title: YBX1 eCLIP, 19-28z-1A T cells, Input2

description: Library name: Input4_1A_2

value: 19-28z-1A T cells


title: YBX1 eCLIP, 19-28z T cells, IP1

status: Public on Jan 22 2026

type: SRA

city: New York

first: Yuzhe

last: Shi

state: NY

address: 1250 First Avenue

department: Immunolgy

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: IP1_28z_1

library_source: other

data_processing:
Samples were processed with Eclipsebio's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). Peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1). For each peak, IP versus input fold enrichments and pvalues were calculated. Peaks were annotated using transcript information from GENCODE v41 with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: hg38
Supplementary files format and content: gene_counts.txt

molecule: other

organism: Homo sapiens

source_name: Primary T cell

extract_protocol:
Cell pellets were lysed using 1mL of eCLIP lysis mix with a modified composition of 6µL of Proteinase Inhibitor Cocktail and 20µL of Murine RNase Inhibitor. Samples were then subjected to one round of sonication for 5 minutes with 30 second ON/OFF at 75% amplitude. Pre-validated antibodies against YBX1 (Abcam cat. Ab76149) were then pre-coupled to Anti-Rabbit IgG Dynabeads (ThermoFisher), added to lysate, and incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers.
IP and input samples were cut from the membrane at the relative band size to 75kDa above. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed.

tag: tissue

value: Primary T cell

tag: disease state

value: Healthy Donor

tag: cell type

value: 19-28z T cells


title: YBX1 eCLIP, 19-28z-1A T cells, IP2

description: Library name: IP4_1A_2


title: Arid1b_1

city: Los Angeles

first: Mingyi

last: Zhang

state: CA

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description:
Library name: Control_Arid1b_1
Epicypher

library_source: genomic

data_processing:
fastq files were trimmed for adapters and low-quality sequences using Galore and subsequently mapped to the mouse mm10 reference genome using Bowtie2 with default parameters.
PCR duplicates were marked using Picard.
Coverage tracks were generated using the bamCoverage tool from deepTools with the RPKM normalization method, and peak calling was conducted using MACS2.
Peak annotation was performed with ChIPseeker (RStudio) to annotate peaks.
Assembly: mm10
Supplementary files format and content: Bigwig files
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: incisor mesenchyme

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Freshly collected proximal mouse incisor fromcontrol mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes . The prepared cells were tested for viability before process the extraction. Cells viability  higher than 80% were used for nucleis extranction for the scATACseq.
Library was performed according to the manufacter's introduction (Epicypher).

treatment_protocol: 20ml/ml concentrated tamxifen was administered to mice via intraperitoneal injection at a dosage of 1.5mg/10g body weight

value: incisor mesenchyme

tag: genotype

value: wild type

tag: treatment


title: Arid1a_1

description:
Library name: Control_Arid1a_1
Epicypher


title: SSC 18day WT Mouse 88_9

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: Library name: samp88_9_SSC_F7_S48

library_source: transcriptomic

data_processing:
Raw fastq files were processed with our pipeline at https://github.com/seanken/BulkIsoform/tree/main/Pipeline. Most notably the data was processed with Salmon to get expression information. This expression information was loaded into R with tximport and processed with DESeq2 for downstream processing.
Assembly: mm10
Supplementary files format and content: The processed files are tab seperated files, as produced from Salmon, with each row corresponding to a transcript, columns with information about expression. See the Salmon documentatiomn for more details

molecule: polyA RNA

source_name: Brain

growth_protocol: brains from 18d and 3mo old male GPR34 KO or Wt C57BL6J mice were microdisected by brain region

extract_protocol:
Each brain region from each animal was then separately prepared for bulk RNA sequencing. RNA was isolated from tissues using the Qiagen RNeasy Mini Kit per manufacturer’s instructions.
. Bulk sequencing libraries were prepared using Illumina TruSeq Stranded mRNA Kit (Catalog #20020595) per manufacturer’s instructions. 300 ng of total RNA from each sample was used and the concentration of resulting cDNA library was measured with High Sensitivity DNA chips (Agilent) using a 2100 Bioanalyzer Instrument (Agilent). A 5 nM normalized library was pooled, and sequencing was performed on a NovaSeq X 25B (Illumina) with 50 bases each for reads 1 and 2 and 8 bases each for index reads 1 and 2. The depth of sequencing for each individual library ranged from 30.5 million to 645 million before downsampling, with a median of 49 million reads.

treatment_protocol: No additional treaments were administered

value: Brain

value: WT

tag: brain region

value: SSC

tag: age

tag: mouse

tag: batch

value: Single Batch


title: Dlx2_1

description:
Library name: Control_Dxl2_1
Epicypher


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep3

city: La Jolla

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Library name: 231107_NG_Sample_12

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

source_name: Lung

growth_protocol: Human pulmonary fibroblasts were cultured in fibroblast media, serum starved prior  cytokine treatment

extract_protocol:
Zymo Direct-zol
NEB mRNA Directional

treatment_protocol: Human pulmonary fibroblasts (HPF) stimulated with 50 ng/ml LIGHT, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or Il17A with LIGHT. HPF were also pretreated with 5 ng/ml of TGFb followed by 50 ng/ml LIGHT treatment.

value: Lung

tag: cell line

value: HPF

value: Fibroblasts

value: IL13 72hrs followed by LIGHT 24hrs


title: SSC 18day WT Mouse 88_6

description: Library name: samp88_6_SSC_F4_S42


title: SSC 18day KO Mouse 88_7

description: Library name: samp88_7_SSC_F5_S44

value: KO


title: YBX1 eCLIP, 19-28z T cells, Input 2

description: Library name: Input2_28z_2


title: MC 18day WT Mouse 88_6

description: Library name: samp88_6_MC_D3_S41

value: MC


title: Arid1a_2

description:
Library name: Control_Arid1a_2
Epicypher


title: flu_b4_organoid scRNAseq

city: Shanghai

first: pei

last: wu

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

description:
Library name: flu_b4_organoid
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcodes processing counting and aggregation were made using the Cell ranger software v8.0.1
Assembly: mm10
Supplementary files format and content: tar file includes matrix files for the sample

molecule: total RNA

source_name: lung

extract_protocol:
Airway epithelial cells (CD45- EPCAM+ CD31- Integrin β4+) from the lungs of influenza-infected mice at 11 days post-infection (dpi) were isolated using FACS. These cells were then cultured in 1:1 mixed SAGM and LPM medium without CHIR medium for 10 days before being digested into single cells for scRNA-seq analysis.
Library was performed according to the manufacture's instructions(single cell 3' v3 protocol, 10x Genomics）

value: lung

value: epithelial cells

value: cultured influenza infected airway epithelial cells

value: flu D11


title: YBX1 eCLIP, 19-28z T cells, IP2

description: Library name: IP2_28z_2

value: Primary T cell

value: Healthy Donor

value: 19-28z T cells


title: MC 18day KO Mouse 88_5

description: Library name: samp88_5_MC_D2_S39

value: Brain


title: MC 18day KO Mouse 88_7

description: Library name: samp88_7_MC_D4_S43


title: HPF cell, IL13, 72 hrs, rep2

description: Library name: 231107_NG_Sample_8

value: IL13 72 hrs


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_6

value: PBS 72 hrs and LIGHT 24 hrs


title: WT4_Aligned.sortedByCoord.out.bam_WT

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

description: Library name: WT4_Aligned.sortedByCoord.out.bam

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the mouse genome (mm10) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R and analysis of differential expression between groups was done using the limma-voom pipeline.
Assembly: mm10
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Calvaria

extract_protocol:
Total RNA was isolated from calvarial cells using a combination of TRI reagent (Molecular Research Center, Cincinnati, OH, USA) and RNeasy-mini columns, including on-column deoxyribonuclease I digestion (Qiagen, Germantown, MD USA). RNA integrity was assessed using a 4200 TapeStation system.
Directional cDNA libraries for mRNA-sequencing were prepared using polyA-mRNA from individual biological replicates using NebNext Ultra reagents. One μg of total RNA was utilized for mRNA isolation using poly-A magnetic beads and was fragmented prior to first and second strand cDNA synthesis. Libraries were generated via PCR including indexed barcodes. Following purification with AmpureXP beads libraries were quantitated using Qubit dsDNA reagents. Pooled cDNA libraries were sequenced using a Nextseq 550 instrument. All libraries were prepared and sequenced in a single batch.

value: Calvaria

value: WT

tag: group


title: HPF cell, PBS, 96 hrs, rep2

description: Library name: 231107_NG_Sample_2

value: Lung

value: HPF

value: PBS 96 hrs


title: Foxo1_1

description:
Library name: Control_Foxo1_1
Epicypher

value: incisor mesenchyme

value: wild type


title: WT3_Aligned.sortedByCoord.out.bam_WT

description: Library name: WT3_Aligned.sortedByCoord.out.bam


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_5

value: Fibroblasts


title: SSC 18day WT Mouse 88_1

description: Library name: samp88_1_SSC_F1_S36

value: SSC

value: Single Batch


title: YBX1 eCLIP, 19-28z-1A T cells, Input1

description: Library name: Input3_1A_1

value: 19-28z-1A T cells


title: YBX1 eCLIP, 19-28z T cells, Input 1

description: Library name: Input1_28z_1

value: Primary T cell


title: SSC 18day WT Mouse 88_8

description: Library name: samp88_8_SSC_F6_S46


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_4


title: HPF cell, LIGHT and IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_17

value: IL17A and LIGHT 24 hrs


title: RNA_untreated_2_13538_2

first: Hyunu

last: Kim

address: 417 E 68th St

department: Immunology

description: Library name: Sample_untreated_2_IGO_13538_2

data_processing:
For RNA-seq dataset generated in this study, transcript quantification was based on the mm10 University of California, Santa Cruz (UCSC) Known Gene models and performed using the quasi-mapping-based mode of Salmon (v0.13.1) correcting for potential GC bias. Transcript was summarized to gene level using tximport (v1.10.1). For ATAC-seq data, reproducible peaks showing an IDR value of 0.05 or less in each condition were retained, aggregated across the experiment and merged via union generate the final atlas, and annotated with the UCSC Known Gene model. Reads were mapped to the final atlas and counted with the summarizeOverlaps function from the GenomicAlignment package (v1.34.1).
Assembly: mm10
Supplementary files format and content: Project_12001_rawCounts.txt
Supplementary files format and content: Project_12002_B_peakAtlas.txt
Supplementary files format and content: Project_12002_B_rawCounts.txt
Supplementary files format and content: Project_12637_rawCounts.txt
Supplementary files format and content: Project_12669_peakAtlas.txt
Supplementary files format and content: Project_12669_rawCounts.txt
Supplementary files format and content: Project_13538_rawCounts.txt

source_name: Spleen

extract_protocol:
For RNA-seq: RNA was isolated from sorted cells and/or stimulated cells as described using PicoPure RNA Isolation Kit (ThermoFisher Scientific, cat. KIT0214). For ex vivo RNAseq analysis in Fig. 1F, Ly49H- NK cells were gated for positivity of Ly49D to reduce the effects of maturation. After RiboGreen quantification and quality control by Agilent BioAnalyzer. For ATAC-seq: ATAC-seq was performed as described previously55. Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37 °C for 30 min. DNA was cleaned with the MinElute PCR Purification kit (QIAGEN, cat. 28004).
For RNA-seq: RNA amplified using SMART-Seq v.4 Ultra Low Input RNA kit (Clontech, cat. 63488). Subsequently, amplified complementary DNA was used to prepare libraries with KAPA HyperPrep Kit (Kapa Biosystems, cat. KK8504). Samples were barcoded and ran on NovaSeq6000 in a 100bp/100bp paired-end run. For ATAC-seq:  DNA materials were amplified and the final product was cleaned by AMPure XP beads (Beckman Coulter catalog no. A63882) at a 1× ratio, and size selection was performed at a 0.5× ratio. Libraries were sequenced on a NovaSeq6000 in a 100 bp/100 bp paired-end run, using the NovaSeq6000 S2 or S4 Reagent kit (Illumina).

