title: DMSO_0_24h_1pool1_S1

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S1


title: WT Hypoxic #1

status: Public on Feb 17 2025

type: SRA

city: San Antonio

first: Astrid

last: Cardona

state: Texas

address: One UTSA Circle

department: Molecular Microbiology and Immunology

country: USA

institute: University of Texas at San Antonio

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v21.0.5 by the Universityof Texas at San Antonio Genomics Core (San Antonio, TX)
Aligned to reference mouse genome GRCm39
Assembly: mm10
Supplementary files format and content: Comma-deliniated files contain verbose output from CLC genomics workbench alignment, uncluding TMP, RPKM and unique counts

molecule: total RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Mechanical homogenization followed by Trizol™ extraction
Libraries were constructed by the University of Texas Health Science Center Genome Sequencing Facility (Greehy Children's Cancer Research Institute, San Antonio Texas) utilizing NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA)

treatment_protocol: Normoxic: animals maintained at ambient oxygen (~22%). Hypoxic: animals maintained at 7.5% oxygen for 7-days

tag: tissue

value: Retina

tag: genotype

value: Wild Type

tag: treatment

value: Hypoxic


title: WT Normoxic #3

value: Normoxic


title: WT Normoxic #2


title: s15_PFC_ATAC

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: Single-cell ATAC sequencing  (10xGenomics)

library_source: genomic

data_processing:
Alignment of reads to reference (GRCh38, ensembl 98), cell caliing and count matrix generation with cellranger-atac v2.0.0.
Processing with ArchR v1.0.2: per-cell quality control with default parameters and removal of doublets with filter ratio of 2.5. Removal of one donor due to overall low data quality.
Dimensionality reduction with iterative LSI and UMAP embedding. Louvain clustering with resolution 1.0. Filtering of one donor and six clusters with low data quality regarding doublet scores and number of fragments, resulting in 399,439 nuclei from 90 donors.
Calculation of gene scores with ArchR and generation of pseudobulk gene scores.
Peak calling with MACS2.
Assembly: GRCh38
Supplementary files format and content: PeakMatrix.mtx is the peak count matrix in mtx format, PeakSet.csv contains peak metadata in csv format and Peak_CellMetadata.csv contains metadata for each nuclei (including cell type annotation).
Supplementary files format and content: GeneScoreMatrix_Pseudobulk_Normalized.csv contains a matrix with gene scores on the pseudobulk level. Each column contains gene score for a pseudosample (donor/cell type combination). Rows represent genes.

molecule: genomic DNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Nuclei were isolated from frozen, dissected brain samples (OFC, BA11; 50 - 60 mg) by dounce-homogenisation in nuclei extraction buffer. Homogenate was layered onto a sucrose cushion and ultra-centrifuged. Nuclei pellet was resuspended in resuspension buffer, filtered through a cell strainer cap, stained with DAPI and counted using a hemocytometer.
Single nuclei ATAC-seq libraries were prepared following the user guide of 10X Genomics (Chromium Single Cell ATAC reagents kits v1.1) with a target recovery of 10,000 nuclei per sample.
Libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent), were then pooled equimolarily and treated with Illumina Free Adapter Blocking Reagent before sequencing on the NovaSeq 6000 System (Illumina).

value: brain

tag: disease status

value: Cases

tag: classification

value: SchizoaffectiveDisorder

tag: age

tag: Sex

value: Male

tag: ethnicity

value: European

tag: ph

tag: pmi

tag: rin

tag: lib batch


title: WT Normoxic #1


title: s12_PFC_ATAC

value: Controls

value: Control

value: Female


title: s14_PFC_ATAC


title: AC33_siU_input

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: siHNRNPU total RNA sample rep 3

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then quantified against the Gencode v43 transcriptome using STAR with default parameters
Assembly: hg38
Supplementary files format and content: raw reads count table

growth_protocol: HCT116 (ATCC CCL-247) cells were grown in DMEM 4.5 g/L glucose supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
RNA extraction was performed with Zymo RNA clean & concentrator -5 R1013 with Dnase treatment, according to manufacturer's protocol
Libraries were built using the Directional RNA library NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 - PerkinElmer, following the manufacturer's protocol

treatment_protocol: siRNAs transfection was performed using the Lipofectamine RNAiMAX for 48h

tag: cell line

value: HNRNPU silencing


title: 3K M17D cells, transfection with scrambled siRNA, day 2 post-transfection, biological replicate 3

city: Piscataway

first: Eleanna

last: Kara

state: New Jersey

address: 683 Hoes Lane West

institute: Rutgers University

data_processing:
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCh38/hg38
Supplementary files format and content: csv file including TPM values for all samples
Supplementary files format and content: csv file including raw counts for all samples

source_name: 3K M17D

extract_protocol:
PureLink RNA mini kit (Thermofisher)
NEB Next Ultra RNA library prep

value: 3K M17D


title: 3K M17D cells, transfection with siRNA against TAX1BP1, day 2 post-transfection, biological replicate 2


title: s13_PFC_ATAC


title: AC33_siU_HP

description: siHNRNPU polysomal RNA sample rep 3

library_source: other

molecule: other


title: WT Hypoxic #2


title: AC33_siCtr_HP

description: wild-type polysomal RNA sample rep 3

value: wild-type


title: 3K M17D cells, transfection with siRNA against TAX1BP1, day 2 post-transfection, biological replicate 1


title: 3K M17D cells, transfection with siRNA against TAX1BP1, day 2 post-transfection, biological replicate 3


title: 3K M17D cells, transfection with scrambled siRNA, day 2 post-transfection, biological replicate 2


title: s11_PFC_ATAC

value: Schizophrenia


title: nascent_dTAG_2

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Raw Bam files underwent processing using the slamseq Nextflow pipeline, accessible at https://github.com/nf-core/slamseq. This pipeline integrates multiple tools including fastqc, trim_galore and slamdunk available at: https://github.com/t-neumann/slamdunk, for quality assessment, adapter trimming, and read mapping. DESeq2 was employed for comparative analysis, facilitating the identification of newly transcribed genes. Heatmaps depicting expression patterns were created using the heatmap.2 function from the gplots R package.
Assembly: Nascent RNA-seq: mm10
Supplementary files format and content: Nascent RNA-seq: tab delimited file with raw counts and normalized expression per gene

growth_protocol: All NUP98::KDM5A cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, 1 mM Sodium pyruvate, 50 µM 2-Mercaptoethanol and 20 mM HEPES at 37 °C, 5% CO2, and 95% humidity. Primary NUP98::KDM5A PDX AML cells were cultured in IMDM containing 15% BIT 9500 Serum Substitute, 100 ng/ml SCF, 50 ng/ml Flt3-Ligand, 20 ng/ml IL-3, 20 ng/ml G-CSF, 100 µM ß-mercaptoethanol, 50 µg/ml gentamicin, 10 µg/ml ciprofloxacin, 500 nM SR1 and 1 µm UM729 at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
Nascent RNA-seq: RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Total RNA was alkylated using 10 mM iodoacetamide and RNA was purified by ethanol precipitation.
Nascent RNA-seq: Sequencing libraries were generated using the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina.

treatment_protocol: Nascent RNA-seq: Cells were treated with dTAG13 (35 nM) or DMSO for 1h, followed by the addition of 100 μM 4-thiouridine for 1h.

tag: cell type

value: acute myeloid leukemia cells


title: AC33_siCtr_input

description: wild-type total RNA sample rep 3


title: 3K M17D cells, transfection with scrambled siRNA, day 2 post-transfection, biological replicate 1


title: s10_PFC_ATAC


title: AC32_siU_HP

description: siHNRNPU polysomal RNA sample rep 2


title: 3K M17D cells, transfection with siRNA against ADAMTS19, day 2 post-transfection, biological replicate 3


title: nascent_dTAG_1


title: s9_PFC_ATAC


title: AC32_siCtr_HP

description: wild-type polysomal RNA sample rep 2


title: nascent_DMSO_3

value: DMSO


title: nascent_dTAG_3


title: AC32_siU_input

description: siHNRNPU total RNA sample rep 2


title: 3K M17D cells, transfection with siRNA against ADAMTS19, day 2 post-transfection, biological replicate 2


title: s8_PFC_ATAC


title: nascent_DMSO_2


title: s7_PFC_ATAC

value: MajorDepression


title: AC32_siCtr_input

description: wild-type total RNA sample rep 2


title: 3K M17D cells, transfection with siRNA against ADAMTS19, day 2 post-transfection, biological replicate 1


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, Tamoxifen 6h, rep1

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam6h rep1

data_processing:
Quality of reads was assessed by FastQC (v. 0.11.9), index and adaptor sequences were trimmed using TrimGalore (v. 0.6.6) and Cutadapt (v. 1.9.1) followed by a second quality check with FastQC.
Sequences were aligned to the mm10 mouse reference genome using Burrows-Wheeler Alignment (BWA, v. 0.7.16) tool with the maximal exact matches (MEM) option.
Fragments were quality filtered (>10) with Samtools (v. 1.6) and PCR duplicates were marked with Picard (v. 2.23.3) and removed with Samtools. Mitochondrial fragments were eliminated with Samtools.
Mapped reads were shifted by +4 bp for the forward strand and -5 bp for the reverse strand. Shifted bam files were transformed into BED files for peak calling using MACS2.
Bigwig tracks were generated with the bamCoverage option in the python-based DeepTools  (v. 3.5.1).
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Cells were routinely cultured in Serum/LIF media on gelatin plates. PGCLC differentiation was perfomed as previosly descrbied (Hayashi et al, 2011). Cells were first kept in 2i/LIF (N2B27 supplemented with CHIR99021 and PD0325901 ) for at least three passages prior to EpiLC and PGCLC differentiation. EpiLCs were derived for 44 hours in EpiLC medium (N2B27 supplemented with human Activin A and Fgf) and then cultured in suspension in GK15 (GMEM 15% KOSR) for 6 days. Cultures with cytokines were also supplemented with BMP4, BMP8a, SCF, LIF and EGF.

extract_protocol:
Nuclei were resuspended in Tagmentation Master Mix containing Assembled Trasposomes (Active Motif, cat. 53150). Tagmentation was performed in a thermocycler at 37°C for 20 minutes. Tagmented DNA was recovered using the DNA Clean and Concentration-5 kit (Zymo Research, cat. D4013).
Library was prepared using NEBNext High Fidelity 2x PCR Master Mix and indexed primers reported in Buenrostro et al, 2013, using the following protocol: 72°C for 5 minutes, and 98°C for 30 seconds followed by 9 cycles of : 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute.

treatment_protocol: Otx2-/- Otx2-ERT2 cells were treated with 1 µM of 4-hydroxytamoxifen for the indicated times. To change tamoxifen containing media, aggregates were collected at day 2, washed, resuspended in GK15 and incubated in 5 mm dishes in rotation until day 4 before collection and analysis.

