single 10X capture well, following manufacturer protocols for Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10X Genomics, User Guide CG000496). Two modifications were required to this protocol for barcode enrichment, as described previously19: first, 1.32µL of 50µM spike-in barcode enrichment oligo was added to the GEM reaction master mix (step 2.1a in 10X protocol); second, the PCR following GEM generation was increased from 12 to 15 cycles (step 2.5a in 10X protocol). Libraries were prepared per manufacturer specifications and analyzed using the TapeStation (Agilent) and Qubit Fluorometer (ThermoFisher).
Final scATAC and barcode libraries were pooled to 10nM concentration for sequencing. Final concentrations for individual libraries in the pool were calculated to achieve a target sequencing depth of 40,000 reads/nuclei (scATAC library) and 1,000 reads/nuclei (barcode library).

treatment_protocol: In Vivo, Human Cells: NOD-Scid-Gamma (‘NSG’, NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ; Strain #: 005557, Jackson Laboratories) were obtained commercially and then bred in-house. For xenograft studies, between 4 and 9 male or female NSG mice (up to 20 weeks of age, same gender in a single experiment) received 1x106 NALM6-CD22Lo leukemia on day -3, followed by 1x106 CAR+ cells (pooled equally from all six CAR conditions) on day 0. Leukemia burden was monitored before CAR injection (day -1), on day 4, and on day 7 before marrow harvest, using the Xenogen In Vivo Imaging System (IVIS) Spectrum (Caliper Life Sciences) after intraperitoneal injection with D-Luciferin Potassium Salt (Revvity, Cat No. 122799A-5). Total flux (photons/s) was measured for each mouse using Living Image software (Revvity, v4.8.2). On day 7, bone marrow was harvested, filtered through a 70µm strainer, and red blood cells were lysed using ACK Lysing Buffer. Cells were then filtered again, and human cells were enriched using MojoSort Mouse CD45 Nanobead (BioLegend, Cat No. 480028) depletion of mouse bone marrow. Cells were stained and FACS sorted (Lymphocytes > Singlets > Live > CD45+/GFP- > CD4+ or CD8+ > mThy1.1+) for scATAC-seq capture (‘ex vivo’ timepoint). Xenograft animal studies were conducted at University of Colorado Anschutz Medical Campus in accordance with an animal protocol approved by the Institutional Animal Care and Use Committee (IACUC, Protocol 751).

value: Mixed Jurkat/EL4

value: T cell

value: Barcoded CAR transduction


title: BALF, Healthy control

first: Han-Bing

last: Chen

address: No. 87, Dingjiaqiao Road, Gulou District

institute: School of Medicine, Southeast University

description:
Library name: HC
10x Genomics

data_processing:
Raw data were processed with Cell Ranger (v7.1.0, hg38 reference), and subsequent analysis was performed in Seurat (v5.1.0).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BALF

extract_protocol:
Cell capture and cDNA synthesis Using single cell 5 'Library and Gel Bead Kit (10x Genomics, 1000006) and Chromium Single Cell A Chip Kit (10x Genomics, 120236), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA.
Single cell RNA-Seq library preparation According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 5’ Library and Gel Bead Kit, Single Cell V(D)J Enrichment Kit, Human T Cell(1000005) and Single Cell V(D)J Enrichment Kit, Human B Cell (1000016). The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: BALF


title: Mixed, barcode-transduced EL4 and Jurkat Cells, In Vitro, scATAC library

description:
Library name: 2024.KRD008
10X Genomics with custom retroviral barcoding


title: Mito(-)ECs-R3

city: Hong Kong

first: Yang

last: Shengyan

address: Prince Philip Dental Hospital, 34 Hospital Road

institute: The University of Hong Kong

description: Library name: SAMPLE6

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.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of p-value below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: RNA-Seq
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell type

growth_protocol: Human dental pulp stem cells (DPSCs) were cultured in α-MEM containing 15% FBS and penicillin–streptomycin. GFP-expressing human umbilical vein endothelial cells (GFP-ECs) were maintained in endothelial cell medium supplemented with 5% FBS, endothelial cell growth supplement, and penicillin–streptomycin.

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

treatment_protocol: MitoTracker-labeled DPSCs and GFP-expressing endothelial cells (GFP-ECs) were co-cultured at a 1:1 cell ratio in a 1:1 mixture of α-MEM and endothelial cell medium (ECM) and incubated under hypoxic conditions (1% O₂, 5% CO₂, 37°C) for 24 h prior to fluorescence-activated cell sorting (FACS) and RNA extraction.

value: cell type

value: HUVECs

value: Endothelial cells

value: Wild type

value: Non-mitochondrial transfer


title: P0-4_scATAC-seq

description: Library name: P0-4_ATAC

source_name: P0 optic lobe

value: P0 optic lobe

value: Canton S x DGRP hybrid

value: female

value: ATAC


title: Mixed untransduced EL4 and Jurkat Cells, In Vitro, scATAC library

description:
Library name: 2024.KRD006
10X Genomics

value: WT


title: 304_P7_25

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: primary human PDL-MSC

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Cells were cultured in a T-225 flask (falcon corning) with the density of 1 x 10⁵ cells. Alpha-minimum essential medium (⍺-MEM; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific),  100 U ml−1 penicillin and 100 μg ml−1 streptomycin (P/S; Thermo Fisher Scientific), was used as a basic medium hPDL-MSCs and medium change was performed twice a week. Cell passaging was done with 0.25% Trypsin EDTA (Thermo Fisher Scientific) for cell detachment.

extract_protocol: EV samples were subjected to miRNA purification using the miRNeasy Micro Kit (Qiagen, 217084).