treatment_protocol: For in vitro stimulation: High-binding 96-well flat-bottom plates were coated with 100 μl per well of 20 μg/ml anti-NK1.1 (Clone PK136, BioLegend, cat. 108759) in PBS at 4 °C overnight. NK cells were cultured in IMDM (10% FBS, 1× L-glutamine, 1× sodium pyruvate, 1× BME, 1× MEM-NAA and 25 mM HEPES). To prevent antigen-receptor signaling in negative controls, we used negative enrichment. Depending on the condition, NK cells were stimulated for 1-3h in 96 wells coated with anti-NK1.1 or in uncoated wells. For cytokine stimulations, we used 50 ng/ml mouse IL-15 (Peprotech, cat. no. 210-15) and 20 ng/ml mouse IL-12 (R&D Systems, cat. no. 419-ML-050) depending on the experiment. For in vivo MCMV experiment: NR4A1-GFP mice were infected with MCMV intraperitoneally and splenic NK cells were isolated from the spleen after 1 day post infection and subjected to RNA- and ATAC-seq.

value: Spleen

value: Total NK cells

value: wild-type

value: untreated


title: WT1_Aligned.sortedByCoord.out.bam_WT

description: Library name: WT1_Aligned.sortedByCoord.out.bam

value: Calvaria


title: KO5_Aligned.sortedByCoord.out.bam_IRE1KO

description: Library name: KO5_Aligned.sortedByCoord.out.bam


title: HPF cell, PBS, 96 hrs, rep1

description: Library name: 231107_NG_Sample_1


title: SSC 18day KO Mouse 88_5

description: Library name: samp88_5_SSC_F3_S40

value: Brain

value: KO


title: HPF cell, LIGHT and IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_16

value: Lung

value: HPF


title: SSC 18day WT Mouse 88_11

description: Library name: samp88_11_SSC_F9_S34

value: WT


title: DKO (Gli1-CreER;Arid1afl/fl;Arid1bfl/fl)_scATAC-seq

description:
Library name: DKO_scATAC-seq
10x Genomics

library_source: genomic single cell

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the Cell Ranger ATAC pipeline.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Freshly collected proximal mouse incisor from Gli1-CreER;Arid1afl/fl;Arid1bfl/fl mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes . The prepared cells were tested for viability before process the extraction. Cells viability  higher than 80% were used for nucleis extranction for the scATACseq.
Library was performed according to the manufacter's introduction (Chromium Next GEM Single Cell ATAC v1.1 ).

value: incisor mesenchyme

value: Tamoxifen induction


title: DKO (Gli1-CreER;Arid1afl/fl;Arid1bfl/fl)_scRNA-seq

description:
Library name: DKO_scRNA-seq
10x Genomics

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 4.0.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Freshly collected proximal mouse incisor from Gli1-CreER;Arid1afl/fl;Arid1bfl/fl mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes. The prepared cells were tested for viability before process the extraction. Cells viability  higher than 75% were used for the scRNAseq.
Library was performed according to the manufacter's introduction (Chromium Next GEM Single Cell 3ʹ v3.1 ).


title: Ribo-seq, 19-28z T cells, RNA 3

description: Library name: RNA_Seq3_28z_6

data_processing:
samples were processed with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next 3' adapters were trimmed from reads using Cutadapt (v3.2). Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a), and during the alignment, multimapping reads were not retained. The exclusion of multimapping reads reduces false positive differential and pausing calls (Halpin, Jangi, and Street). The removal of multimapping reads may lead to underestimates of counts for genes with high rates of pseudogenization or duplication events. PCR duplicates were removed using UMI-tools (v1.1.1). Gene coverage was calculated using Subread featureCounts (v2.0.1) and ribosome occupancy was calculated by dividing coverage in the ribosome protected footprint (RPF) library by the RNA-Seq library. Differentially expressed and occupied genes were identified using DESeq2. For transcriptome analyses, reads were also aligned to the transcriptome with STAR (v2.7.7a). Transcriptome aligned reads were processed with riboWaltz and custom analysis programs developed by Eclipsebio to determine codon usage, stall sites, 5' UTR loading, and 3' read through. ORF detection was performed on genome alignments using ribotricer (v1.3.3).
Assembly: hg38
Supplementary files format and content: counts, TPM, FPKM
Library strategy: Ribo-Seq

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

value: Healthy Donor

value: 19-28z T cells


title: RNA_untreated_1_13538_1

description: Library name: Sample_untreated_1_IGO_13538_1


title: SSC 18day KO Mouse 88_2

description: Library name: samp88_2_SSC_F2_S38

value: SSC

value: Single Batch


title: MC 18day KO Mouse 88_2

description: Library name: samp88_2_MC_D1_S37

value: MC


title: HPF cell, PBS, 96 hrs, rep3

description: Library name: 231107_NG_Sample_3

value: Fibroblasts

value: PBS 96 hrs


title: WT2_Aligned.sortedByCoord.out.bam_WT

description: Library name: WT2_Aligned.sortedByCoord.out.bam


title: MC 18day KO Mouse 88_10

description: Library name: samp88_10__MC_D7


title: RNA_IL12_2_13538_4

description: Library name: Sample_IL12_2_IGO_13538_4

value: Spleen

value: Total NK cells

value: wild-type


title: KO2_Aligned.sortedByCoord.out.bam_IRE1KO

description: Library name: KO2_Aligned.sortedByCoord.out.bam

value: Calvaria


title: HPF cell, IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_14

value: IL17A 24 hrs


title: SSC 18day KO Mouse 88_10

description: Library name: samp88_10_SSC_F8_S31

value: Brain

value: KO


title: HPF cell, LIGHT and IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_18

value: Lung

value: HPF

value: IL17A and LIGHT 24 hrs


title: HPF cell, LIGHT and IL13, 24 hrs, rep3

description: Library name: 230428_NG_Sample_12

value: IL13 and LIGHT 24 hrs


title: MC 18day WT Mouse 88_1

description: Library name: samp88_1_MC_C12_S35

value: WT


title: RNA_NK11_IL12_1_13538_7

description: Library name: Sample_NK11_IL12_1_IGO_13538_7


title: KO1_Aligned.sortedByCoord.out.bam_IRE1KO

description: Library name: KO1_Aligned.sortedByCoord.out.bam


title: RNA_NK11_2_13538_6

description: Library name: Sample_NK11_2_IGO_13538_6


title: Multiome, PBMC, COVID-19 patients 14, ATAC

city: Gwangju

first: Donggun

address: 123, Cheomdangwagi-ro

department: Life Science

country: South Korea

institute: Gwangju Institute of Science and Technology

description:
Library name: PB14_ATAC
10x Genomics

data_processing:
Raw sequencing data were processed by 10x genomics Cell Ranger-arc version 2.0.1 (https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/release-notes/release-notes). FASTQ files were aligned to the GRCh38 human reference genome, and expression, fragment count matrices were generated.
Demultiplexed data was processed using the Demuxlet.
Assembly: GRCh38
Supplementary files format and content: CellRanger-ARC output files: Hierarchical Data Format version 5 (RNA) and tab-separated values files (ATAC)

source_name: PBMC

extract_protocol:
PBMCs were isolated by density gradient centrifugation using Histopaque®-1077 (Sigma-Aldrich, Cat. No. 10771). Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using 10x chromium with Chromium Next GEM Chip J Single Cell Kit
The libraries were generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (PN-1000283) (10x Genomics) in accordance with the manufacturer's guidelines. First, nuclei were incubated with Transposition Mix at 37°C for 60 minutes. The resulting mixture was loaded onto Chromium Next GEM Chip J Single Cell Kit (PN-1000234, 10x Genomics), and GEMs (Gel Beads-in-Emulsions) were formed following the manufacturer’s protocol. After GEM processing and cleanup, barcoded transposed DNA and barcoded full-length cDNA fragments underwent pre-amplification via PCR. For library construction, ATAC libraries were prepared using the Library Construction Kit (PN-1000190), while full-length pre-amplified cDNA fragments underwent additional PCR amplification. RNA libraries were assembled using the Library Construction Kit B (PN-1000279). Finally, the completed libraries were subjected to sequencing on an HiSeq X Ten platform.

value: PBMC


title: KO4_Aligned.sortedByCoord.out.bam_IRE1KO

description: Library name: KO4_Aligned.sortedByCoord.out.bam


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_2_12669_20

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_2_IGO_12669_20

value: Ly49H+ NK cells


title: RNA_IL12_1_13538_3

description: Library name: Sample_IL12_1_IGO_13538_3


title: KO3_Aligned.sortedByCoord.out.bam_IRE1KO

description: Library name: KO3_Aligned.sortedByCoord.out.bam


title: Hipp 3month WT Mouse 81_2

description: Library name: samp81_2_Hipp_A4_S28

value: Hipp

value: Single Batch


title: RNA_NK11_1_13538_5

description: Library name: Sample_NK11_1_IGO_13538_5


title: SSC 3month WT Mouse 81_1

description: Library name: samp81_1_SSC_E11_S27

value: SSC


title: SSC 3month WT Mouse 81_2

description: Library name: samp81_2_SSC_E12_S30


title: HPF cell, IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_13

value: Fibroblasts


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_2_12669_23

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_2_IGO_12669_23

value: Spleen


title: HPF cell, IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_15


title: HPF cell, IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_8

value: IL13 24 hrs


title: HPF cell, IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_7


title: Multiome, PBMC, COVID-19 patients 13, ATAC

description:
Library name: PB13_ATAC
10x Genomics


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_2_12669_17

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_2_IGO_12669_17


title: Multiome, PBMC, COVID-19 patients 9, ATAC

description:
Library name: PB09_ATAC
10x Genomics


title: Multiome, PBMC, COVID-19 patients 12, ATAC

description:
Library name: PB12_ATAC
10x Genomics


title: HPF cell, IL13 24 hrs, rep3

description: Library name: 230428_NG_Sample_9


title: MC 18day WT Mouse 88_11

description: Library name: samp88_11_MC_D8_S33

value: MC


title: MC 3month WT Mouse 7_4

description: Library name: samp07_4_MC_C9_S23


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_1_2_12669_14

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_1_2_IGO_12669_14


title: RNA_NK11_IL12_2_13538_8

description: Library name: Sample_NK11_IL12_2_IGO_13538_8

value: Total NK cells

value: wild-type


title: Multiome, PBMC, COVID-19 patients 11, ATAC

description:
Library name: PB11_ATAC
10x Genomics


title: HPF cell, LIGHT and IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_10


title: HPF cell, LIGHT and IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_11