value: Otx2-/- OTX2-ERT2

value: EpiLC

tag: time point

value: day 2

value: Activin A + bFGF, tamoxifen 6h


title: nascent_DMSO_1


title: AC31b_siCtr_HP

description: wild-type polysomal RNA sample rep 1


title: CD45+mCherry+_1

city: Cambridge

first: Qiuchen

last: Zhao

state: UK

address: Downing College, Regent St, Room45

department: Department of Pathology, CRUK Cambridge Centre

institute: University of Cambridge

data_processing:
Quality assessment of the raw sequencing reads was conducted using FastQC, and the HISAT2 aligner was utilized to map the reads to the human genome (hg38), resulting in SAM files for each sample. Samtools was subsequently used to convert and sort these files into BAM format. Gene-level abundance and raw counts were derived using htseq-count, providing the necessary data for principal component analysis (PCA) and differential gene expression analysis in DESeq2 (version 1.30.1). The raw single-cell RNA sequencing (scRNA-seq) data were subjected to an initial preprocessing stage employing the Cell Ranger toolkit (version 7.1.0), a product of 10x Genomics. This stage involved the filtration of low-quality reads, alignment of reads to the mouse reference genome (GRCm38), demultiplexing of cellular barcodes, and generation of the unique molecular identifier (UMI) matrix.
Assembly: Human reference genome (hg38); Mouse reference genome (GRCm38)
Supplementary files format and content: Normalised counts for each sample; Tab-separated values files and matrix files

source_name: CD45+ cells

extract_protocol:
RNA samples were isolated using RNeasy Plus Mini Kit (Qiagen). For scRNA-seq, the process began with sorting samples into PBS-0.04% BSA solution, which were then loaded into Chromium microfluidic chips. The chips utilized 10X Genomics' 5′ v2 chemistry to create gel-bead emulsions in a Chromium controller, targeting around 10,000 emulsions with unique cell barcodes.
The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. Single-cell RNA sequencing libraries were employed the Chromium Next GEM Single Cell 5' Kit v2, along with other specialized kits and guides provided by 10X Genomics.

value: CD45+ cells


title: AC31b_siU_HP

description: siHNRNPU polysomal RNA sample rep 1


title: CD45+mCherry+_2


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, Tamoxifen 1h, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam1h rep1

value: Activin A + bFGF, tamoxifen 1h


title: s6_PFC_ATAC

value: brain

value: European


title: s5_PFC_ATAC

value: Cases

value: Male


title: AC31b_siU_input

description: siHNRNPU total RNA sample rep 1

value: HNRNPU silencing


title: s3_PFC_ATAC

value: Female


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, untreated, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam0h rep1

value: Activin A + bFGF


title: CD45+mCherry-_1


title: CD45+mCherry-_2


title: AC31b_siCtr_input

description: wild-type total RNA sample rep 1

value: wild-type


title: s2_PFC_ATAC


title: Replicate 3 Medium MFI Sorted Infected Cells

city: Ann Arbor

first: Alice

last: Telesnitsky

state: MI

address: 1150 W. Medical Center Drive, 6714 MSII

department: Microbiology & Immunology

institute: University of Michigan

description: Library name: Sample 20

data_processing:
Barcode abundances were tabulated using a custom suite of tools implemented in Python.
Supplementary files format and content: A text file of barcode abundances for each sample

organism: Human immunodeficiency virus 1

source_name: Jurkat T cells

extract_protocol:
Genomic DNA samples were isolated from cells using the Dneasy Blood & Tissue Kit per manufacturer protocol. Total RNA samples were isolated from cells using Trizol Reagent. Unspliced capture RNA was enriched from total RNA samples using affinity capture. Viral RNA was isolated from concentrated extracellular viral particles using Trizol Reagent.
Amplicons were prepared for sequencing using PCR either directly from cellular genomic DNA samples or from cDNA generated from RNA samples.

value: Jurkat T cells


title: Replicate 3 High MFI Sorted Infected Cells

description: Library name: Sample 21


title: Replicate 3 Low MFI Sorted Infected Cells

description: Library name: Sample 19


title: s1_PFC_ATAC

value: Schizophrenia


title: Ctrl_2

value: WT


title: DCs_GC5

description:
DC10
row_counts_norm_MoDC.csv

source_name: Dendritic cells

value: Dendritic cells


title: Replicate 2 High MFI Sorted Infected Cells

description: Library name: Sample 18


title: Ctrl_1


title: Replicate 2 Medium MFI Sorted Infected Cells

description: Library name: Sample 17


title: Cyp11a1KO_3

value: Cyp11a1 KO


title: Replicate 2 Low MFI Sorted Infected Cells

description: Library name: Sample 16


title: DCs_Ctrl5

description:
DC9
row_counts_norm_MoDC.csv


title: s4_PFC_ATAC


title: Replicate 1 High MFI Sorted Infected Cells

description: Library name: Sample 15


title: Cyp11a1KO_2


title: DCs_GC4

description:
DC8
row_counts_norm_MoDC.csv


title: DCs_Ctrl4

description:
DC7
row_counts_norm_MoDC.csv


title: Replicate 1 Medium MFI Sorted Infected Cells

description: Library name: Sample 14


title: DCs_GC3

description:
DC6
row_counts_norm_MoDC.csv


title: DCs_Ctrl3

description:
DC5
row_counts_norm_MoDC.csv


title: Cyp11a1KO_1


title: Replicate 1 Low MFI Sorted Infected Cells

description: Library name: Sample 13


title: D8 CD8T, scATAC-seq

city: Guangzhou

first: Zhonghui

last: Tang

state: Guangdong

address: No. 74 Zhongshan Second Road, Guangzhou

country: China

institute: Sun Yat-sen University

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw scATAC-seq data was processed using 10x Genomics Cell Ranger ATAC pipeline (v1.2.0), including aligning the demultiplexed FASTQ reads to the mouse reference genome (mm10, v1.2.0, from 10x Genomics)
Counting the unique molecular identifier (UMI) for each cell barcode by using the ‘cellranger-atac count’ function
Downstream scATAC-seq analysis was performed in R (v4.0.0) using Seurat (v4.0.6), Signac (v1.1.1), and ArchR (v1.0.1)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, peaks.bed.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Binary data with h5 format

source_name: Lymphocytes

growth_protocol: For effector CD8+ T cell sorting, 5x10^3 OT-1 CD8+ T cells were transferred into congenically distinct CD45.2+ mice by intravenous (i.v.) injection and then infected with 1x10^5 CFU of Lm-OVA intravenously 1 day later. For experiments where OT-1 cells were collected two days after infection, 1x10^6 OT-I CD8+ T cells were transferred and then infected with 2x10^6 CFU of Lm-OVA intravenously. Activated OT-I T cells (CD8+Vα2+CD45.1+CD44+) were sorted from the spleen.

extract_protocol:
Briefly, approximately 50,000 FACS-sorted CD8+ T cells  were used for the nuclei preparation according to the manufacturer’s instructions. Then, 15,000 nuclei were loaded into a 10x Chromium controller. All library preparation was performed according to the manufacturer’s instructions.
The single-cell ATAC-seq (scATAC-seq) libraries were prepared using 10x Genomics Chromium Cell ATAC Reagent Kit (v1) according to the manufacturer’s protocol.

value: Lymphocytes

tag: strain

tag: infection

value: Lm-OVA, D8

tag: sorted cells

value: CD45.1+CD44+CD8+ T cells


title: D2 CD8T, scATAC-seq

description: 10x Genomics

tag: tissue

tag: genotype

value: Lm-OVA, D2


title: DCs_GC2

description:
DC4
row_counts_norm_MoDC.csv


title: Ctrl_3

value: CD45+ cells


title: Pool B Extracellular Viral RNA

description: Library name: Sample 12


title: DCs_Ctrl2

description:
DC3
row_counts_norm_MoDC.csv


title: Naïve CD8T, scATAC-seq

description: 10x Genomics

value: Naïve

value: CD45.1+CD44-CD8+ T cells


title: Pool B Unspliced Capture RNA

description: Library name: Sample 10


title: Pool A Extracellular Viral RNA

description: Library name: Sample 11


title: DCs_GC1

description:
DC2
row_counts_norm_MoDC.csv


title: Hindbrain pain neuronal ensemble SNI with brush

city: Bethesda

first: Tianming

last: Li

state: MD

address: 35A Convent Drive

department: NIDCR

institute: National Institutes of Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cells were excluded following the Seurat pre-processing protocol (Stuart, Butler, et al., 2019). Briefly, cells with fewer than 4000 unique features and more than 5% mitochondrial reads were excluded.
Non-neuronal hindbrain cells were excluded, after integrating and clustering cells following the Seurat protocol (Stuart, Butler, et al., 2019), using previously identified markers for non-neuronal cells (Nguyen et al., 2021).
Assembly: mm10
Supplementary files format and content: Comma separated values files
Supplementary files format and content: Tab separated values files

molecule: nuclear RNA

source_name: Hindbrain

extract_protocol:
Mouse hindbrains (~ -7.3- -5.2 mm posterior to the bregma) were rapidly dissected under sterile conditions and stored in -80°C. Hindbrains from the same treatment were pooled together for nuclear isolation. In breif, pooled brain tissues were homogenized (2ml Dounce homogenizer) in 1 ml freshly prepared lysis buffer, filtered (40 µm cell strainer), and centrifuged at 300g for 5 min (4°C). The pellet was gently resuspended in 500 µl 1xPBS (1% BSA and 0.2 U/µl SUPERaseIn RNase Inhibitor) and loaded on top of 900 µl 1.8M Sucrose Cushion Solution (Sigma, NUC-201). After 45 min of ultracentrifuge (13,000 g, 4°C), the nuclei were resuspended in 500 µl FACS buffer with the addition of 2.5 µl of 5 mM nuclear marker DRAQ5 (ThermoFisher).
Library was constructed folowing the manufacturer's protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit v3)

treatment_protocol: Different types of pain

value: neuron

value: Hindbrain

tag: treatment

value: SNI with brush


title: Pool A Unspliced Capture RNA

description: Library name: Sample 9


title: Memory CD8T RNAPII ChIA-PET

data_processing:
Filtering linker sequence in ChIA-PET using in-house script
Mapping ChIA-PET reads to reference genome using BWA MEM (v0.7.9a)
Deduplicating ChIA-PET reads using Picard (MarkDuplicates)
Peak-calling for ChIA-PET using MACS (v1.4.2)
Assembly: mm10
Supplementary files format and content: bedpe files
Supplementary files format and content: bedgraph files

growth_protocol: 200 ug GP33-41 peptide was intravenously injected into the P14 mice. 36 h later, mice were sacrificed, and cells from the spleen and lymph node were harvested. The cells were then washed and cultured in fresh tissue-culture flasks in a medium supplemented with the 20 ng/ml rIL-2 or 20 ng/ml rIL-15 and 1 ng/ml rIL-2. Media supplemented with cytokines were replaced every two days. All experiments were done using cells cultured for 9 days.

