title: K562, RNA, RepC

city: Seattle

first: Abby

middle: V

last: McGee

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Library name: LAMPRA RNA RepC

data_processing:
PacBio consensus reads were processed through a series of custom scripts to associate unique barcodes with sCRLs. First, all reads were oriented to the same direction to ensure consistent downstream processing. Next, elements and barcodes were extracted by identifying fiducials – known fixed sequences that serve as positional markers – flanking the insert regions and extracting the downstream sequences following the fiducials. Element sequences were then annotated by comparing extracted sequences against the designed enhancer, synthetic insulator, and shuffled negative control sequences. Sequences that exactly matched the first 12 bp of a known element were annotated with the corresponding element name and orientation. Random barcode sequences were extracted using the same method, identifying 16 bp sequences between the fiducial sequences flanking the barcode insertion region. Each read was represented as the combination of elements in slots 1-5 and its corresponding barcode, and counts were collapsed by aggregating reads by unique element-barcode combinations to generate a final sCRL-barcode dictionary.  Sequencing data were demultiplexed using bcl2fastq. Forward and reverse barcode reads were merged and error-corrected using PEAR (v0.9.11) with parameters set to the barcode length (options -v 16 -m 16 -n 16 -t 16). Using custom Python and R scripts, successfully assembled barcode reads were combined with UMI reads, BC-UMI pairs were counted, and the read and UMI counts per BC were determined. The read and UMI counts for barcodes present in the initial plasmid library (determined a priori; see above) were collected for downstream analysis.
Assembly: hg19
Supplementary files format and content: BC-sCRL association dictionary
Supplementary files format and content: LAMPRA activity scores

growth_protocol: K562 cells (ATCC, CCL-243) were grown in RPMI 1640 medium (Thermo Fisher, 11875119), supplemented with 10% FBS (Fisher Scientific, Cytiva HyClone fetal bovine serum, SH3039603) and 1× penicillin/streptomycin (Thermo Fisher, 15140122). Cells were kept at 37 °C and 5% CO2, and passaged every 2-3 days.

extract_protocol:
Genomic DNA and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, 80204) with vortexing to lyse cells.  Libraries were electroporated in NEB 3020K electro-competent cells. Plasmids from cells were bottlenecked and extracted using the ChargeSwitch MidiPrep kits per manufacture's instructions.
MPRA amplicon libraries from genomic DNA were generated in two steps of PCR amplification with OneTaq (NEB, M0482S). Approximately 10 µg of genomic DNA input was used per replicate. For the first low-cycle PCR (PCR1), gDNA was mixed with 200 µl 2× OneTaq master mix, 2 µl 100 µM indexed P5 primer (rand-P5-E##), 2 µl 100 µM P7-pLSmp-assUMI-gfp primer, and water to a final volume of 400 µl. This mix was prepared for each replicate and then split over 16 wells for PCR. Cycling parameters were: 2 min at 95 °C, followed by three cycles of 20 s at 95 °C, 30 s at 55 °C, and 2 min at 72 °C, with a final extension of 5 min at 72 °C, followed by a 4 °C hold. Primer P7-pLSmp-assUMI-gfp contains ten random nucleotides (Ns) to serve as a pseudo-UMI (hereafter referred to as UMIs for brevity) to correct for PCR jackpotting. Reactions were pooled for each replicate, cleaned up with AMPure XP beads (Beckman Coulter, A63881) at 1.8×, and eluted in 97 µl of 10 mM Tris pH 8.0. A second round of PCR (PCR2) was performed for each replicate with primers P5 and P7, which amplified the library for sequencing without adding additional UMIs. The entire 97 µl of eluate from PCR1 was used as input and combined with 100 µl OneTaq master mix, 1 µl 100× SYBR Green (Thermo Fisher, S7563), 1 µl 100 µM P5 primer, and 1 µl 100 µM P7 primer. This mix was split over 8 reactions for each replicate. Libraries were amplified and monitored in real-time by qPCR with 2 min at 95 °C, followed by cycles up to the qPCR inflection point consisting of 15 s at 95 °C, 20 s at 60 °C, and 2 min at 72 °C. Libraries were then pooled by replicate and cleaned up with AMPure XP beads (Beckman Coulter, A63881) at 1.8×.  Amplicon libraries from RNA were obtained by first DNase-treating the RNA (up to 100 µl total RNA) by adding 0.1 volume 10× TURBO DNase buffer and 0.5 µl TURBO DNase (Thermo Fisher, AM1907), then incubating at 37 °C for 30 min. An additional 0.5 µl of TURBO DNase was then added followed by a second incubation. DNase was removed by adding 0.1 volume of DNase Inactivation Reagent. For each replicate, 40 µg of DNase-treated RNA was then used for eight reverse transcription reactions. For each reaction, 5 µg RNA was mixed with 1 µl 2 µM P7-pLSmp-assUMI-gfp and 1 µl of 10 mM dNTPs (NEB, N0447L), incubated at 65 °C for 5 min, and placed on ice. 6 µl of reverse transcription master mix was then added (4 µl 5× FS buffer, 1 µl 0.1 M dithiothreitol, and 1 µl SSIV (Thermo Fisher, 18091050)), and the reaction was incubated at 55 °C for 60 min, followed by 80 °C for 10 min. Each reverse transcription reaction was combined and split into 32 total PCR reactions per replicate. For PCR1, reactions contained 160 µl template, 640 µl 2× OneTaq master mix, 8 µl 100 µM indexed P5 primer (rand-P5-E##), 8 µl 100 µM P7 primer, and 464 µl water, and were split over 32 wells with the following cycling parameters: 2 min at 95 °C, followed by three cycles of 20 s at 95 °C, 30 s at 55 °C, and 2 min at 72 °C, with a final extension of 5 min at 72 °C, followed by a 4 °C hold. Reactions were pooled by replicate, cleaned up with AMPure XP beads at 1.8×, and eluted in 291 µl of 10 mM Tris pH 8.0. For PCR2, the entire 291 µl of eluate from PCR1 was used as input and combined with 300 µl OneTaq master mix, 3 µl 100× SYBR Green (Thermo Fisher, S7563), 3 µl 100 µM P5 primer, and 3 µl 100 µM P7 primer. This mix was split over 24 reactions for each replicate. Libraries were amplified and monitored in real-time by qPCR with 2 min at 95 °C, followed by cycles up to the qPCR inflection point consisting of 15 s at 95 °C, 20 s at 60 °C, and 2 min at 72 °C. Libraries were then pooled by replicate.  The three DNA libraries were pooled together, as were the three RNA libraries, and these two final pools were size-selected on 1% agarose gel for the expected band (156 bp). The RNA and DNA pooled libraries were quantified with Qubit dsDNA HS (Thermo Fisher) and diluted to 2 nM. Libraries were loaded at a ratio of 2:1 RNA:DNA and paired-end sequencing was performed on a NextSeq 2000 with the following primers and cycle numbers: read1 (BC forward): 16 cycles with primer TruSeq-R1; index1 (UMI): 10 cycles with primer randMPRAseq-I1; read2 (BC reverse): 16 cycles with primer randMPRAseq-R2; index2 (sample index): 10 cycles with primer TruSeq-I2.


title: 4_HKM7VBGXT.4.ACTCGCTA_AGAGGATA

status: Public on Jul 28 2026

type: SRA

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 4_SM-NBW7D_plate1
DHMT_0.5hr_a

library_source: transcriptomic

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

tag: cell line

tag: cell type

value: iPSC-derived excitatory neuron, astrocyte

tag: genotype

value: WT

tag: day

tag: guide rna

value: no guide

tag: barcode


title: K562, RNA, RepB

country: USA

description: Library name: LAMPRA RNA RepB


title: KO_18h4

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

description:
Library name: Sample 16
Column name in raw_read_quant.table.txt: KO_18h4

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

organism: Mus musculus

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from the femurs and tibias of male WT and Nur77-KO mice aged 6-12 weeks. The cells were differentiated into macrophages by culturing them in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 15% L929-conditioned medium, 1 mM sodium pyruvate, 1x MEM Non-Essential Amino Acids Solution, and 1x MEM Vitamin Solution for a period of 7 days. After the differentiation process, the cells were lifted, counted, and re-seeded at a density of 1 × 10^6 cells per ml.

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were stimulated with 100 ng/ml LPS for 0, 1, 5 and 18h

tag: tissue

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

value: cre

tag: treatment

value: 18h 100 ng/ml LPS


title: 3_HKM7VBGXT.3.ACTCGCTA_AGAGGATA

description:
Library name: 3_SM-NBW7D_plate1
DHMT_0.5hr_a


title: K562, RNA, RepA

description: Library name: LAMPRA RNA RepA


title: 2_HKM7VBGXT.2.ACTCGCTA_AGAGGATA

description:
Library name: 2_SM-NBW7D_plate1
DHMT_0.5hr_a


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells aged, biol repl2

city: Suzhou

first: zhengxia

last: Ni

state: Jiangsu

address: 188 Shizi Road

department: Department of Orthopedics

country: China

institute: The First Affiliated Hospital of Soochow University

description:
Library name: B2
counts_anno.txt: B2

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GCF_036323735.1
Supplementary files format and content: txt file includes gene counts for all Sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Bone Marrow Mesenchymal Stem Cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Bone Marrow Mesenchymal Stem Cells

value: aged


title: KO_18h3

description:
Library name: Sample 15
Column name in raw_read_quant.table.txt: KO_18h3


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells aged, biol repl3

description:
Library name: B3
counts_anno.txt: B3


title: KO_18h2

description:
Library name: Sample 14
Column name in raw_read_quant.table.txt: KO_18h2


title: K562, DNA, RepC

description: Library name: LAMPRA DNA RepC

library_source: genomic

molecule: genomic DNA


title: 1_HKM7VBGXT.1.ACTCGCTA_AGAGGATA

description:
Library name: 1_SM-NBW7D_plate1
DHMT_0.5hr_a


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells aged, biol repl1

description:
Library name: B1
counts_anno.txt: B1


title: K562, DNA, RepB

description: Library name: LAMPRA DNA RepB


title: KO_18h1

description:
Library name: Sample 13
Column name in raw_read_quant.table.txt: KO_18h1


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells Young, biol repl3

description:
Library name: A3
counts_anno.txt: A3

value: Young


title: 4_HKM7VBGXT.4.TCGACGTC_ATAGAGAG

description:
Library name: 4_SM-NBW7C_plate1
DHMT_48hr_LRP1_A_d

value: LRP1 knockdown


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells Young, biol repl2

description:
Library name: A2
counts_anno.txt: A2


title: KO_5h4

description:
Library name: Sample 12
Column name in raw_read_quant.table.txt: KO_5h4

value: 5h 100 ng/ml LPS


title: K562, DNA, RepA

description: Library name: LAMPRA DNA RepA


title: 3_HKM7VBGXT.3.TCGACGTC_ATAGAGAG

description:
Library name: 3_SM-NBW7C_plate1
DHMT_48hr_LRP1_A_d


title: KO_5h3

description:
Library name: Sample 11
Column name in raw_read_quant.table.txt: KO_5h3


title: RNA-Seq of Rattus norvegicus Bone Marrow Mesenchymal Stem Cells Young, biol repl1

description:
Library name: A1
counts_anno.txt: A1


title: Ribo-seq C2_RS Control replicate 2

city: San Diego

first: Khalyd

last: Clay

state: CA

address: 10550 N. Torry Pines. Rd.