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_2_12669_24

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_2_IGO_12669_24


title: Hipp 3month WT Mouse 81_1

description: Library name: samp81_1_Hipp_A3_S26

value: Brain


title: Multiome, PBMC, COVID-19 patients 6, ATAC

description:
Library name: PB06_ATAC
10x Genomics


title: ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_2_12669_16

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_2_IGO_12669_16

value: Ly49D+ NK cells


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_2_12669_21

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_2_IGO_12669_21


title: Multiome, PBMC, COVID-19 patients 5, ATAC

description:
Library name: PB05_ATAC
10x Genomics


title: SSC 3month WT Mouse 7_4

description: Library name: samp07_4_SSC_E10_S24


title: HPF cell, LIGHT, 24 hrs,rep3

description: Library name: 230428_NG_Sample_6

value: Lung

value: HPF

value: LIGHT 24 hrs


title: ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_1_2_12669_15

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_1_2_IGO_12669_15


title: HPF cell, PBS, 24 hrs, rep3

description: Library name: 230428_NG_Sample_3

value: PBS 24 hrs


title: Multiome, PBMC, COVID-19 patients 7, ATAC

description:
Library name: PB07_ATAC
10x Genomics

value: PBMC


title: Multiome, PBMC, COVID-19 patients 10, ATAC

description:
Library name: PB10_ATAC
10x Genomics


title: NA NA NA Mouse NA

description: Library name: samp81_099999999999994_MC_C10_S25


title: MC 3month KO Mouse 7_3

description: Library name: samp07_3_MC_C8_S20

value: KO


title: Multiome, PBMC, COVID-19 patients 8, ATAC

description:
Library name: PB08_ATAC
10x Genomics


title: Multiome, PBMC, COVID-19 patients 4, ATAC

description:
Library name: PB04_ATAC
10x Genomics


title: Hipp 3month WT Mouse 7_4

description: Library name: samp07_4_Hipp_A2_S22

value: WT

value: Hipp


title: ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_2_12669_22

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_2_IGO_12669_22


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_12637_8

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_3_IGO_12637_8

value: Ly49H+ NK cells


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_12637_11

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_4_IGO_12637_11


title: Multiome, PBMC, COVID-19 patients 3, ATAC

description:
Library name: PB03_ATAC
10x Genomics


title: HPF cell, PBS, 24 hrs, rep2

description: Library name: 230428_NG_Sample_2

value: Fibroblasts


title: SSC 3month KO Mouse 7_3

description: Library name: samp07_3_SSC_E9_S21

value: SSC

value: Single Batch


title: HPF cell, LIGHT, 24 hrs, rep1

description: Library name: 230428_NG_Sample_4


title: Multiome, PBMC, COVID-19 patients 2, ATAC

description:
Library name: PB02_ATAC
10x Genomics


title: HPF cell, LIGHT, 24 hrs, rep2

description: Library name: 230428_NG_Sample_5


title: Hipp 3month KO Mouse 7_3

description: Library name: samp07_3_Hipp_A1_S19


title: ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_1_2_12669_13

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_1_2_IGO_12669_13

value: Spleen


title: ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_2_12669_19

description: Library name: Sample_ATAC_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_2_IGO_12669_19


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_12637_5

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPpos_2_IGO_12637_5


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_12637_12

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_4_IGO_12637_12


title: SKNBE2_DFMO_3

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: Library name: SKNBE2_DFMO_3

data_processing:
Reads were mapped to the human genome (version GRCh38) using vast-tools “align” module (-IR_version 2 -stepSize 25 -mismatchNum 2).
Aligned single datasets were merged with the “merge” module.
We combined the samples using “combine” with parameters “-IR_version 2 -extra_eej 5”. We identified differentially spliced events using Matt v. 1.3.0 with minimum abs(deltaPSI) > 10% and Wilcoxon p-value <0.1 after excluding events with PSIRANGE_ALL = NA and LENGTH= 0.
Assembly: GRCh38
Supplementary files format and content: RNAseq data of SKNBE2 neuroblastoma cells treated with DFMO.

source_name: Neuroblastoma Cancer Cells

extract_protocol:
At sub-confluency cells were washed with ice-cold PBS and RNA was isolated from cell extracts by direct addition of 3-volumes of QIAzol® (Qiagen, Cat. No. 79306).
RNA were sent to Genomic Platform (UNIGE) for stranded mRNA libraries preparation.

value: Neuroblastoma Cancer Cells

value: Neuroblast

value: MYCN Amplified

value: DFMO


title: MC 3month KO Mouse 7_2

description: Library name: samp07_2_MC_C7_S17

value: Brain

value: MC


title: HPF cell, PBS, 24 hrs, rep1

description: Library name: 230428_NG_Sample_1

value: Lung

value: HPF


title: Multiome, PBMC, healthy control 3, ATAC

description:
Library name: HC03_ATAC
10x Genomics

value: PBMC


title: Hipp 3month KO Mouse 7_2

description: Library name: samp07_2_Hipp_H12_S16

value: KO


title: MC 3month WT Mouse 81_2

description: Library name: samp81_2_MC_C11_S29

value: WT


title: SKNBE2_Control_3

description: Library name: SKNBE2_Control_3

value: Control


title: MC 3month WT Mouse 7_1

description: Library name: samp07_1_MC_C6_S14


title: SKNBE2_DFMO_1

description: Library name: SKNBE2_DFMO_1


title: Multiome, PBMC, COVID-19 patients 1, ATAC

description:
Library name: PB01_ATAC
10x Genomics


title: SKNBE2_Control_2

description: Library name: SKNBE2_Control_2


title: Multiome, PBMC, healthy control 1, ATAC

description:
Library name: HC01_ATAC
10x Genomics


title: SSC 3month WT Mouse 7_1

description: Library name: samp07_1_SSC_E7_S15


title: Hipp 3month WT Mouse 7_1

description: Library name: samp07_1_Hipp_H11_S13

value: Hipp


title: Multiome, PBMC, healthy control 2, ATAC

description:
Library name: HC02_ATAC
10x Genomics


title: SSC 3month KO Mouse 7_2

description: Library name: samp07_2_SSC_E8_S18


title: SKNBE2_Control_1

description: Library name: SKNBE2_Control_1


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_12637_9

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_3_IGO_12637_9

value: Ly49H+ NK cells


title: A549 RNaseL-KO, transfected with poly(I:C), 4sU-seq replicate 3

city: Berkeley

first: Britt

middle: Aspen

last: Glaunsinger

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

description:
Library name: BGXM001L
All samples are nascent RNA profiling by 4sU-seq

data_processing:
The raw reads were pre-processed with HTStream v1.3.2 (https://github.com/s4hts/HTStream), including separation of rRNA and non-rRNA reads into separate files by HTStream SeqScreener.
The rRNA reads were aligned to the rDNA repeat (GenBank Accession U13369.1) concatenated to ERCC sequences and the non-rRNA reads were aligned to the human genome (hg38) concatenated to ERCC sequences using STAR (v2.6.1b). When aligning rRNA reads, options --alignIntronMax 1 and --alignSJDBoverhangMin 999 were set to suppress gapped alignment.
Aligned reads were counted using FeatureCounts and differential gene expression analysis was performed with limma-Voom, normalized to 4sU-labeled spike-ins. Segments of pre-rRNA (i.e., 5’ ETS, 18S, ITS1, 5.8S, ITS2, 28S, 3’ ETS) were included in the differential expression analysis.
Scaled, stranded BigWig files were generated with Deeptools (v3.5.5) bamCoverage function, using scaling factors generated in limma-Voom (proportional to the reciprocal of norm.factors × lib.sizes). BigWig files of biological replicates were averaged using Deeptools bigwigAverage function. For both operations, bin sizes were set to 20bp.
Assembly: hg38, Human ribosomal DNA complete repeating unit (Genbank U13369.1)
Supplementary files format and content: raw count file by FeatureCounts; Scaled, stranded BigWig files by Deeptools
Library strategy: 4sU-seq

source_name: Cell line

growth_protocol: A549 WT and RNase L-KO cells were maintained in DMEM supplemented with 10% FBS in humidified incubator with 5% CO2 at 37°C

extract_protocol:
The plates were washed once with PBS then lysed with 2ml TRIzol. RNA was extracted from the TRIzol lysate, followed by isopropanol precipitation. 100μg or 300μg (WT with poly(I:C)) total RNA was mixed in-vitro-transcribed RNA 4sU-labeled- or 4sU-unlabeled-spike-in RNA and biotinylated with HPDP-biotin (Thermo Scientific cat # PI21341, 50μg per 25μg of RNA) for 2 hours, followed by two chloroform extraction and isopropanol precipitation.  The RNA samples were denatured at 65°C for 5 minutes, then incubated with Dynabeads MyOne Streptavidin C1 magnetic beads (Thermo Fisher cat # 65002) previously blocked with glycogen for 1 hour. The beads were washed twice with wash buffer (100 mM Tris-HCl, 10 mM EDTA, 1 M sodium chloride, and 0.1% Tween 20) at 65°C then twice at room temperature. To increase the stringency of the washes, the beads were further washed with TE buffer (10mM Tris-HCl pH 7.4, 1mM EDTA) twice at 55°C. 4sU-RNA was then eluted from beads twice with 100μL 100mM DTT, and the combined eluent was precipitated with isopropanol.
The sequencing library was constructed using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche, cat # KK8484, 07962304001) and KAPA Single-Indexed Adapter Kit (Roche, cat # KK8700, 08005699001) following manufacturer’s instructions, with the following modifications: Briefly, 60ng to 100ng RNA was used as input without rRNA depletion and fragmented at 85 °C for 6 minutes; the PCR cycle numbers were determined empirically by qPCR.

treatment_protocol: Six million A549 WT or RLKO cells were seeded in 15cm tissue culture dishes and cultured overnight before transfection. Then cells were then transfected with RNAiMAX alone (i.e., mock-transfected) or with 0.73 μg/ml poly(I:C) for 4 hours, followed by pulse labeling with 500μM 4sU dissolved in DMEM media supplemented with 10% FBS for 10 minutes.