extract_protocol:
Briefly, approximately 100-200 million cultured primary T cells were harvested and fixed with 45 mL of 1.5 mM Ethylene glycol-bis (succinic acid N-hydroxysuccinimide ester) in DPBS buffer for 20 min at room temperature with 15 rpm rotating. A final concentration of 1% formaldehyde was added directly and followed by a rotation with 15 rpm at room temperature for 15 min. Before washing, quenched the crosslinked sample by adding a final concentration of 125 mM glycine at 15 rpm rotating for 10 min at room temperature. Collected all cell pellets with 1000 rcf for 5 min at 4℃ and washed the cell twice with 45 mL PBS before harvesting the cells. The dual crosslinked were aliquoted into 10 million cells each 1.5 mL LowBand tube for following library constraction or storing at a -80 ℃ freezer.
The chromatin was obtained and sonicated to generate fragments with an average length of 1-3 kb. The monoclonal antibody against RNA Polymerase II pre-incubated protein G beads were used to enrich RNAPII-bound chromatin fragments by overnight rotating with 10 rpm at 4℃. The on beads chromatin DNA fragments were washed following 4 different cold buffers and rinsed in 100 μL TE-1% SDS solution for 1 hour at 65℃ with 1100 rpm rotation. The solution was added 150 μL Qiagen EB buffer for another 45 min decrosslink. Collected all supernatant, added 10 μL proteinase K, and rotated at 900 rpm overnight at 65℃. The DNA fragments were purified with Zymo genomic DNA clean&concentrator kit and eluted with 20 μL nuclease-free water. Proceed with tagmentation for 50ng ChIP-DNA in each 200 μL PCR tube using 5 μL Tn5 transposase at 55℃ for 10 min to obtain a 0.1-1kb tagmentated DNA profile. Purified the tagmentated DNA with DNA cleanup columns and immobilized with the pre-blocked and pre-cleaned M280 streptavidin dynabeads in final 1X binding and washing buffer at RT for 45 min with 15 rpm rotation. The supernatant was discarded and the beads were washed 5 times with 500 μL pre-warmed at 37℃ 0.5% SDS/2X SSC buffer and the beads were resined in 30 μL elution buffer. A 11-13 cycles on-beads PCR was performed to construct the in situ ChIA-PET libraries and the PCR products were purified with 1X AMPure beads. These final libraries were then subjected to a 0.6X-0.8X double-size selection using AMPure beads and paired-end sequencing (2 x 150bp) using Illumina NovaSeq 6000.

tag: cell subtype

value: CD45.1+CD44+CD8+CD62L+ T cells


title: Hindbrain pain neuronal ensemble hot water

description: 10x Genomics

tag: age

value: Hot water bath


title: MNB_Tx, scRNAseq

city: Tokyo

first: Satoshi

last: Hatsuse

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

data_processing:
scRNA-seq reads were processed using the CellRanger 7.1.0 pipeline against the Rnor_6.0-104 reference genome in 3’ v3 chemistry mode (10x Genomics).
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix file

organism: Rattus norvegicus

source_name: Transplanted embryonic kidneys

extract_protocol:
Parenchyma from the transplanted kidney was collected, minced into millimetre-sized pieces, and thoroughly mixed. Approximately 100 mg of the sample was digested with 1 mL of Accutase (Innovative Cell Technologies) at 37 °C for 15 min and gently pipetted, followed by neutralisation of enzymatic activity with 1 mL of minimum essential medium α (Gibco) with 20% foetal bovine serum (FBS) and 0.4% penicillin/streptomycin. Cell suspensions were filtered through a 35 μm nylon cell strainer and centrifuged at 400 ×g for 5 min, after which the supernatant was discarded. Following debris removal using a debris removal solution (Miltenyi Biotec) according to the manufacturer’s protocol, the cell pellets were washed three times with Dulbecco's phosphate-buffered saline (DPBS)+10% FBS. Finally, the cells were resuspended in an appropriate volume of DPBS+10% FBS after confirmation of viable cell abundance through cell counts. The cells were loaded onto a Chromium Single-Cell Instrument (10x Genomics) targeting 10,000 cells to generate single-cell gel bead-in-emulsions (GEMs).
single-cell RNA sequencing (scRNA-seq) libraries were prepared using the Chromium Next GEM Single Cell 3ʹ GEM Kit v3.1 (10x Genomics). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from polyadenylated mRNA. After incubation, the GEMs were broken, the pooled post-GEM-RT reaction mixtures were recovered, and cDNA was purified using silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, Thermo Fisher Scientific). The purified post-GEM-RT product was amplified via PCR. Sequencing libraries were prepared following the manufacturer’s instructions.

value: Transplanted embryonic kidneys

value: Kidney cells


title: Naïve CD8T RNAPII ChIA-PET

value: CD45.1+CD44-CD8+CD62L+ T cells

value: WT


title: Effector CD8T RNAPII ChIA-PET

value: CD45.1+CD44+CD8+CD62L- T cells


title: eGFP- Sorted Pool B Cellular Genomic DNA

description: Library name: Sample 6

value: Jurkat T cells


title: eGFP- Sorted Pool A Cellular Genomic DNA

description: Library name: Sample 5


title: D180 CD8T scATAC-seq

description: 10x Genomics

growth_protocol: For effector and memory CD8+ T cell sorting, 5x10^3 P14 CD8+ T cells were transferred into congenically distinct CD45.2+ mice by intravenous (i.v.) injection and then infected with 2x10^5 PFU of LCMV Armstrong intraperitoneally 1 day later. For experiments where P14 cells were collected two days after infection, 1x10^6 P14 CD8+ T cells were transferred and then infected with 2x10^6 PFU of LCMV Arm+ intravenously. Activated P14 T cells (CD8+Vα2+CD45.1+CD44+) were sorted from the spleen.

value: Lymphocytes

value: LCMV-Armstrong

tag: time


title: eGFP+ Sorted Pool B Cellular Genomic DNA

description: Library name: Sample 4


title: D8-2 CD8T scATAC-seq

description: 10x Genomics

value: CD45.1+CD44+CD8+ T cells


title: eGFP+ Sorted Pool A Cellular Genomic DNA

description: Library name: Sample 3


title: AS-340505-LR-42842

city: Berlin

first: Clemens

last: Schmitt

address: Augustenburger Platz 1

department: Hematology, Oncology, Tumorimmunology

institute: Charite

description:
Library name: M_9
TIS_high

data_processing:
Quantification of the transcripts was performed using Salmon.
Downstream analyses were performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-separated txt files with normalized and raw read count

source_name: Blood

growth_protocol: Primary human AML cells were cultured on BJhTERT feeders in 35% DMEM, 35% IMDM (both Thermo Fisher Scientific), 10% FBS and 20% 5637 cell line-conditioned DMEM/IMDM, supplemented with 100 IE/ml penicillin/streptomycin, 200 mM L-glutamine (Sigma-Aldrich), 14.3 M -mercaptoethanol (Bio-Rad Laboratories), 100 ng/ml SCF (stem cell factor), 20 ng/ml IL-6 (interleukin-6), 10 ng/ml TPO (thrombopoietin, all from PeproTech), 10 ng/ml IL-3 and 10 ng/ml FLT3 (fms-like tyrosine kinase 3) ligand (both from Miltenyi Biotec). 5637-conditioned medium was collected and filtered after incubation of 45% DMEM/ 45% IMDM/ 10% FBS containing 100 IE/ml penicillin/streptomycin on a subconfluent dish of 5637 cells for 48 hours.

extract_protocol:
RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions
Targeted next-generation sequencing was performed with the TruSight Myeloid Sequencing Panel (Illumina). Samples for RNA sequencing were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) and sequenced on a HiSeq 2000.

treatment_protocol: Daunorubicin (50 ng/ml, Sigma-Aldrich) was added to freshly reseeded purified blasts, and cells were analyzed 5 days after treatment.

value: Blood

value: AML blasts

value: nt


title: D8-1 CD8T scATAC-seq

description: 10x Genomics


title: AS-335489-LR-42843

description:
Library name: M_21
TIS_high


title: Unsorted Pool B Cellular Genomic DNA

description: Library name: Sample 2


title: D2 CD8T scATAC-seq

description: 10x Genomics


title: PY65938_11

type: RNA

city: Houston

first: Robin

last: Parihar

address: 1102 Bates Avenue

department: Immunology

institute: Baylor College of Medicine

description: Total RNA was isolated using the Qiagen RNeasy Micro Kit and analyzed via NanoString Human Immunology V2 Panel.

hyb_protocol: Depending on sample quality, either 100ng or 300ng of total RNA were hybridized with the Nanostring Technologies nCounter Immune Immunology V2 Panel containing 608 unique pairs of 35-50bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occured for 16.8 hours at 65°C. Wash protocol: Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3' end to remove excess reporter probes, then by its 5' end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric curent (negative to positive), and immobolized. Photobleaching and flurophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobolized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 fields of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.

data_processing: The raw data was analyzed with the nSolver Analysis Software 3.0 program to generate the normalized data. The median values of negative controls were used for background subtraction and the geometric mean was used for normalization.

label: not provided

source_name: Primary Human NK Cells

extract_protocol: Qiagen RNEasy Micro Kit

value: Primary Human NK Cells

tag: donor

tag: nk condition

tag: tumor exposure

value: After


title: Naïve CD8T scATAC-seq

description: 10x Genomics

value: CD45.1+CD44-CD8+ T cells

value: Naive


title: AS-335488-LR-42843

description:
Library name: M_19
TIS_low


title: PY65935_08


title: PY65936_09

value: Unmodified


title: DCs_Ctrl1

description:
DC1
row_counts_norm_MoDC.csv

value: Dendritic cells


title: Unsorted Pool A Cellular Genomic DNA

description: Library name: Sample 1


title: Pool B Total Cellular RNA

description: Library name: Sample 8


title: Pool A Total Cellular RNA

description: Library name: Sample 7


title: PY65939_12


title: WT3

city: Shanghai

first: Si

middle: qin

last: Chen

address: No. 180 of Road Fenglin, District Xuhui.

institute: Fudan university

data_processing:
Hisat2（version:2.0.4）[2] software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Assembly: mmu10
Supplementary files format and content: Excel file include FPKM values for each Sample.

source_name: cardiac macrophages from WT mice

growth_protocol: Permanent left anterior descending artery (LAD) ligation or sham operation was performed on experimental animals

extract_protocol:
Total RNA was extracted using PAXgene Blood miRNA Kit (Cat# 763134, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Single cell suspensions were generated from the hearts as described by follows: The hearts were dissected, carefully cut into small pieces with fine scissors, and enzymatically digested with type II collagenase (1.5 mg mL-1, Worthington Biochemical, Lakewood, NJ, USA), elastase (0.25 mg mL-1, Worthington Biochemical), and DNase I (0.5 mg mL-1, Worthington Biochemical) for 1 h at 37 °C. Following digestion, the tissues were passed through 70-μm cell strainers, washed, and stained with antibody for fluorescence-activated cell sorter (FACS) analysis. To block the non-specific binding of antibodies to Fcγ receptors, isolated cells were incubated first with anti-CD16/32 antibody at 4 °C for 5 min. Cells were stained with CD45, CD64, CD11b monoclonal antibodies. LIVE/DEAD dye was used for exclusion of dead cells.

value: heart

value: 8 week

value: cardiac macrophages


title: AS-335487-LR-42843

description:
Library name: M_12
TIS_low

value: tr


title: PY65933_06

value: TIGITKO


title: AS-335486-LR-42842

description:
Library name: M_11
TIS_low


title: AS-335490-LR-42843

description:
Library name: M_22
TIS_high


title: PY65937_10


title: PY65932_05


title: WT2

value: WT


title: AuDC_DOX_10

city: Hsinchu City

first: ShengLiang

last: Cheng

address: No. 101, Sec. 2, Guangfu Rd., East Dist.

