title: H1703, TMP, rep4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to the hg38 (GENCODE GRCh38) using STAR
Read count extraction per gene was performed using featureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: Four NSCLC line lines (H460, H838, H1703, H1755) were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS).

extract_protocol:
RNA was collected using NucleoSpin RNA, Mini kit for RNA purification (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) according to the manufacturer's protocols.

treatment_protocol: 1 day post plating, cells were treated with DMSO, MYCi975 5 µM, TMP195 25 µM, or combination for 24 hours.

tag: cell line

tag: treatment


title: H1703, MYCi, rep4

status: Public on Apr 23 2025

type: SRA

city: Baltimore

first: Jina

last: Park

state: Maryland

address: 1650 Orleans St

department: Oncology

country: USA

institute: Johns Hopkins University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: PBS-14-d28

type: other

city: Irvine

first: Li

last: Liang

state: CA

address: MedSurge II

institute: University of California Irvine

description: Total IgG

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

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

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

molecule: other

organism: Mus musculus

source_name: Plasma

tag: days post prime immunization


title: pat. 2, MRA, antrum, repl.1

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v. 3.7.5
Fastq were preprocessed for QC by fastp.
Alignment was performed with STAR 2.6.
Quantification at gene level was determined using htseq-count 0.6.1p1.
Assembly: Illumina iGenome Homo sapiens UCSC hg38
Supplementary files format and content: Tab-delimited files including raw counts for each sample

molecule: polyA RNA

source_name: Gastric

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) following manufacturer’ instructions.
10ng of total RNA were processed using the NEBNext Low Input RNA Library Prep Kit (New England Biolabs p/n E6420) according to manufacturer’s instructions.

tag: tissue

value: Gastric

tag: subtissue

value: Antrum

tag: culture system

value: MRA


title: ATAC Day_8_Hdac1-KO_Term-1

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

description:
Day_8_Hdac1-KO_Term_peaks.narrowPeak
Day_8_Hdac1-KO_Term_scaled.bw

library_source: genomic

data_processing:
The sequencing quality of Cut&Run libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Low-quality bases and adapters were removed through Trim Galore (v0.6.7)(MAPQ > 30)
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling ATAC-seq peaks, where stringent criteria of FDR < 1e-5, --fe-cutoff 4 and --llocal 7500.
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig

molecule: genomic DNA

source_name: Hdac1-deficient Tex-Term cells

extract_protocol:
Gzmb-Cre; Rosa26-lsl-GFP; Hdac1 wild-type or floxed mice were directly infected with LCMV Clone 13. On day 8 post-infection, Gp33 tetramer-positive cells were sorted into three populations based on surface markers Cx3cr1 and Slamf6 for ATAC-seq analysis.
Sort-purified cells  were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina Nova seq platform.

value: splenocytes

tag: cell population

value: Tex-Term cells

tag: genotype


title: H1703, Veh, rep4

value: Vehicle


title: PBS-12-d28

description: Total IgG


title: HA mRNA 23-d28

description: Total IgG


title: pat. 2, organoid, body, repl.1

value: Body

value: Organoid


title: NRVM_Nit_2_1

city: Dover

first: David

middle: C

last: Zebrowski

state: DE

address: 1151 Walker Rd

institute: GenKardia Inc.

data_processing:
Raw sequence reads were mapped to the RAT genome (RN6) and human genome (hg38) using Tophat2 with Bowtie2 option where adaptor sequences were removed using trim_galore before read mapping.
BAM files containing the alignment results were sorted according to the mapping position. Raw read counts for each gene were calculated using featureCounts from Subread package.
Differential expression analysis was performed using DEseq2, with raw counts as input. The differentially expressed genes were identified by adjusted p value for multiple testing using Benjamini-Hochberg correction with False Discovery Rate (FDR) values less than 0.1.
Assembly: rat genome (RN6) and human genome (hg38)
Supplementary files format and content: Excel file includes results from differential expression analysis and normalized counts per gene and sample