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells

value: RNase L-KO

value: transfected with 0.73 μg/ml poly(I:C)


title: RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_2_12637_6

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49H_Nur77GFP_GFPneg_2_IGO_12637_6

value: Spleen


title: SKNBE2_DFMO_2

description: Library name: SKNBE2_DFMO_2

value: Neuroblastoma Cancer Cells

value: Neuroblast


title: Multiome, PBMC, COVID-19 patients 14, GEX

description:
Library name: PB14_GEX
10x Genomics


title: RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_12637_4

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_2_IGO_12637_4

value: Ly49D+ NK cells


title: Multiome, PBMC, COVID-19 patients 13, GEX

description:
Library name: PB13_GEX
10x Genomics


title: ATAC_TotalNK_Unstim_3hr_1_12002_B_1

description: Library name: Sample_ATAC_TotalNK_Unstim_3hr_1_IGO_12002_B_1

value: Total NK cells

value: wild-type


title: RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_12637_7

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_3_IGO_12637_7


title: Multiome, PBMC, COVID-19 patients 11, GEX

description:
Library name: PB11_GEX
10x Genomics


title: A549 WT, transfected with poly(I:C), 4sU-seq replicate 3

description:
Library name: BGXM001J
All samples are nascent RNA profiling by 4sU-seq


title: Multiome, PBMC, COVID-19 patients 10, GEX

description:
Library name: PB10_GEX
10x Genomics


title: Hipp 3month WT Mouse 5_4

description: Library name: samp05_4_Hipp_H10_S10

value: Brain

value: Single Batch


title: SSC 3month WT Mouse 5_4

description: Library name: samp05_4_SSC_E6_S12

value: SSC


title: ATAC_TotalNK_Unstim_3hr_2_12002_B_2

description: Library name: Sample_ATAC_TotalNK_Unstim_3hr_2_IGO_12002_B_2


title: Multiome, PBMC, COVID-19 patients 12, GEX

description:
Library name: PB12_GEX
10x Genomics

value: PBMC


title: MC 3month WT Mouse 5_4

description: Library name: samp05_4_MC_C5_S11

value: WT

value: MC


title: ATAC_TotalNK_NK11_3hr_3_12002_B_10

description: Library name: Sample_ATAC_TotalNK_NK11_3hr_3_IGO_12002_B_10


title: Multiome, PBMC, COVID-19 patients 8, GEX

description:
Library name: PB08_GEX
10x Genomics


title: RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_12637_10

description: Library name: Sample_RNA_NK_Spleen_D1_Ly49D_Nur77GFP_All_4_IGO_12637_10


title: A549 RNaseL-KO, mock-transfected, 4sU-seq replicate 3

description:
Library name: BGXM001K
All samples are nascent RNA profiling by 4sU-seq

value: mock-transfected with RNAiMAX


title: A549 RNaseL-KO, mock-transfected, 4sU-seq replicate 2

description:
Library name: BGXM001G
All samples are nascent RNA profiling by 4sU-seq


title: ATAC_TotalNK_NK11_3hr_2_12002_B_9

description: Library name: Sample_ATAC_TotalNK_NK11_3hr_2_IGO_12002_B_9


title: ATAC_TotalNK_NK11_3hr_1_12002_B_8

description: Library name: Sample_ATAC_TotalNK_NK11_3hr_1_IGO_12002_B_8


title: A549 WT, mock-transfected, 4sU-seq replicate 3

description:
Library name: BGXM001I
All samples are nascent RNA profiling by 4sU-seq


title: MC 3month KO Mouse 5_2

description: Library name: samp05_2_MC_C3_S5

value: KO


title: SSC 3month KO Mouse 5_3

description: Library name: samp05_3_SSC_E5_S9


title: Hipp 3month KO Mouse 5_3

description: Library name: samp05_3_Hipp_H9_S7

value: Hipp


title: MC 3month KO Mouse 5_3

description: Library name: samp05_3_MC_C4_S8


title: Multiome, PBMC, COVID-19 patients 9, GEX

description:
Library name: PB09_GEX
10x Genomics


title: Multiome, PBMC, COVID-19 patients 7, GEX

description:
Library name: PB07_GEX
10x Genomics


title: A549 RNaseL-KO, transfected with poly(I:C), 4sU-seq replicate 2

description:
Library name: BGXM001H
All samples are nascent RNA profiling by 4sU-seq

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells

value: RNase L-KO


title: RNA_TotalNK_NK11_3hr_2_12001_6

description: Library name: Sample_RNA_TotalNK_NK11_3hr_2_IGO_12001_6

value: Spleen


title: SSC 3month KO Mouse 5_2

description: Library name: samp05_2_SSC_E4_S6


title: MC 3month KO Mouse samp05_1

description: Library name: samp05_1_MC_C2_S2


title: Hipp 3month KO Mouse samp05_1

description: Library name: samp05_1_Hipp_H7_S1


title: RNA_TotalNK_NK11_3hr_1_12001_5

description: Library name: Sample_RNA_TotalNK_NK11_3hr_1_IGO_12001_5


title: A549 WT, mock-transfected, 4sU-seq replicate 1

description:
Library name: BGXM001A
All samples are nascent RNA profiling by 4sU-seq


title: RNA_TotalNK_Unstim_3hr_1_12001_1

description: Library name: Sample_RNA_TotalNK_Unstim_3hr_1_IGO_12001_1


title: Multiome, PBMC, COVID-19 patients 4, GEX

description:
Library name: PB04_GEX
10x Genomics


title: A549 WT, transfected with poly(I:C), 4sU-seq replicate 1

description:
Library name: BGXM001B
All samples are nascent RNA profiling by 4sU-seq

value: transfected with 0.73 μg/ml poly(I:C)


title: NKCells_TimeCourse_CITE_HTO

description: Library name: Pooled CITE_HTO

data_processing:
The cell–gene count matrix was constructed using the 10x Cell Ranger (v7.1.0) pipeline based on mm10 2020-A reference. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. After mitochondrial and doublet cleanup, the raw count matrix was normalized by median library size normalization followed by log transformation.
Assembly: mm10
Supplementary files format and content: HTO_doubletFiltered.h5ad
Supplementary files format and content: adataGEX_processed.h5ad
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Splenic Ly49H+ NK cells (CD3/TCRb/CD19−NK1.1+CD49b+Ly49H+) from uninfected or MCMV-infected WT C57BL/6 mice were sorted as described and stained with barcoded antibodies (Total-Seq B, BioLegend). After hash-staining, NK cells were pooled and the single-cell RNA-seq from these pooled FACS-sorted cell suspensions was performed on a Chromium instrument (10x Genomics) following the user guide manual for 3′ v.3.1. In brief, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in 1× PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan blue staining (Countess II). Cells were captured in droplets.
Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA-purified using Dynabeads MyOne SILANE (Thermo Fisher, cat. 37002D) followed by PCR amplification as per the manual instructions. Samples were multiplexed together on one lane of 10x Chromium (using Hash Tag Oligonucleotides (HTOs)). Final libraries were sequenced on Illumina NovaSeq6000 S4 platform (R1, 28 cycles; i7, 8 cycles; and R2, 90 cycles).

treatment_protocol: WT C57BL/6 mice were intected with MCMV (intraperitoneally) at different days and spleens of infected / uninfected animals were isolated on the same day.

value: MCMV


title: A549 WT, mock-transfected, 4sU-seq replicate 2

description:
Library name: BGXM001E
All samples are nascent RNA profiling by 4sU-seq


title: A549 RNaseL-KO, transfected with poly(I:C), 4sU-seq replicate 1

description:
Library name: BGXM001D
All samples are nascent RNA profiling by 4sU-seq


title: Multiome, PBMC, COVID-19 patients 6, GEX

description:
Library name: PB06_GEX
10x Genomics


title: 19-1XX-week2 rep3

description: Library name: 19-1XX-week2 rep3

data_processing:
DESeq2
Assembly: hg38
Supplementary files format and content: Proj_13276_B_htseq_all_samples25.txt

source_name: T cell

extract_protocol:
Trizol
Two ng RNA with integrity numbers ranging from 9.1 to 9.3 underwent amplification using the SMART-seq v4 Ultra Low Input RNA Kit (63488, Clonetech) with 12 cycles of amplification: 95°C for 60 s, 12 times (98°C for 10 s, 65°C for 30 s, 68°C for 180 s) and 72°C for 10 min. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (KK8504, Kapa Biosystems) using 8 cycles of PCR. The final DNA library was double-size purified (0.8-1x) with Ampure XP beads (Beckman coulter)

value: T cell

value: primary T cell

value: immune cell


title: Multiome, PBMC, COVID-19 patients 5, GEX

description:
Library name: PB05_GEX
10x Genomics


title: SCC cell, Itga6 high CD80 negative, replicate 1

city: Chicago

first: weijie

last: guo

state: IL

address: 929 East 57th Street, GCIS W423N

institute: university of Chicago

description: Library name: a6Hi_CD80neg_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutdapt (v3.2)
Genes were counted by using kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: skin SCC

extract_protocol:
RNA was harvested using zymo Quick-RNA Microprep Kit
RNA libraries for RNA-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit following manufacturer's protocols.

value: skin SCC


title: RNA_TotalNK_NK11_3hr_3_12001_7

description: Library name: Sample_RNA_TotalNK_NK11_3hr_3_IGO_12001_7

value: Total NK cells

value: wild-type


title: Multiome, PBMC, COVID-19 patients 3, GEX

description:
Library name: PB03_GEX
10x Genomics

value: PBMC


title: Hipp 3month KO Mouse 5_2

description: Library name: samp05_2_Hipp_H8_S4

value: Brain

value: Single Batch


title: A549 WT, transfected with poly(I:C), 4sU-seq replicate 2

description:
Library name: BGXM001F
All samples are nascent RNA profiling by 4sU-seq

value: WT


title: RNA_TotalNK_Unstim_3hr_2_12001_2

description: Library name: Sample_RNA_TotalNK_Unstim_3hr_2_IGO_12001_2


title: A549 RNaseL-KO, mock-transfected, 4sU-seq replicate 1

description:
Library name: BGXM001C
All samples are nascent RNA profiling by 4sU-seq

value: mock-transfected with RNAiMAX


title: SCC cell, Itga6 high CD80 negative, replicate 2

description: Library name: a6Hi_CD80neg_2


title: Multiome, PBMC, COVID-19 patients 2, GEX

description:
Library name: PB02_GEX
10x Genomics


title: SSC 3month KO Mouse samp05_1

description: Library name: samp05_1_SSC_E3_S3

value: KO

value: SSC


title: mouse OT-1 CD8+ T cells, SIIQFEHL + IL-12 stimulated, STAT4, rep1

description: Library name: CD8_600k_STAT4_Q4H7IL12_fix_1

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie 2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as a control using narrow peak parameters with cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
The peak atlas was generated by merging via union of peaks called by each sample after filtering out bottom 25% of peaks by MACS2 calculated qValue. Resulting peak atlas was further filtered to only retain peaks that were called by two or more replicates within each sample group, as well as peaks that do not overlap the Encode’s DAC Exclusion List Regions (ENCFF547MET).
Assembly: mm10
Supplementary files format and content: NK_peakatlas_normCounts.tsv
Supplementary files format and content: CD8T_peakatlas_normCounts.tsv
Library strategy: CUT&Run

extract_protocol:
Following CUT&RUN preparation, DNA was extracted using the Qiagen MinElute Kit.
For library preparation, we used the KAPA Hyper Prep Kit and followed the kit's instructions. Amplification cycle number was determined by running qPCR after 4 cycles of amplification and assessing required additional cycles.