treatment_protocol: Once confluency reached over 95%, cells were gently washed three times with Dulbecco’s phosphate buffered saline (DPBS) (Fujiwako, 045-29795),   then the culture medium was replaced with serum and antibiotic-free α‑MEM basal medium. Conditioned medium was collected after culturing for 24 hours under 5% CO₂ at different settings (passage number: P7 and P10, temperatures: 37 °C and 25 °C). Adapted from our previous protocol (Sjoqvist, Ishikawa et al. 2019, Sjoqvist, Kasai et al. 2019), conditioned medium was centrifuged at 300 × g and then 3,000 × g for 10 minutes each at 4 °C. Further ultrafiltration was achieved with 100 kDa (Amicon Ultra‑14, Merck Millipore) and 10 kDa membrane (Amicon Ultra‑4, Merck Millipore). EVs were separated by sizeexclusion chromatography (qEV, Gen2 original/35, Izon). Fractions 8 to 10 were collected as the “EVs fraction”, while 11 to 14 were separated as “non-EVs fractions”. Nanoparticle-Tracking Analysis (NTA) platforms included Videodrop (Myriade, France), ZetaView (Particle Metrix, Germany), and NanoFCM Flow-NanoAnalyzer (NanoFCM, China). EVs' diameter and concentration were measured. All samples were stored at -80 °C at 5×109 particles/mL until further use.

tag: passage number

tag: culture tempeture


title: P0-4_scRNA-seq

description: Library name: P0-4_GEX

tag: tissue

tag: strain

value: mRNA


title: Mito(+) ECs-R3

description: Library name: SAMPLE5

tag: treatment

value: Mitochondrial transfer


title: 304_P10_37


title: P0-3_scATAC-seq

description: Library name: P0-3_ATAC

tag: age


title: Mito(-)ECs-R2

description: Library name: SAMPLE4


title: HCT116, PABPC1&PABPC4 AID, PABP1212 expression

city: Cambridge

first: Ryan

middle: Yue

last: Muller

state: Massachusetts

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description:
Library name: P1212
direct RNA sequencing with polyA tail measurement

data_processing:
The thirteen barcoded samples were demultiplexed with a custom trained Support Vector Classifier (SVC) model and replicates were aggregated. The model was trained on thirteen different in vitro transcribed sequences, each ligated to a barcoded adapter, to generate unique IVT transcript-barcode label pairs, with approximately 4000 reads per label. Ground-truth labels were established by mapping IVT transcripts to reference sequences using Minimap2 for long IVT sequences and Bowtie2 for short IVT sequences. The electric current magnitude and dwell time of the barcode region in each read, termed “fingerprint”, was captured using WarpDemuX. A Dynamic Time Warping (DTW)-based kernel was learned from the barcode fingerprints, and used, together with the ground-truth labels, to train the SVC. The SVC outputs the probability that a given read belongs to each of the thirteen classes. The predicted label was assigned as the class with the highest probability, and the confidence score was defined as the difference between the highest and second-highest probabilities. The trained model was then applied to RNA-seq data for demultiplexing, and tail lengths of the demultiplexed reads were calculated using Dorado (v0.9.5, Oxford Nanopore Technologies).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes sample, PAS_ID (gene coordinates of the 3' end of the mapped transcript), and tail lengths

growth_protocol: Cells were cultured in McCoy's 5A Medium supplemented with 10% FBS and incubated at 37 °C and 5% CO2. Cell lines were passaged by subcultivation (1:5 ratio) every 2–3 days at 70–90% confluency using 0.25% Trypsin-EDTA.

extract_protocol:
Total RNA was phenol chloroform extracted and 1μg total RNA was used as an input for sequencing preparation.
Sequencing libraries were prepared according to manufacturer instructions (Oxford Nanopore direct RNA kit SQK-RNA004) with one specific adaptation. The first ligation set was modified to instead ligate a set of custom adapters that would allow for sample barcoding and demultiplexing.

treatment_protocol: To induce PABPC1 and PABPC4 degradation and expression of PABPC variants, cells were treated with 1μg/mL doxycycline and 0.5 mM Indole-3-acetic acid (IAA) for 13 days

value: colon cancer

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1-with RRM1&RRM2 domain duplication

tag: time

value: 13 days

tag: metadata file


title: HCT116, PABPC1&PABPC4 AID, PABPC1 expression

description:
Library name: WT
direct RNA sequencing with polyA tail measurement

value: PABPC1 & PABPC4 degron tag, sleeping beauty transposon expression of PABPC1


title: Mito(+) ECs-R2

description: Library name: SAMPLE3


title: 304_P7_37_2


title: P0-3_scRNA-seq

description: Library name: P0-3_GEX


title: 309_P7_37


title: K181A_3

city: Chang Chun

first: Zhang

last: Chang

address: yong chang street

department: key laboratory of pathobiology, ministry of education,

institute: jilin university

description:
Library name: K181A_3
HeLa cells overexpressing HNRNPU K181A mutant, biological replicate 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: gene count and fpkm/TPM value for each Sample

source_name: HeLa cells

extract_protocol:
For cell line RNA extraction in PromethION full-length transcriptome library prep: lyse cells in TRIzol, add chloroform, centrifuge, and collect the aqueous phase. Precipitate RNA with isopropanol, wash with ethanol, and dissolve in RNase-free water. Use DNase I treatment to remove genomic DNA, then quantify RNA integrity and concentration.
The PromethION full-length transcriptome library preparation involves: reverse transcription of poly(A) RNA using a primer with a strand-switching adapter. The resulting cDNA is amplified by PCR, then subjected to adapter ligation (including sequencing adapters and motor proteins). Size selection and quality control steps remove smaller fragments. The final library is loaded onto a PromethION flow cell for long-read, direct RNA or cDNA sequencing, enabling isoform-level transcript analysis.