organism: Rattus norvegicus

source_name: primary cells

growth_protocol: Neonatal Rat Ventricular Cardiomyocyte Isolation and Culture: Ventricular cardiomyocytes were isolated from 6-day old neonatal Sprague-Dawley rats as described previously (18). Cardiomyocytes were seeded and cultured in DMEM/F-12, GlutamaxTM-I (ThermoFisher Scientific, catalogue number: 10565018) + Penicillin (100 U/ml)/Streptomycin (100 µg/ml) (Pen/Step) (ThermoFisher Scientific, catalogue number: 15140122) for 2 days prior to experimentation.Cells were plated in 24-well plates on glass coverslips (ThermoScientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Fibronectin for at least 2 hours at RT prior to seeding. Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Human iPSC-derived Cardiomyocytes and Culture: Human induced-PSC-derived cardiomyocytes (hiPSC-CMs) were acquired from Fujifilm Cellular Dynamics International, Inc. (CDI) (iCell Cardiomyocytes, catalogue number: CMC-100-010-001). hiPSC-CMs from CDI were seeded and cultured according to manufacture´s directions (https://cellulardynamics.com/assets/CDI_iCellCardiomyocytes_UG.pdf). CDI iCell Cardiomyocyte lot numbers used in this study: #1833511, #1099441, #1098841. In brief, hiPSC-CMs were thawed and cultured in plating medium (CDI, catalogue number: M1003) for 2 days and then cultured in maintenance medium (CDI, catalogue number: M1001) for 4 days. Afterwards, hiPSC-CMs were treated with compounds for 2 days prior to fixation or RNA isolation. hiPSC-CMs were plated in 24-well plates on glass coverslips (Thermo Fisher Scientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Matrigel (Corning, catalogue number: 356255) for at least 2 hours at RT.

extract_protocol:
P6-NRVMs and CDI-CMs were treated with Nitrendipine or 1-NA-PP1 for 2 days prior to RNA extraction. In addition, both P6-NRVMs and CDI-CMs during treatment with Nitrendipine or 1-NA-PP1 were cultured in the presence of araC. AraC was used to reduce overgrowth of contaminating cardiac fibroblasts (which generally amount to ~3% of cultured cells in primary cardiomyocyte isolation procedure). RNA was extracted from sub-confluent 10-cm plates using Qiagen RNeasy mini kit. RNA quality (RNA integrity number, RIN) and quantity was measured in a Bioanalyzer 2100 (Agilent) using the Agilent RNA 6000 Nano Kit (part number 5067-1511). The sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England Biolabs), starting with 200 ng of total RNA. In brief, mRNA was isolated and fragmented using the NEBNext poly(A) mRNA magnetic isolation module (E7490S, New England Biolabs), with the first and second strands of cDNA synthesized and purified using AmPure XP SPRI beads (A63880, Beckman Coulter). Then adaptor ligation and size selection wereperformed according to the manufacturer’s protocol. Next, the adaptor ligated cDNA was PCR enriched to incorporate an Illumina compatible index sequence (NEBNext Oligos for Illumina, Dual Index Primers Set1 (E7600S, New England Biolabs). All libraries were purified using AmPure XP SPRI beads, and the size distribution of the libraries was analyzed at the Bioanalyzer 2100 using the Agilent High Sensitivity DNA Kit (part number 5067-4626). Subsequently, the quantification of the libraries was performed with the Qubit® 2.0 Fluorometer (ThermoFisher Scientific) and QubitTMdsDNA HS Assay Kits (Q32851, Invitrogen). Finally, all 19 libraries were pooled and diluted to 3.5 nM for sequencing on one lane of a Hiseq 3000 sequencer (Illumina), using a single read 50 bp and dual indexed sequencing strategy.
The sequencing libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacture's protocols.

treatment_protocol: Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Treatment of CDI cardiomyocytes with Nitrendipine and 1-NA-PP1 was done in the presence of CDI culture medium for 2 days prior to fixation or RNA-isolation.

value: primary cells

tag: cell type

value: cardiomyocytes

tag: developmental stage

value: neonatal

value: Nitrendipine, 48 hours

tag: time

value: day 7 (P7)