institute: Scripps Research

description:
Library name: C2_RS
HEK293 ribosome-protected fragments. One processed gene-count matrix (RiboSeq_C1C2.27_29.gene_counts.clean.tsv) covers the two uploaded C1/C2 Ribo-seq libraries.

library_source: other

data_processing:
Raw paired-end reads were adapter-trimmed and merged with PEAR without 5-prime clipping. Empirical length windows were aligned to hg19; rDNA/rRNA-mapping reads were separated from genic reads, and a MAPQ >= 2 filter was applied to the genic branch. Annotation- and length-bin QC identified the 27-29 nt mRNA-associated footprint branch. P-site assignment, frame/periodicity QC, metagene profiles, and codon-occupancy estimates used the in-house riboWaltz/RiboToolkit pipeline. The uploaded processed file RiboSeq_C1C2.27_29.gene_counts.clean.tsv is a C1/C2-only gene-level count matrix derived from the 27-29 nt branch.
Remote GEO upload subfolder: RiboSeq
Ribo-seq raw FASTQ upload includes only C1_RS and C2_RS for this manuscript-use set.
Only one Ribo-seq processed data file is uploaded: RiboSeq_C1C2.27_29.gene_counts.clean.tsv.
Assembly: hg19
Supplementary files format and content: RiboSeq_C1C2.27_29.gene_counts.clean.tsv: gene-level 27-29 nt RPF raw count matrix for C1_RS and C2_RS.
Library strategy: Ribo-Seq

molecule: other

source_name: HEK293 (ATCC CRL-1573)

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 C with 5% CO2; mycoplasma testing every 6 months through TSRI.

extract_protocol:
For each sample, two 15-cm plates at approximately 80 percent confluency were harvested. Medium was removed, cells were washed three times with ice-cold 1x DPBS, scraped, pelleted, and flash-frozen. Cells were lysed in ice-cold mammalian polysome buffer containing Triton X-100, DTT, cycloheximide, DNase I, and nuclease-free water, homogenized on ice through a 26-gauge needle, and clarified at 20,000 x g for 10 min at 4 C.
Clarified lysate was digested with RNase I to generate ribosome-protected fragments. Monosomes were isolated by size-exclusion chromatography (MicroSpin S-400 HR). RNA was extracted without rRNA depletion, and 20-38 nt RPFs were PAGE-purified, end-phosphorylated, ligated to 5-prime and 3-prime TruSeq adapters, reverse-transcribed, PCR-amplified, and sequenced on Illumina paired-end 150 nt by CD Genomics.

treatment_protocol: Vehicle or minocycline (100 uM) for 12 h under basal conditions; harvested without heat shock for sequencing assays.

value: HEK293 (ATCC CRL-1573)

value: Control; compound:DMSO vehicle; dose:vehicle; duration:12 h

tag: batch


title: 2_HKM7VBGXT.2.TCGACGTC_ATAGAGAG

description:
Library name: 2_SM-NBW7C_plate1
DHMT_48hr_LRP1_A_d


title: KO_5h2

description:
Library name: Sample 10
Column name in raw_read_quant.table.txt: KO_5h2


title: Ribo-seq C1_RS Control replicate 1

description:
Library name: C1_RS
HEK293 ribosome-protected fragments. One processed gene-count matrix (RiboSeq_C1C2.27_29.gene_counts.clean.tsv) covers the two uploaded C1/C2 Ribo-seq libraries.


title: 1_HKM7VBGXT.1.TCGACGTC_ATAGAGAG

description:
Library name: 1_SM-NBW7C_plate1
DHMT_48hr_LRP1_A_d


title: KO_5h1

description:
Library name: Sample 9
Column name in raw_read_quant.table.txt: KO_5h1


title: RNA-seq M3_RNA Minocycline replicate 3

description:
Library name: M3_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.

data_processing:
RNA-seq reads were processed with the in-house pipeline described in the manuscript and aligned to hg19. The uploaded processed data file RNAseq.hg19.gene_counts.clean.tsv is a gene-level raw count matrix for all six RNA-seq libraries.
Remote GEO upload subfolder: RNAseq
RNA-seq raw FASTQ upload includes all six RNA-seq libraries.
Only one RNA-seq processed data file is uploaded: RNAseq.hg19.gene_counts.clean.tsv.
No compressed archive files were uploaded for this GEO HTS set.
Assembly: hg19
Supplementary files format and content: RNAseq.hg19.gene_counts.clean.tsv: gene-level raw count matrix.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Samples were lysed and homogenized under RNase-free conditions, and genomic DNA was removed by on-column DNase digestion. RNA was purified using silica membrane spin columns, washed, and eluted in nuclease-free water. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was assessed using an Agilent Bioanalyzer before RNA-seq library preparation.
Library preparation and paired-end 150 nt Illumina sequencing were performed by CD Genomics (order CGRPML200520) using the NEBNext Ultra II RNA Library Prep Kit; TODO add exact selection/strandedness if available.

value: Minocycline; compound:minocycline; dose:100 uM; duration:12 h


title: KO_1h4

description:
Library name: Sample 8
Column name in raw_read_quant.table.txt: KO_1h4

value: 1h 100 ng/ml LPS


title: 4_HKM7VBGXT.4.TGCAGCTA_ATAGAGAG

description:
Library name: 4_SM-NBW7B_plate1
DHMT_48hr_LRP1_A_c


title: RNA-seq M2_RNA Minocycline replicate 2

description:
Library name: M2_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.


title: 3_HKM7VBGXT.3.TGCAGCTA_ATAGAGAG

description:
Library name: 3_SM-NBW7B_plate1
DHMT_48hr_LRP1_A_c


title: iSAE_PIWIL4_siRNA_Uninfected

type: RNA

city: Galveston

first: Tiziana

last: Corsello

address: 301 University Blvd

institute: UTMB

description: iSAE cells transfected with PIWIL4-targeting siRNA (300 nM), harvested uninfected (basal condition).

hyb_protocol: Labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies). Sample preparation and array hybridization were performed by Arraystar Inc. based on the manufacturer's standard protocols.

scan_protocol: After washing, arrays were scanned using the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing: Scanned images were analyzed with Agilent Feature Extraction software v11.0.1.1 to obtain background-subtracted, spatially-detrended processed signal intensities (gProcessedSignal). The gProcessedSignal values of the four arrays were then quantile-normalized together to generate the normalized signal-intensity matrix provided here. In the associated study, quantile normalization and downstream processing were performed with Agilent GeneSpring GX v12.1; after normalization, features flagged as Detected (All Targets Value) in at least 1 of 4 samples were retained and differentially expressed genes were identified by Volcano plot filtering with a fold-change cutoff of >=1.5.

source_name: Immortalized small airway epithelial (iSAE) cells, PIWIL4-targeting siRNA, uninfected control

label_protocol: Total RNA was transcribed into fluorescent cRNA using Agilent's Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

growth_protocol: Primary human small airway epithelial (SAE) cells (Lonza, CC-2547) and immortalized SAE (iSAE) cells (established by transduction with human telomerase and cyclin-dependent kinase-4 retrovirus constructs) were grown in growth medium containing 7.5 mg/ml bovine pituitary extract, 0.5 mg/ml hydrocortisone, 0.5 ug/ml hEGF, 0.5 mg/ml epinephrine, 10 mg/ml transferrin, 5 mg/ml insulin, 0.1 ug/ml retinoic acid, 0.5 ug/ml triiodothyronine, 50 mg/ml gentamicin and 50 mg/ml bovine serum albumin.

extract_protocol: Total RNA was extracted using the ToTALLY RNA kit (Ambion/Life Technologies). RNA concentration was quantified using a Nanodrop spectrophotometer and integrity assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: iSAE cells were transfected by electroporation (Amaxa Nucleofector, Basic Nucleofector Kit for epithelial cells) with either PIWIL4-targeting siRNA (a mixture of three custom 21-mer duplexes, Sigma VC30002; SASI_Hs01_00210309, SASI_Hs02_00366170, SASI_Hs01_00210310) or non-targeting control siRNA (Sigma SIC001-10NMOL), each at a final concentration of 300 nM. At 24-30 hours post-transfection, cells were switched to basal medium (no supplements) 4 hours prior to infection, then infected with RSV Long strain at MOI 5, or mock-treated with an equivalent volume of 30% sucrose solution (uninfected control), and harvested 15 hours post-infection.

value: iSAE cells

tag: sirna treatment

value: PIWIL4-targeting siRNA

tag: infection status

value: uninfected (control)


title: KO_1h3

description:
Library name: Sample 7
Column name in raw_read_quant.table.txt: KO_1h3


title: iSAE_NonTargeting_siRNA_RSV_15h

description: iSAE cells transfected with non-targeting control siRNA (300 nM), then infected with RSV Long strain (MOI 5) and harvested 15 hours post-infection.

source_name: Immortalized small airway epithelial (iSAE) cells, non-targeting siRNA, RSV-infected

value: non-targeting siRNA

value: RSV infection, MOI 5, 15 hours post-infection


title: iSAE_PIWIL4_siRNA_RSV_15h

description: iSAE cells transfected with PIWIL4-targeting siRNA (300 nM), then infected with RSV Long strain (MOI 5) and harvested 15 hours post-infection.

source_name: Immortalized small airway epithelial (iSAE) cells, PIWIL4-targeting siRNA, RSV-infected


title: RNA-seq M1_RNA Minocycline replicate 1

description:
Library name: M1_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.


title: 2_HKM7VBGXT.2.TGCAGCTA_ATAGAGAG

description:
Library name: 2_SM-NBW7B_plate1
DHMT_48hr_LRP1_A_c

value: iPSC-derived excitatory neuron, astrocyte


title: Cal27 erlotinib resistant, bio rep 2

city: PHILADELPHIA

first: Flaviane

middle: Nunes da

last: Silva

state: PENNSYLVANIA

address: 333 COTTMAN AVENUE

institute: Fox Chase Cancer Center

description:
Library name: Sample 12
HiSeq 2x150bp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: .txt files contain raw counts for each sample
Supplementary files format and content: .csv files contain normalized gene hit counts of all samples used in the comparison

source_name: Tongue Squamous Cell Carcinoma

growth_protocol: Fadu cells were maintained in EMEM supplemented with 10%FBS and 1% penstrep at 5% CO2 at 37C. Cal27 cells were maintained in DMEM supplemented with 10% FBS,

extract_protocol:
Frozen cell pellets were shipped out to Azenta for RNA extraction and further processing
Library preparation, Illumina, RNA with PolyA selection with ERCC spike in, 20M reads per sample

value: Tongue Squamous Cell Carcinoma

value: tumor

value: WT

value: Erlotinib Resistant


title: iSAE_NonTargeting_siRNA_Uninfected

description: iSAE cells transfected with non-targeting control siRNA (300 nM), harvested uninfected (basal condition).