treatment_protocol: NK cells were stimulated with aNK1.1 for 3h (or unstimulated as control), sorted, and stimulated for 1h with IL-12. OT-1 CD8+ T cells were stimulated with the respective peptide ((presented by splenocytes) for 16h, sorted, and stimulated for 1h with IL12.

tag: cell count

tag: antibody

tag: stimulation

tag: replicate

tag: batch id


title: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_3_(250715_BT_Mm_P03)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_3
Biological replicate with on-slide dissection

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the mm10 Mus musculus reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the mm10 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .mm10.bw)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: brain tumor FFPE

extract_protocol:
dx.doi.org/10.17504/protocols.io.5jyl88pp7l2w/v1
CUTAC for FFPE Slides

value: brain tumor FFPE

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: Multiome, PBMC, COVID-19 patients 1, GEX

description:
Library name: PB01_GEX
10x Genomics


title: mouse OT-1 CD8+ T cells, SIINFEKL + IL-12 stimulated, STAT4, rep2

description: Library name: CD8_600k_STAT4_N4IL12_fix_2


title: mouse OT-1 CD8+ T cells, SIINFEKL + IL-12 stimulated, STAT4, rep1

description: Library name: CD8_600k_STAT4_N4IL12_fix_1


title: 19-1XX-week2 rep2

description: Library name: 19-1XX-week2 rep2


title: mouse OT-1 CD8+ T cells, SIIQFEHL + IL-12 stimulated, STAT4, rep2

description: Library name: CD8_600k_STAT4_Q4H7IL12_fix_2


title: Multiome, PBMC, healthy control 3, GEX

description:
Library name: HC03_GEX
10x Genomics


title: Peritoneal macrophage-like cells in vitro 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the hg19 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: cell culture

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide

tag: mouse strain

value: 8-12 weeks

tag: Sex

value: female


title: Seq-Scope-X-Spleen3

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description:
Library name: Seq-Scope-X-Spleen3
Seq-Scope-X-Spleen

data_processing:
Seq-Scope-X transcriptome data were processed using the Seq-Scope pipeline with adjustments for experimentally determined expansion factors, following the NovaScope and NEDA workflows. Processing included generation of spatial barcode maps, alignment to reference genomes, construction of spatial gene expression matrices, and clustering using Seurat v5.  Spatial factor discovery was performed using Latent Dirichlet Allocation, and FICTURE was used to project cell-type factors into raw pixel space. Microscopy images, which lacked fiducial markers, were aligned to transcriptomic data using QGIS and further processed with CellProfiler and Photoshop. Differential expression, clustering, and integration analyses were conducted on hexagonally binned data to enable spatial and functional interpretation.
Other data could be found at Deep Blue Repository at (https://doi.org/10.7302/kj26-7j44)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz Digital Gene Expression Data in Matrix Market Format
Supplementary files format and content: transcripts.sorted.tsv.gz Spatial Digital Expression Spreadsheet
Library strategy: Spatial Transcriptomics

source_name: spleen

growth_protocol: Mouse liver, colon, and spleen tissues were collected from 8-week-old male C57BL/6 wild-type mice, and brain tissue was obtained from a 6-month-old male mouse. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Michigan (protocol PRO00011369).  Human tonsil tissue was obtained from the UCLA Pathology Biobank as a discarded surgical specimen from an adult patient with chronic tonsillitis. The sample was fully de-identified prior to acquisition and classified as IRB-exempt under institutional and federal guidelines, with no access to identifiable patient information.

extract_protocol:
Fresh frozen tissues were cryosectioned, mounted on charged slides, fixed with formaldehyde, and permeabilized with methanol. Anchor probes were hybridized in a formamide-containing buffer under humidified conditions. Tissues were then embedded in a polyacrylate-based monomer solution, polymerized, and cleared using digestion buffer with Proteinase K.
Tissue expansion was performed by incubation in diluted SSC, and DAPI staining was used to assess tissue integrity. Expanded gels were trimmed for imaging and alignment, then placed onto Seq-Scope Chips. Probe release and transcript transfer were achieved by heat incubation, followed by standard Seq-Scope library preparation, omitting tissue digestion as tissues were not directly attached to the chip.

treatment_protocol: For spatial proteomic analysis, tissues were permeabilized with methanol, blocked with a BSA-containing solution, and incubated overnight with TotalSeq™-A oligonucleotide-tagged antibody cocktails. After washing and post-fixation, tissues were processed using the same embedding, clearing, and expansion steps as in the transcriptome workflow.  Library preparation was modified to capture antibody-bound DNA oligonucleotides. Following reverse transcription, antibody tag libraries were eluted, purified, amplified by AT-PCR and indexing PCR, size-selected to isolate ~250 bp fragments, and sequenced on an Illumina NovaSeq-X platform.

tag: tissue

value: spleen

value: Normal


title: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_4_(250715_BT_Mm_P04)

description:
Library name: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_4
Biological replicate with on-slide dissection

tag: cell type


title: Multiome, PBMC, healthy control 1, GEX

description:
Library name: HC01_GEX
10x Genomics


title: Peritoneal macrophages FACS sorted ex vivo 3

source_name: peritoneum


title: 19-28z-1A-week2 rep2

description: Library name: 19-28z-1A-week2 rep2

value: T cell

value: primary T cell

value: immune cell


title: 19-28z-week2

description: Library name: 19-28z-week2


title: NKCells_TimeCourse_scRNA

description: Library name: Pooled scRNA

data_processing:
The cell–gene count matrix was constructed using the 10x Cell Ranger (v7.1.0) pipeline based on mm10 2020-A reference. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. After mitochondrial and doublet cleanup, the raw count matrix was normalized by median library size normalization followed by log transformation.
Assembly: mm10
Supplementary files format and content: HTO_doubletFiltered.h5ad
Supplementary files format and content: adataGEX_processed.h5ad

value: Spleen

value: Total NK cells

tag: genotype

value: wild-type

value: MCMV


title: 19-28z-1A-week2 rep3

description: Library name: 19-28z-1A-week2 rep3


title: 19-1XX-week2 rep1

description: Library name: 19-1XX-week2 rep1


title: Peritoneal macrophage-like cells in vitro 3


title: 19-28z-1A-week2 rep1

description: Library name: 19-28z-1A-week2 rep1


title: Multiome, PBMC, healthy control 2, GEX

description:
Library name: HC02_GEX
10x Genomics

value: PBMC


title: mouse NK cells, IL-12 stimulated, STAT4, rep2

description: Library name: mNK_400k_STAT4_IL12_2

source_name: NK

value: NK


title: Peritoneal macrophages FACS sorted ex vivo 1


title: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_1_(250715_BT_Mm_P01)

description:
Library name: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_1
Biological replicate with on-slide dissection


title: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_2_(250715_BT_Mm_P02)

description:
Library name: FFPE-CUTAC_RNAPol2-Ser5_Normal_brain_onslide_2
Biological replicate with on-slide dissection


title: Seq-Scope-X-DMAA-Spleen

description:
Library name: Seq-Scope-X-DMAA-Spleen
Seq-Scope-X-DMAA-Spleen

tag: treatment


title: mouse OT-1 CD8+ T cells, SIINFEKL + IL-12 stimulated, input, rep1

description: Library name: CD8_150k_input_N4IL12_fix_1

value: input


title: 19-28z-1A-week1 rep3

description: Library name: 19-28z-1A-week1 rep3


title: mouse NK cells, IL-12 stimulated, STAT4, rep3

description: Library name: mNK_400k_STAT4_IL12_3


title: 19-1XX-week1 rep3

description: Library name: 19-1XX-week1 rep3


title: Seq-Scope-X-oYoLINK2

description:
Library name: Seq-Scope-X-oYoLINK2
Seq-Scope-X-oYoLINK2

source_name: muscle

value: muscle

value: C57BL/6 CKM-TD


title: Seq-Scope-X-Spleen

description:
Library name: Seq-Scope-X-Spleen
Seq-Scope-X-Spleen


title: 19-28z-1A-week1 rep2

description: Library name: 19-28z-1A-week1 rep2


title: 19-1XX-week1 rep1

description: Library name: 19-1XX-week1 rep1


title: Microglia-like cells in vitro 3


title: Microglia-like cells in vitro 1


title: Peritoneal macrophages FACS sorted ex vivo 2


title: 19-1XX-week1 rep2

description: Library name: 19-1XX-week1 rep2


title: Microglia-like cells in vitro 2


title: mouse NK cells, IL-12 stimulated, input, rep1

description: Library name: mNK_400k_input_IL12_1


title: Seq-Scope-X-Colon

description:
Library name: Seq-Scope-X-Colon
Seq-Scope-X-Colon

source_name: colon

value: colon


title: mouse NK cells, IL-12 stimulated, STAT4, rep1

description: Library name: mNK_400k_STAT4_IL12_1


title: mouse NK cells, antiNK1.1 + IL-12 stimulated, STAT4, rep2

description: Library name: mNK_400k_STAT4_aNK11IL12_2


title: Seq-Scope-X-Brain

description:
Library name: Seq-Scope-X-Brain
Seq-Scope-X-Brain

source_name: brain

value: brain


title: 19-28z-1A-week1 rep1

description: Library name: 19-28z-1A-week1 rep1


title: Seq-Scope-X-Spleen2

description:
Library name: Seq-Scope-X-Spleen2
Seq-Scope-X-Spleen


title: 19-28z-week1 rep3

description: Library name: 19-28z-week1 rep3


title: 19-28z-week1 rep2

description: Library name: 19-28z-week1 rep2


title: Microglia FACS sorted ex vivo 3

value: 8-12 weeks

value: female


title: Microglia FACS sorted ex vivo 2


title: lung PBS CD4+ T repeat3

data_processing:
The raw paired end reads were trimmed and quality controlled by Skewer with default parameters
STAR software was used to compare the preprocessed sequecnces with the reference genome sequences of sequenced species
STringTie was used to count the original sequence of known genes
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

extract_protocol:
RNA was harvested using Direct-zolTM RNA MicroPrep（Zymo research), 2ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Kit following manufacture's protocols

treatment_protocol: CD45-Epcam+Integrin β4+ cells, CD45-Epcam+Integrin β4- cells, and CD3+CD4+ T cells from 3 mice each group (PBS, flu D11) were sorted by FACS. RNA was harvested using EastepTM Super Total RNA extraction kit（Promega), 2ug of total RNA was used for the construction of sequencing libraries

value: lung

value: CD4+ T cells

value: WT

value: PBS


title: lung PBS CD4+ T repeat2


title: Microglia FACS sorted ex vivo 1


title: murine AT2s-2

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

description: Library name: SK8

data_processing:
Quality of sequenced reads were assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
PolyA/T tails were trimmed using Cutadapt(Martin M et al., EMBnet journal,2011).
Adaptor sequences were trimmed and reads shorter than 24 bp were trimmed using Trimmomatic(Bolger AM et al., Bioinformatics,2014).
Normalization and extraction of differentially expressed genes (DEGs) between samples were performed using an R package, DESeq2(Love MI et al.,Genome Biology, 2014).
Assembly: GRCm38
Supplementary files format and content: tab delimited text file includes FPKM for each sample

source_name: Primary cells

growth_protocol: The FACS-purified primary murine AT2s were seeded on collagen-1 or on fibronectin in 12-well plates.