title: PBS-13-d28

description: Total IgG


title: H838, Combo, rep4

value: Combo


title: S mRNA-32-d28

description: Total IgG


title: NRVM_Nit_2_0


title: HA/S Protein-54-d14

description: Total IgG


title: PBS-11-d28

description: Total IgG


title: H1703, Combo, rep4


title: HA/S Protein-55-d14

description: Total IgG


title: ATAC Day_8_Hdac1-KO_Int-1

description:
Day_8_Hdac1-KO_Int_peaks.narrowPeak
Day_8_Hdac1-KO_Int_scaled.bw

source_name: Hdac1-deficient Tex-Int cells

value: Tex-Int cells


title: HA/S Protein-53-d14

description: Total IgG


title: H838, TMP, rep4


title: H838, MYCi, rep4


title: NRVM_Nit_1_2


title: NRVM_Nit_1_1


title: HA/S Protein-52-d14

description: Total IgG


title: HA/S Protein-51-d14

description: Total IgG


title: HA/S mRNA-44-d14

description: Total IgG


title: HA/S mRNA-43-d14

description: Total IgG


title: HA/S mRNA-45-d14

description: Total IgG


title: H1755, Combo, rep4


title: NRVM_Ctrl_2_2

value: DMSO, 48 hours


title: HA/S mRNA-42-d14

description: Total IgG


title: H1755, TMP195, rep4


title: S mRNA-34-d14

description: Total IgG


title: NRVM_Ctrl_2_1


title: H1755, MYCi975, rep4


title: HA/S mRNA-41-d14

description: Total IgG


title: S mRNA-33-d14

description: Total IgG


title: NRVM_Nit_1_0


title: NRVM_Ctrl_2_0


title: H1755, Vehicle, rep4


title: H460, Combo, rep4


title: HA mRNA 25-d14

description: Total IgG


title: NRVM_Ctrl_1_2


title: NRVM_Ctrl_1_1


title: HA mRNA 24-d14

description: Total IgG


title: NRVM_Ctrl_1_0


title: HA mRNA 23-d14

description: Total IgG


title: S mRNA-35-d14

description: Total IgG


title: H838, Veh, rep4


title: H460, TMP195, rep4


title: H460, MYCi975, rep4


title: S mRNA-31-d14

description: Total IgG


title: HA mRNA 22-d14

description: Total IgG


title: PBS-15-d14

description: Total IgG


title: S mRNA-32-d14

description: Total IgG


title: NRVM_PP1_2_2

value: 1-NA-PP1, 48 hours


title: H460, Vehicle, rep4


title: NRVM_PP1_2_1


title: PBS-13-d14

description: Total IgG


title: PBS-12-d14

description: Total IgG


title: H838, TMP, rep3


title: H838, TMP, rep2


title: PBS-11-d14

description: Total IgG


title: NRVM_PP1_1_2


title: H441, Combo, rep 2

growth_protocol: Four NSCLC line lines (H460, H1703, HCC827, H441) were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS).

treatment_protocol: 1 day post plating, cells were treated with DMSO, MYCi975 5 µM, TMP195 25 µM, or combination for 48 hours.


title: Kpy_2

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

country: China

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

description: Library name: Sample 2

data_processing:
Sequencing reads were mapped to the Illumina iGenomes UCSC hg38 reference genome using Bowtie, retaining only uniquely mapped reads. The aligned files were then converted to bam format, sorted, and PCR duplicates were removed using SAMtools. The average profiling of sequencing reads was generated using Ngs.plot. Peak calling was performed with MACS (FDR = 0.01), and data visualization was conducted using IGV.
Assembly: hg38
Supplementary files format and content: bigWig,csv
Library strategy: CUT&Tag

source_name: HEK293T cells

extract_protocol:
CUT&Tag experiments were performed following the instructions of the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (N259-YH01, Novoprotein). A total of 100,000 cells were immobilized on concanavalin A (ConA)-coated magnetic beads, followed by permeabilization using digitonin. Each sample was incubated overnight at 4°C with 1 μg of either anti-pan Kpy or anti-pan Kla antibodies. Subsequent steps included secondary antibody incubation, transposome integration, and fragmentation reactions.
The reaction products were subjected to DNA extraction, PCR amplification, and purification to construct next-generation sequencing libraries. Libraries were sequenced on a HiSeq X Ten platform (Illumina) with 150-bp paired-end reads, following the manufacturer's instructions for sequencing read length and dual indexing (Annoroad).