value: HeLa cells

value: overexpressing HNRNPU K181A mutant


title: 304_P7_37_1


title: P0-2_scATAC-seq

description: Library name: P0-2_ATAC


title: K181A_2

description:
Library name: K181A_2
HeLa cells overexpressing HNRNPU K181A mutant, biological replicate 2


title: Mito(+) ECs-R1

description: Library name: SAMPLE1

value: cell type

value: HUVECs


title: K181A_1

description:
Library name: K181A_1
HeLa cells overexpressing HNRNPU K181A mutant, biological replicate 1


title: Scramble_control_rep5

city: Bethlehem

first: Michael

middle: John

last: Layden

state: PA

address: 111 Research Dr

department: Biological Sciences

institute: Lehigh University

description:
Library name: LA48_2B
Scramble control replicate 5

data_processing:
Raw reads were quality filtered and trimmed by Novogene Inc.
Reads were mapped to the Nematostella vectensis Nvec200 genome using the Galaxy web platform.
Transcript-level quantification was performed using Salmon.
Differential gene expression analysis was performed using DESeq2 on the Galaxy web platform.
Differentially expressed genes were identified using a false discovery rate of p ≤ 0.05 and log2(FC) of ± 0.585.
Assembly: Nematostella vectensis Nvec200
Supplementary files format and content: Salmon quant files (.tabular): transcript-level quantification including transcript name, length, effective length, TPM, and NumReads for each sample.
Supplementary files format and content: Tab-delimited text format. Columns: Name, Length, EffectiveLength, TPM, NumReads.

organism: Nematostella vectensis

source_name: gastrula embryo 28hpf

growth_protocol: Nematostella vectensis embryos were raised at 24°C. Gastrula-stage embryos were collected at 28 hours post fertilization (28hpf)

extract_protocol:
RNA was stabilized by placing embryos from each replicate in 1 ml of TRI Reagent (Sigma-Aldrich) and storing at -20°C until total RNA isolation. RNA concentration and purity were measured with an Agilent 2100 Bioanalyzer. All samples had RIN ≥ 8.0.
Library preparation and Illumina NovaSeq 6000 paired-end (150bp) mRNA sequencing were performed by Novogene Inc. Read quality filtering and trimming were performed by Novogene Inc.

treatment_protocol: Embryos were injected with Nvznf845 shRNA for knockdown or scramble RNA as control. Each replicate consisted of approximately 1000 injected embryos.

value: gastrula embryo 28hpf

value: whole embryo

value: wildtype

value: scramble RNA control

tag: batch


title: P0-2_scRNA-seq

description: Library name: P0-2_GEX

value: P0 optic lobe

value: Canton S x DGRP hybrid

value: female


title: C3R5X116, RaPID-BFP, clone A3.1-C5, sgBFP, AZD7648

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description: Library name: LentiMap_RaPID-BFP_clone_A3.1-C6_sgBFP_AZD7648

data_processing:
Illumina NGS adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
conversion to coverage (deepTools bamCoverage), separated by first-of-read-pair maaping strand.  Parameters: (--binSize 250 --normalizeUsing CPM --minMappingQuality 10 --extendReads) with either (--samFlagInclude 99) or (--samFlagInclude 83)
Assembly: hg38
Supplementary files format and content: bigWig with CPM normalization

molecule: protein

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum (tetracycline-screened), GlutaMAX, 1X PenStrep, 1ug/mL puromycin. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
chromatin immunoprecipitation
xGen ssDNA & Low-Input DNA Library Prep Kit

treatment_protocol: pre-treatment with 100nM doxycycline (20h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with 1uM Shield1 treatment

value: blood

value: K-562, RaPID-BFP, clone A3.1-C5

value: myelogenous leukemia

value: CRISPR/Cas9, sgBFP, AZD7648


title: P0-1_scATAC-seq

description: Library name: P0-1_ATAC

data_processing:
Multiome data were processed with CellRanger-ARC v2.0.2 using the D. melanogaster BDGP6.88 genome, beginning with FASTQ file generation via cellranger-arc mkfastq.
RNA-based cell calling from CellRanger v7 was used due to high ATAC background, followed by stringent filtering on gene/peak counts, mitochondrial/ribosomal RNA content, ATAC quality metrics, and doublet removal with demuxlet.
Cells were classified using supervised neural network models trained on a prior atlas and unsupervised WNN clustering, yielding refined P48 subclusters that served as a new reference for label transfer across stages.
Assembly: ENSEMBL-release-88-BDGP6
Supplementary files format and content:
Multiome.rds: A merged Seurat object (.rds format) containing each stage includes raw, normalized and scaled expression values for each cell in addition to the identities determined using different methods, as detailed in the paper.
RNAmarkers.csv: Table of neuron-enriched RNA markers identified across P24, P48, and Adult datasets. Each row corresponds to a gene with significantly enriched expression (adjusted p < 0.05, log2FC > 0.5), with metadata on statistical results and developmental stage.
ATACmarkers.csv: Table of neuron-enriched ATAC peaks identified across P24, P48, and Adult datasets. Each row corresponds to a genomic region with significantly enriched accessibility (adjusted p < 0.05, log2FC > 0.5), with metadata on statistical results and developmental stage.
atac_fragments.tsv.gz: Tab-separated file containing ATAC-seq fragment information (chromosome, start, end, cell barcode, and fragment count) for all profiled cells. This file is used to generate accessibility profiles across the genome.
atac_fragments.tsv.gz.tbi: Index file accompanyingatac_fragments.tsv.gz, generated to allow efficient querying of genomic intervals.
Links.xlsx: Excel table containing Seurat/Signac LinkPeaks outputs across all stages (Adult, P48, P24, and P0), individual stages, P0 OPC progenitor, and P0 OPC neuronal clusters.

extract_protocol:
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits (10x Genomics)
Performed following the manufacturer's instructions: The nuclei were subjected to Tn5 transposition for 1 hour at 37°C and were then immediately loaded into a Chip J for generation of nanoliter-scale gel bead-in-emulsions (GEMs) using Chromium Controller. Following reverse-transcription, cleanup and pre-amplification PCR, the samples were split into two for the ATAC library PCR (9 cycles) and for cDNA amplification (7 cycles) followed by fragmentation, adaptor ligation and sample index PCR for the RNA library (11 cycles). We used 20 µl of the amplified cDNA for RNA library preparation (even though 10 µl is normally recommended), and the final resuspension of the ATAC libraries was done using 40 µl of EB buffer, even though 20 µl is normally recommended. We produced 5 different multiomic libraries (technical replicates) for the P48 stage, and 4 libraries for other stages (P0, P24 and Adult), aiming for ~20,000 cells per library (Detailed in Methods).