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

description: Library name: AuDC_DOX_10

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: tumor

growth_protocol: Murine TNBC 4T1 cells were orthotopically implanted in the mammary gland of 6–8-week-old female Balb/c mice. 1 × 10^5 4T1 cells were injected in the fatpad through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine TNBC (4T1) cells in Balb/c mice on day 0, followed by surgical removal of the primary tumor and cryogel implantation on day 14. Subsequent transcriptome analysis of the tumors was performed on day 16.

value: tumor

value: TNBC

value: DOX and AuNP treated BMDC co-loaded cryogel


title: AuDC_DOX_6

description: Library name: AuDC_DOX_6


title: AS-335485-LR-42842

description:
Library name: M_10
TIS_high

value: Blood

value: AML blasts


title: WT1


title: AuDC_DOX_4

description: Library name: AuDC_DOX_4


title: AS-335483-LR-42842

description:
Library name: M_6
TIS_high


title: PY65930_03

value: Primary Human NK Cells


title: PY65931_04

value: After


title: KO4

source_name: cardiac macrophages from LGMN-KO mice

value: LGMN-KO


title: AS-335482-LR-42842

description:
Library name: M_5
TIS_high

value: nt


title: KO2


title: PY65934_07


title: AS-334643-LR-42843

description:
Library name: M_20
TIS_low


title: KO1


title: PY65929_02


title: Control_8

description: Library name: Control_8

value: Untreated


title: AS-250545-LR-36069

description:
Library name: M_26
TIS_high


title: PY60277_12

value: Before


title: L4 stage animals, u49, PA, 3

city: Changsha

first: Xibin

last: Tian

address: Tianma Road

institute: Hunan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clean reads were mapped to the C. elegans genome sequence using Hisat2 v2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of three biological replicates per condition was performed using the DESeq R package (1.18.0).
Genome_build: WBcel2
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all Samples

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1 worms were placed onto NGM plates seeded with OP50 and grown at 20oC till L4 stage.

extract_protocol:
Animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01-01). Total RNA was obtained using the kit (Transgen, ER501-01) and 1 ug total RNA from each sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: L4 stage animals were collected and washed with M9 solution before being transferred to modified NGM plates containing OP50 or PA14 for 24 h at 25oC.

tag: developmental stage

value: P. aeruginosa (PA14)

value: L4 animal exposed for 24 h


title: Control_5_1

description: Library name: Control_5


title: Equal amount of DMSO incubated with RNA extract from E. Coli - copy 3

city: Nijmegen

first: Daphne

middle: Ai Lin

last: van den Homberg

address: Heyendaalseweg

department: Physical Organic Chemistry

country: Netherlands

institute: Radboud University

data_processing:
RNAFramework
Sequences were trimmed and mapped to ASM584v2_genomic.gff using RNAFrameworks rf-map using the default parameters
Read count was performed using featureCounts
Assembly: NC_000913.3
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Bacteria were cultured at 37 °C in liquid Luria Broth (LB) medium supplemented with 25 µM tetracycline until OD600=0.8. RNA was extracted afterwards. RNA was incubated with the probe or DMSO for photoaffinity labeling and downstream analysis

extract_protocol:
RNA was isolated after biotin-streptavidin bead pulldown using 50 mM DTT. Eluted RNA samples were cleaned up using RNA Clean and ConcentratorTM-5 (Zymo) and dissolved in nuclease-free water. 25 ng of RNA was used per sample for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the KAPA RNA Hyperprep kit following manufacturer's protocols

treatment_protocol: RNA was isolated from the bacteria. Isolated RNA was used to incubate TMP photoaffinity probe or DMSO in folding buffer at 37 oC for 30 min and irradiated with 365 nm light. RNA was isolated and a biotin handle was ligated to the RNA-probe complexes. RNA was isolated, Biotin-Streptavidin bead enrichments were performed and next-generation RNA library preparation and sequencing were performed.

value: bacterial cell

value: LAM-; rpoS396(Am); tolC6::mini-Tn10; rph-1

value: control


title: Equal amount of DMSO incubated with RNA extract from E. Coli - copy 2


title: PY65928_01

value: Unmodified


title: AS-250544-LR-36069

description:
Library name: M_25
TIS_high


title: TMP photoaffinity probe incubated with RNA extract from E. Coli - copy 3

value: TMP photoaffinity probe


title: PY60276_11


title: AS-250543-LR-36069

description:
Library name: M_24
TIS_low

value: tr


title: Equal amount of DMSO incubated with RNA extract from E. Coli - copy 1


title: L4 stage animals, u49, PA, 1


title: Control_6

description: Library name: Control_6

value: tumor

value: TNBC


title: AS-250542-LR-36069

description:
Library name: M_23
TIS_low

value: Blood

value: AML blasts


title: TMP photoaffinity probe incubated with RNA extract from E. Coli - copy 2


title: PY60275_10

value: Primary Human NK Cells


title: PY60274_09


title: AS-250541-LR-36068

description:
Library name: M_18
TIS_low


title: L4 stage animals, u49, OP, 2


title: TMP photoaffinity probe incubated with RNA extract from E. Coli-copy 1


title: AS-250540-LR-36068

description:
Library name: M_17
TIS_low


title: PY60273_08


title: PY60272_07


title: PY60271_06

value: TIGITKO


title: PGC, dRNA-ONT

first: Kin Fai

last: Au

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

description: Direct RNA sequencing (SQK-DCS109 Kit) for Library prepration; R9.4.1 flow cell for sequencing

data_processing:
For ONT long-read RNA-seq, only the long reads with a quality score (qscore ≥7, passed reads) are used for our study, and these passed reads are uploaded to NCBI GEO.  For Illumina short-read RNA-seq, sequencing adapters are trimmed by Cutadapt (v1.8.1)  with the parameter “-q 20,20 -m 20 --max-n 0.01 --trim-n”.
For identification of gene isoforms, based on the hg38 reference genome and GENCODE annotation (v39), IsoQuant (v3.3.0) is run with the parameter “-d nanopore” for cDNA-ONT data merged from ESC, PE and PGC; and with the parameter “-d nanopore --stranded forward” for dRNA-ONT data merged from ESC, PE and PGC. For each of three samples (ESC, PE and PGC), two sets of gene annotations are derived from IsoQuant using cDNA-ONT and dRNA-ONT data.
To estimate the abundance of these gene isoforms, for each of three samples (ESC, PE, PGC), miniQuant (v1.0.0) is run separately with the two sets of gene annotations (constructed by IsoQuant) and the two dataset combinations: (1) cDNA-ONT derived annotation and cDNA-ONT plus Illumina data, with the parameter "--pretrained_model_path cDNA-ONT --EM_choice hybrid"; (2) dRNA-ONT derived annotation and dRNA-ONT plus Illumina data, with the parameter "--pretrained_model_path dRNA-ONT --EM_choice hybrid". Of note, for each sample, the Illumina data are combined from three replicates when running miniQuant.
For Illumina RNA-seq data alone, for each of three replicates from ESC, ES, PE and PGC sample, we estimate the expression abundance using Kallisto (v0.46.1) with the default parameter, based on GENECODE annotation (v39).
Assembly: hg38
Supplementary files format and content: GTF format files included the gene isoforms identified by IsoQuant from ESC, PE and PGC samples, using cDNA-ONT and dRNA-ONT data, respectively.
Supplementary files format and content: Tab-delimited text files included the expression value (Transcripts per million, TPM) of gene isoforms quantified by Kallisto for each replicate of ESC, DE, PE and PGC samples, using Illumina data.
Supplementary files format and content: Tab-delimited text files included the expression value (Transcripts per million, TPM) of gene isoforms quantified by miniQuant for ESC, PE and PGC samples, using cDNA-ONT plus Illumina data and dRNA-ONT plus Illumina data, respectively.

molecule: polyA RNA

source_name: H1-hESC derived primordial germ cell-like cells

growth_protocol: Definitive endoderm (DE) and pharyngeal endoderm (PE), and primordial germ cell-like cells (PGC) (reference: PMID: 37709760) are differentiated from human ESC (H1-hESC cell line), respectively. See the details in the manuscripts: (1)  DOI: https://doi.org/10.1101/2022.06.26.497457 (from ESC to DE and PE); and (2) PMID: 37709760 (from ESC to PGC).

extract_protocol:
Total RNA is extracted by TRIzol Reagent (Thermo Fisher Scientific), followed by polyA+ RNA enrichment using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific).
For ESC, PE and PGC, ONT sequencing libraries are prepared using the SQK-PCS109 Kit for PCR-cDNA sequencing (cDNA-ONT), and the SQK-DCS109 Kit for direct RNA sequencing (dRNA-ONT). ONT sequencing is conducted using MiniON/GridION flow cells with R9.4.1 chemistry, with real-time base calling performed by the Guppy software. For ESC, DE, PE and PGC, the library preparation and sequencing of Illumina RNA-seq data are conducted by Novogene company.


title: AS-250539-LR-36068

description:
Library name: M_16
TIS_high


title: AS-250538-LR-36068

description:
Library name: M_15
TIS_high

value: nt


title: L4 stage animals, u49, PA, 2


title: L4 stage animals, WT, PA, 3

value: wild-type (N2)


title: L4 stage animals, u49, OP, 1


title: PY60270_05

value: Before


title: L4 stage animals, u49, OP, 3


title: PE, dRNA-ONT

source_name: H1-hESC derived pharyngeal endoderm

value: H1-hESC derived pharyngeal endoderm


title: PY60269_04


title: AS-250537-LR-36068

description:
Library name: M_8
TIS_high


title: AS-250535-LR-36067

description:
Library name: M_3
TIS_low


title: ESC, dRNA-ONT

value: human embryonic stem cells


title: L4 stage animals, WT, PA, 1

value: P. aeruginosa (PA14)

value: L4 animal exposed for 24 h


title: PY60267_02


title: PY60266_01


title: AS-250536-LR-36067

description:
Library name: M_7
TIS_high


title: L4 stage animals, WT, OP, 3

value: control


title: PE, cDNA-ONT

description: PCR-cDNA sequencing (SQK-PCS109 Kit) for Library prepration; R9.4.1 flow cell for sequencing


title: L4 stage animals, WT, OP, 2


title: PY60268_03

value: Unmodified


title: H660 DOX_negative_3

status: Public on Feb 16 2025

city: Boston

first: Keisuke

last: Shigeta

state: MA

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

description: Library name: Sample 3

data_processing:
RNA-seq
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: prostate

growth_protocol: H660 cells were maintained in Gibco RPMI 1640 Media containing 10% heat inactivated FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: prostate

value: prostate cancer

value: total RNA

value: wild-type


title: L4 stage animals, WT, OP, 1


title: AS-250534-LR-36067

description:
Library name: M_4
TIS_low

value: Blood

value: tr


title: ZC3H12A/N4BP1, M003.1, replicate 3

city: Berkeley

first: Brenna

middle: C

last: Remick

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Library name: BRRV30
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_M003_rep3

data_processing:
Sequencing quality of fastq files was evaluated with FastQC, and adaptors were trimmed using Cutadapt (1.18).
Paired end RNA-seq reads were aligned to the reference genome (GRCh38) using STAR (2.7.1a).
Fragment counts were quantified using featureCounts from the Subread (2.0.3) package. (featureCounts -p --countReadPairs -B)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: BLaER1 cells were cultured in RPMI 1640 medium (Gibco) supplemented with L-glutamine, sodium pyruvate, 100 U/ml penicillin-streptomycin, and 10% (v/v) FBS (Gibco).

extract_protocol:
RNA was isolated using the Omega Biotek Total RNA Kit I according to the manufacturer’s instructions. DNA was removed with TURBO DNase (Invitogen) in the presence of RNasin Plus Ribonuclease Inhibitor (Promega), and RNA was isolated with RNAClean XP beads (Beckman Coulter).
NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Polyclonal gene-deficient BLaER1 cells were made by nucleofecting cells with Cas9 and two gRNAs targeting the indicated gene. 1.4 million BLaER1 B cells were transdifferentiated into monocytes for 5 days in RPMI medium containing 10 ng/ml of human recombinant (hr) IL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech), and 100 nM β-Estradiol (Sigma-Aldrich). BLaER1 monocytes were treated with 1 µg/ml doxycycline hyclate (Sigma-Aldrich) for 24 hours to induce expression of either mCherry or myxoma virus M003.1.