value: HEK293T cells

value: human embryonic kidney cells

value: WT


title: H441, Vehicle, rep 2


title: NRVM_PP1_1_0


title: HA mRNA-21-d14

description: Total IgG


title: H838, MYCi, rep3


title: HCC827, Vehicle, rep 2


title: H838, TMP, rep1


title: H1703, Combo, rep2


title: H1703, Combo, rep 2


title: HCC827, Combo, rep 2


title: H1703, Vehicle, rep 2


title: H460, Combo, rep 2


title: H1755, Combo, rep3


title: H460, Vehicle, rep 2


title: H1755, TMP, rep3


title: LECs, GF sample 12

city: Mainz

first: Hristo

last: Todorov

address: Duesbergweg 6

country: Germany

institute: University Medical Center Mainz

description:
Library name: Samples12
G06-L1_S107

data_processing:
The quality of raw sequencing reads was inspected using FastQC (v0.11.9). Adapters and low-quality bases were removed using BBDuk (BBMap 38.86) with the following settings: ktrim=r k=23 mink=11 hdist=1 tpe tbo minlen=10 ziplevel=2 overwrite=true qtrim=rl trimq=10. Trimmed reads were mapped to the UCSC mm10 mouse reference genome using STAR (v2.7.5a). Gene expression was quantified with featureCounts (v2.0.1) from the Subread package. Differential expression analysis was performed using DESeq2 (v1.42.1) with default settings.
Assembly: mm10 USCS
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Liver endothelial cells

extract_protocol:
Total RNA extracted from LECs were sequenced as described previously (REF DOI: 10.1016/j.isci.2021.103092) with the following modifications. RNA concentration and integrity were analysed using a TapeStation 4200 System (Agilent) and a Qubit 4 fluorometer (ThermoFisher Scientific).
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions. All samples were sequenced using an Illumina NovaSeq6000 sequencer (Illumina, San Diego,CA)

value: Liver endothelial cells

value: wild type

tag: group

value: GF


title: NRVM_PP1_2_0


title: PBS-14-d14

description: Total IgG


title: H441, Combo, rep 1


title: H441, Vehicle, rep 1

value: Vehicle


title: H1755, MYCi, rep3


title: HCC827, Combo, rep 1


title: NRVM_PP1_1_1


title: Kpy_1

description: Library name: Sample 1


title: LECs, GF sample 10

description:
Library name: Samples10
E06-L1_S89


title: LECs, GF sample 13

description:
Library name: Samples13
H06-L1_S116


title: H1703, Combo, rep 1


title: LECs, GF sample 9

description:
Library name: Samples9
D06-L1_S79


title: H1703, Vehicle, rep 1


title: H1703, TMP, rep3


title: LECs, GF sample 8

description:
Library name: Samples8
C06-L1_S69


title: H460, Combo, rep 1


title: H1703, Combo, rep3


title: P120 Malignant Line, WES

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem.63 Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated peripheral blood mononuclear cells.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json
Library strategy: WES

source_name: Patient-derived malignant cell line

extract_protocol:
Bulk RNAseq: Total RNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol. RNA concentration and quality were assessed using NanoDrop.  Whole exome sequencing: Genomic DNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen DNeasy Blood & Tissue Kit following the manufacturer’s instructions. DNA concentration and purity were assessed with NanoDrop. Extracted DNA was used for exome library preparation. Single-cell sequecing: Single-cell suspensions were prepared from tumor or PBMCs, and viable cells were loaded into the 10x Genomics Chromium platform for partitioning. RNA from individual cells was reverse-transcribed, and libraries were prepared according to the 10x Genomics protocol. Spatial: Slides were processed through the 10x Genomics Gene Expression workflow with pre-sequencing H&E imaging completed on the Keyence Microscope per 10x Genomics workflows. Next, transcripts were de-crosslinked, hybridized to a probe panel, ligation completed, and probes released for capture on the gridded, barcoded surface of the Visium slide (CytAssist, 10x Genomics, RRID:SCR_024570). After barcoding, the samples underwent library preparation, amplification, and clean-up with quality assessment ensuring that fragments were ~240bp.
Bulk RNAseq: RNA was extracted and used for mRNA library preparation with poly(A) enrichment, following Novogene's standard protocol. Library construction and sequencing were performed on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Whole exome sequencing: Genomic DNA was extracted and used for library preparation with the Agilent V6 kit, according to Novogene's standard workflow. Library quality was assessed, and sequencing was conducted on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Single-cell sequencing: Library preparation was completed at the MCW Mellowes Center (RRID:SCR_022926) with 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits (10X Genomics, sample dual indexes with cellular and molecular barcodes with VDJ amplification). Target capture of 10,000 cells per sample was used. Prior to sequencing, libraries were quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems). Spatial: Libraries were sequenced at the Mellowes Center Facility on the Illumina NovaSeq6000 with paired end reads per the 10x Genomics protocol and generating 25 million read pairs per spot covered by tissue. The quality control of raw reads was processed by FastQC.