source_name: Immortalized small airway epithelial (iSAE) cells, non-targeting siRNA, uninfected control


title: KO_1h2

description:
Library name: Sample 6
Column name in raw_read_quant.table.txt: KO_1h2

value: bone marrow

value: bone marrow-derived macrophages

value: cre


title: RNA-seq C3_RNA Control replicate 3

description:
Library name: C3_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.

value: HEK293 (ATCC CRL-1573)


title: 1_HKM7VBGXT.1.TGCAGCTA_ATAGAGAG

description:
Library name: 1_SM-NBW7B_plate1
DHMT_48hr_LRP1_A_c

value: LRP1 knockdown


title: Cal27 erlotinib resistant, bio rep 1

description:
Library name: Sample 11
HiSeq 2x150bp


title: KO_1h1

description:
Library name: Sample 5
Column name in raw_read_quant.table.txt: KO_1h1


title: RNA-seq C2_RNA Control replicate 2

description:
Library name: C2_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.

value: Control; compound:DMSO vehicle; dose:vehicle; duration:12 h


title: 4_HKM7VBGXT.4.CGATCAGT_ATAGAGAG

description:
Library name: 4_SM-NBW7A_plate1
DHMT_48hr_LRP1_A_b


title: KO_0h4

description:
Library name: Sample 4
Column name in raw_read_quant.table.txt: KO_0h4

value: untreated


title: Cal27 afatinib resistant, bio rep 2

description:
Library name: Sample 10
HiSeq 2x150bp

value: Afatinib Resistant


title: 3_HKM7VBGXT.3.CGATCAGT_ATAGAGAG

description:
Library name: 3_SM-NBW7A_plate1
DHMT_48hr_LRP1_A_b


title: KO_0h3

description:
Library name: Sample 3
Column name in raw_read_quant.table.txt: KO_0h3


title: Cal27 afatinib resistant, bio rep 1

description:
Library name: Sample 9
HiSeq 2x150bp


title: RNA-seq C1_RNA Control replicate 1

description:
Library name: C1_RNA
HEK293 matched total RNA. One processed gene-count matrix (RNAseq.hg19.gene_counts.clean.tsv) covers all six RNA-seq libraries.


title: hiPSC MNase-seq, 10 U, Low Depth

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

description: Library name: hiPSC_MNase_10U_LowDepth

data_processing:
Paired-end reads were adapter- and quality-trimmed with Trimmomatic v0.40 (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 with orphan-read retention :1:true; LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:33).
For 150 bp NovaSeq X reads, reads were additionally cropped to 50 bp where required to recover subnucleosomal fragments and harmonize fragment-size classification across platforms.
Reads were processed with the nucMACC pipeline v3.1 (Nextflow v25.10.4), running the MNaseQC and nucMACC analysis modules; reads were aligned to GRCh38.
ENCODE blacklist regions (636 intervals) were excluded. The internal read-depth filtering threshold in get_nucMACC_scores.R was adjusted to 14 (values of 8 and 11 also evaluated) to enable recovery of mono-nucleosomal outputs from high-depth libraries.
nucMACC scores were computed across the MNase titration to classify mono- and subnucleosomal fragments, derive hyper- and hypo-accessible nucleosome classes (LOESS-slope cutoffs on rank-normalized scores), and generate TSS-centered occupancy and accessibility profiles.
Assembly: GRCh38
Supplementary files format and content: bigWig: genome-wide normalized MNase coverage tracks (GRCh38).
Supplementary files format and content: BED/bedGraph: nucMACC nucleosome positions with accessibility scores, including hyper- and hypo-accessible nucleosome classifications.

source_name: not applicable (cell line)

growth_protocol: hiPSC line PB010.5 (MCRIi010-A; RRID:CVCL_UK91) was maintained under feeder-free conditions on hESC-qualified Matrigel (Corning 354277) in mTeSR Plus (STEMCELL 100-0276) with 0.5% (v/v) penicillin-streptomycin, passaged with ReLeSR (STEMCELL 100-0483), and used between passages 30-45. Cells were dissociated to single cells with TrypLE (Thermo 12604013) and counted prior to digestion.

extract_protocol:
RNA was removed with RNase A (42°C, 30 min) and protein digested with 20% SDS plus Proteinase K (55°C, 15 min). MNase-digested DNA was purified with the GeneJET PCR Purification Kit (Thermo K0701) and quantified by NanoDrop. Saccharomyces cerevisiae (BY4742) mononucleosomal spike-in DNA — prepared by Zymolyase spheroplasting and 60 U MNase digestion (10 min, 37°C) of log-phase cells followed by GeneJET purification — was added to each sample at 0.5 ng per 10 ng hiPSC DNA (~5% of total) immediately before library preparation.
Libraries were prepared from 10 ng MNase-digested hiPSC DNA plus 0.5 ng BY4742 spike-in DNA using the Active Motif DNA Library Kit for Illumina (53220): end repair, indexed Illumina adapter ligation, SPRI bead cleanup, 12-cycle PCR enrichment, and SPRI size selection. Library quality and size distribution were assessed by capillary electrophoresis (Agilent TapeStation, D1000 ScreenTape).

treatment_protocol: Single-cell hiPSC suspensions (typically 250,000-500,000 cells) were permeabilized in MNase digestion Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.1% (v/v) NP-40, 1 mM β-mercaptoethanol) for 10 min at 22°C, supplemented with CaCl2 to 2 mM, and digested with micrococcal nuclease (Thermo EN0181) at 0.5, 1, 3, 6, or 10 U for 5 min at 37°C with shaking (450 rpm). Digestion was stopped with ice-cold 50 mM EDTA / 50 mM EGTA.

value: not applicable (cell line)

value: hiPSCs RRID:CVCL_UK91

value: Human


title: 2_HKM7VBGXT.2.CGATCAGT_ATAGAGAG

description:
Library name: 2_SM-NBW7A_plate1
DHMT_48hr_LRP1_A_b


title: ptLNPIFN-Y2

city: shenzhen

first: yongfei

last: Zhou

address: Yutang Subdistrict, Guangming District

institute: Shenzhen Bay Laboratory

description:
Library name: Sample17
ptLNPIFN-Y2

data_processing:
Raw sequencing data were filtered using SOAPnuke to obtain clean reads, which were then aligned to the reference genome with HISAT2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Gene expression levels were quantified using RSEM. Novel transcripts were predicted with StringTie and Cuffmerge, compared against the reference annotation using Cuffcompare, and evaluated for coding potential by CPC.Differential expression analysis was performed with DESeq2. Genes showing a fold change ≥ 2 and an adjusted P_x001E_value ≤ 0.001 were considered significantly differentially expressed.

source_name: Ovary

growth_protocol: Mouse ovarian tissue samples were snap-frozen and stored in liquid nitrogen prior to RNA extraction.

extract_protocol:
After the addition of a chloroform:isopentanol mixture (24:1) and centrifugation, the supernatant was transferred to a deep_x001E_well plate pre_x001E_loaded with binding solution and magnetic beads. RNA purification was carried out using an automated nucleic acid extractor, and the purified RNA was eluted with RNase_x001E_free water.
For library construction, mRNA was captured using oligo(dT)-conjugated magnetic beads, fragmented, and then reverse_x001E_transcribed into first_x001E_strand and second_x001E_strand cDNA. The resulting double_x001E_stranded cDNA was subjected to end repair, A_x001E_tailing, adaptor ligation, and PCR amplification.Following library quality control, single_x001E_stranded circular DNA was generated and sequenced on a DNBSEQ platform via rolling circle amplification combined with combinatorial Probe_x001E_Anchor Synthesis (cPAS).

treatment_protocol: Tissue specimens were homogenized in lysis buffer.

value: Ovary

value: ovarian cancer/ptLNPIFN-Y


title: ptLNPIFN-Y5

description:
Library name: Sample20
ptLNPIFN-Y5


title: KO_0h2

description:
Library name: Sample 2
Column name in raw_read_quant.table.txt: KO_0h2


title: 1_HKM7VBGXT.1.CGATCAGT_ATAGAGAG

description:
Library name: 1_SM-NBW7A_plate1
DHMT_48hr_LRP1_A_b

value: iPSC-derived excitatory neuron, astrocyte


title: hiPSC MNase-seq, 6 U, Low Depth

description: Library name: hiPSC_MNase_6U_LowDepth


title: 1_HW7KJBGXT.1.GGAGCTAC_ATAGAGAG

description:
Library name: 1_SM-NBW9S_plate2
DHMT_48hr_Astrocyte_Mono_b

value: Astrocyte

value: no guide


title: Cal27 parental, bio rep 2

description:
Library name: Sample 8
HiSeq 2x150bp

value: Tongue Squamous Cell Carcinoma

value: tumor

value: WT

value: Parental


title: hiPSC MNase-seq, 3 U, Low Depth

description: Library name: hiPSC_MNase_3U_LowDepth


title: Cal27 parental, bio rep 1

description:
Library name: Sample 7
HiSeq 2x150bp


title: KO_0h1

description:
Library name: Sample 1
Column name in raw_read_quant.table.txt: KO_0h1

value: bone marrow

value: bone marrow-derived macrophages

value: cre


title: Fadu erlotinib resistant, bio rep 2

description:
Library name: Sample 6
HiSeq 2x150bp

source_name: Hypopharyngeal Squamous Cell Carcinoma

value: Hypopharyngeal Squamous Cell Carcinoma

value: FaDu

value: Erlotinib Resistant


title: 4_HKM7VBGXT.4.CCTAAGAC_ATAGAGAG

description:
Library name: 4_SM-NBW79_plate1
DHMT_48hr_LRP1_A_a

value: LRP1 knockdown


title: hiPSC MNase-seq, 1 U, Low Depth

description: Library name: hiPSC_MNase_1U_LowDepth

value: not applicable (cell line)

value: hiPSCs RRID:CVCL_UK91

value: Human


title: 3_HKM7VBGXT.3.CCTAAGAC_ATAGAGAG

description:
Library name: 3_SM-NBW79_plate1
DHMT_48hr_LRP1_A_a

value: iPSC-derived excitatory neuron, astrocyte


title: Fadu erlotinib resistant, bio rep 1

description:
Library name: Sample 5
HiSeq 2x150bp


title: kq791_20uM_24h_IFNb_003

city: Montreal

first: Michel

last: Tremblay

state: Quebec

address: 1160 Pine Avenue West

country: Canada

institute: Goodman Cancer Research Centre

description:
Library name: A_030
Data2/A030_quant

data_processing:
Salmon
Assembly: MM_grch38_ens94
Supplementary files format and content: .csv

growth_protocol: DMEM 10% FBS + 1X Pen Strep. Cell were kept at

extract_protocol:
Quiiagen Plus mini kit
NEBNext_dual_i7

value: IFN-beta, 6h, 20ng/mL


title: kq791_20uM_24h_IFNb_002

description:
Library name: A_029
Data2/A029_quant


title: hiPSC MNase-seq, 0.5 U, Low Depth

description: Library name: hiPSC_MNase_0.5U_LowDepth


title: 2_HKM7VBGXT.2.CCTAAGAC_ATAGAGAG

description:
Library name: 2_SM-NBW79_plate1
DHMT_48hr_LRP1_A_a


title: Fadu afatinib resistant, bio rep 2

description:
Library name: Sample 4
HiSeq 2x150bp

value: Afatinib Resistant


title: 1_HKM7VBGXT.1.CCTAAGAC_ATAGAGAG

description:
Library name: 1_SM-NBW79_plate1
DHMT_48hr_LRP1_A_a


title: Isolated Male 2

city: Princeton

first: Elisabeth

last: Tawa

state: NJ

address: Lewis Thomas Lab, Washington Road

institute: Princeton University

description: Library name: 2919__Isolated-Male2

data_processing:
Sequences were aligned to the Drosophila melanogaster genome (BDGP.46) using STAR (v. 2.7.10b). Duplicates were removed using the Picard Toolkit (v. 2.27.5) MarkDuplicates function. The number of reads mapping to each gene was determined using htseq-count (HTSeq v. 2.0.5). Differential gene expression analysis was performed in R (v. 4.4.0). All read counts from rRNA and pseudo-rRNA genes were removed. Normalization was performed using edgeR (v. 4.4.1).
Assembly: Drosophila melanogaster genome (BDGP.46)
Supplementary files format and content: csv file containing raw read counts for each sample