extract_protocol:
For total RNA extraction, cells were resuspended in TRIzol reagent (Thermo Fisher Scientific, 15596026) and total RNA was extracted using a Direct-zol RNA Microprep kit (Zymo, R2061) with DNase I treatment according to the manufacturer’s protocol.
Purified RNA (1 µg) from each sample was enriched for Poly-A RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, #E7490). Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, #E7770).

value: Lung

value: primary cultured murine AT2s

value: days 5 on collagen-1


title: mutine AT2s-3

description: Library name: SK9


title: 19-1XX-preinfusion rep3

description: Library name: 19-1XX-preinfusion rep3

value: T cell

value: primary T cell

value: immune cell


title: Kupffer cell-like cells in vitro 3


title: 19-1XX-preinfusion rep1

description: Library name: 19-1XX-preinfusion rep1


title: lung PBS Integrin β4+ repeat3

source_name: lung

value: distal airway epithelial cells


title: Kupffer cell-like cells in vitro 2


title: murine AT1s-3

description: Library name: SK6

value: primary cultured murine AT1s

value: days 9 on fibronectin


title: murine AT1s-2

description: Library name: SK5


title: Peritoneal macrophage-like cells in vitro 1


title: 19-1XX-preinfusion rep2

description: Library name: 19-1XX-preinfusion rep2


title: lung PBS Integrin β4+ repeat2


title: 19-28z-1A-preinfusion rep3

description: Library name: 19-28z-1A-preinfusion rep3


title: Kupffer cells FACS sorted ex vivo 3

source_name: liver


title: Seq-Scope-X-oYoLINK1

description:
Library name: Seq-Scope-X-oYoLINK1
Seq-Scope-X-oYoLINK1

value: muscle

value: C57BL/6 CKM-TD

value: Normal


title: murine PATS-3

description: Library name: SK3

value: primary cultured murine PATS

value: days 5 on fibronectin


title: Kupffer cell-like cells in vitro 1

value: 8-12 weeks

value: female


title: murine AT1s-1

description: Library name: SK4

value: WT


title: Kupffer cells FACS sorted ex vivo 2


title: 19-28z-1A-preinfusion rep2

description: Library name: 19-28z-1A-preinfusion rep2


title: lung PBS CD4+ T repeat1

value: lung

value: CD4+ T cells

value: PBS


title: 19-28z-week1 rep1

description: Library name: 19-28z-week1 rep1

value: T cell


title: lung PBS Integrin β4- repeat3

value: alveolar epithelial cells


title: murine PATS-1

description: Library name: SK1

value: Lung


title: murine PATS-2

description: Library name: SK2


title: 19-28z-1A-preinfusion rep1

description: Library name: 19-28z-1A-preinfusion rep1

value: primary T cell

value: immune cell


title: lung PBS Integrin β4- repeat1


title: Kupffer cells FACS sorted ex vivo 1


title: lung PBS Integrin β4- repeat2


title: Alveolar macrophage-like cells in vitro 3


title: cultured cortical astrocyte, control, 3days, 2

city: Sendai

first: Momono

last: Segawa

state: Miyagi

address: Katahira 2-1-1, Aoba-ku

department: Graduate School of Life Sciences

country: Japan

institute: Tohoku University

description: Library name: Sample17

data_processing:
The raw data underwent quality control with fastp (v0.23.4), followed by alignment to the mouse genome (mm39) with Salmon (v1.8.0).
Gene count matrices and TPM matrices  were generated using the tximport (v1.34.0) and TxDb.Mmusculus.UCSC.mm39.knownGene (v3.20.0) libraries in R.
Assembly: mm39
Supplementary files format and content: csv file includes raw counts for each sample in 90-min group
Supplementary files format and content: csv file includes raw counts for each sample in 3-days group

growth_protocol: Cells were plated onto plates pretreated with poly-L-lysine (Sigma-Aldrich, #P2336) at 37°C under 5% CO₂, using high-glucose Dulbecco’s Modified Eagle Medium (DMEM, Wako) supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin (PS, Wako). Cells were transferred to new dishes before confluence.

extract_protocol:
Total RNA was collected from cultured astrocytes after 90 minutes after DCZ application, using Phenol-chloroform based RNA extraction. For, experiment aimed at assessing the long-term effect of DREADD stimulation, the cells were treated with DCZ for 90 min and the medium was replaced to a fresh medium without DCZ. Then, the RNA was collected from the culture three days after.
RNA libralies for RNA-seq were prepared by Novogene. Briefly, the purified total RNA samples underwent mRNA purification, poly-A mRNA enrichment library preparation.

treatment_protocol: Plasmid transfection was performed using HilyMax reagent (Dojindo) according to the manufacturer’s instructions. The medium was replaced to a fresh medium on the next day of transfection. Cultured astrocytes were treated with DCZ (8μM, Deschloroclozapine dihydrochloride; MedChemExpress, #HY-42110A) for 90 min, seven days after plasmid transfection.

value: brain

value: cultured cortical astrocyte

value: Control (mCherry) + DCZ, 3days


title: cultured cortical astrocyte, control, 3days, 3

description: Library name: Sample18


title: lung flu D11 CD4+ T repeat2

value: flu D11


title: 19-28z-preinfusion rep2

description: Library name: 19-28z-preinfusion rep2


title: cultured cortical astrocyte, control, 3days, 1

description: Library name: Sample16


title: lung flu D11 CD4+ T repeat1


title: Alveolar macrophage-like cells in vitro 1


title: cultured cortical astrocyte, hM3Dq, 3days, 3

description: Library name: Sample15

value: hM3Dq + DCZ, 3days


title: lung flu D11 Integrin β4+ repeat2

value: distal airway epithelial cells


title: Alveolar macrophage-like cells in vitro 2

value: 8-12 weeks


title: Alveolar macrophages FACSsorted ex vivo 2

value: female


title: CAOV3_Bezafibrate_Ascites_Rep3

first: Jen-Tsan Ashley

last: Chi

address: 101 Science Dr

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Trimmomatic v0.39 was used to trim raw reads
STAR v2.7.9a was used to align reads to the transcriptome and the genome
RSEM v1.3.3 was used to generate raw counts, TPM and FPKM values
DESeq2 v1.28.1 was used for pairwise differential analysis
GSEA v4.2.3 and MSigDB v7.4 was used for pathway analysis
Assembly: GRCh38 human genome build and GENCODE v39 annotation
Supplementary files format and content: TSV file includes raw counts for each sample

source_name: ovary

growth_protocol: CAOV3 cells were maintained in DMEM media, supplied with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed with PBS and RNA was harvested using the Rneasy mini kit (Qiagen). RNA extracts were further treated with the RNAse-free DNAse set (Qiagen). 1 ug of RNA was sent for to the Duke SGT facility for library prep and sequencing
Library was constructed by the Duke SGT facility

treatment_protocol: 2.5 x 10^5 CAOV3 cells were seeded in 1.5 mL of DMEM media supplied with 10% FBS and antibiotics in 6-well plates. 150 uL of ovarian cancer ascites (10%), or 200 uM bezafibrate (Sigma), or both were added to the cell media and cells were incubated with the treatment for 16 hours.

value: ovary

value: epithelial high grade serous

value: WT

value: Bezadibrate (200 uM) and 10% ovarian cancer ascites for 16 hours


title: lung flu D11 Integrin β4+ repeat1

value: lung


title: 19-28z-preinfusion rep1

first: Yuzhe

address: 1250 First Avenue

description: Library name: 19-28z-preinfusion rep1

value: T cell


title: 19-28z-preinfusion rep3

description: Library name: 19-28z-preinfusion rep3


title: lung flu D11 Integrin β4- repeat2

value: alveolar epithelial cells


title: CAOV3_Bezafibrate_Ascites_Rep1


title: cultured cortical astrocyte, hM3Dq, 3days, 2

description: Library name: Sample14


title: lung flu D11 Integrin β4- repeat1


title: Alveolar macrophages FACS sorted ex vivo 1


title: 5-M-V

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: Library name: 5-M-V

data_processing:
cellranger mkfastq
cellranger count
Assembly: GRCh38
Supplementary files format and content: h5 sparse matrix of feature counts

source_name: Liver

growth_protocol: 72hr post mono and or coculture cells were collected to carry out the scRNA seq

extract_protocol: Single-cell RNA sequencing was conducted using the 10X Genomics Chromium System (10X Genomics, Pleasanton, CA) by the Molecular Genomics Core at Moffitt Cancer Center and Research Institute. Following tissue harvest and dissociation, single-cell suspensions were prepared, washed twice with 1X PBS (calcium- and magnesium-free) containing 0.04% BSA (w/v), and resuspended in the same buffer according to the 10X Genomics cell preparation protocol.