value: Patient-derived malignant cell line

value: Pre-Treatment


title: H1703, MYCi, rep3


title: LECs, CONV-R sample7

description:
Library name: Samples7
H09-L1_S119

value: CONV-R


title: P120 Malignant Line, Bulk_RNA

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem.63 Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated peripheral blood mononuclear cells.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json


title: H1703, Veh, rep3


title: P120N, Bulk_RNA

source_name: Cancer lymph node

value: Cancer lymph node


title: LECs, CONV-R sample5

description:
Library name: Samples5
F09-L1_S101


title: LECs, CONV-R sample6

description:
Library name: Samples6
G09-L1_S110


title: P120PBMC, WES

description: This PBMC sample does not have processed data as it is the germline reference used to produce the VCF files for the tumor samples.

source_name: PBMC

value: PBMC


title: H838, Combo, rep3


title: P120N, WES


title: LECs, GF sample 11

description:
Library name: Samples11
F06-L1_S98


title: P120T, WES

source_name: Oral cancer

value: Oral cancer


title: HyPR-HN 02_3_PBMC, WES

value: 6 Weeks Post-Radiation


title: LECs, CONV-R sample4

description:
Library name: Samples4
D10-L1_S83


title: HCC827, Vehicle, rep 1


title: H1755, Veh, rep3


title: H838, Vehicle, rep3


title: HyPR-HN 02_3, WES


title: P120T, Bulk_RNA


title: LECs, CONV-R sample3

description:
Library name: Samples3
C10-L1_S73


title: H460, Vehicle, rep 1


title: HyPR-HN 02_3_Bulk_RNA


title: H460, Combo, rep3

value: Combo


title: HyPR-HN 02_1, WES


title: H460, TMP195, rep3


title: HyPR-HN 02_1_Bulk_RNA


title: LECs, CONV-R sample2

description:
Library name: Samples2
B10-L1_S63


title: H838, Combo, rep4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic version 0.39.
Trimmed sequence reads were mapped to the GENCODE hg38 (GRCh38) genome using Bowtie2 version 2.3.5.1.
ATAC-seq reads that are unmapped, mate unmapped, not primary alignment, failing platform, PCR duplicates, mapping to chrM or MAPQ < 20 were discarded.
Peaks were called using MACS3.
Assembly: hg38
Supplementary files format and content: xls (MACS3 output)

growth_protocol: Two NSCLC line lines (H460, H838) were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS).

extract_protocol:
50,000 viable cells were collected and lysed with cold lysis buffer containing 0.1 % v/v NP-40, 0.1 % v/v Tween-20, and 0.01 % v/v Digitonin. Following the centrifuging of the cell lysate, the pellet (nuclei) was incubated with Tn5 Transposase (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits, 20034197) for 30 minutes at 37°C on a thermomixer at 1,000 rpm. DNA was extracted from the lysate.
ATAC-seq libraries were prepared following the Omni-ATAC method (Corces, M. Ryan, et al. 2017). Briefly, extracted DNA was subjected to PCR amplification with the number of cycles determined by qPCR. ATAC-seq libraries were purified with AMPure XP beads (Beckman Coulter, A63880).


title: LECs, CONV-R sample1

description:
Library name: Samples1
A10-L1_S53


title: H460, MYCi975, rep3


title: H838, TMP195, rep4


title: H838, MYCi975, rep4


title: H838, Vehicle, rep4


title: H460, Combo, rep4


title: H460, MYCi975, rep4


title: NEGR1_control, ventral hippocampus, rep1

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

description:
Library name: NEGR1_control_ventral hippocampus tissues_rep1
C17

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.36. (parameter: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:15)
High-quality reads were then imported into STAR 2.7.10 for alignment into BAM files. (parameter: --genomeDir /path/to/ensembl_mm10/ --outSAMtype BAM SortedByCoordinate)
Gene read counts were calculated by featureCounts v2.0.3. (parameter: -T 24 -s 0 --primary -p -t exon -Q 10 -g gene_id -a /path/to/Mus_musculus.GRCm39.110.chr.gtf)
Assembly: ensembl_mm10
Supplementary files format and content: whitespace-delimited text file including raw counts for each ventral hippocampus Sample

source_name: ventral hippocampus

extract_protocol:
Total RNA was extracted by Trizol.
RNA library for Strand-specific RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template without U was enriched by PCR, and the PCR product was purified to obtain the final library.