value: ATAC


title: Scramble_control_rep4

description:
Library name: LA48_1B
Scramble control replicate 4


title: WT_3

description:
Library name: WT_3
HeLa cells overexpressing HNRNPU WT, biological replicate 3

value: overexpressing HNRNPU WT


title: C3R5X116, RaPID-BFP, clone A3.1-C5, sgBFP

description: Library name: LentiMap_RaPID-BFP_clone_A3.1-C6_sgBFP

value: CRISPR/Cas9, sgBFP


title: P0-1_scRNA-seq

description: Library name: P0-1_GEX

value: mRNA


title: WT_2

description:
Library name: WT_2
HeLa cells overexpressing HNRNPU WT, biological replicate 2

value: HeLa cells


title: C3R5X116, RaPID-BFP, clone A3.1-C5, baseline

description:
Library name: LentiMap_RaPID-BFP_clone_A3.1-C6_baseline
input sample for baseline/background


title: Scramble_control_rep3

description:
Library name: LA45_1B
Scramble control replicate 3


title: WT_1

description:
Library name: WT_1
HeLa cells overexpressing HNRNPU WT, biological replicate 1


title: Nvznf845_shRNA_rep3

description:
Library name: LA45_1A
Nvznf845 knockdown replicate 3

value: Nvznf845 shRNA


title: HCM10_myo59049

city: Guildford

first: Ayman

last: Ibrahim

state: Surrey

address: Daphne Jackson Road

country: United Kingdom

institute: University of Surrey

description:
Library name: myo59049
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM10_myo59049

data_processing:
Tuxedo protocol
Quality assessment of the paired-end raw reads was done using FastQC (version 0.11.5) before and after trimming with Trimmomatic (version 0.36).
Trimmed reads were aligned to the GENCODE GRCh38 primary assembly (release 44) using STAR (version 2.7.10).
The Tuxedo protocol (version 2.2.1) was used for differential expression analysis with the GENCODE basic annotation. Differentially expressed genes were filtered using q-value ≤ 0.05 and log fold-change ≥ 1.5.
Assembly: GENCODE GRCh38 (release 44)
Supplementary files format and content: genes.count_tracking
Supplementary files format and content: genes.fpkm_tracking
Supplementary files format and content: FPKM_Counts_All_Samples
Supplementary files format and content: Raw_Counts_All_Samples
Supplementary files format and content: All Tuxedo DEGs.xlsx

source_name: cardiac fibroblasts

growth_protocol: Cardiac fibroblasts were briefly grown in DMEM-F12 media supplemented with 10% Fetal bovine serum

extract_protocol:
RNA was extracted from Cardiac fibroblasts using RNeasy mini kit (Qiagen) for total RNA extraction
Isolated total RNA was sequenced using TruSeq Stranded Total RNA with Ribo Zero Gold kit 1 (Illumina, San Diego, CA), following manufacture recommendations.

value: cardiac fibroblasts


title: PT22_Pooled_Input

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

description: Library name: 7_097E_PT22_Pooled_Input_i55

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms were stored in bigWig (.bw) files.
Assembly: GRCm38
Supplementary files format and content: bigWig files

source_name: Kidney

growth_protocol: Modified PT-22 cells were cultured in DMEM supplemented with 3% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Cells were crosslinked for 10 min with 1% w/v formaldehyde, quenched in 0.125 M glycine, washed twice with ice-cold PBS, scraped, and harvested by centrifugation. Cell pellets were sent on dry ice to Active Motif, Inc. (Carslbad, CA) for ChIP-Seq analyses as fee-for-service. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of chromatin (30 µg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 µg of antibody against PAX8 (Proteintech 10336-1-AP) or specific histone modifications (H3K4me3-Active Motif 39159; H3K27me3-Active Motif 39155). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65⁰C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Cells were treated with 1 uM 4-hydroxytamoxifen 2 d to deplete PAX8 or with vehicle. Chromatin was collected at 6 d.

value: Kidney

value: Proximal tubule

value: both (pooled)


title: Scramble_control_rep2

description:
Library name: LA42_B
Scramble control replicate 2

value: gastrula embryo 28hpf

value: whole embryo

value: wildtype

value: scramble RNA control


title: RNA-seq, MDA-MB-231, SRPK2 overexpression (OE), biol rep 1

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

institute: The Second Hospital of Dalian Medical University

description: Library name: OE_1

data_processing:
Illumina bcl2fastq software used for basecalling. The raw reads were trimmed of low-quality bases using a FASTX-Toolkit (v.0.0.13;   http://hannonlab.cshl.edu/fastx_toolkit/).  Then the clean reads were evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Clean reads were aligned to the human GRch38 genome by HISAT2. Uniquely mapped reads were ultimately used to calculate read number and fragments per kilobase of exon model per pillion mapped fragments (FPKM) for each gene. The expression levels of genes were evaluated using FPKM.
Read counting and FPKM calculation were performed for each gene based on the uniquely mapped reads.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
The selected treatment cells were subjected to total RNA extraction using TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and sequenced on an Illumina NovaSeq 6000 system in paired-end mode.

value: breast cancer


title: HCM8_60773MF

description:
Library name: 60773MF
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM8_60773MF


title: Nvznf845_shRNA_rep2

description:
Library name: LA42_A
Nvznf845 knockdown replicate 2


title: HCM7_58862Myo

description:
Library name: 58862Myo
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM7_58862Myo


title: RNA-seq, MDA-MB-231, empty vector control (NC), biol rep 3

description: Library name: NC_3


title: Scramble_control_rep1

description:
Library name: LA40_B
Scramble control replicate 1


title: PT22T_H3K4me3

description: Library name: 4_097C_PT22T_H3K4me3_i53

value: 4-hydroxytamoxifen (1 uM)


title: RNA-seq, MDA-MB-231, empty vector control (NC), biol rep 2

description: Library name: NC_2


title: HCM6_57050Myo

description:
Library name: 57050Myo
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM6_57050Myo


title: Nvznf845_shRNA_rep1

description:
Library name: LA40_A
Nvznf845 knockdown replicate 1


title: RNA-seq, MDA-MB-231, empty vector control (NC), biol rep 1

description: Library name: NC_1


title: HCM5_56253Myo

description:
Library name: 56253Myo
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM5_56253Myo


title: Scramble_control_rep5

description:
Library name: LA70_1_E2
Scramble control replicate 5

treatment_protocol: Embryos were injected with NvpaxA shRNA for knockdown or scramble RNA as control. Each replicate consisted of approximately 1000 injected embryos.