treatment_protocol: Samples are from either mono (MP41) or coculture (MP41+LX2 coculture)

value: Liver

value: Epithelial


title: Alveolar macrophages FACS sorted ex vivo 3


title: CAOV3_Bezafibrate_Ascites_Rep2


title: Flu_immune_cells scRNAseq rep2

description: 10X Genomics

data_processing:
The demultiplexing, barcodes processing counting and aggregation were made using the Cell ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: tar file includes matrix files for each sample

extract_protocol:
Tissue resident immune cells (CD45+ EPCAM- CD31- i.v.CD45-) from influenza 11 dpi and PBS (control) lungs were isolated by FACS
Library was performed according to the manufacture's instructions(single cell 3' v3 protocol, 10x Genomics）

tag: strain

value: Immune cells


title: cultured cortical astrocyte, hM3Dq, 3days, 1

description: Library name: Sample13

value: brain

value: cultured cortical astrocyte


title: cultured cortical astrocyte, control, 90min, 3

description: Library name: Sample12

value: Control (EGFP) + DCZ, 90min


title: Flu_immune_cells scRNAseq rep1

description: 10X Genomics

value: flu D11


title: cultured cortical astrocyte, control, 90min, 2

description: Library name: Sample11


title: 1-E-V

description: Library name: 1-E-V

source_name: Uveal melanoma

value: Uveal melanoma


title: mouse NK cells, antiNK1.1 + IL-12 stimulated, STAT4, rep3

institute: Memorial Sloan Kettering Cancer Center

description: Library name: mNK_400k_STAT4_aNK11IL12_3

value: NK


title: CAOV3_Bezafibrate_Rep3

value: Bezadibrate (200 uM) for 16 hours


title: TC32-siNEG-30hr-biolrep3

first: Patrick

middle: J

last: Grohar

address: 1600 Huron Pkwy

institute: University of Michigan Medical School

description:
Library name: TC3230hrN3
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrN3

data_processing:
Sequence quality by FASTQc
low quality sequence removed with cutadapt v2.10
log2 ratios determined with  DESeq2 v1.32.0
Assembly: HG38
Supplementary files format and content: FASTq

growth_protocol: 10% FBS + L-gln

extract_protocol:
Purified on column
NEB Next Small RNA library

treatment_protocol: Plate on siRNA incubate for 30hours

value: Ewing sarcoma

value: siNEG


title: TC32-siNEG-30hr-biolrep2

description:
Library name: TC3230hrN2
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrN2

value: WT


title: lung PBS Integrin β4+ repeat1

value: distal airway epithelial cells

value: PBS


title: CAOV3_Bezafibrate_Rep2

value: ovary

value: epithelial high grade serous


title: CAOV3_Ascites_Rep3

value: 10% ovarian cancer ascites and DMSO for 16 hours


title: cultured cortical astrocyte, control, 90min, 1

description: Library name: Sample10


title: CAOV3_Bezafibrate_Rep1


title: cultured cortical astrocyte, rM3Ds, 90min, 3

description: Library name: Sample9

value: rM3Ds + DCZ, 90min


title: CAOV3_Ascites_Rep2


title: cultured cortical astrocyte, rM3Ds, 90min, 2

description: Library name: Sample8


title: TC32-siNEG-30hr-biolrep1

description:
Library name: TC3230hrN1
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrN1


title: CAOV3_Ascites_Rep1


title: TC32-Media-30hr-biolrep2

description:
Library name: TC3230hrM2
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrM2

value: Media


title: Brain coronal slice (between -2.03 and -2.18 mm posterior to the bregma), WT_SCDi

city: Montreal

first: Valerie

last: Mongrain

state: QC

address: 333 rue Saint-Antoine Est

department: Research center

country: Canada

institute: CRCHUM

description: Visium Spatial Gene Expression libraries comprise standard Illumina paired-end constructs that are flanked with P5/P7, necessary for binding to the Illumina flow cell. TruSeq Read 1 is used for priming and sequencing the 16 bp Spatial Barcode and 12 bp UMI, and TruSeq Read 2 is used for priming and sequencing the cDNA insert. The two 10bp sample indexes are sequenced in the i5 and i7 read respectively. Sequencing data from the libraries are provided for each sample here.

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger count pipeline. Spaceranger count takes a microscope slide image and FASTQ sequencing files and performs alignment, tissue detection, fiducial detection, and barcode/UMI counting. The pipeline uses Visium Spatial Barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis.
Sequence were aligned to mus musculus mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: _possorted_genome_bam.bam: binary files containing position-sorted, genome-aligned sequencing reads
Supplementary files format and content: _raw_feature_bc_matrix.h5: HDF5 files storing raw counts of features (e.g., genes) associated with barcodes
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: alignes_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactor in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: Brain

growth_protocol: Habituation to individual cage for 10 days; housing in a 12h light:12h dark cycle with food and water available ad libitum

extract_protocol:
10X Genomics protocol CG000239-Rev D
Paired-end dual indexed RNA sequencing with Illumina NovaSeq 6000 S4 PE100 sequencer (Genome Quebec Innovation Centre, Montreal, QC, Canada), at a sequencing depth of approximately 2500M read pairs per sample. RNAseq was performed according to instructions of 10x Genomics for the Visium Spatial Gene Expression kit: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.

treatment_protocol: stearoyl-CoA desaturase inhibitor (SCDi; final infusion concentration of 80 µM; 0.11 μl/hour infusion rate) or vehicle (DMSO + aCSF); intracerebroventricular administration for 28 days

value: Brain

value: B6129SF2/J, Jackson Laboratory strain #101045

value: female

value: Stearoyl-CoA desaturase inhibitor (SCDi; final infusion concentration of 80 µM; 0.11 μl/hour infusion rate)


title: TC32-Media-30hr-biolrep3

description:
Library name: TC3230hrM3
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrM3


title: cultured cortical astrocyte, rM3Ds, 90min, 1

description: Library name: Sample7

value: brain

value: cultured cortical astrocyte


title: CAOV3_Control_Rep3

value: DMSO


title: Brain coronal slice (between -2.03 and -2.18 mm posterior to the bregma), 3xTg_veh

value: B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax, Jackson Laboratory MMRRC strain #034830-JAX

value: Control (DMSO; 0.11 μl/hour infusion rate)


title: PBS_immune_cells scRNAseq

first: pei

address: 393 Middle Huaxia Road

description: 10X Genomics

value: lung

value: Immune cells

value: WT


title: Brain coronal slice (between -2.03 and -2.18 mm posterior to the bregma), WT_Veh


title: TC32-Media-30hr-biolrep1

description:
Library name: TC3230hrM1
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrM1

value: Ewing sarcoma


title: TC32-siEF-30hr-biolrep3

description:
Library name: TC3230hrEF3
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrEF3

value: siEF


title: Liver, SSO, rep4

city: china

first: Yao

last: Tao

state: zhejiang

address: zhejiang province

institute: First Affiliated Hospital, Zhejiang University

data_processing:
In this study, we implemented a series of precise quality control and analysis steps for the sequenced data collected. Initially, Trim Galore version 0.6.1 was used for quality control of raw reads, removing those with Phred quality scores below 20 and lengths less than 35 bp after trimming. Subsequently, these quality-filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using HISAT2 version 2.2.1 with default settings. Post-alignment, duplicates were marked using Sambamba version1.0.1. Quantification of the aligned reads was then conducted using featureCounts version 2.0.2, based on gene IDs from the mouse Gencode version 20. Finally, normalization of read counts and differential gene expression analysis were performed using the R package DESeq2.
Assembly: mm10
Supplementary files format and content: text files of normalized counts for every sample and every gene.

growth_protocol: 8-week-old C57BL/6J male mice were randomized into two groups for the experiment. n=8 mice each groups.

extract_protocol:
Total RNA was isolated from freshly frozen liver tissues of mice treated with SSO by TRIzol reagent (#T9424, Invitrogen), following their PHx surgery.
RNA library for RNA-seq was prepared as following: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments. The first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis.

treatment_protocol: 8-week-old C57BL/6J male mice were randomly splited into two groups with 8 mice each group. The mice in SSO treatment group were adminstered with  SSO at a dose of 40mg/kg and The mice in control group were injected with solvent as vehicle control one day before PHx surgery. Liver samples were collected 48 hours post-surgery for RNA sequencing.

value: Liver


title: CAOV3_Control_Rep2

value: ovary

value: epithelial high grade serous


title: CAOV3_Control_Rep1


title: Brain coronal slice (between -2.03 and -2.18 mm posterior to the bregma), 3xTg_SCDi

value: Brain


title: Liver, Vehicle, rep4


title: TC32-siEF-30hr-biolrep2

description:
Library name: TC3230hrEF2
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrEF2


title: TOV21G_Ascites_Rep_3

data_processing:
TrimGalore toolkit
The TrimGalore toolkit was used to trim low quality bases via Cutadapt (removed <20nt reads)
Reads were mapped to the GRCh38v93 version of human genome using the STAR RNA-seq alignment tool
Counts were compiled using the HTSeq tool
DESeq and GSEA were used for normalization, differential expression, and gene enrichment analyses
Assembly: GRCh38v93 human genome
Supplementary files format and content: CSV file includes normalized counts for each sample

growth_protocol: CAOV3 and TOV21G cells were maintained in DMEM media, supplied with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

treatment_protocol: 2.5 x 10^5 CAOV3 and TOV21G cells were seeded in 1.5 mL of DMEM media supplied with 10% FBS and antibiotics in 6-well plates. 150 uL of ovarian cancer ascites (10%) was added to the cell media and cells were incubated with the ascites for 16 hours.

value: epithelial clear

value: 10% ovarian cancer ascites for 16 hours


title: CD36+ MDM, rep3

source_name: Macrophage

growth_protocol: 8-week-old C57BL/6J male mice or MDM-Ern1KO male mice were initially acclimatized under controlled conditions. These were subjected to 2/3 PHx and sacrificed for liver samples 48 hours post-surgery.

extract_protocol:
Total RNA was isolated using TRIZol (#T9424, Invitrogen) from four specific cell populations sorted from mouse liver tissues: Kupffer cells, LY6C+ MDMs, CD36+ MDMs, and CD36+ MDMs of Mac-Ern1KO mice.
RNA library for RNA-seq was prepared as following: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments. The first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis.

treatment_protocol: The mice were subjected to 2/3 PHx and sacrificed for liver samples 48 hours post-surgery. Liver tissues were subsequently enzymatically digested for single cell suspentions before sorting distinct macophages subpopulations, including Kupffer cells, LY6C+ MDMs, CD36+ MDMs retrived from C57BL/6 wild type mice, as well as CD36+ MDMs retrived MDM-Ern1KO mice. For each of these macrophage subpopulations, we prepared three replicate samples. Each samples were pooled of the cells from three or more mice.

value: Macrophage


title: cultured cortical astrocyte, hM4Di, 90min, 3

description: Library name: Sample3

value: brain

value: hM4Di + DCZ, 90min


title: MDM-Ern1KO_CD36+ MDM, rep3


title: TOV21G_Ascites_Rep_2


title: cultured cortical astrocyte, hM3Dq, 90min, 3

description: Library name: Sample6

value: cultured cortical astrocyte

value: hM3Dq + DCZ, 90min


title: TC32-siEF-30hr-biolrep1

description:
Library name: TC3230hrEF1
Sample name in siEWS-FLI_RNAseq_genes_count.csv: TC3230hrEF1


title: TOV21G_Ascites_Rep_1


title: KC, rep3


title: TOV21G_Control_Rep_3


title: LY6C+ MDM, rep3


title: deltaCTR mycLARP6-3

city: Oxford

first: Faraz

middle: K.