value: ventral hippocampus

value: total RNA


title: H460, Vehicle, rep3


title: NEGR1_control, ventral hippocampus, rep2

description:
Library name: NEGR1_control_ventral hippocampus tissues_rep2
C19


title: H460, TMP195, rep4


title: H460, Vehicle, rep4


title: NEGR1_overexpression, ventral hippocampus, rep3

description:
Library name: NEGR1_overexpression_ventral hippocampus tissues_rep3
N10


title: H838, TMP195, rep3


title: H838, MYCi975, rep3


title: H1755, TMP, rep2


title: H1755, Combo, rep2


title: NEGR1_overexpression, ventral hippocampus, rep2

description:
Library name: NEGR1_overexpression_ventral hippocampus tissues_rep2
N8


title: H838, Combo, rep3


title: H1755, MYCi, rep2


title: H1755, Veh, rep2


title: H460, Combo, rep3


title: H838, Vehicle, rep3


title: NEGR1_overexpression, ventral hippocampus, rep1

description:
Library name: NEGR1_overexpression_ventral hippocampus tissues_rep1
N7


title: H1703, TMP, rep2


title: H460, Vehicle, rep3


title: WT_activte_repeat1

city: Shanghai

first: Wei

last: Lu

state: Shanghai

address: 320 YueYang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
Library name: WT_RNAseq_activte_repeat1
W_A_1

data_processing:
The trimmed reads were mapped to the mouse reference genome (GRCm38.p6). Read count extraction
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

extract_protocol:
Naïve CD8+ T cells were purified by using MojoSort™ Mouse Naive CD8 T Cell Isolation Kit (BioLegend).
RNA was purified with Trizol (Invitrogen). 500 ng RNA was used to construct libraries
NextSeq 500 High Output v2 Kit