value: monocyte

value: gRNA:ZC3H12A/N4BP1 expressing doxycycline-inducible M003.1

value: doxycycline, 24 hours


title: ESC, cDNA-ONT


title: H660 DOX_positive_2

description: Library name: Sample 5


title: H660 DOX_positive_1

description: Library name: Sample 4


title: H660 DOX_positive_3

description: Library name: Sample 6


title: PGC, cDNA-ONT

value: H1-hESC derived primordial germ cell-like cells


title: TRIM25, mCherry, replicate 3

description:
Library name: BRRV27
column name in raw_feature_counts2.txt: TRIM25_cherry_rep3

value: gRNA:TRIM25 expressing doxycycline-inducible mCherry


title: ZC3H12A/N4BP1, mCherry, replicate 3

description:
Library name: BRRV29
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_cherry_rep3

value: gRNA:ZC3H12A/N4BP1 expressing doxycycline-inducible mCherry


title: L4 stage animals, WT, PA, 2

value: wild-type (N2)


title: N4BP1, mCherry, replicate 3

description:
Library name: BRRV23
column name in raw_feature_counts2.txt: N4BP1_cherry_rep3

value: gRNA:N4BP1 expressing doxycycline-inducible mCherry


title: H660 DOX_negative_2

description: Library name: Sample 2


title: NTC, M003.1, replicate 3

description:
Library name: BRRV22
column name in raw_feature_counts2.txt: NTC_M003_rep3

value: gRNA:NTC expressing doxycycline-inducible M003.1


title: ZC3H12A, mCherry, replicate 3

description:
Library name: BRRV25
column name in raw_feature_counts2.txt: ZC3H12A_cherry_rep3

value: gRNA:ZC3H12A expressing doxycycline-inducible mCherry


title: ZC3H12A, M003.1, replicate 3

description:
Library name: BRRV26
column name in raw_feature_counts2.txt: ZC3H12A_M003_rep3

value: gRNA:ZC3H12A expressing doxycycline-inducible M003.1


title: TRIM25, M003.1, replicate 3

description:
Library name: BRRV28
column name in raw_feature_counts2.txt: TRIM25_M003_rep3

value: gRNA:TRIM25 expressing doxycycline-inducible M003.1


title: ZC3H12A/N4BP1, M003.1, replicate 2

description:
Library name: BRRV20
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_M003_rep2


title: NTC, mCherry, replicate 3

description:
Library name: BRRV21
column name in raw_feature_counts2.txt: NTC_cherry_rep3

value: gRNA:NTC expressing doxycycline-inducible mCherry


title: N4BP1, M003.1, replicate 3

description:
Library name: BRRV24
column name in raw_feature_counts2.txt: N4BP1_M003_rep3

value: gRNA:N4BP1 expressing doxycycline-inducible M003.1


title: ZC3H12A/N4BP1, mCherry, replicate 2

description:
Library name: BRRV19
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_cherry_rep2


title: TRIM25, M003.1, replicate 2

description:
Library name: BRRV18
column name in raw_feature_counts2.txt: TRIM25_M003_rep2


title: ZC3H12A, mCherry, replicate 2

description:
Library name: BRRV15
column name in raw_feature_counts2.txt: ZC3H12A_cherry_rep2


title: ZC3H12A, M003.1, replicate 2

description:
Library name: BRRV16
column name in raw_feature_counts2.txt: ZC3H12A_M003_rep2


title: TRIM25, mCherry, replicate 2

description:
Library name: BRRV17
column name in raw_feature_counts2.txt: TRIM25_cherry_rep2


title: N4BP1, mCherry, replicate 2

description:
Library name: BRRV13
column name in raw_feature_counts2.txt: N4BP1_cherry_rep2


title: N4BP1, M003.1, replicate 2

description:
Library name: BRRV14
column name in raw_feature_counts2.txt: N4BP1_M003_rep2


title: H660 DOX_negative_1

description: Library name: Sample 1

value: prostate

value: prostate cancer

value: total RNA

value: wild-type


title: NTC, M003.1, replicate 2

description:
Library name: BRRV12
column name in raw_feature_counts2.txt: NTC_M003_rep2

value: monocyte


title: TRIM25, M003.1, replicate 1

description:
Library name: BRRV8
column name in raw_feature_counts2.txt: TRIM25_M003_rep1

value: doxycycline, 24 hours


title: N4BP1, mCherry, replicate 1

description:
Library name: BRRV3
column name in raw_feature_counts2.txt: N4BP1_cherry_rep1


title: NTC, mCherry, replicate 2

description:
Library name: BRRV11
column name in raw_feature_counts2.txt: NTC_cherry_rep2


title: M003.1, replicate 3

description:
Library name: Sample 6
column name in raw_feature_counts.txt: m3_rep3

data_processing:
Paired end RNA-seq reads were aligned to the reference genome (GRCh38) using STAR (2.7.1a).
Fragment counts were quantified using featureCounts from the Subread (2.0.3) package. (featureCounts -p --countReadPairs -B)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
RNA was isolated using the Omega Biotek Total RNA Kit I according to the manufacturer’s instructions. DNA was removed with TURBO DNase (Invitogen) in the presence of RNasin Plus Ribonuclease Inhibitor (Promega), and RNA was isolated with RNAClean XP beads (Beckman Coulter).
KAPA mRNA Hyper Prep kit (Roche KK8581)

treatment_protocol: 1.4 million BLaER1 B cells were transdifferentiated into monocytes for 5 days in RPMI medium containing 10 ng/ml of human recombinant (hr) IL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech), and 100 nM β-Estradiol (Sigma-Aldrich). BLaER1 monocytes were treated with 1 µg/ml doxycycline hyclate (Sigma-Aldrich) for 24 hours to induce expression of either mCherry or myxoma virus M003.1.

value: MYD88/TRIF knockout expressing doxycycline-inducible M003.1


title: ZC3H12A/N4BP1, M003.1, replicate 1

description:
Library name: BRRV10
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_M003_rep1

value: gRNA:ZC3H12A/N4BP1 expressing doxycycline-inducible M003.1


title: N4BP1, M003.1, replicate 1

description:
Library name: BRRV4
column name in raw_feature_counts2.txt: N4BP1_M003_rep1


title: mCherry, replicate 2

description:
Library name: Sample 3
column name in raw_feature_counts.txt: cherry_rep2

value: MYD88/TRIF knockout expressing doxycycline-inducible mCherry


title: M003.1, replicate 2

description:
Library name: Sample 4
column name in raw_feature_counts.txt: m3_rep2


title: mCherry, replicate 1

description:
Library name: Sample 1
column name in raw_feature_counts.txt: cherry_rep1


title: ZC3H12A, M003.1, replicate 1

description:
Library name: BRRV6
column name in raw_feature_counts2.txt: ZC3H12A_M003_rep1


title: NTC, M003.1, replicate 1

description:
Library name: BRRV2
column name in raw_feature_counts2.txt: NTC_M003_rep1


title: ZC3H12A, mCherry, replicate 1

description:
Library name: BRRV5
column name in raw_feature_counts2.txt: ZC3H12A_cherry_rep1


title: TRIM25, mCherry, replicate 1

description:
Library name: BRRV7
column name in raw_feature_counts2.txt: TRIM25_cherry_rep1

value: gRNA:TRIM25 expressing doxycycline-inducible mCherry


title: mCherry, replicate 3

description:
Library name: Sample 5
column name in raw_feature_counts.txt: cherry_rep3


title: M003.1, replicate 1

description:
Library name: Sample 2
column name in raw_feature_counts.txt: m3_rep1


title: NTC, mCherry, replicate 1

description:
Library name: BRRV1
column name in raw_feature_counts2.txt: NTC_cherry_rep1


title: 12Z p40, Control siRNA (Ambion #4390846) 72 hours, replicate B

first: Quanah

middle: J

last: Hudson

address: Währinger Gürtel 18-20

institute: Medical University of Vienna

description: Ribo-zero 2x50bp

data_processing:
FASTQ files were aligned with STAR (v2.7.10b) based an index from GRCh38 genome assembly and gencode v42 gene annotation. Read counts as prepared from STAR were used for downstream analyses in R (v4.2.1).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts aligned to ENSEMBL transcripts

growth_protocol: 12Z cells were maintained in DMEM-F12 with penicillin (50 U/mL), streptomycin (50 µg/mL) and 10% v/v fetal calf serum (FCS) in a humidified incubator at 37°C with 5% CO2

extract_protocol:
Qiagen RNeasy mini kit
RNA-seq libraries were prepared with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) and the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA).

treatment_protocol: cells were transfected with a siRNA using Lipofectamine RNAiMAX (Thermo Fisher Scientific) following the manufacturers protocol, and harvested after 72 hours of culture.

value: endometriosis epithelial cells

value: control siRNA


title: 12Z p40, LINC01638 siRNA (LINC01638_2) 72 hours, replicate A

description: Ribo-zero 2x50bp

value: LINC01638 siRNA


title: KOPN-8 Cas9 cells_sgZNF217 #2_rep 1

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
KOPN-8_sgZNF217_1164_rep1
genes.RSEM.counts.tsv
sgZNF217-1164_vs_sgScramble.DESeq2.txt

data_processing:
The reads were mapped to the human transcriptome built with genome sequences (hg38 version) and gene annotations (GENCODE v37) by STAR (v2.7.2b) software. The gene expressions were calculated by RSEM (v1.3.3) and quantified as expected count. The expected count matrixes were used as the input of DESeq2 (v1.32.0) package to calcualte the differential expressions (DE) of genes between different conditions.
Assembly: hg38
Supplementary files format and content: The TSV file contains the raw reads count from RSEM for genes in all samples
Supplementary files format and content: The txt file contains the results from DESeq2

source_name: peripheral blood

growth_protocol: Single-cloned KOPN-8 Cas9 cells transduced with sgRNA were cultivated in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 10 mM HEPES, 2.5 μg/ml Plasmocin prophylactic, 5 μg/ml blasticidin, and 1 μg/ml puromycin. The cells were maintained at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNAs were isolated from whole cells using QIAzol reagent (QIAGEN) and the miRNeasy Kit (QIAGEN).
The double-stranded cDNA libraries were constructed by Novogene Corporation Inc. (Sacramento, CA). In brief, mRNA was enriched from the RNA samples using oligo(dT) beads, then underwent random fragmentation, reverse transcription, second-strand synthesis, and sequencing adaptor ligation. The adaptors used were 5'-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3' (5' Adapter) and 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3' (3' Adapter).