title: PT22T_PAX8

description: Library name: 2_09ZT_PT22T_PAX8_i60


title: HCM4_56091Myo

description:
Library name: 56091Myo
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM4_56091Myo


title: NvpaxA_shRNA_rep5

description:
Library name: LA70_1_E1
NvpaxA knockdown replicate 5

value: NvpaxA shRNA


title: PT22_PAX8

description: Library name: 1_09ZS_PT22_PAX8_i59

value: vehicle


title: Thyroid MALT lymphoma Visium HD spatial transcriptomics

city: Shanghai

first: Jiadai

last: Xu

address: Xuhui District, Zhongshan Hospital Fudan University

institute: Zhongshan Hospital Fudan University

description:
Library name: LC_23S060453
Thyroid MALT lymphoma FFPE tissue profiled by 10x Genomics Visium HD Spatial Gene Expression.

data_processing:
FASTQ files were generated from Illumina paired-end sequencing reads.
FASTQ files were processed with Space Ranger v3.0 using the human reference genome.
Spatial transcriptomics downstream analyses were performed using Seurat, SPOTlight, CellChat, AddModuleScore, and related R workflows as described in the manuscript.
Processed Space Ranger matrix and spatial image outputs will be supplied as supplementary processed data files before final GEO release.
Assembly: GRCh38 human reference genome used by Space Ranger v3.0. Confirm exact reference package before final submission.
Supplementary files format and content: Processed data will include Space Ranger filtered feature-barcode matrices, spatial coordinate and image files, and selected downstream annotation and result tables. LC_24G22292 processed matrix is pending transfer from another computer.
Library strategy: Spatial Transcriptomics

source_name: thyroid

growth_protocol: FFPE tissue sections from MALT lymphoma biopsy samples were used for Visium HD spatial transcriptomics.

extract_protocol:
Total RNA was isolated from FFPE tissue blocks. RNA quality was assessed by DV200, and samples passing quality control were processed using the 10x Genomics Visium HD Spatial Gene Expression workflow.
FFPE tissue sections were deparaffinized, stained and imaged, followed by probe hybridization, ligation, probe release, extension, library construction, and paired-end sequencing according to the 10x Genomics Visium HD Spatial Gene Expression protocol.

treatment_protocol: No ex vivo treatment was applied to the submitted tissue sections.

value: thyroid

value: MALT lymphoma tissue

value: first-line orelabrutinib plus obinutuzumab cohort; pretreatment biopsy

value: Visium HD


title: HCM3_53311

description:
Library name: 53311
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM3_53311


title: Scramble_control_rep4

description:
Library name: LA70_1_D2
Scramble control replicate 4


title: LD 6mpk T 15mpk 10

city: San Diego

first: Aarash

last: Bordbar

address: 3210 Merryfield Row

institute: Sinopia Biosciences

data_processing:
FastQ files were quality controlled using FastQC. Reads were mapped to the Norway rat genome (Rnor_6.0.94) using STAR. Aligned reads were counted using HTseq using the “intersection_strict” mode.
Assembly: Rnor_6.0.94
Supplementary files format and content: raw_counts.txt contains the HTseq output

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Total RNA was obtained from homogenized striatum using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared using polyA capture and reverse transcription of cDNA

value: Striatum

tag: gender

value: female

value: Sprague Dawley


title: HCM2_50940MF

description:
Library name: 50940MF
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM2_50940MF

value: cardiac fibroblasts


title: A23LUN_2

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 8

data_processing:
Sequencing reads were quality filtered and adapter trimmed prior to alignment.
Trimmed reads were aligned to the human reference genome.
Aligned reads were filtered to remove duplicates and low-quality mappings.
Accessible chromatin regions were identified using peak calling and normalized signal tracks were generated.
Assembly: hg38
Supplementary files format and content: BigWig files represent normalized ATAC-seq signal tracks for each sample.
Supplementary files format and content: avg_BigWig files represent normalized ATAC-seq signal tracks for averaged samples

source_name: Lung

growth_protocol: Human tumor samples were obtained from surgical resections and processed according to institutional protocols. Samples were flash frozen and stored at −80 °C until chromatin accessibility profiling.

extract_protocol:
Nuclei were isolated from frozen tumor tissue and subjected to transposition using Tn5 transposase to tag accessible chromatin regions.
ATAC-seq libraries were prepared using a standard transposase-based protocol followed by PCR amplification and size selection according to the manufacturer’s instructions.

treatment_protocol: No in vitro treatment was applied. Samples represent primary and metastatic tumor tissues collected at the time of surgery.