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
For each sample, flies were decapitated on dry ice. RNA was extracted and purified from homogenized whole heads using a phenol chloroform organic extraction. Samples were also treated using either the RQ1 RNase-Free DNase kit (Promega Corporation) or the TURBO DNA-free Kit (Invitrogen) to address genomic DNA contamination. The samples submitted for RNA-seq were extracted from 200 whole heads each.
RNA-seq was performed by the Princeton University Genomics Core Facility. The integrity of total RNA samples was assessed on the 2100 Bioanalyzer system using the RNA 6000 Pico Chip (Agilent Technologies, CA). The poly-A containing RNA transcripts were enriched from one microgram of total RNA for each sample using oligo-dT beads, further fragmented, and converted to cDNA and Illumina sequencing libraries using the PrepX RNA-seq library preparation protocol on the Apollo 324 NGS Library Prep System (Takara Bio, CA). Different DNA barcodes were attached to each library. The RNA-seq libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA), and pooled at equal molar amounts. Each library pool was denatured and sequenced on one Illumina NovaSeq 6000 S Prime lane using the 100 cycle v1.5 kit. Raw sequencing reads were filtered by Illumina NovaSeq Control software, and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: Newly-eclosed male and female flies were housed together for three to five days to acquire social experience. Flies were then housed either singly or in same-sex groups of 25 for seven days. Within 24 hours of the final day of isolation or group housing, flies were frozen on dry ice for RNA extraction.

value: Head

tag: developmental stage

value: Adult

tag: Sex

value: Male

value: ORE-R

value: Social Isolation


title: Fadu afatinib resistant, bio rep 1

description:
Library name: Sample 3
HiSeq 2x150bp

value: tumor

value: WT


title: Isolated Male 1

description: Library name: 2919__Isolated-Male1_merged


title: kq791_20uM_24h_UNST_003

description:
Library name: A_027
Data2/A027_quant

value: NT


title: kq791_20uM_24h_IFNb_001

description:
Library name: A_028
Data2/A028_quant


title: Fadu parental, bio rep 2

description:
Library name: Sample 2
HiSeq 2x150bp

value: Hypopharyngeal Squamous Cell Carcinoma

value: FaDu

value: Parental


title: 3_HKM7VBGXT.3.ACTGAGCG_ATAGAGAG

description:
Library name: 3_SM-NBW78_plate1
DHMT_24hr_d

value: no guide


title: 4_HKM7VBGXT.4.ACTGAGCG_ATAGAGAG

description:
Library name: 4_SM-NBW78_plate1
DHMT_24hr_d


title: Fadu parental, bio rep 1

description:
Library name: Sample 1
HiSeq 2x150bp


title: Isolated Female 1

description: Library name: 2919__Isolated-Female1

value: Female


title: kq791_20uM_24h_UNST_001

description:
Library name: A_025
Data2/A025_quant


title: Isolated Female 2

description: Library name: 2919__Isolated-Female2


title: kq791_20uM_24h_UNST_002

description:
Library name: A_026
Data2/A026_quant


title: 2_HKM7VBGXT.2.ACTGAGCG_ATAGAGAG

description:
Library name: 2_SM-NBW78_plate1
DHMT_24hr_d


title: A22LP062Z1

city: Shanghai

first: Xiaojie

last: Yang

address: No. 639 Zaozhiju Rd., Huangpu District

department: Department of Oral Medicine

institute: Shanghai Ninth People's Hospital

description:
Library name: Sample42
one sample from oral mucosa tissue from oral lichenoid lesions

data_processing:
Raw sequence reads were processed using CLC Genomics Workbench v11.0.1. Adapter sequences and low-quality bases were trimmed with a quality limit of 0.05. Trimmed reads were mapped to the human reference genome (GRCh38/hg38) using the following alignment parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, and similarity fraction = 0.8. Gene-level read counts were extracted, and normalization was performed using the default settings in CLC Genomics Workbench.
Assembly: GRCh38
Supplementary files format and content: txt,gene counts expression

source_name: oral mucosa

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: oral mucosa

value: oral mucosal cell

tag: disease state

value: Oral lichenoid lesions


title: sgDKO_IFNb_003

description:
Library name: A_024
Data2/A024_quant

value: sgDKO

value: IFN-beta, 6h, 20ng/mL


title: 1_HKM7VBGXT.1.ACTGAGCG_ATAGAGAG

description:
Library name: 1_SM-NBW78_plate1
DHMT_24hr_d

value: iPSC-derived excitatory neuron, astrocyte


title: A22LP061Z1

description:
Library name: Sample41
one sample from oral mucosa tissue from oral lichenoid lesions


title: Control Male 2

description: Library name: 2919__Control-Male2

value: Head

value: Adult

value: Male

value: Group Housing (Control)


title: sgDKO_IFNb_002

description:
Library name: A_023
Data2/A023_quant


title: Control Male 1

description: Library name: 2919__Control-Male1

value: ORE-R


title: 4_HKM7VBGXT.4.TAGCGCTC_ATAGAGAG

description:
Library name: 4_SM-NBW77_plate1
DHMT_24hr_c

value: WT


title: A22LP060Z1

description:
Library name: Sample40
one sample from oral mucosa tissue from oral lichenoid lesions


title: sgDKO_IFNb_001

description:
Library name: A_022
Data2/A022_quant


title: Control Female 2

description: Library name: 2919__Control-Female2


title: Control Female 1

description: Library name: 2919__Control-Female1


title: 4_HKM7VBGXT.4.TGCAGCTA_TATGCAGT

description:
Library name: 4_SM-NBW8C_plate1
DHMT_48hr_LDLR_A_c

value: LDLR knockdown


title: A22LP059Z1

description:
Library name: Sample39
one sample from oral mucosa tissue from oral lichenoid lesions


title: A22LP055Z1

description:
Library name: Sample38
one sample from oral mucosa tissue from oral lichenoid lesions


title: 2_HKM7VBGXT.2.TAGCGCTC_ATAGAGAG

description:
Library name: 2_SM-NBW77_plate1
DHMT_24hr_c


title: mouseNSCs, Commd3-Bmi1_multiplex, 3

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

description: Library name: Mouse_ComBmi_3

data_processing:
Adaptor and imcomplete sequences were removed by Trim Galore (ver. 0.6.6)
Human and mouse short reads were mapped to the COMMD3–BMI1 locus on human chromosome 10 and mouse chromosome 2, respectively, using TopHat2 to visualize junction reads.
For the quantification of junction reads, BMI1 exon 2–containing reads were mapped to COMMD3 exons using Bowtie2, and the read ends opposite to the BMI1 exon 2–containing sequences were assigned to their corresponding COMMD3 exons.
Assembly: hg38, mm10
Supplementary files format and content: BED file includes read data for each COMMD3 exon.

source_name: Forebrain on E11

extract_protocol:
RNA was extracted using Sepazol Super G RNA (Nakarai Tesque) by the phenol-chloroform method.
Total RNA was reverse‑transcribed using the ReverTra Ace® qPCR RT Master Mix with gDNA Remover (Toyobo, FSQ‑301), following the manufacturer’s instructions. Multiplex PCR was performed using KOD‑Multi & Epi‑ (Toyobo) under the following conditions: 94 °C for 2 min, followed by 40 cycles of 98 °C for 10 s and 65 °C for 30 s. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: Forebrain on E11

value: neural stem cells


title: mouseNSCs, Commd3-Bmi1_multiplex, 2

description: Library name: Mouse_ComBmi_2


title: sgDKO_UNST_003

description:
Library name: A_021
Data2/A021_quant

value: NT


title: 4_HKM7VBGXT.4.CGATCAGT_TATGCAGT

description:
Library name: 4_SM-NBW8B_plate1
DHMT_48hr_LDLR_A_b


title: 3_HKM7VBGXT.3.TAGCGCTC_ATAGAGAG

description:
Library name: 3_SM-NBW77_plate1
DHMT_24hr_c

value: no guide


title: sgDKO_UNST_002

description:
Library name: A_020
Data2/A020_quant


title: 1_HKM7VBGXT.1.TAGCGCTC_ATAGAGAG

description:
Library name: 1_SM-NBW77_plate1
DHMT_24hr_c


title: Isolated Male 0

description: Library name: 2558__Isolated-Males

value: Social Isolation


title: A22LP047Z1

description:
Library name: Sample37
one sample from oral mucosa tissue from oral lichenoid lesions

value: oral mucosa

value: oral mucosal cell


title: sgDKO_UNST_001

description:
Library name: A_019
Data2/A019_quant

value: sgDKO


title: 4_HKM7VBGXT.4.ATGCGCAG_ATAGAGAG

description:
Library name: 4_SM-NBW76_plate1
DHMT_24hr_b


title: sgPtpn2_IFNb_003

description:
Library name: A_018
Data2/A018_quant

value: IFN-beta, 6h, 20ng/mL


title: A22LP043Z1

description:
Library name: Sample36
one sample from oral mucosa tissue from oral lichenoid lesions

value: Oral lichenoid lesions


title: Control Male 0

description: Library name: 2558__Cont-Males

value: Head


title: A22LP042Z1

description:
Library name: Sample35
one sample from oral mucosa tissue from oral lichenoid lesions


title: Control Female 0

description: Library name: 2558__Cont-Females

value: Adult

value: Female


title: A22LP041Z1

description:
Library name: Sample34
one sample from oral mucosa tissue from oral lichenoid lesions


title: 2_HKM7VBGXT.2.ATGCGCAG_ATAGAGAG

description:
Library name: 2_SM-NBW76_plate1
DHMT_24hr_b

value: iPSC-derived excitatory neuron, astrocyte


title: sgPtpn2_UNST_003

description:
Library name: A_015
Data2/A015_quant


title: A22LP035Z1

description:
Library name: Sample33
one sample from oral mucosa tissue from oral lichenoid lesions


title: sgPtpn2_IFNb_001

description:
Library name: A_016
Data2/A016_quant


title: 1_HKM7VBGXT.1.ATGCGCAG_ATAGAGAG

description:
Library name: 1_SM-NBW76_plate1
DHMT_24hr_b


title: 4_HKM7VBGXT.4.TACGCTGC_ATAGAGAG

description:
Library name: 4_SM-NBW75_plate1
DHMT_24hr_a


title: A22LP032Z1

description:
Library name: Sample32
one sample from oral mucosa tissue from oral lichenoid lesions