treatment_protocol: Without special treatment

value: peripheral blood

value: B cell precursor


title: 12Z p40, Control siRNA (Ambion #4390846) 72 hours, replicate C

description: Ribo-zero 2x50bp


title: 12Z p40, LINC01638 siRNA (LINC01638_2) 72 hours, replicate B

description: Ribo-zero 2x50bp


title: 12Z p40, Control siRNA (Ambion #4390846) 72 hours, replicate A

description: Ribo-zero 2x50bp


title: KOPN-8 Cas9 cells_sgScramble_rep 2

description:
KOPN-8_sgScramble_rep2
genes.RSEM.counts.tsv


title: ZC3H12A/N4BP1, mCherry, replicate 1

description:
Library name: BRRV9
column name in raw_feature_counts2.txt: ZC3H12A_N4BP1_cherry_rep1

value: gRNA:ZC3H12A/N4BP1 expressing doxycycline-inducible mCherry


title: KOPN-8 Cas9 cells_sgScramble_rep 1

description:
KOPN-8_sgScramble_rep1
genes.RSEM.counts.tsv


title: KOPN-8_shZNF217_anti-H3K27ac_rep2

description:
KOPN8_znf217KD_H3K27ac.narrowPeak
KD_H3K27ac_round2

data_processing:
*library strategy: CUT&RUN
The CUT&RUN-seq reads in two replciates were merged and processed by CUT&RUNTools 2.0 with the following parameters: {fastq_sequence_length: 101, peak_caller: macs2, num_bp_from_summit: 100, frag_120: FALSE, num_peaks: 15000, total_peaks: 15000, num_motifs: 25, motif_scanning_pval: 0.01, meme_minw:5, meme_maxw: 10}.
After peak calling, we remove the non-specific binding background from the target peaks by exclude the peaks that intersecting with IgG peaks. Finally the peaks were annotated by gene annotations from GENCODE v37 (hg38) using in-house scripts.
Assembly: hg38
Supplementary files format and content: The narrowPeak files contains the binding or histone modification peaks in narrowPeak format

growth_protocol: KOPN-8 cells transduced with shRNA were cultivated in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 10 mM HEPES, 2.5 μg/ml Plasmocin prophylactic, and 1 μg/ml puromycin. The cells were maintained at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
The CUT&RUN-enriched DNAs were extracted from live cells (i.e., ZNF217 group, LSD1 group) and lightly cross-linked cells (i.e., H3K4me1 group, H3K4me2 group, and H3K27ac group) using the CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher), following the manufacturer's instructions.
For each sample, 10 ng of CUT&RUN-enriched DNA was used for library construction, employing the CUTANA CUT&RUN Library Prep Kit (14-1002, EpiCypher). Index primers used included CUTANA_i501, CUTANA_i502, CUTANA_i503, CUTANA_i504, CUTANA_i505, CUTANA_i506, CUTANA_i707, and CUTANA_i708.

treatment_protocol: In the ZNF217 and LSD1 groups, live cells were used, while in the H3K4me1, H3K4me2, and H3K27ac groups, cells were lightly cross-linked with 0.1% formaldehyde for 1 minute.

tag: cut&run antibody

value: H3K27ac (Active Motif, #39034)


title: KOPN-8_shZNF217_anti-H3K4me2_rep2

description:
KOPN8_znf217KD_H3K4me2.narrowPeak
KD_H3K4me2_round2

tag: cell line

value: H3K4me2 (Active Motif, #9725T)


title: KOPN-8 Cas9 cells_sgZNF217 #1_rep 2

description:
KOPN-8_sgZNF217_833_rep2
genes.RSEM.counts.tsv
sgZNF217-833_vs_sgScramble.DESeq2.txt

tag: cell type


title: KOPN-8_shZNF217_anti-H3K4me1_rep1

description:
KOPN8_znf217KD_H3K4me1.narrowPeak
KD_H3K4me1_round1

value: H3K4me1 (Active Motif, #5326T)


title: KOPN-8_shZNF217_anti-IgG_rep2


title: KOPN-8_shZNF217_anti-LSD1_rep1

description:
KOPN8_znf217KD_LSD1.narrowPeak
KD_LSD1_round1

value: LSD1 (Cell Signaling Technology, #2139S)


title: KOPN-8_shZNF217_anti-H3K4me2_rep1

description:
KOPN8_znf217KD_H3K4me2.narrowPeak
KD_H3K4me2_round1


title: KOPN-8_shZNF217_anti-H3K27ac_rep1

description:
KOPN8_znf217KD_H3K27ac.narrowPeak
KD_H3K27ac_round1


title: KOPN-8_shZNF217_anti-H3K4me1_rep2

description:
KOPN8_znf217KD_H3K4me1.narrowPeak
KD_H3K4me1_round2


title: KOPN-8_shScramble_anti-H3K4me2_rep2

description:
KOPN8_WT_H3K4me2.narrowPeak
WT_H3K4me2_round2

value: wild-type


title: 12Z p40, LINC01638 siRNA (LINC01638_2) 72 hours, replicate C

description: Ribo-zero 2x50bp


title: KOPN-8_shZNF217_anti-IgG_rep1


title: KOPN-8_shZNF217_anti-LSD1_rep2

description:
KOPN8_znf217KD_LSD1.narrowPeak
KD_LSD1_round2


title: KOPN-8_shScramble_anti-H3K4me1_rep2

description:
KOPN8_WT_H3K4me1.narrowPeak
WT_H3K4me1_round2


title: KOPN-8_shZNF217_anti-ZNF217_rep1

description:
KOPN8_znf217KD_ZNF217.narrowPeak
KD_ZNF217_round1

value: ZNF217 (Thermo Fisher Scientific, #A303-265A)


title: KOPN-8_shScramble_anti-H3K27ac_rep1

description:
KOPN8_WT_H3K27ac.narrowPeak
WT_H3K27ac_round1


title: KOPN-8 Cas9 cells_sgZNF217 #2_rep 2

description:
KOPN-8_sgZNF217_1164_rep2
genes.RSEM.counts.tsv
sgZNF217-1164_vs_sgScramble.DESeq2.txt


title: KOPN-8_shScramble_anti-H3K4me1_rep1

description:
KOPN8_WT_H3K4me1.narrowPeak
WT_H3K4me1_round1


title: KOPN-8_shScramble_anti-IgG_rep1


title: KOPN-8_shScramble_anti-ZNF217_rep2

description:
KOPN8_WT_ZNF217.narrowPeak
WT_ZNF217_round2


title: KOPN-8_shScramble_anti-ZNF217_rep1

description:
KOPN8_WT_ZNF217.narrowPeak
WT_ZNF217_round1


title: KOPN-8_shZNF217_anti-ZNF217_rep2

description:
KOPN8_znf217KD_ZNF217.narrowPeak
KD_ZNF217_round2


title: 293T, DIS3-sh2+D146N, fraction 8, rep2

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Pair-end RNA-seq reads were firstly trimmed by Trimmomatics (v0.32, parameters: PE -threads 5 -phred33 ILLUMINACLIP:TruSeq3PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) to remove adaptors and low quality bases.
the reads were mapped to the hg38 rDNA sequences (5S, 5.8S,18S, 28S) by Bowtie2 (version 2.3.5, parameters: -p 10 --score-min L,-16,0 --rfg 0,7 --rdg 0,7 --mp 7,7) to remove reads from ribosomal RNAs. Then, the rest reads were uniquely mapped to the human hg38 reference genome with HISAT2 (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 --dta -k 1)
The HISAT2 generated SAM files were then converted to BAM files by samtools.
Fragment counts of genes were obtained using featureCounts (version 1.5.1, parameters: -s 2 -p --fraction -O -T 16 -t exon -g gene_id) based on GENCODE v4 gene annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene read counts for samples

molecule: cytoplasmic RNA

extract_protocol:
RNA from fractions in sucrose density gradient centrifugation assay were extracted using TRIzol reagent (Invitrogen), and then used for the construction of  sequencing library.
RNAs in each fraction were processed with KAPA RiboErase Kit (HMR) (KR1142) to deplete most ribosomal RNAs. Then, the ribo– RNA libraries for sequencing were prepared with KAPA RNA HyperPrep Kit (KR1350). These libraries were sequenced with NovaSeq 6000 at Sequanta Technologies, Shanghai, China.FastQC was applied for raw read qualities assessment.
ribo- RNA-seq

value: DIS3 konckdown + DIS3 D146N rescue

value: DIS3-sh2 + DIS3 D146N rescue


title: 293T, DIS3-sh2+D146N, fraction 8, rep1


title: KOPN-8 Cas9 cells_sgZNF217 #1_rep 1

description:
KOPN-8_sgZNF217_833_rep1
genes.RSEM.counts.tsv
sgZNF217-833_vs_sgScramble.DESeq2.txt


title: 293T, DIS3-sh2+D146N, fraction 8, rep3


title: 293T, DIS3-sh2+D146N, fraction 7, rep3


title: KOPN-8_shScramble_anti-H3K4me2_rep1

description:
KOPN8_WT_H3K4me2.narrowPeak
WT_H3K4me2_round1


title: KOPN-8_shScramble_anti-LSD1_rep2

description:
KOPN8_WT_LSD1.narrowPeak
WT_LSD1_round2


title: KOPN-8_shScramble_anti-LSD1_rep1

description:
KOPN8_WT_LSD1.narrowPeak
WT_LSD1_round1


title: 293T, DIS3-sh2+D146N, fraction 7, rep2


title: 293T, DIS3-sh2+D146N, fraction 4, rep1


title: 293T, DIS3-sh2+D146N, fraction 4, rep3


title: 293T, DIS3-sh2+D146N, fraction 4, rep2


title: 293T, DIS3-sh2+D146N, fraction 3, rep2


title: KOPN-8_shScramble_anti-IgG_rep2


title: 293T, DIS3-sh2+D146N, fraction 3, rep3


title: KOPN-8_shScramble_anti-H3K27ac_rep2

description:
KOPN8_WT_H3K27ac.narrowPeak
WT_H3K27ac_round2


title: 293T, DIS3-sh2+D146N, fraction 3, rep1


title: 293T, DIS3-sh2+DIS3 WT, fraction 7, rep3

value: DIS3 konckdown + DIS3 WT rescue

value: DIS3-sh2 + DIS3 WT rescue


title: 293T, DIS3-sh2+DIS3 WT, fraction 8, rep1


title: 293T, DIS3-sh2+DIS3 WT, fraction 8, rep2


title: 293T, DIS3-sh2+DIS3 WT, fraction 7, rep1


title: 293T, DIS3-sh2+DIS3 WT, fraction 8, rep3


title: 293T, DIS3-sh2+DIS3 WT, fraction 7, rep2


title: 293T, DIS3-sh2+DIS3 WT, fraction 4, rep3


title: 293T, DIS3-sh2+DIS3 WT, fraction 4, rep1


title: 293T, DIS3-sh2+DIS3 WT, fraction 3, rep3


title: 293T, DIS3-sh2+DIS3 WT, fraction 3, rep1


title: 293T, DIS3-sh2, rep1

extract_protocol:
Total RNA from cells was extracted using TRIzol reagent (Invitrogen), 1 ug of total RNA was used for the construction of  sequencing library.
Total RNAs were processed with RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete most ribosomal RNAs. Then, the ribo– RNA libraries for sequencing were prepared with illumina TruSeq® Stranded Total RNA Library Prep Gold (20020598) kit. These libraries were sequenced with X-ten at GENEWIZ, Suzhou, China. FastQC was applied for raw read qualities assessment.

value: DIS3 konckdown

value: DIS3-sh2 shRNA


title: 293T, DIS3-sh2, rep3


title: 293T, DIS3-sh1, rep2

value: DIS3-sh1 shRNA


title: 293T, DIS3-sh1, rep3


title: 293T, DIS3-sh1, rep1


title: 293T, DIS3-sh2+D146N, fraction 7, rep1


title: 293T, Scramble, rep3

value: WT

value: Scramble shRNA


title: 293T, Scramble, rep2


title: KMS34, ambroxol 200 mM for 24 hours

first: Yutaka

last: Hattori

state: Japan

address: 1-5-30 Shiba-koen, Minato-ku

institute: Keio University, Faculty of Pharmacy

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic-039.
Trimmed sequence reads were mapped to Human hg38 using STAR ver.2.7.9a and StrandNGS 4.0.
Raw read counts were normalized to TPM.
Assembly: Human hg38, Annotation information was obtained from Ensemble Genes (2016.12.01).
Supplementary files format and content: TPM-Ensemble excel file includes raw read counts and TPM values for each sample.