value: Lung

value: lung metastatic tumor cells


title: Nvznf845_shRNA_rep4

description:
Library name: LA48_1A
Nvznf845 knockdown replicate 4

value: gastrula embryo 28hpf

value: whole embryo

value: Nvznf845 shRNA


title: NvpaxA_shRNA_rep4

description:
Library name: LA70_1_D1
NvpaxA knockdown replicate 4

value: wildtype


title: LD 6mpk T 15mpk 9


title: HCM11_myo63988

description:
Library name: myo63988
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM11_myo63988


title: RNA-seq, MDA-MB-231, SRPK2 overexpression (OE), biol rep 3

description: Library name: OE_3

value: breast cancer


title: RXRG CUT&Tag of human mid-fetal dlPFC DFC2

city: New Haven

first: Saejeong

last: Park

state: Connecticut

address: 100 College St

institute: Yale University

description:
Library name: DFC2_RXRG
RXRG CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RXRG.bw
Human mid-fetal dlPFC RXRG peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

data_processing:
Single-nucleus multiomic data were processed using Cell Ranger ARC (v2.0.1, 10x Genomics) with default parameters. Reads were aligned to the reference genome, and gene expression matrices and chromatin accessibility fragment files were generated. CUT&Tag sequencing reads were processed using standard pipelines, including read alignment to the reference genome and identification of enriched regions. Bulk RNA-seq data were processed using standard pipelines, including read alignment to the reference genome and quantification of gene expression levels to generate gene-level count matrices.
Assembly: Human: hg38 Mouse: mm10
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for each sample. For single-nucleus multiomic data, processed files include gene expression matrices and chromatin accessibility fragment files. For CUT&Tag data, processed files include BigWig files and peak files. For bulk RNA-seq, processed files include gene-level count matrices for each sample as well as differential gene expression analysis results.
Library strategy: CUT&Tag

source_name: dlPFC

extract_protocol:
For human samples, nuclei were isolated from mid-fetal dorsolateral prefrontal cortex (dlPFC) tissue using a Dounce homogenization-based protocol in ice-cold lysis buffer, followed by filtration and iodixanol gradient centrifugation. The resulting nuclear pellets were resuspended in nuclei buffer supplemented with RNase inhibitor and DTT. For mouse samples, nuclei were isolated from medial prefrontal cortex (mPFC) and motor cortex (MC) tissues at postnatal day 1 (P1) using a similar homogenization-based protocol followed by filtration and centrifugation. For CUT&Tag experiments, nuclei were isolated from fresh frozen human cortical tissue using a commercial nuclei isolation kit according to the manufacturer’s instructions. For bulk RNA-seq, total RNA was extracted from dissociated mouse mPFC cells following enzymatic digestion and cell dissociation.
Single-nucleus multiomic libraries for gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. CUT&Tag libraries were prepared using a Hyperactive Universal CUT&Tag Assay Kit (Vazyme) following standard protocols. Briefly, isolated nuclei were incubated with primary antibodies targeting transcription factors (RARA, RARB, RXRG, MEIS2) or histone modifications (H3K27ac, H3K4me3), followed by secondary antibody incubation, Tn5 transposase binding, tagmentation, and PCR amplification. Bulk RNA-seq libraries were prepared from mouse mPFC cells using the VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s protocol.

value: dlPFC

tag: antibody

value: RXRG


title: HCM1_48977

description:
Library name: 48977
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM1_48977


title: HCM9_myo49610

description:
Library name: myo49610
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM9_myo49610


title: RNA-seq, MDA-MB-231, SRPK2 overexpression (OE), biol rep 2

description: Library name: OE_2


title: PT22T_H3K27me3

description: Library name: 6_09ZR_PT22T_H3K27me3_i57

value: Kidney

value: Proximal tubule

value: 4-hydroxytamoxifen (1 uM)


title: Scramble_control_rep3

description:
Library name: LA70_1_C2
Scramble control replicate 3

value: scramble RNA control


title: RARB CUT&Tag of human mid-fetal dlPFC DFC2

description:
Library name: DFC2_RARB
RARB CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RARB.bw
Human mid-fetal dlPFC RARB peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

value: RARB


title: HCM0_23011

description:
Library name: 23011
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: HCM0_23011


title: LD 6mpk T 15mpk 8

value: Striatum

value: female


title: NvpaxA_shRNA_rep3

description:
Library name: LA70_1_C1
NvpaxA knockdown replicate 3

value: NvpaxA shRNA


title: PT22_H3K27me3

description: Library name: 5_09ZQ_PT22_H3K27me3_i56

value: vehicle


title: LD 6mpk T 15mpk 7

value: Sprague Dawley


title: Control2_Myo182

description:
Library name: Myo182
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: Control2_Myo182

value: cardiac fibroblasts


title: Scramble_control_rep2

description:
Library name: LA61_1_B2
Scramble control replicate 2

value: gastrula embryo 28hpf

value: whole embryo


title: RARA CUT&Tag of human mid-fetal dlPFC DFC2

description:
Library name: DFC2_RARA
RARA CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RARA.bw
Human mid-fetal dlPFC RARA peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

value: RARA


title: LD 6mpk T 15mpk 6


title: Control1_Myoc169

description:
Library name: Myoc169
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: Control1_Myoc169


title: Labial gland MALT lymphoma Visium HD spatial transcriptomics

description:
Library name: LC_23S061111
Labial gland MALT lymphoma FFPE tissue profiled by 10x Genomics Visium HD Spatial Gene Expression.

source_name: labial gland

value: labial gland

value: MALT lymphoma tissue

value: first-line orelabrutinib plus obinutuzumab cohort; pretreatment biopsy

value: Visium HD


title: MEIS2 CUT&Tag of human mid-fetal dlPFC DFC2

description:
Library name: DFC2_MEIS2
MEIS2 CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC MEIS2.bw
Human mid-fetal dlPFC MEIS2 peak.bed

value: dlPFC


title: NvpaxA_shRNA_rep2

description:
Library name: LA61_1_B1
NvpaxA knockdown replicate 2

value: wildtype


title: LD 6mpk T 15mpk 5


title: Control0_Myo96

description:
Library name: Myo96
Column name in Raw_Counts_All_Samples.txt and FPKM_Counts_All_Samples.txt: Control0_Myo96


title: H3K4me3 CUT&Tag of human mid-fetal dlPFC DFC2

description:
Library name: DFC2_H3K4me3
H3K4me3 CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC H3K4me3.bw
Human mid-fetal dlPFC H3K4me3 peak.bed