title: sgPtpn2_UNST_002

description:
Library name: A_014
Data2/A014_quant


title: 3_HKM7VBGXT.3.TACGCTGC_ATAGAGAG

description:
Library name: 3_SM-NBW75_plate1
DHMT_24hr_a


title: A22LP031Z1

description:
Library name: Sample31
one sample from oral mucosa tissue from oral lichenoid lesions


title: sgPtpn2_UNST_001

description:
Library name: A_013
Data2/A013_quant


title: 2_HKM7VBGXT.2.TACGCTGC_ATAGAGAG

description:
Library name: 2_SM-NBW75_plate1
DHMT_24hr_a


title: Control_1, drosophila head, 5 days

city: Hangzhou

first: Yuyu

state: Zhejiang

address: 79 Qingchun Rd., Shangcheng District

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/
Supplementary files format and content: A tab-delimited text file that includes raw counts for each sample
Supplementary files format and content: A tab-delimited text file that includes FPKM for each sample

source_name: head

growth_protocol: Using the Glass Multiple Repeat (GMR, TB00094 from Tsinghua Fly Center) driver allowed for the expression of transgenes in the pupal retina and adult eye. All crosses were maintained at 25°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: 5-d-old Drosophila heads were dissected, and total RNA was extracted using RNAiso Plus (TaKaRa, Dalian, China)

value: head

value: 5 days old, adult

value: Control


title: A22LP029Z1

description:
Library name: Sample30
one sample from oral mucosa tissue from oral lichenoid lesions


title: sgPtpn1_IFNb_003

description:
Library name: A_012
Data2/A012_quant


title: 1_HKM7VBGXT.1.TACGCTGC_ATAGAGAG

description:
Library name: 1_SM-NBW75_plate1
DHMT_24hr_a

value: WT


title: A22LP028Z1

description:
Library name: Sample29
one sample from oral mucosa tissue from oral lichenoid lesions


title: Rab7 RNAi_3, drosophila head, 5 days

value: GMR-Gal4/UAS-Rab7 RNAi

value: RNA interference


title: A22LP023Z1

description:
Library name: Sample28
one sample from oral mucosa tissue from oral lichenoid lesions


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319481a

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
The fragments of genes were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization.
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software
Supplementary files format and content: "standard processed data.xlsx" represents TMM-normalized data

source_name: lymph node/skin tissue

extract_protocol:
Total RNA was extracted from FFPE tissues followed by library preparation according to Illumina standard instruction (SMARTer Stranded Total RNA-Seq Kit v2).
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina NovaSeq6000.

value: previously untreated advanced ENKTL

value: lymph node/skin tissue

value: Sintilimab with P-GEMOX chemotherapy

tag: medical center

value: Sun Yat-sen University Cancer Center

tag: age

value: male

tag: Stage

value: IV


title: sgPtpn1_IFNb_001

description:
Library name: A_010
Data2/A010_quant

tag: cell line

value: IFN-beta, 6h, 20ng/mL


title: Rab7 RNAi_2, drosophila head, 5 days

tag: genotype


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319480a

value: female


title: A22LP022Z1

description:
Library name: Sample27
one sample from oral mucosa tissue from oral lichenoid lesions

value: oral mucosa

tag: cell type

value: oral mucosal cell

value: Oral lichenoid lesions


title: sgPtpn1_UNST_003

description:
Library name: A_009
Data2/A009_quant

value: NT


title: Rab7 RNAi_1, drosophila head, 5 days

value: head

value: 5 days old, adult


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319479a


title: A22LP065Z1

description:
Library name: Sample26
one sample from oral mucosa tissue from oral lichen planus

value: Oral lichen planus


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319478a


title: sgPtpn1_UNST_002

description:
Library name: A_008
Data2/A008_quant


title: Rab5 RNAi_5, drosophila head, 5 days

value: GMR-Gal4/UAS-Rab5 RNAi


title: A22LP058Z1

description:
Library name: Sample25
one sample from oral mucosa tissue from oral lichen planus


title: sgPtpn1_UNST_001

description:
Library name: A_007
Data2/A007_quant


title: Rab5 RNAi_4, drosophila head, 5 days

value: RNA interference


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319477a

value: previously untreated advanced ENKTL


title: CTL_IFNb_003

description:
Library name: A_006
Data2/A006_quant

value: sgCTL


title: A22LP057Z1

description:
Library name: Sample24
one sample from oral mucosa tissue from oral lichen planus


title: Rab5 RNAi_3, drosophila head, 5 days


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319476a

value: lymph node/skin tissue

value: Sintilimab with P-GEMOX chemotherapy


title: A22LP056Z1

description:
Library name: Sample23
one sample from oral mucosa tissue from oral lichen planus


title: CTL_IFNb_002

description:
Library name: A_005
Data2/A005_quant


title: Rab5 RNAi_2, drosophila head, 5 days


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319475a

value: Sun Yat-sen University Cancer Center

value: male


title: Rab5 RNAi_1, drosophila head, 5 days


title: A22LP053Z1

description:
Library name: Sample22
one sample from oral mucosa tissue from oral lichen planus


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319472a

value: IV


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319471a


title: SW1990, EPZ-3

city: Changchun

first: Ziyu

last: Liu

address: 1 Xinmin Street

institute: Jilin University

description: Library name: Sample 6

data_processing:
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: SW1990 pancreatic ductal adenocarcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and integrity were assessed using the Agilent 2100 Bioanalyzer, and RNA concentration was measured with a Qubit Fluorometer.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using dUTP. The cDNA fragments then underwent end repair, A-tailing, adapter ligation, USER enzyme digestion, PCR amplification, and purification. Libraries were quantified using Qubit and real-time PCR and size-checked with a Bioanalyzer.

treatment_protocol: Cells in the treatment group were exposed to 5 µM EPZ-5676 (MedChemExpress), a selective DOT1L inhibitor. Cells in the control group were treated with equal volumes of DMSO.

value: pancreatic ductal adenocarcinoma (PDAC) cell line

value: DOT1L inhibitor EPZ-5676


title: SW1990, EPZ-2

description: Library name: Sample 5


title: CTL_USNT_002

description:
Library name: A_002
Data2/A002_quant


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319470a

value: female


title: A22LP048Z1

description:
Library name: Sample19
one sample from oral mucosa tissue from oral lichen planus

value: oral mucosa

value: oral mucosal cell


title: A22LP039Z1

description:
Library name: Sample18
one sample from oral mucosa tissue from oral lichen planus


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319469a


title: Nur77_input_LPS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
Tag directories were created using the makeTagDirectory command in HOMER
BigWigs were produced from HOMER tag directories
Nur77 binding peaks were identified by using HOMER peak calling with default settings, Pol II and H3K27ac binding was called using the regions setting (broad peaks)
For the peak files, the reproducible peaks in three or two biological replicates were merged using HOMER’s mergePeaks.pl script. The BigWigs were merged using bigwigAverage from deepTools2
Assembly: mm10
Supplementary files format and content: tab-delimited text files with identiified peaks (except for input samples), bigWig files

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of HA-tagged Nur77 or GFP were seeded at a density of 3.75x10^5 cells/ml and after two days Nur77 or GFP expression was induced by incubation with 50ng/ml doxycyclin for 18 h

extract_protocol:
Only for the Nur77 ChIP, cells were crosslinked directly in culture flasks with 2mM Di(N-succinimidyl) glutarate in PBS for 30 min at room temperature. For all ChIP targets including Nur77, cells were then crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, the chromatin was sonicated into approximately 400bp fragments using a Bioruptor Pico (Diagenode) for 4 cycles (double cross-linked) or 3 cycles (single cross-linked) of 10sec on and 50sec off. Immunoprecipitation was performed using HA (for Nur77),  RNA polymerase, or H3K27ac antibody
Strrand-specific ChIP seq libraries were prepared using the KAPA hyperprep kit protocol. Concentration and fragment size of chromatin was confirmed using the Tapestation4200 (Agilent).

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0 and 1h

value: macrophages

value: 1h 500 ng/ml LPS

tag: chip antibody


title: A22LP038Z1

description:
Library name: Sample17
one sample from oral mucosa tissue from oral lichen planus

value: Oral lichen planus


title: SW1990, NC-2

description: Library name: Sample 2

value: none; untreated


title: Nur77_input_Ctrl

value: untreated


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319468a

value: previously untreated advanced ENKTL


title: A22LP037Z1

description:
Library name: Sample16
one sample from oral mucosa tissue from oral lichen planus


title: GFP_input_LPS

value: GFP


title: SW1990, NC-1

description: Library name: Sample 1


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319465a

value: lymph node/skin tissue


title: GFP_input_Ctrl


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319464a

value: Sintilimab with P-GEMOX chemotherapy


title: A22LP034Z1

description:
Library name: Sample14
one sample from oral mucosa tissue from oral lichen planus


title: Nur77_H3K27ac_LPS2

value: H3K27ac (Diagenode, C15410196)


title: SW1990, NC

description: Library name: Sample 1

data_processing:
Raw reads were processed using fastp v0.20.0 for quality filtering, adapter trimming, and removal of low-quality sequences.
Assembly: hg38
Supplementary files format and content: EPZ.bw
Supplementary files format and content: NC.bw

extract_protocol:
After treatment, cells were harvested and bound to Concanavalin A-coated magnetic beads. The plasma membrane was permeabilized with Digitonin, followed by antibody binding with anti-H3K79me2. pA-Tn5 transposase was added to perform targeted tagmentation. The resulting DNA was enriched by PCR to prepare sequencing libraries.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using dUTP. The cDNA fragments then underwent end repair, A-tailing, adapter ligation, USER enzyme digestion, PCR amplification, and purification. Libraries were quantified using Qubit and real-time PCR and size-checked with a Bioanalyzer.