source_name: plasma cell

extract_protocol:
Total RNA was isolated by RNeasy Plus Mini Kit (QIAGEN).
Truseq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).

value: multiple myeloma

value: treated with ambroxol


title: KMS21 cells, ambroxol 200 mM for 24 hours


title: 293T, DIS3-sh2+DIS3 WT, fraction 4, rep2


title: LPTC-2, replicate 1, scRNAseq

first: Yu

last: Zeng

address: Fangsong Street

institute: Shanghai Jiaotong University

description: 10x Genomics

data_processing:
The raw ST sequencing reads were mapped to the human reference genome (hg38) using Space Ranger (version 1.3.1). Raw scRNA-seq reads were processed by the Cell Ranger software (version 3.1.0) for sample demultiplexing, barcode processing, and genome mapping.
Low-quality cells were detected and removed as described in previous studies
Cells were also filtered out as low-quality cells if mitochondrial gene proportions are larger than the median value of all cells minus three times of median absolute deviation
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files and 10X visium image files

source_name: Thyroid

extract_protocol:
Fresh surgical specimens were delivered within MACS Tissue Storage Solution, and were frozen in optimum cutting temperature (OCT) compound. OCT-embedden specimens were cut to 10 μm thickness cryosections and then were layered in the Visium Spatial Gene Expression Slide  includes 4 capture areas (6.5*6.5 mm2). The slides were fixed, stained, and then permeabilized for different times. After the optimal conditions was established, the slides were processed immediately. Primer spots were stained by hybridization of fluorescently labeled probes and imaged on by Leica SCN400. The resulting spot image was loaded into Spaceranger to generate spatial feature counts for a single library from fresh frozen sample using automatic fiducial alignment and tissue detection on a brightfield image input. The images were aligned and the Spaceranger will extract spots covered by tissue automatic. Tissue sections on the Visium Slide were processed in the optimal staining procedure by fixing in methanol for 30 min at -20°C, staining in isopropanol for 1 min, in Hematoxylin for 7 min, in Bluing Buffer for 2 min and in Eosin Mix for 1 min at room temperature. Lastly, slides were incubated for 5 min at 37°C in the Thermocycler Adaptor. The slides were washed in ultrapure water after each staining step. Then, the stained tissue sections are imaged. For tissue permeabilization, the slides were first placed in the Slide Cassette. Permeabilization Enzyme was used to permeabilize the tissue sections for 12min. Wells were then washed with 0.1*SSC.
Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification. Library construction was performed with Library Construction Kit. A Visium Spatial Gene Expression library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The 16 bp Spatial Barcode and 12 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. i7 and i5 sample index sequences are incorporated. TruSeq Read 1 and TruSeq Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing.

value: total cell

value: Thyroid

tag: Stage

value: Locally advanced papillary thyroid carcinoma

tag: time point

value: 0 week


title: PTC-4, replicate 3, scRNAseq

description: 10x Genomics

value: Papillary thyroid carcinoma


title: PTC-3, replicate 2, scRNAseq

description: 10x Genomics


title: KMS21, no treatment

value: untreated


title: N-4, replicate 3, scRNAseq

description: 10x Genomics

value: Normal


title: N-3, replicate 2, scRNAseq

description: 10x Genomics


title: PTC-2, replicate 1, scRNAseq

description: 10x Genomics


title: LPTC-4, replicate 3, scRNAseq

description: 10x Genomics


title: 293T, DIS3-sh2+DIS3 WT, fraction 3, rep2


title: N-2, replicate 1, scRNAseq

description: 10x Genomics


title: ATC-4, replicate 4, 10X visium

description: 10x Genomics

data_processing:
library strategy: spatial transcriptome
The raw ST sequencing reads were mapped to the human reference genome (hg38) using Space Ranger (version 1.3.1). Raw scRNA-seq reads were processed by the Cell Ranger software (version 3.1.0) for sample demultiplexing, barcode processing, and genome mapping.
Low-quality cells were detected and removed as described in previous studies
Cells were also filtered out as low-quality cells if mitochondrial gene proportions are larger than the median value of all cells minus three times of median absolute deviation
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files and 10X visium image files

value: Anaplastic thyroid cancer


title: ATC-3, replicate 3, 10X visium

description: 10x Genomics


title: LPTC-3, replicate 2, scRNAseq

description: 10x Genomics


title: 293T, DIS3-sh2, rep2


title: ATC-2, replicate 2, 10X visium

description: 10x Genomics


title: ATC-1, replicate 1, 10X visium

description: 10x Genomics


title: LPTC-2, replicate 2, 10X visium

description: 10x Genomics


title: PTC-4, replicate 4, 10X visium

description: 10x Genomics


title: LPTC-1, replicate 1, 10X visium

description: 10x Genomics


title: LPTC-3, replicate 3, 10X visium

description: 10x Genomics


title: PTC-3, replicate 3, 10X visium

description: 10x Genomics


title: KMS34, no treatment


title: PTC-2, replicate 2, 10X visium

description: 10x Genomics


title: 293T, Scramble, rep1


title: PTC-1, replicate 1, 10X visium

description: 10x Genomics


title: PBa3D10

city: Victoria

first: Dawei

last: Ma

state: BC

address: 3800 Finnerty Road

department: Biology

country: Canada

institute: University of Victoria

description: Library name: PBa3D10

data_processing:
The alignment of sequence was performed using HISAT2 (version 2.1.0). A P. trichocarpa genome sequence (version 4.1) was used as reference genome (Sjödin et al., 2009; https://phytozome-next.jgi.doe.gov).
Cufflinks and Cuffmerge (version 2.2.1.OSX_x86_64) were used to generate a reference transcriptome and use a Populus trichocarpa transcriptome as reference (https://phytozome-next.jgi.doe.gov).
Htseq-count (version 0.6.1) was used to calculate the raw count. DESeq package in R (version 3.4.0) was used to perform the differential expression analysis.
Assembly: Phytozome Populus trichocarpa v4.1
Supplementary files format and content: raw count in csv files

organism: Populus balsamifera

source_name: bud break lateral leaf buds

growth_protocol: The twigs were placed in water in a growth chamber at 22 °C under 16 h of light and sampled at 2 d intervals.

extract_protocol:
Total RNA was extracted from frozen ground leaf bud powder using the modified cetyl trimethyl ammonium bromide method for polyphenol-rich plant tissue described by Muoki et al. (2012).
MagJET enrichment kit (ThermoScientific) was used to purify mRNA from crude RNA. The mRNA was fragmented by heating the samples at 94℃ for 5 minutes. To make cDNA libraries with adaptors NEBNext ultra RNA Library Prep Kit for Illumina (NEB) was used. GeneJET NGS Cleanup Kit (ThermoScientific) was used to clean the extra adaptors.  Primers for RNA-Seq were added to cDNA using NEBNext Multiplex Oligo kit (NEB). MagJET NGS Cleanup and Size Selection kit (ThermoScientific) was used to select DNA fragments around 350bp. Twelve libraries with same concentration (250 ng/ul) each were pooled and sent to University of British Columbia Sequencing and Bioinformatics Consortium (Vancouver, BC, Canada).

treatment_protocol: For each time point, leaf buds were collected from one individual cutting as a replicate to prevent wound-induced effects during the time course. Samples were collected from three replicates of P. balsamifera and two replicates of P. trichocarpa. Each sampling consisted of 10 leaf buds, and samples were collected over 12 d. Samples collected at day 0 (D0), day 4 (D4), and day 10 (D10) were selected to represent dormant, pre-bud break, and bud break phases of the lateral leaf buds, respectively.

value: bud break lateral leaf buds

value: growth chamber


title: PBa2D10

description: Library name: PBa2D10


title: N-4, replicate 4, 10X visium

description: 10x Genomics


title: PBa1D10

description: Library name: PBa1D10


title: PBa2D4

description: Library name: PBa2D4

source_name: pre-bud break lateral leaf buds

value: pre-bud break lateral leaf buds


title: PBa3D0

description: Library name: PBa3D0

source_name: dormant lateral leaf buds

value: dormant lateral leaf buds


title: N-1, replicate 1, 10X visium

description: 10x Genomics


title: 22Rv1 Normoxia Zota RNA biol rep 3

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

description: Library name: Sample12

data_processing:
Salmon quant using default parameters was used to quantify paired-end RNA-Seq reads.
Reads were imported into DESeq using tximport. Raw read counts were extracted at this step.
Pairwise comparisons were performed using default DESeq2 parameters.
Assembly: hg38
Supplementary files format and content: csv file with raw counts for each sample
Supplementary files format and content: xlsx file with DESeq2 output from pairwise compairsons corresponding to supplemental table from paper

growth_protocol: 22Rv1 cells were seeded in triplicates in a 6-well plate, and one set was incubated in normoxia and the other in hypoxia (1% oxygen) overnight.

extract_protocol:
Cells were harvested by trypsinization and RNA was isolated by Trizol.
Libraries were prepared using the Takara Smarter Stranded Total RNA-Seq kit per the manufacturer’s protocol.

treatment_protocol: 24h post-seeding, cells were treated with 10nM Zotatifin for 24 hours.

value: Normoxia

value: Zotatifin


title: PBa3D4

description: Library name: PBa3D4


title: PBa2D0

description: Library name: PBa2D0


title: N-3, replicate 3, 10X visium

description: 10x Genomics


title: PBa1D0

description: Library name: PBa1D0


title: N-2, replicate 2, 10X visium

description: 10x Genomics


title: 22Rv1 Normoxia Vehicle RNA biol rep 3

description: Library name: Sample9


title: 22Rv1 Normoxia Zota RNA biol rep 2

description: Library name: Sample11


title: 22Rv1 Normoxia Zota RNA biol rep 1

description: Library name: Sample10


title: 22Rv1 Normoxia Vehicle RNA biol rep 2

description: Library name: Sample8


title: LPTC-4, replicate 4, 10X visium

description: 10x Genomics


title: PTr2D10

description: Library name: PTr2D10

organism: Populus trichocarpa


title: PTr1D10

description: Library name: PTr1D10


title: 22Rv1 Normoxia Vehicle RNA biol rep 1

description: Library name: Sample7


title: PTr2D4

description: Library name: PTr2D4


title: PTr1D4

description: Library name: PTr1D4


title: 22Rv1 Hypoxia Zota RNA biol rep 2

description: Library name: Sample5

value: Hypoxia


title: 22Rv1 Hypoxia Zota RNA biol rep 3

description: Library name: Sample6


title: 22Rv1 Hypoxia Zota RNA biol rep 1

description: Library name: Sample4


title: 22Rv1 Hypoxia Vehicle RNA biol rep 3

description: Library name: Sample3


title: PTr2D0

description: Library name: PTr2D0


title: PTr1D0

description: Library name: PTr1D0


title: 22Rv1 Hypoxia Vehicle RNA biol rep 1

description: Library name: Sample1


title: Cat_#3_ConA

city: Ube

first: Yoichi

last: Mizukami

institute: Yamaguchi　University

data_processing:
FASTQ files produced by Illumina NovaSeq 6000 were imported to CLC Genomics Workbench software (ver.22.0.1).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with low quality scores were removed using CLC Genomics Workbench software (ver.22.0.1).
The reads were trimmed and mapped to the feline reference genome (felCat9) by using the CLC Genomics Workbench ver. 22.0.1.
Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.22.0.1).
Assembly: felCat9
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

organism: Felis catus

source_name: peripheral blood lymphocytes

extract_protocol:
Total RNA was isolated from the melanoma cells using the RNeasy Plus Universal Kit  (QIAGEN). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Tapestation 4200 D1000 (Agilent). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NovaSeq 6000 with 50 bp paired-end cycle sequencing kit (Illumina).