title: PT22_H3K4me3

description: Library name: 3_097B_PT22_H3K4me3_i52

value: Kidney

value: Proximal tubule


title: Scramble_control_rep1

description:
Library name: LA61_1_A2
Scramble control replicate 1

value: scramble RNA control


title: LD 6mpk T 15mpk 4

value: Striatum

value: female


title: Lac, 3 weeks, bio rep 5 and 6

city: La Jolla

first: Bianca

last: Pena

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

description:
Library name: Sample 12
Column name in RNAseq_LP SBI_counts.csv: Sample 12_Lac3w.3

data_processing:
Salmon software tool was used for quantification. R software was used for further analysis.
Assembly: Taxonomy ID: 10116, Rattus norvegicus
Supplementary files format and content: csv file includes raw counts for each sample

source_name: skeletal muscle

extract_protocol:
Pubocaudalis muscle was extracted and stored in RNAlater at -80C until RNA isolation. 30 mg of tissue was excised and underwent RNA isolation using Rneasy fibrous tissue mini kit (Qiagen). mRNA was checked for degradation using the TapeStation 4200. RNA was then pooled with two biological replicates per RNA pool. Pools were quantified using a Qubit 3.0 with a Qubit™ RNA High Sensitivity kit.
Samples were prepared using the Illumina Stranded mRNA kit according to manufacturer protocols. Final libraries were sizes using a D1000 ScreenTape on a TapeStation 4200 and quantified using a Qubit 3.0 with a Qubit™ 1x ds DNA High Sensitivity kit. Libraries were pooled and sequenced on one lane of the 10B PE100 flow cell using the Illumina NovaSeq X Plus.

value: skeletal muscle


title: H3K27ac CUT&Tag of human mid-fetal dlPFC DFC2

description:
Library name: DFC2_H3K27ac
H3K27ac CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC H3K27ac.bw
Human mid-fetal dlPFC H3K27ac peak.bed


title: LD 6mpk T 15mpk 3

value: Sprague Dawley


title: RXRG CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_RXRG
RXRG CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RXRG.bw
Human mid-fetal dlPFC RXRG peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

value: RXRG


title: LD 6mpk T 15mpk 2


title: Scramble_control_rep4

description:
Library name: LA20_3_E2
Scramble control replicate 4

treatment_protocol: Embryos were injected with NvfoxE-like shRNA for knockdown or scramble RNA as control. Each replicate consisted of approximately 1000 injected embryos.

value: gastrula embryo 28hpf

value: Whole embryo


title: Lac, 3 weeks, bio rep 3 and 4

description:
Library name: Sample 11
Column name in RNAseq_LP SBI_counts.csv: Sample 11_Lac3w.2


title: NvpaxA_shRNA_rep1

description:
Library name: LA61_1_A1
NvpaxA knockdown replicate 1

value: whole embryo

value: NvpaxA shRNA


title: RARB CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_RARB
RARB CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RARB.bw
Human mid-fetal dlPFC RARB peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

value: RARB


title: Lac, 3 weeks, bio rep 1 and 2

description:
Library name: Sample 10
Column name in RNAseq_LP SBI_counts.csv: Sample 10_Lac3w.1


title: NvfoxE-like_shRNA_rep4

description:
Library name: LA20_3_E1
NvfoxE-like knockdown replicate 4

value: NvfoxE-like shRNA


title: RARA CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_RARA
RARA CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC RARA.bw
Human mid-fetal dlPFC RARA peak.bed
Human mid-fetal dlPFC RAR_RXR.bw

value: RARA


title: LD 6mpk T 15mpk 1


title: Non Lac, 3 weeks, bio rep 5 and 6

description:
Library name: Sample 9
Column name in RNAseq_LP SBI_counts.csv: Sample 9_NLac3w.3


title: LD 6mpk T 7.5mpk 10


title: Scramble_control_rep3

description:
Library name: LA20_3_C2
Scramble control replicate 3


title: MEIS2 CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_MEIS2
MEIS2 CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC MEIS2.bw
Human mid-fetal dlPFC MEIS2 peak.bed

value: dlPFC


title: Non Lac, 3 weeks, bio rep 3 and 4

description:
Library name: Sample 8
Column name in RNAseq_LP SBI_counts.csv: Sample 8_NLac3w.2


title: H3K4me3 CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_H3K4me3
H3K4me3 CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC H3K4me3.bw
Human mid-fetal dlPFC H3K4me3 peak.bed


title: NvfoxE-like_shRNA_rep3

description:
Library name: LA20_3_C1
NvfoxE-like knockdown replicate 3

value: wildtype


title: Non Lac, 3 weeks, bio rep 1 and 2

description:
Library name: Sample 7
Column name in RNAseq_LP SBI_counts.csv: Sample 7_NLac3w.1


title: LD 6mpk T 7.5mpk 8


title: H3K27ac CUT&Tag of human mid-fetal dlPFC DFC1

description:
Library name: DFC1_H3K27ac
H3K27ac CUT&Tag of human mid-fetal dlPFC
Human mid-fetal dlPFC H3K27ac.bw
Human mid-fetal dlPFC H3K27ac peak.bed


title: Lac, 1 week, bio rep 5 and 6

description:
Library name: Sample 6
Column name in RNAseq_LP SBI_counts.csv: Sample 6_Lac1w.3


title: LD 6mpk T 7.5mpk 7


title: DSP-1001660019865-E-F02

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: Library name: Sample 301

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: PF

tag: scan name

tag: roi

tag: segment

value: Desmin


title: Scramble_control_rep1

description:
Library name: LA19_2_A2
Scramble control replicate 1

tag: cell type

value: scramble RNA control


title: Lac, 1 week, bio rep 3 and 4

description:
Library name: Sample 5
Column name in RNAseq_LP SBI_counts.csv: Sample 5_Lac1w.2


title: LD 6mpk T 7.5mpk 6

value: Striatum

value: female


title: DSP-1001660019865-E-F01

description: Library name: Sample 300


title: Lac, 1 week, bio rep 1 and 2

description:
Library name: Sample 4
Column name in RNAseq_LP SBI_counts.csv: Sample 4_Lac1w.1

value: skeletal muscle


title: NvfoxE-like_shRNA_rep1

description:
Library name: LA19_2_A1
NvfoxE-like knockdown replicate 1

tag: genotype


title: DSP-1001660019865-E-E12

description: Library name: Sample 299


title: Non Lac, 1 week, bio rep 5 and 6

description:
Library name: Sample 3
Column name in RNAseq_LP SBI_counts.csv: Sample 3_NLac1w.3


title: H5/ALC/CpG+MPLA-105-d28

type: protein

city: Irvine

first: Li

last: Liang

address: 847 Health Sciences

institute: University of California Irvine

hyb_protocol: The microarray slides were probed with mouse sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. Mouse IgG  secondary antibody conjugated to AF647, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.