title: A22LP033Z1

description:
Library name: Sample13
one sample from oral mucosa tissue from oral lichen planus


title: Nur77_H3K27ac_LPS1


title: Plasmid DNA

description:
Library name: LAMPRA plasmid DNA
plasmid DNA, PacBio Vega

data_processing:
PacBio consensus reads were processed through a series of custom scripts to associate unique barcodes with sCRLs. First, all reads were oriented to the same direction to ensure consistent downstream processing. Next, elements and barcodes were extracted by identifying fiducials – known fixed sequences that serve as positional markers – flanking the insert regions and extracting the downstream sequences following the fiducials. Element sequences were then annotated by comparing extracted sequences against the designed enhancer, synthetic insulator, and shuffled negative control sequences. Sequences that exactly matched the first 12 bp of a known element were annotated with the corresponding element name and orientation. Random barcode sequences were extracted using the same method, identifying 16 bp sequences between the fiducial sequences flanking the barcode insertion region. Each read was represented as the combination of elements in slots 1-5 and its corresponding barcode, and counts were collapsed by aggregating reads by unique element-barcode combinations to generate a final sCRL-barcode dictionary.  Sequencing data were demultiplexed using bcl2fastq. Forward and reverse barcode reads were merged and error-corrected using PEAR (v0.9.11) with parameters set to the barcode length (options -v 16 -m 16 -n 16 -t 16). Using custom Python and R scripts, successfully assembled barcode reads were combined with UMI reads, BC-UMI pairs were counted, and the read and UMI counts per BC were determined. The read and UMI counts for barcodes present in the initial plasmid library (determined a priori; see above) were collected for downstream analysis.
Assembly: hg19
Supplementary files format and content: BC-sCRL association dictionary
Supplementary files format and content: LAMPRA activity scores

extract_protocol:
Genomic DNA and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, 80204) with vortexing to lyse cells.  Libraries were electroporated in NEB 3020K electro-competent cells. Plasmids from cells were bottlenecked and extracted using the ChargeSwitch MidiPrep kits per manufacture's instructions.
MPRA amplicon libraries from genomic DNA were generated in two steps of PCR amplification with OneTaq (NEB, M0482S). Approximately 10 µg of genomic DNA input was used per replicate. For the first low-cycle PCR (PCR1), gDNA was mixed with 200 µl 2× OneTaq master mix, 2 µl 100 µM indexed P5 primer (rand-P5-E##), 2 µl 100 µM P7-pLSmp-assUMI-gfp primer, and water to a final volume of 400 µl. This mix was prepared for each replicate and then split over 16 wells for PCR. Cycling parameters were: 2 min at 95 °C, followed by three cycles of 20 s at 95 °C, 30 s at 55 °C, and 2 min at 72 °C, with a final extension of 5 min at 72 °C, followed by a 4 °C hold. Primer P7-pLSmp-assUMI-gfp contains ten random nucleotides (Ns) to serve as a pseudo-UMI (hereafter referred to as UMIs for brevity) to correct for PCR jackpotting. Reactions were pooled for each replicate, cleaned up with AMPure XP beads (Beckman Coulter, A63881) at 1.8×, and eluted in 97 µl of 10 mM Tris pH 8.0. A second round of PCR (PCR2) was performed for each replicate with primers P5 and P7, which amplified the library for sequencing without adding additional UMIs. The entire 97 µl of eluate from PCR1 was used as input and combined with 100 µl OneTaq master mix, 1 µl 100× SYBR Green (Thermo Fisher, S7563), 1 µl 100 µM P5 primer, and 1 µl 100 µM P7 primer. This mix was split over 8 reactions for each replicate. Libraries were amplified and monitored in real-time by qPCR with 2 min at 95 °C, followed by cycles up to the qPCR inflection point consisting of 15 s at 95 °C, 20 s at 60 °C, and 2 min at 72 °C. Libraries were then pooled by replicate and cleaned up with AMPure XP beads (Beckman Coulter, A63881) at 1.8×.  Amplicon libraries from RNA were obtained by first DNase-treating the RNA (up to 100 µl total RNA) by adding 0.1 volume 10× TURBO DNase buffer and 0.5 µl TURBO DNase (Thermo Fisher, AM1907), then incubating at 37 °C for 30 min. An additional 0.5 µl of TURBO DNase was then added followed by a second incubation. DNase was removed by adding 0.1 volume of DNase Inactivation Reagent. For each replicate, 40 µg of DNase-treated RNA was then used for eight reverse transcription reactions. For each reaction, 5 µg RNA was mixed with 1 µl 2 µM P7-pLSmp-assUMI-gfp and 1 µl of 10 mM dNTPs (NEB, N0447L), incubated at 65 °C for 5 min, and placed on ice. 6 µl of reverse transcription master mix was then added (4 µl 5× FS buffer, 1 µl 0.1 M dithiothreitol, and 1 µl SSIV (Thermo Fisher, 18091050)), and the reaction was incubated at 55 °C for 60 min, followed by 80 °C for 10 min. Each reverse transcription reaction was combined and split into 32 total PCR reactions per replicate. For PCR1, reactions contained 160 µl template, 640 µl 2× OneTaq master mix, 8 µl 100 µM indexed P5 primer (rand-P5-E##), 8 µl 100 µM P7 primer, and 464 µl water, and were split over 32 wells with the following cycling parameters: 2 min at 95 °C, followed by three cycles of 20 s at 95 °C, 30 s at 55 °C, and 2 min at 72 °C, with a final extension of 5 min at 72 °C, followed by a 4 °C hold. Reactions were pooled by replicate, cleaned up with AMPure XP beads at 1.8×, and eluted in 291 µl of 10 mM Tris pH 8.0. For PCR2, the entire 291 µl of eluate from PCR1 was used as input and combined with 300 µl OneTaq master mix, 3 µl 100× SYBR Green (Thermo Fisher, S7563), 3 µl 100 µM P5 primer, and 3 µl 100 µM P7 primer. This mix was split over 24 reactions for each replicate. Libraries were amplified and monitored in real-time by qPCR with 2 min at 95 °C, followed by cycles up to the qPCR inflection point consisting of 15 s at 95 °C, 20 s at 60 °C, and 2 min at 72 °C. Libraries were then pooled by replicate.  The three DNA libraries were pooled together, as were the three RNA libraries, and these two final pools were size-selected on 1% agarose gel for the expected band (156 bp). The RNA and DNA pooled libraries were quantified with Qubit dsDNA HS (Thermo Fisher) and diluted to 2 nM. Libraries were loaded at a ratio of 2:1 RNA:DNA and paired-end sequencing was performed on a NextSeq 2000 with the following primers and cycle numbers: read1 (BC forward): 16 cycles with primer TruSeq-R1; index1 (UMI): 10 cycles with primer randMPRAseq-I1; read2 (BC reverse): 16 cycles with primer randMPRAseq-R2; index2 (sample index): 10 cycles with primer TruSeq-I2.


title: A22LP051Z1

description:
Library name: Sample21
one sample from oral mucosa tissue from oral lichen planus


title: A22LP049Z1

description:
Library name: Sample20
one sample from oral mucosa tissue from oral lichen planus


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319462a

value: Sun Yat-sen University Cancer Center

value: male


title: Nur77_H3K27ac_Ctrl2


title: SW1990, EPZ-1

description: Library name: Sample 4

value: pancreatic ductal adenocarcinoma (PDAC) cell line


title: iSAE_PIWIL4_siRNA_RSV_15h_piRNA

description: iSAE cells transfected with PIWIL4-targeting siRNA (300 nM), then infected with RSV Long strain (MOI 5) and harvested 15 hours post-infection. Same RNA source sample as the companion gene expression array (GPL28885, Sample Targ_RSV).

hyb_protocol: Labeled samples were hybridized onto the Arraystar Human piRNA Microarray (HG19), which targets 23,677 unique piRNAs. Sample preparation and array hybridization were performed by Arraystar Inc. (Rockville, MD) based on the manufacturer's standard protocols.

scan_protocol: After washing, arrays were scanned using the Agilent Scanner G2505C. Agilent Feature Extraction software was used to analyze the acquired array images and derive processed signal intensities (gProcessedSignal) for each probe.

data_processing: Raw signal intensities (Agilent Feature Extraction gProcessedSignal) were quantile-normalized across the four arrays using GeneSpring GX v12.1 (Agilent Technologies). piRNAs with a detection flag of Present or Marginal (All Targets Value) in at least 1 of 4 samples were retained for further analysis. The value reported for each sample in the matrix table is the log2-transformed quantile-normalized signal intensity. Differentially expressed piRNAs were identified by Fold Change filtering; hierarchical clustering was performed using the R software package.

label_protocol: cDNA was labeled following Arraystar Inc.'s standard piRNA microarray labeling protocol (Arraystar Human piRNA Microarray, HG19).

extract_protocol: Total RNA was extracted using the ToTALLY RNA kit (Ambion/Life Technologies). RNA concentration was quantified using a Nanodrop spectrophotometer and integrity assessed by standard denaturing agarose gel electrophoresis. 600 ng of total RNA was reverse transcribed into cDNA in 1x RT buffer, 50 nM RT primers, 250 nM dNTPs, 0.6 U RNase Inhibitor, and 3 U M-MuLV Reverse Transcriptase in a 20 ul reaction volume.

value: iSAE cells

value: PIWIL4-targeting siRNA

value: RSV infection, MOI 5, 15 hours post-infection


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319461a

value: IV


title: A22LP021Z1

description:
Library name: Sample11
one sample from oral mucosa tissue from oral lichen planus

value: oral mucosa

value: oral mucosal cell


title: Nur77_H3K27ac_Ctrl1

value: macrophages


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319460a


title: iSAE_PIWIL4_siRNA_Uninfected_piRNA

description: iSAE cells transfected with PIWIL4-targeting siRNA (300 nM), harvested uninfected (basal condition). Same RNA source sample as the companion gene expression array (GPL28885, Sample Targ_Ctrl).

value: uninfected (control)


title: A22HC076Z1

description:
Library name: Sample10
one sample from oral mucosa tissue from healthy individual

value: healthy


title: GFP_H3K27ac_LPS2

value: 1h 500 ng/ml LPS


title: iSAE_NonTargeting_siRNA_RSV_15h_piRNA

description: iSAE cells transfected with non-targeting control siRNA (300 nM), then infected with RSV Long strain (MOI 5) and harvested 15 hours post-infection. Same RNA source sample as the companion gene expression array (GPL28885, Sample NTarg_RSV).

value: non-targeting siRNA


title: SW1990, EPZ

description: Library name: Sample 2


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319459a

value: previously untreated advanced ENKTL

value: lymph node/skin tissue


title: A22HC075Z1

description:
Library name: Sample9
one sample from oral mucosa tissue from healthy individual


title: GFP_H3K27ac_LPS1

value: GFP

value: H3K27ac (Diagenode, C15410196)


title: iSAE_NonTargeting_siRNA_Uninfected_piRNA

description: iSAE cells transfected with non-targeting control siRNA (300 nM), harvested uninfected (basal condition). Same RNA source sample as the companion gene expression array (GPL28885, Sample NTarg_Ctrl).