value: peripheral blood lymphocytes

value: ConA


title: chk1chk2-cpt-1

city: beijing

first: Yulin

state: Beijing

address: Institute of Microbiology

institute: University of Chinese Academy of Sciences

data_processing:
FastQC v0.11.5
trimmomatic v0.39
Hisat2 v2.1.0
Stringtie v1.3.3
DEseq2 v1.16.1
Assembly: Neurospora crassa OR74A
Supplementary files format and content: tpm TPM of all strains

organism: Neurospora crassa

extract_protocol:
The purity of the sample was determined by NanoPhotometer ® (IMPLEN, CA, USA)；The concentration and integrity of RNA samples were detected by Agilent 2100 RNA nano 6000 assay kit (Agilent Technologies, CA, USA).
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02) (Annoroad Gene Technology Co., Ltd, Beijing)  following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: chk1chk2 knockout

value: 2% glucose with 0.2ug/mL CPT at 25C , DD18


title: 5xFAD, Microglia, PKR KO, rep4

description: Library name: Sample13

data_processing:
Pair-end RNA-seq reads were firstly trimmed by Trimmomatics (v0.32, parameters: PE -threads 5 -phred33 ILLUMINACLIP:TruSeq3PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) to remove adaptors and low quality bases.
The reads were mapped to the mm10 rDNA sequences for rRNAs (5S, 5.8S,18S, 28S) and pre-rRNAs (45S) to remove reads from ribosomal RNA by Bowtie2 (version: 2.3.5, parameters: -p 10 --score-min L,-16,0 --rfg 0,7 --rdg 0,7 --mp 7,7) and the rest paired reads were then mapped to the mouse mm10 genome reference with HISAT2 (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 --dta -k 1)
Fragment counts of genes were obtained using featureCounts (v1.5.1, parameters: -s 2 -p --fraction -O -T 16 -t exon -g gene_id) based on gencode vM25 gene annotation and normalized to FPKM (fragments per kilobase of gene per million fragments mapped)
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized gene expression values (FPKM) for samples

source_name: Microglia

extract_protocol:
Total RNA from tissues was extracted using TRIzol reagent (Invitrogen), 1 ug of total RNA was used for the construction of  sequencing library.
Total RNAs were processed with RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete most ribosomal RNAs (ribo- RNA). The ribo- RNA libraries for sequencing were prepared with illumina TruSeq® Stranded Total RNA Library Prep Gold (#20020598) kit. All libraries were sequenced with NovaSeq 6000 system at Sequanta Technologies. FastQC was applied for raw read qualities assessment.

value: Microglia

value: 5xFAD; PKR KO

value: PKR KO


title: wt-cpt-2

value: WT


title: Cat_#3_ALA

value: ALA


title: Cat_#3_Control

value: Control


title: 5xFAD, Microglia, PKR KO, rep3

description: Library name: Sample12


title: PBa1D4

description: Library name: PBa1D4


title: 22Rv1 RPS5 5UTR DMS Zota biol rep 2

description: Library name: Sample32

data_processing:
Reads were trimmed using trim galore (default parameters), and then aligned to the reference 5’UTR sequence using bowtie, using the parameters -local --no-unal --no-discordant --no-mixed -X 1000 -L 12.
Bam files were then input into the perl-based rnaframework toolkit (v2.8.9).Mutations were counted using rf-count -m and normalized using rf-norm (parameters -sm 4 -nm 2 -rb AC -nf float,float) with experiment-wide normalization factors obtained from rf-normfactor (parameters -sm 4 -nm 2 -rb AC).
Normalized replicate xml files were combined using rf-combine.
Structural prediction was done using rf-fold with parameters -g -ct --folding-method 2 -dp. Predicted secondary structures were compared using rf-compare.
Assembly: hg38
Supplementary files format and content: xlsx files with normalized per-condition and delta bp reactivities for endogenous AR, HIF1a, and control transcripts (DNAJA1, APEX1, RPS5) corresponding to supplemental tables from paper
Library strategy: DMS MaPSeq

growth_protocol: 22Rv1 cells were cultured in RPMI 1640 medium supplemented with 10% Fetal Bovine serum and Penicillin/Streptomycin (GIBCO).

extract_protocol:
Cells were resuspended in 2.8ml RPMI media, mixed with 800ul warm 1M bicine (pH 8.57 at room temperature) buffer followed by 400ul 16% DMS diluted in EtOH to have a final 1.6% DMS concentration in the fume hood. Cells were then incubated in a 37 ˚C water bath for 5 min, and DMS was quenched by adding 2 ml cold beta-mercaptoethanol (BME), followed by centrifugation at 300 g for 5min at 4C. Cells were washed once with 7ml 30% BME in PBS and lysed in 1ml Trizol (Invitrogen). RNA was isolated following the manufacturer’s protocol. Any trace of DNA was removed by Turbo DNase I followed by phenol:chloroform extraction, and RNA was used as a template for cDNA synthesis using Induro reverse transcriptase (NEB). cDNA was cleaned up using SPRIselect beads and is used as a template to amplify the full-length 5’UTRs of corresponding transcripts using Prime Star Max DNA polymerase (Takara).
The libraries were prepared by the NEBNext® Ultra™ II DNA Library Prep (NEB) and sequenced on Novaseq X.

treatment_protocol: 22Rv1 cells were seeded on a 6 cm plate and incubated overnight. The following day, the cells were treated with zotatifin (10nM) or enzalutamide (1mM) for 2 hours and harvested immediately by trypsinization.

value: Prostate cancer cell line


title: chk1chk2-cpt-2


title: 22Rv1 RPS5 5UTR DMS Vehicle biol rep 2

description: Library name: Sample30


title: 22Rv1 Hypoxia Vehicle RNA biol rep 2

description: Library name: Sample2


title: 22Rv1 RPS5 5UTR DMS Zota biol rep 1

description: Library name: Sample31


title: 5xFAD, Microglia, PKR KO, rep2

description: Library name: Sample11


title: Cat_#2_ALA+ConA

value: ALA+ConA


title: 5xFAD, Microglia, PKR KO, rep1

description: Library name: Sample10


title: 22Rv1 RPS5 5UTR DMS Vehicle biol rep 1

description: Library name: Sample29


title: WT, Input, 2

data_processing:
Basecalls were performed using Peaks were called using MACS2 (v.2.2.8, macs2 callpeak) with parameter -t -c -g 4.3e8 -q 0.05 --broad --max-gap 500 -n. Peaks annotation was performed by the package makeTxDbFromGFF (makeTxDbFromGFF function - RDocumentation) of R.
Assembly: Neurospora crassa OR74A
Supplementary files format and content: bigWig,

extract_protocol:
The purity of the sample was determined by NanoPhotometer ® (IMPLEN, CA, USA)；The concentration and integrity of RNA samples were detected by Agilent 2100 RNA nano 6000 assay kit (Agilent Technologies, CA, USA).
Sequencing libraries were generated using TIANSeq DirectFast Library Kit (illumina) (NG101)  following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: 2% glucose with 1mg/mL HU in DD14


title: Cat_#2_ALA


title: M24-superior

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0.1.
Data matrixes were imported into Seurat v4.3.0 (Satija, et al. 2015) in the R v4.2.1 statistical environment. Initial matrix filtering of >5 cells per gene, >200 features per cell, and cells with mitochondria reads <20% was performed.
Sample count matrixes of the same age were merged and ambient RNA was removed using decontX function in the celda v1.14.2 package. DecontX adjusted counts matrixes were split into individual samples prior to doublet detection and removal using DoubletFinder v2.0.3 with a target doublet rate of 5%.
Sample decontX adjusted count matrixes were merged into a single Seurat object and normalized and variance stabilized using SCTransform v2 (Choudhary and Satija, 2022). PCA (50 dimensions), FindNeighbors (30 dimensions), RunUMAP (30 dimensions), and FindClusters were performed using Seurat.
Cell types were assigned using scType (https://github.com/IanevskiAleksandr/sc-type) with sctype 'eye' database "Astrocytes", "Immune cells", "Retinal pigment epithelial cells", and custom cell type gene lists (https://github.com/NEI-NNRL/2023_Mouse_Retina_Aging/blob/main/src/Retina_Cell_type_MB_v2.xlsx). High resolution clustering (108 clusters) was performed to assess and remove clusters exhibiting expression of canonical cell type markers from more than one cell type.
Assembly: GRCm38.p6/ENSEMBL v98
Supplementary files format and content: HDF5 file of filtered CellRanger output

source_name: Retina

extract_protocol:
Mouse retinas were dissected and dissociated as previously described (Fadl, et al. Mol Vis 2020). A 1mm punch of superior or inferior retina dissociate at each age was used as input for 10X Genomics Chromium controller using v2 (Chromium Next GEM Single Cell 3ʹ GEM, Library and Gel Bead Kit v2) chemistry. Approximately 10,000 live cells per sample were loaded into the Chromium chip following the Cell Suspension Volume Calculator Table to capture transcripts from approximately 6,000 cells.
Libraries were performed according to the manufacturer’s instructions (Single Cell 3’ v2 protocol, 10x Genomics)

value: Retina

value: 24 months

tag: region

value: superior

tag: Sex

value: male


title: 22Rv1 APEX1 5UTR DMS Zota biol rep 2

description: Library name: Sample28

value: Zotatifin


title: M24-inferior

description: 10X Genomics

tag: tissue

value: inferior

tag: genotype


title: WT, Input, 1

tag: treatment


title: Cat_#2_Control

value: peripheral blood lymphocytes


title: chk1chk2, Input, 2

value: chk1chk2 knockout


title: Cat_#2_ConA

value: ConA


title: 22Rv1 APEX1 5UTR DMS Zota biol rep 1

description: Library name: Sample27


title: Cat_#3_ALA+ConA


title: M12-superior

description: 10X Genomics

tag: age

value: 12 months


title: Cat_#1_ALA+ConA


title: wt-cpt-1

value: 2% glucose with 0.2ug/mL CPT at 25C , DD18


title: 22Rv1 APEX1 5UTR DMS Vehicle biol rep 2

description: Library name: Sample26


title: chk1chk2, Input, 1


title: M12-inferior

description: 10X Genomics


title: 22Rv1 APEX1 5UTR DMS Vehicle biol rep 1

description: Library name: Sample25


title: 22Rv1 HIF1A set 2 5UTR DMS Enza biol rep 2

description: Library name: Sample24

value: Enzalutamide


title: WT, H3T11ph, ChIP, 2

value: WT


title: Cat_#1_ALA

value: ALA


title: M8-superior

description: 10X Genomics

value: 8 months


title: Cat_#1_Control

value: Control


title: WT, H3T11ph, ChIP, 1

value: 2% glucose with 1mg/mL HU in DD14


title: M3-inferior

description: 10X Genomics

value: Retina

value: 3 months