last: Mardakheh

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: CLIP_CTR1_3

data_processing:
iCLIP data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were uploaded on the webserver iMAPS (imaps.goodwright.com) for primary iCLIP data analysis. The human genome GRCh38.p13 GENCODE V42 was used with the primary assembly comprehensive annotation. Reads were first trimmed with TrimGalore! (software developed by Felix Krueger), to remove remaining adapters and low-quality reads, then pre-mapped to rRNA and tRNA sequences with Bowtie 2 and discarded. This step ensured that reads mapping to repetitive regions were not misaligned to mRNA. The remaining unmapped reads were then mapped to the genome with STAR. PCR duplicates were removed with UMI-tools based on the presence of identical UMIs in reads mapping to the same position. The exact crosslink position was then identified as the first nucleotide after the experimental barcode, and this data was downloaded from the webserver and processed further offline. The crosslink information was used to call the peaks, which represent the binding sites of LARP6, for each individual replicate. The peak caller Clippy (version 1.5.0) was used with the following settings: rolling mean 15; minimum counts per gene 3; minimum counts per peak 3; prominence 1 (default); peak threshold 0.4 (default). The peaks called for the individual replicates were then combined into one file per mutant by merging the peaks and summing their peak scores using bedtools (version 2.30.0), with the peak scores indicative of the binding strength. Background normalisation was performed by subtracting the peaks that were called in the parental negative control from each combined peak file, using bedtools.
Total RNA-Seq data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were trimmed with TrimGalore! (version 0.6.10) to remove the remaining adapter sequences and low-quality reads. Reads were then mapped to the human genome GRCh38.p13 GENCODE V42 with STAR (version 2.7.10b). Default parameters were used, and gene counts were generated directly from the mapping step by enabling the –quantMode GenerateCounts option. The gene counts from the RNAseq were used for iCLIP data normalisation. The iCLIP peak scores were normalised for transcript abundance according to the following formula: normalised peak score=((peak score)/(gene count)*1000).
Assembly: GRCh38.p13 GENCODE V42
Supplementary files format and content: peaks.bed (iCLIP peak scores)
Supplementary files format and content: .out (INPUT RNA-seq read counts)
Library strategy: iCLIP

growth_protocol: U-87 MG (PURCHASED FROM ATCC) cells were grown in DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. U-87 MG myc-LARP6 inducible cell lines were grown as above, and myc-LARP6 expression was induced with 60 ng/mL Doxycycline. All cells were maintained in a humidified incubator at 37°C, 5% CO2. Cells were passaged consistently before reaching confluence with Trypsin-EDTA (Gibco), and tested regularly for mycoplasma, using the MycoAlert Mycoplasma Detection Kit (Lonza Bioscience).

extract_protocol:
For iCLIP, cells were UV-C crosslinked, lysed, and subjected to iCLIP as indicated in (https://doi.org/10.1101/2024.09.20.614075). Briefly, 20 million cells per condition were grown in 15 cm dishes and myc-LARP6 mutants were induced with 60 ng/mL doxycycline for 24 hours. Cells were crosslinked on ice at 150 mJ/cm2 at 254 nm in a Hoefer Scientific UV crosslinker to form covalent bonds between RBPs and RNAs that were in direct contact, then scraped in PBS and pelleted. Cell pellets were lysed in iCLIP lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate, cOmplete protease inhibitor cocktail (Roche), 1 mM PMSF), cleared, and diluted to 1 mg/mL in 1 mL volume. Samples were then treated with 0.2 units/mL lysate RNase I (Thermo Scientific, catalogue number EN0602) and 2 μL Turbo DNase (Ambion) for 3 minutes at 37°C to partially digest the RNA. 50 μL Dynabeads Protein G (Invitrogen) per sample were first conjugated with 4 μg (10 μL) mouse anti-myc-tag antibody (Cell Signaling, 9B11) for one hour at RT in a rotating wheel, then added to the samples to perform the immunoprecipitation (IP) for one hour at 4°C in a rotating wheel. After the IP, samples were stringently washed twice with high-salt wash buffer (50 mM Tris-HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate), then once with PNK wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20).
For Input RNA-seq, cells grown under the same conditions as the ones used in the iCLIP experiment was subjected to RNA extraction with TRIzol. The purified RNAs were quantified with the Qubit RNA High-sensitivity assay, and the quality was validated with the Agilent High Sensitivity RNA ScreenTape assay, with all samples having a RIN ≥ 9.3. The whole transcriptome RNAseq library preparation and sequencing was outsourced to Novogene.
For iCLIP, The RNA fragments were dephosphorylated on the beads at the 3’ end, followed by 3’ end ligation of different barcoded adapters, to allow for downstream multiplexing of each replicate into one sample. The samples were then eluted from the beads, run on an SDS-PAGE gel, followed by isolation of the RNA fragments and subsequent library preparation as described previously. The amplified libraries were quantified and validated with the Qubit dsDNA High-sensitivity and Agilent D1000 high sensitivity ScreenTape assays, pooled in an equimolar ratio, and deep sequenced on an Illumina NextSeq 500 instrument, using a single-end 100 nt workflow. Sequencing was performed at the Barts and The London Genome Centre.
For Input RNA-seq, rRNA depletion whole transcriptome sequencing using two protocols (short and long RNAs) was performed by Novogene (https://www.novogene.com/eu-en/services/research-services/transcriptome-sequencing/whole-transcriptome-sequencing/)

treatment_protocol: 60 ng/mL Doxycycline for 24hrs.

value: Glioblastoma

value: LARP6 deltaCTR

value: myc-tag


title: deltaLa-Mod mycLARP6-3

description: Library name: CLIP_LaMod_3

value: LARP6 deltaLa-module


title: cultured cortical astrocyte, hM4Di, 90min, 1

description: Library name: Sample1


title: cultured cortical astrocyte, hM3Dq, 90min, 2

description: Library name: Sample5


title: deltaNTD mycLARP6-3

description: Library name: CLIP_NTD_3

value: LARP6 deltaNTD


title: TOV21G_Control_Rep_2

value: WT


city: Winston-Salem

first: Keith

last: Gagnon

address: 575 Patterson Ave

department: Biochemistry

institute: Wake Forest Baptist Medical Center

description: Library name: IDT synthesized fragment (asp gene, no Mods)

data_processing:
Reads were called from the POD5 files with Dorado software (v1.0.0) with settings for RNA modifications (RNA basecalling model rna004_130bps_sup@v5.2.0), and aligned to a HIV-1 genome (AF324493.2, included as NL43_AF324493.2_R2R.fasta), producing a BAM file.
modkit was used to generate a bedgraph of each modification, using a command such as: modkit pileup [location_of_BAM] --ref [loc_of_reference] -t 18 --region NL43_AF324493.2_R2R --max-depth 10000000 --bedgraph ./ --filter-threshold .7 --motif DRACH 2 --prefix m6A
Bedgraph files were filtered to remove modification calls at positions with fewer than 10 reads to reduce noise from low-call areas.
Reads unaligned to HIV-1 reference genome were removed from BAM file to reduce file size and protect PLWH data.
Assembly: NL43_AF324493.2_R2R.fasta
Supplementary files format and content: bedgraph files. Tab-seperated text files, one per modification. Columns in file are: column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters 5 | total calls | Number of calls passing filters, both modified and unmodified column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position  int 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 | total calls | Number of calls passing filters, both modified and unmodified column  name  description  type ------------------------------------ 1  chrom  name of reference sequence from BAM header  str 2  start position  0-based start position  int 3  end position  0-based exclusive end position  int 4 fraction modified Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 total calls Number of calls passing filters, both modified and unmodified int

organism: Human immunodeficiency virus 1

source_name: Synthesized

growth_protocol: Jurkat cells (HIV repository) were cultured in RPMI-1640 medium supplemented with 10% FBS, 1x P/S, and non-essential amino acids (NEAA).  CD4+ T cells were harvested from whole blood tubes from unidentified healthy donors or leukopaks (Red Cross Blood). Negative cell separation was conducted following the vendors protocol with EasySep Direct Human CD4+ T cell Isolation Kits or RosetteSep Human CD4+ T cell Enrichment Cocktail (Stem Cell Technologies) with Lymphoprep (Stem Cell Technologies) as density medium, respectively. Before infection, we activated T cells by adding anti-CD3 and anti-CD28 antibodies along with IL-2.

extract_protocol:
Total RNA was harvested via TRIZol (Invitrogen), using the manufacturer's protocol.
After extraction, total RNA was divided, and approximately 15-20 μg was used for poly-A selection and RNaseH ribosomal RNA depletion. For poly-A selection, the NEBNext High Input Poly(A) mRNA Isolation Module (E3370S) was used according to the manufacturer's protocol. For the RNaseH treatment, total RNA was hybridized with DNA oligonucleotides complementary to rRNA. The solution was heated to 95°C and slow cooled to 65°C to enable oligonucleotide hybridization. RNase H (McLabs, HTRH-200) was added (200 U) and the solution incubated at 65°C for 5 min to degrade rRNA. DNA was then degraded using 150 U of Turbo DNase (Invitrogen, AM2239) at 37°C for 20 min. RNA was then purified using AMPure XP beads. A polyadenylation reactions was performed using E. coli Poly(A) Polymerase (New England Biolabs, M0276L).  The final library was loaded on a PromethION RNA flow cell (FLO-PRO004RA) and sequenced on a PromethION P2 solo using MinKNOW (v. 24.06.10) with POD5 and live base-calling on.

treatment_protocol: Jurkat cells: When infecting with replicative NL4-3 and pHIVdEnv-GFP, we used a high cell density of ~2.5 x 106 cells/mL with a working concentration of HIV p24 (determined by ELISA) of 500-600 ng/mL. Cells were harvested at 45-48 h post-infection.  CD4+ T cells: Activation was confirmed 3 days post-treatment by measuring CD4+/CD69+ double-positive cell percentage by flow cytometry.  Day 0, isolate CD4+ T cells from blood and activate T cells  Day 3: test activation % and infect CD4+ T cells with WT-HIV.  Day 4: TRIUMEQ cART treatment when applicable  Day 6: harvest CD4+ T cells for TRIzol lysis as well as quantify infection rate by flow cytometry with KC57 antibody  cART treatment: To model current cART therapy, we added TRIUMEQ with the respective concentrations for each of the antiretrovirals based on reported plasma levels: ABC 140 ng/mL, 3TC 670 ng/mL, DTG 3.9 ug/mL.

value: Synthesized


title: TOV21G_Control_Rep_1

value: ovary