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319457a

value: Sintilimab with P-GEMOX chemotherapy

value: Sun Yat-sen University Cancer Center

value: male


title: A22HC074Z1

description:
Library name: Sample8
one sample from oral mucosa tissue from healthy individual


title: GFP_H3K27ac_Ctrl2

value: untreated


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319463a


title: Spinal cord snRNA-seq

city: New York

first: Hyemin

last: Lee

state: NY

address: 435 E 30th St

department: Neuroscience

institute: NYU Langone Medical Center

description:
Library name: sample 3
PIPseq snRNA-seq (Fluent/Illumina)

library_source: transcriptomic single cell

data_processing:
The chromosome-level genome assembly and annotated transcriptome of the little skate were accessed from NCBI (RefSeq: GCF_028641065.1). Chromosome names in the genome were edited to match the transcriptome chromosome names, then the edited .fna and .gtf files were used to make an indexed genome using STAR. This indexed genome was used to process raw .fastq files via PIPseeker (v2.1.4), a wrapper function for STARsolo. Ambient RNA was removed and cell-containing droplets were called using CellBender remove-background (v0.3.x) with default parameters (FPR 0.01, 150 epochs, learning rate 1e-4). Quality control metrics for each nucleus included the number of detected genes (nFeature_RNA) and total UMI counts (nCount_RNA). Nuclei were excluded if they had fewer than 2,500 detected genes (nFeature_RNA <2500) or fewer than 5,000 total UMIs (nCount_RNA <5000). Standard preprocessing and normalization were performed in Seurat (v5.1.0), and data were integrated across samples. Marker genes for each cluster and related differential expression (DE) analyses were calculated using the Wilcoxon rank-sum test implemented in Seurat. No data were excluded from the analyses, except during quality-control filtering as described above.
Assembly: Leucoraja erinacea, little skate, RefSeq GCF_028641065.1
Supplementary files format and content: Per-sample gene-by-nucleus UMI count matrices in HDF5 (.h5), output by CellBender remove-background (ambient-RNA-corrected counts filtered to droplets with >50% posterior probability of containing a nucleus)

molecule: nuclear RNA

organism: Leucoraja erinaceus

source_name: Spinal cord

growth_protocol: Leucoraja erinacea embryos were obtained from the Marine Biological Laboratory (Woods Hole, MA) and staged to embryonic stages 31-32.

extract_protocol:
Spinal cords and dorsal root ganglia (DRG) were dissected from st31 and st32 Leucoraja erinacea embryos (Marine Biological Laboratory, Woods Hole, MA) in seawater and collected in 500 μL filtered sEBSS (~45 mL EBSS supplemented with 1 g urea, 0.7 g NaCl, and 0.2 g TMAO). Samples were centrifuged at 300 × g for 4 minutes at 4°C, supernatant was removed, and pellets were snap-frozen on dry ice and stored at −80°C. Nuclei were isolated from spinal cords (6 embryos) and individually dissected DRG (14 embryos). Frozen samples were mechanically homogenized in 2 mL cold EZ Lysis Buffer (Sigma) using a Dounce homogenizer (20 strokes loose pestle, 20 strokes tight pestle). The homogenizer was rinsed with 1 mL EZ Lysis Buffer, samples were brought to 5 mL total volume and incubated on ice for 5 minutes. Samples were centrifuged at 500 × g for 5 minutes at 4°C, resuspended in EZ Lysis Buffer, and the lysis step was repeated. Pellets were resuspended in nuclei suspension buffer (PBS containing 0.1 mg/mL BSA and 0.2 U/μL RNase inhibitor), centrifuged, resuspended in ~1 mL nuclei suspension buffer, filtered through a 40 μm cell strainer, centrifuged again, and resuspended in 20 μL cell suspension buffer.
Approximately 45,000 nuclei (DRG) and 60,000 nuclei (SC) were loaded for library preparation following the manufacturer's instructions. Single nuclei were partitioned into pre-templated instant partitions (PIPs) following the manufacturer's instructions (Fluent BioSciences, now Illumina). Briefly, 40,000–60,000 nuclei were combined with template beads (thawed on ice), mixed gently by pipetting, and then vortexed for 175 seconds to generate single-nucleus partitions. Reverse transcription and library prep were then performed according to the manufacturer's protocol. Samples were sequenced on an Illumina NovaSeq X.

value: Spinal cord

value: embryonic stage 31-32


title: Ppn1 mutant (W501A), Rep2

city: Oxford

first: Abigail

last: Southers

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: YP1995_rep2

data_processing:
Reads trimmed and quality controlled with fastp (0.20.0)
Reads were aligned to concatenated genome of S.pombe and S. cerevisiae using STAR (2.7.3a)
Reads were split to each of the organisms keeping all alignments with samtools and bash command line
Reads which had too distant pairs were further filtered using a custom script
Aligned, filtered files were sorted and indexed using samtools
Bigwig files were prepared and separated by strand with bedtools genomecov (including -bg -strand -du -split -scale options). As scaling factor spike-in value was used. Bedgraphs were sorted and transformed to bigwigs using bedGraphToBigWig.
Assembly: ASM294v2 from pombase.org
Supplementary files format and content: bigwig with normalised coverage using spiked-in reads for plus strand
Supplementary files format and content: bigwig with normalised coverage using spiked-in reads for minus strand

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Strains were grown in YES media (with reduced uracil to 10mg/L) to OD600=~0.5

extract_protocol:
Total RNAs were extracted by a standard hot phenol method from 4-thiouracil labelled cells (S.pombe mixed with S.cerevisiae as a spike-in).
Library was prepared following TT-seq (chem) protocol. Briefly, RNA was treated with DNAse, subjected to NaOH fragmentation, followed by RNA biotinylation and purification on streptavidin beads. Purified RNA (50ng) was used in library preparation following manufacture recommendations for NEBNext ultra II directional RNA library prep kit for Illumina.

treatment_protocol: Auxin (1 mM final) treatment for 24 hours at 25°C. Non treated cells were grown at 30°C.Thiouracil labelling (5 mM final) for 6 minutes. Cells harvested and snap-frozen in liquid nitrogen

value: yeast

value: h+ leu1-32 ura4-D18 ade6-M216 his3::1 ppn1::KanMX; Leu::Ppn1(W501A)-FTP

value: no treatment


title: A22HC073Z1

description:
Library name: Sample7
one sample from oral mucosa tissue from healthy individual

value: oral mucosa

value: oral mucosal cell


title: GFP_H3K27ac_Ctrl1

value: macrophages


title: DRG snRNA-seq, replicate 2

description:
Library name: sample 2
PIPseq snRNA-seq (Fluent/Illumina)

source_name: Dorsal root ganglia

value: Dorsal root ganglia


title: Ppn1 mutant (W501A), Rep1

description: Library name: YP1995_rep1


title: A22HC072Z1

description:
Library name: Sample6
one sample from oral mucosa tissue from healthy individual

value: healthy


title: Nur77_RNApol_LPS2

value: 1h 500 ng/ml LPS

value: RNA Pol II (Diagenode, C1510055)


title: DRG snRNA-seq, replicate 1

description:
Library name: sample 1
PIPseq snRNA-seq (Fluent/Illumina)


title: Ppn1 deletion, Rep2

description: Library name: YP1892_rep2

value: h+ leu1-32 ura4-D18 ade6-M216 his3::1 ppn1::KanMX


title: A22HC070Z1

description:
Library name: Sample5
one sample from oral mucosa tissue from healthy individual


title: Nur77_RNApol_LPS1


title: A22LP025Z1

description:
Library name: Sample12
one sample from oral mucosa tissue from oral lichen planus

value: Oral lichen planus


title: Multiplexed_Splenocytes_OVA_Allergic_Day80_HTO

city: Würzburg

first: Manfred

last: Lutz

address: Versbacher Straße 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

description:
Library name: Sample 1 HTO
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
After assessing sequencing quality using FASTQC, libraries were processed with Cell Ranger 7.2.0, mapping them to the mouse reference GRCm38. Subsequently, demultiplexing was performed separately for each cell type using the HOT Demux function from the Seurat package, with a positive quantile set to 0.85. Cells with fewer than 200 detected genes, more than 10% mitochondrial genes, or over 60% ribosomal genes were considered low quality and removed. Doublets were identified with the DoubletFinder R package and excluded. The data then underwent normalization and scaling, while variable features were identified using the vst method in Seurat. The top 2000 variable genes were used to conduct PCA, followed by 30 PCs for further dimensional reduction. Cell types were assigned using canonical markers. Signatures were calculated with the AddModuleScore function in Seurat. Visualization was accomplished using the SCPubr and scCstomize R packages.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.: Tab-separated file of cell barcodes
Supplementary files format and content: features.tsv: Tab-separated file of gene names and feature name
Supplementary files format and content: matrix.mtx: gene expresion count data in Matrix Market Exchange
Supplementary files format and content: feature_reference.csv, contains the HTO info for demultiplexing

molecule: protein

source_name: Spleen

growth_protocol: C57BL/6 mice, 8 weeks old, were bred and maintained under SPF conditions in the animal facilities of the Institute of Hygiene and Microbiology and the Institute of Virology and Immunobiology of the University of Würzburg.

extract_protocol:
On day 80, mice were euthanized. Spleens were harvested, and single-cell suspensions were prepared by passing the tissue through a 70 µm cell strainer followed by red blood cell (RBC) lysis. For each group At day 80 the spleen cells of all mice were were restimulated for 3h with PMA/Ionomycin. Thereafter cells were sorted into CD45+ CD11b- and CD45+ and CD11b+ fractions, which were then pooled at a 1:1 ratio to enrich for myeloid cells and then used for scRNA-seq. Then the cells were frozen until processed using the 10x Genomics Chromium Single Cell 3′ v3.1 platform (10x Genomics) according to the manufacturer’s protocol (CG000315_RevF). To enable multiplexing of multiple samples within a single library preparation, cells were labeled with TotalSeq-A hashtag oligonucleotide (HTO) antibodies (BioLegend).
The pooled cells were loaded onto the Chromium Controller, where individual cells were encapsulated into Gel Bead Emulsions (GEMs), droplets containing a gel bead with barcoded oligonucleotides. Each oligonucleotide includes a 10x cell barcode, a unique molecular identifier (UMI), and an oligo-dT sequence that captures polyadenylated mRNA molecules. Inside each droplet, cells were lysed, and mRNA molecules were reverse-transcribed to produce barcoded cDNA, ensuring that transcripts from each cell were uniquely labelled. After reverse transcription, emulsions were broken, and the barcoded cDNA was purified, amplified, and used to create both gene expression and hashtag oligonucleotide (HTO) libraries. Approximately 10,000 cells were targeted for capture per reaction. Libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics), following the manufacturer’s recommendations for amplification and indexing. Sequencing was performed on an Illumina NextSeq 2000 system using a P3 flow cell in paired-end (PE) mode with the following read configuration: Read 1: 28 bp (cell barcode and UMI), i7 index: 10 bp, i5 index: 10 bp, Read 2: 90 bp (transcript sequence). Libraries were sequenced to a depth of approximately 50,000 reads per cell for the gene expression libraries and 5,000 reads per cell for the HTO libraries, in accordance with 10x Genomics recommendations.

treatment_protocol: All mice were sensitized at days 0 and 10 to develop allergy against ovalbumin (OVA) and then groups of mice were 1) left untreated, 2) treated with a standard desensitization at days 20, 22 and 24 with OVA in PBS and again with OVA in Alum at days 40 and 60, or 3) treated at days 20, 22, and 24 with a DCIR-2-Fusion protein connected to OVA.