source_name: Plasma

tag: days post prime immunization


title: DSP-1001660019865-E-E11

description: Library name: Sample 298


title: Non Lac, 1 week, bio rep 3 and 4

description:
Library name: Sample 2
Column name in RNAseq_LP SBI_counts.csv: Sample 2_NLac1w.2


title: H5/ALC/CpG+MPLA-103-d28


title: LD 6mpk T 7.5mpk 3

value: Sprague Dawley


title: LD 6mpk T 7.5mpk 4


title: DSP-1001660019865-E-E10

description: Library name: Sample 297


title: Non Lac, 1 week, bio rep 1 and 2

description:
Library name: Sample 1
Column name in RNAseq_LP SBI_counts.csv: Sample 1_NLac1w.1


title: LD 6mpk T 7.5mpk 2


title: DSP-1001660019865-E-E09

description: Library name: Sample 296


title: H5/ALC/CpG+MPLA-101-d28


title: SRPK2 iRIP-seq, MDA-MB-231, input replicate 2

description: Library name: SRPK2_Input_2

data_processing:
Illumina bcl2fastq software used for basecalling. Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of SPRK2 on genome using “ABLIRC” strategy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

extract_protocol:
The SRPK2-bound RNA was isolated from the immunoprecipitation of anti-SRPK2 using Trizol (Invitrogen).
Complementary DNA (cDNA) libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according to the manufacturer’s procedure and high-throughput sequencing of the cDNA libraries was performed on an Illumina Xtenplatform for 150 bp paired-end sequencing.

tag: cell line

value: breast cancer


title: LD 6mpk T 7.5mpk 1

tag: tissue


title: DSP-1001660019865-E-E08

description: Library name: Sample 295


title: H5/ALC/CpG-95-d28


title: Mito(-)ECs-R1

description: Library name: SAMPLE2

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.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of p-value below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: RNA-Seq
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: cell type

value: HUVECs

value: Endothelial cells

value: Wild type

value: Non-mitochondrial transfer


title: LD 6mpk 5

tag: strain


title: SRPK2 iRIP-seq, MDA-MB-231, IP replicate 2

description: Library name: SRPK2_IP_2


title: H5/ALC/CpG-93-d28


title: LD 6mpk 4


title: DSP-1001660019865-E-E06

description: Library name: Sample 293

tag: treatment


title: Nvznf845_shRNA_rep5

description:
Library name: LA48_2A
Nvznf845 knockdown replicate 5

value: gastrula embryo 28hpf

value: whole embryo

value: Nvznf845 shRNA


title: H5/ALC/CpG-92-d28


title: SRPK2 iRIP-seq, MDA-MB-231, IP replicate 1

description: Library name: SRPK2_IP_1


title: LD 6mpk 3


title: DSP-1001660019865-E-E05

description: Library name: Sample 292

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: THP-1 cells, MPXV lineage B.1-infected, 24h pi, replicate 3

city: London

first: Rebecca

last: Sumner

address: 2nd Floor Borough Wing, Guy's Hospital

department: Department of Infectious Diseases

institute: King's College London

description: Library name: THPB1_3

data_processing:
RNA-seq reads were aligned to the Homo Sapiens genome using HISAT2 and featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene and the FPKM of each gene was calculated based on the length of the gene and reads count mapped to it. Differentially expressed genes (DEG) were calculated using DESeq2. The resulting P-values from DESeq2 were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: csv file includes FPKM data for each sample

source_name: PMA-differentiated THP-1

growth_protocol: HFFF2 cells were cultured in Dulbecco modified Eagle medium (Sigma) and THP-1 cells were cultured in RPMI medium (Gibco), all supplemented with 10 % foetal bovine serum (FBS, Biowest) and 100 U/mL penicillin and 100 µg/mL streptomycin (Pen/Strep; Life Technologies).

extract_protocol:
Total RNA was extracted using the RNeasy mini RNA extraction kit (QIAgen) including on-column DNase treatment according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesised using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were then pooled and sequenced on an Illumina platform.

treatment_protocol: THP-1 cells were differentiated for 48 h in the presence of 50 ng/mL PMA (Peprotech).

value: PMA-differentiated THP-1

value: acute monoctyic leukaemia

value: THP-1 IFIT-1 Luc

value: PMA-differentiation, infected with MPXV B.1


title: H5/ALC/CpG-91-d28


title: LD 6mpk 2

value: Striatum

value: female


title: THP-1 cells, MPXV lineage B.1-infected, 24h pi, replicate 2

description: Library name: THPB1_2


title: DSP-1001660019865-E-E04

description: Library name: Sample 291

value: PF

value: Desmin


title: LD 6mpk T 7.5mpk 9

value: Sprague Dawley


title: LD 6mpk 1


title: H5/ALC-85-d28


title: Scramble_control_rep2

description:
Library name: LA19_2_B2
Scramble control replicate 2

value: Whole embryo

value: wildtype

value: scramble RNA control


title: THP-1 cells, MPXV lineage B.1-infected, 24h pi, replicate 1

description: Library name: THPB1_1


title: DSP-1001660019865-E-E03

description: Library name: Sample 290


title: H5/ALC-83-d28


title: NvfoxE-like_shRNA_rep2

description:
Library name: LA19_2_B1
NvfoxE-like knockdown replicate 2

value: NvfoxE-like shRNA