value: Spleen

value: CD11B Enriched

tag: library type

value: HTO

value: WT

value: Stimulated


title: Isolated Female 0

description: Library name: 2558__Isolated-Females

tag: tissue

value: Head

value: Adult

value: Female

value: ORE-R

value: Social Isolation


title: A22HC069Z1

description:
Library name: Sample4
one sample from oral mucosa tissue from healthy individual

value: oral mucosa

value: oral mucosal cell


title: Ppn1 deletion, Rep1

description: Library name: YP1892_rep1

value: yeast

value: no treatment


title: Nur77_RNApol_Ctrl2

city: Amsterdam

first: Claudia

address: Meibergdreef 15

institute: Amsterdam UMC

value: macrophages

value: untreated

value: RNA Pol II (Diagenode, C1510055)


title: 3_HKM7VBGXT.3.ATGCGCAG_ATAGAGAG

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

institute: University of Helsinki

description:
Library name: 3_SM-NBW76_plate1
DHMT_24hr_b

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

value: iPSC-derived excitatory neuron, astrocyte

tag: day

tag: guide rna

value: no guide

tag: barcode


title: Control_4, drosophila head, 5 days

value: head

value: 5 days old, adult

tag: treatment

value: Control


title: Control_3, drosophila head, 5 days


title: Multiplexed_Splenocytes_OVA_Allergic_Day80_Gene expression

description:
Library name: Sample 1
polyA RNA
Pooled splenocytes from OVA-sensitized C57BL/6 mice. This multiplexed single-cell library contains three biological conditions: 1) Untreated , 2) Standard OVA desensitization , and 3) DCIR-2-Fusion protein treated . Cells were sorted (CD45+ CD11b- and CD45+ CD11b+ fractions pooled 1:1) and restimulated for 3h with PMA/Ionomycin.

value: Spleen

tag: strain

value: CD11B Enriched

value: mRNA

value: WT

value: Stimulated


title: sgPtpn2_IFNb_002

description:
Library name: A_017
Data2/A017_quant

value: IFN-beta, 6h, 20ng/mL

tag: batch


title: Swd2.2 deletion, Rep2

description: Library name: YP1890_rep2

value: h+ leu1-32 ura4-D18 ade6-M216 his3::1 swd2.2::KanMX


title: A22HC068Z1

description:
Library name: Sample3
one sample from oral mucosa tissue from healthy individual

value: oral mucosa

value: oral mucosal cell

value: healthy


title: Nur77_RNApol_Ctrl1

last: van Tiel

value: macrophages

value: untreated


title: DEC1 (BHLHE40) ChIP-seq in wild-type bone marrow-derived macrophages (IL-4-treated)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Library name: mm_ChIP_BMDM_DEC1_IL4

data_processing:
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
peak prediction with callpeak function of MACS2
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: bone marrow-derived macrophage

growth_protocol: We applied mouse mouse bone marrow-derived macrophages (BMDMs) from C57BL6 background control mice. Isolation and differentiation were completed as described earlier (Daniel et al. Genes Dev. (2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
ChIP was performed with minor modifications of the previously described protocol (Daniel et al. Methods Mol Biol. (2014). Briefly, 1x107 BMDMs were double cross-linked with DSG (45 min) and formaldehyde (10 min). Nuclei were isolated using a lysis buffer containing 0.15M NaCl, 0.005M EDTA pH 7.5, 0.05M Tris-HCl pH 7.5, 0.5% NP40, supplemented with protease inhibitor (Roche) prior to use. chromatin was sheared with sonication and immunoprecipitated overnight with the DEC1 antibody (NB100-1800, Novus Biologicals). Chromatin-antibody complexes were extensively washed and eluted after pull-down by paramagnetic beads. Eluted complexes were decrosslinked overnight and purified by the MinElute PCR Purification Kit. Immunoprecipitated DNA was quantified by a Qubit fluorometer.
Libraries were prepared from 10ng DNA withTruSeq ChIP library systems (Illumina) according to the manufacturer's instructions. Libraries were sequenced on NextSeq 2000.

treatment_protocol: We have generated untreated and IL-4-treated cells. On day 5, differentiated BMDMs were treated with a final concentration of 20 ng/ml IL-4 (Peprotech; 214-14) for 24 hours.

value: bone marrow-derived macrophage

value: wild-type


title: Control_2, drosophila head, 5 days

value: head

tag: developmental stage


title: Swd2.2 deletion, Rep1

description: Library name: YP1890_rep1

value: yeast

value: no treatment


title: GFP_RNApol_LPS2

value: GFP

value: 1h 500 ng/ml LPS

value: RNA Pol II (Diagenode, C1510055)


title: A22HC052Z1

description:
Library name: Sample2
one sample from oral mucosa tissue from healthy individual

tag: disease state


title: DEC1 (BHLHE40) ChIP-seq in wild-type bone marrow-derived macrophages (untreated)

description: Library name: mm_ChIP_BMDM_DEC1_untreated


title: A22HC050Z1

description:
Library name: Sample1
one sample from oral mucosa tissue from healthy individual


title: Dis2 catalytic mutant (R245Q) , Rep2

description: Library name: YP611_rep2

value: h- leu1 dis2-11


title: GFP_RNApol_LPS1


title: Dis2 catalytic mutant (R245Q) , Rep1

description: Library name: YP611_rep1


title: 3D culture from BT474 cells at day 6 replicate

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Library name: BT-C3D2

data_processing:
Sequencing reads were aligned to the human reference genome (hg38) using Bowtie2 within the pipe4C analysis pipeline. The assembly version used was hg38. Supplementary files format and content: .bedgraph files. The library preparation strategy corresponded to 4C-seq.
Assembly: hg38
Supplementary files format and content: .bedGraph
Library strategy: 4C-Seq

source_name: cell line

growth_protocol: 2D culture of BT-474 and T47D cell lines (ATCC) were cultured in Hybri-Care or RPMI medium (Gibco) supplemented with 10% FBS. To establish 3D cultures, 120 µL of Geltrex (Thermo Fisher) was dispensed into 24-well plates and incubated at 37 °C for 30 minutes to solidify. Then, 3.1 × 10⁴ cells from 2D cultures were seeded in 250 µL of medium and incubated for another 30 minutes. An additional 250 µL of medium containing 5% Geltrex was added. From the following day, 3D cultures were maintained by replacing the medium with 500 µL of fresh complete medium every three days.

extract_protocol:
A total of 15 million BT-474 and T47D cells were fixed with 2% formaldehyde in PBS for 10 minutes at room temperature to crosslink chromatin. The reaction was stopped by adding glycine (0.125 M), followed by a 5-minute incubation at 4 °C. Cells were then washed twice with cold PBS to remove residual formaldehyde. Lysis was performed in 5 mL of buffer containing Tris-HCl (50 mM, pH 8.0), NaCl (150 mM), EDTA (5 mM), Igepal CA-630 (0.5%), and Triton X-100 (1%) for 30 minutes on ice. For 3D cultures, cells were additionally dissociated with cold TrypLE™ Express to ensure single-cell suspension prior to lysis. Nuclei were isolated and 10 million were resuspended in 500 µL of 1X NEBuffer r2.1, followed by heat inactivation steps (60 °C for 10 min, then 37 °C for 50 min). Chromatin was digested using 200 U of EcoRI at 37 °C for 6 hours in a thermomixer (900 rpm), with a second enzyme dose added for overnight digestion. Subsequently, proximity ligation was carried out overnight at 16 °C using 100 U of T4 DNA ligase in 7 mL final volume with 5% PEG. To reverse crosslinking, samples were treated with Proteinase K (30 µL, 10 mg/mL) at 65 °C for 6 hours, followed by RNase A (30 µL, 10 mg/mL) at 37 °C for 45 minutes. DNA was purified by phenol–chloroform–isoamyl alcohol extraction and ethanol precipitation. The resulting DNA was then digested overnight with the secondary restriction enzyme Csp6I, purified again, and circularized via a second ligation step (overnight at 16 °C, then 1 hour at room temperature). Circular DNA was purified once more and used as template for 4C library amplification via inverse PCR.
Circularized DNA was used as a template for 4C library amplification via PCR, employing the primers CTD-2566J3.1-Reading (5′-ATGAACTAGGCACAGTGTAC-3′) and CTD-2566J3.1-Non-reading (5′-TTCCAGGGAAACTGCAAATTG-3′). Eight parallel reactions were performed using 100–200 ng of DNA each and amplified with Hot Start Phusion II High-Fidelity DNA Polymerase. PCR products were pooled and purified using the Qiagen PCR Purification Kit. Final 4C libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) and subjected to high-throughput sequencing on the Illumina platform.

value: cell line

value: Breast cancer


title: CD64 positive cell fraction from the spleen of a P.chabaudi infected mouse, mouse 99

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str. 31

department: Developmental Biology of the Immune System

institute: Life & Medical Sciences Institute, University of Bonn

description:
Library name: CD65pos_Malaria6020
10X Genomics

data_processing:
The raw sequencing data was  processed with the ‘count’ command of the Cell Ranger software (v7.1.0) provided by 10X Genomics using the refdata-gex-mm10-2020-A reference genome.  All other options were used as per default.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-delimited text files include cell-barcode names (barcodes.tsv) as well as gene names (features.tsv) corresponding to the count data in matrix.mtx.

source_name: spleen

extract_protocol:
FACS/MACS enrichment
ChromiumNext GEMSingle Cell 3ʹ Reagent Kits v3.1 (Dual Index)

value: spleen

value: 5-6 months

value: Tnfrsf11aCre; Rosa26LSL-YFP; Ms4a3FlpO; Rosa26FSF-tdTomato

tag: condition

value: Malaria


title: sgPtpn1_IFNb_002

description:
Library name: A_011
Data2/A011_quant

data_processing:
Salmon
Assembly: MM_grch38_ens94
Supplementary files format and content: .csv

extract_protocol:
Quiiagen Plus mini kit
NEBNext_dual_i7

value: IFN-beta, 6h, 20ng/mL


title: CD64 positive cell fraction from the spleen of a P.chabaudi infected mouse, mouse 2

description:
Library name: CD65pos_Malaria1
10X Genomics

tag: age


title: GFP_RNApol_Ctrl2

value: macrophages

value: untreated


title: Rab7 RNAi_4, drosophila head, 5 days

value: 5 days old, adult

value: GMR-Gal4/UAS-Rab7 RNAi

value: RNA interference


title: Dis2 deletion, Rep2

description: Library name: YP606_rep2

value: yeast

value: h- leu1 ura4 dis2::ura4+

value: no treatment


title: 3D culture from BT474 cells at day 6

description: Library name: BT-C3D1


title: GFP_RNApol_Ctrl1

value: GFP

value: RNA Pol II (Diagenode, C1510055)


title: CD64 positive cell fraction from the spleen of a PBS treated control mouse, mouse 99

description:
Library name: CD65pos_Ctrl99
10X Genomics

value: PBS

value: Ctrl


title: 2D culture from BT474 cells at day 6 replicate

description: Library name: BT-C2D2

value: cell line

value: Breast cancer


title: Dis2 deletion, Rep1

description: Library name: YP606_rep1


title: Nur77_HA_LPS3

value: 1h 500 ng/ml LPS

value: HA (Diagenode, C15200190)


title: CD64 positive cell fraction from the spleen of a PBS treated control mouse, mouse 2

description:
Library name: CD65pos_Ctrl2
10X Genomics

value: spleen

value: 5-6 months

value: Tnfrsf11aCre; Rosa26LSL-YFP; Ms4a3FlpO; Rosa26FSF-tdTomato


title: 2D culture from BT474 cells at day 6

description: Library name: BT-C2D1


title: WT, Rep2

description: Library name: YP144_rep2


title: Nur77_HA_LPS2

value: macrophages


title: CD45 negative cell fraction from the spleen of a P.chabaudi infected mouse, mouse 99

description:
Library name: CD45neg_Malaria6020
10X Genomics

value: Malaria


title: WT, Rep1

description: Library name: YP144_rep1


title: Nur77_HA_LPS1