value: spleen

value: anti-CD3/CD28 stimulate for 24h


title: H460, MYCi975, rep3


title: NEGR1_control, ventral hippocampus, rep3

description:
Library name: NEGR1_control_ventral hippocampus tissues_rep3
C20


title: H838, Combo, rep2


title: WT_activte_repeat2

description:
Library name: WT_RNAseq_activte_repeat2
W_A_2

value: WT


title: H838, TMP195, rep2


title: H838, Vehicle, rep2


title: H838, MYCi975, rep2


title: H1703, Veh, rep2


title: WT_activte_repeat3

description:
Library name: WT_RNAseq_activte_repeat3
W_A_3


title: E134G_activate_repeat1

description:
Library name: E134G_RNAseq__activate_repeat1
E_A_1

value: Card11 E134G


title: H460, Combo, rep2


title: H460, TMP195, rep2


title: H838, MYCi975, rep2


title: H838, Vehicle, rep2


title: H460, Vehicle, rep2


title: H460, MYCi975, rep2


title: E134G_activate_repeat2

description:
Library name: E134G_RNAseq__activate_repeat2
E_A_2


title: H838, Combo, rep1


title: E134G_activate_repeat3

description:
Library name: E134G_RNAseq__activate_repeat3
E_A_3


title: H460, Combo, rep2


title: H838, TMP195, rep1


title: H838, MYCi975, rep1


title: H460, TMP195, rep3


title: H1703, MYCi, rep2


title: H838, Vehicle, rep1


title: H460, TMP195, rep2


title: H460, TMP195, rep1


title: H460, Combo, rep1


title: K215M_activated_repeat3

description:
Library name: K215M_RNAseq_activated_repeat3
K_A_3

value: Card11 K215M


title: H460, MYCi975, rep1


title: H460, Vehicle, rep1


title: H838, Combo, rep2


title: H460, MYCi975, rep2


title: H460, Vehicle, rep2


title: WT_naive_repeat1

description:
Library name: WT_RNAseq_naive_repeat1
W_N_1

value: naïve


title: LEC3

city: Auckland

first: Justin

last: Rustenhoven

address: 133 Rangatira Road

department: Pharmacology

country: New Zealand

institute: The University of Auckland

description: Paired end runs, two lanes per sample

data_processing:
CD Genomics
The quality of the original reads including sequencing error rate distribution and GC content distribution, æwas evaluated using FastQC. The original sequencing sequences contain low quality reads and adapter sequences. To ensure the quality of data analysis, raw reads were filtered to get clean reads, and the subsequent analysis was based on clean reads. Data filtering was carried out using fastp mainly including the removal of adapter sequences in the reads, the removal of reads with high proportion of N (N denotes the unascertained base information), and the removal of low-quality reads.
The reference genome index was created by the build-index function in HISAT2 software package with default options.  Then the filtered clean reads were mapped to reference genome by HISAT2, and the position and gene characteristics were acquired.
FeatureCounts software of subread package was used to quantify transcripts and the gene expression  levels using mapped reads’ positional information on the gene. The differential expression levels of the gene, as well as the expression level of each single gene were analyzed. DESeq2 was used to analyze the DEGs (differentially expressed genes).
Assembly: GRCh38
Supplementary files format and content: Tab-delineated text file includes raw counts for each Sample

source_name: iPSC

growth_protocol: iPSC were maintained in StemFlex culture media. iPSCs were converted to LECs via mesoderm differentiation with  0.5 X DMEM/F12, 0.5 X Neurobasal, 1X Glutamax, 1X N2, 1X B27, 8 uM CHIR99021, and 100 ug/mL BMP4. Mesoderm was converted to LECs with 1X StemPro34, 1X Glutamax, 2 uM Forskolin, 100 ng/mL VEGFC, 100 ng/,mL Wnt5b, 20 ng/mL VEGFA, 20 ng/mL Ang1, 20 ng/mL BMP4, 20 ng/mL IL3.

extract_protocol:
RNA was harvested using the RNAqueous micro kit (ThermoFisher). 500 ng of RNA was used for the construction of sequencing libraries.
Illumina® Stranded mRNA Prep to enrich for mRNA using PolyA capture with ligation-based addition of adapters and indexes was used to make stranded libraries for Illumina sequencing. Twelve cycles of PCR were used to amplify the libraries according to manufacturer instructions.

value: iPSC

value: iPSC-differentiation to LECs


title: H1755, Combo, rep1


title: LEC2

description: Paired end runs, two lanes per sample


title: WT_naive_repeat2

description:
Library name: WT_RNAseq_naive_repeat2
W_N_2


title: LEC1

description: Paired end runs, two lanes per sample


title: iPSC3

description: Paired end runs, two lanes per sample

value: Base iPSC line


title: iPSC2

description: Paired end runs, two lanes per sample


title: H1755, TMP, rep1


title: iPSC1

description: Paired end runs, two lanes per sample


title: WT_naive_repeat3

description:
Library name: WT_RNAseq_naive_repeat3
W_N_3


title: Nurse (scATAC-Seq)

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

library_source: genomic single cell

data_processing:
‘cellranger-arc mkref’ (version 2.0.0) from 10x Genomics was used to creating a reference package with Amel_HAv3.1 genome and the modified annotation gtf file. Raw sequencing scRNA- and scATAC-seq fastq files were aligned to the Amel_HAv3.1 reference genome by ‘cellranger -arc count’ to generate barcoded count matrices of gene expression and chromatin accessibility data. All ambiguous UMIs that mapped to multiple genes were removed from the BAM file with custom scripts using samtools and pysam to prevent double-counting UMIs. The gene expression matrix was then recalculated by counting the number of different UMIs per cell barcode for each gene(Tsukahara et al. 2021).
Assembly: Amel_HAv3.1 genome
Supplementary files format and content: tsv file include barcode, peak position and peak signal for each sample

organism: Apis mellifera

source_name: Nurse bees

extract_protocol:
Dissected antennae were thawed on wet ice, and all subsequent steps were performed on wet ice. Once samples were thawed, antennae were centrifuged in a bench top microcentrifuge for 5–10 s, Schneider’s Medium was removed and replaced with 1 mL of homogenization buffer (ref). And transfer 1 ml homogenized sample into the 1 ml dounce (Wheaton #357538). Dounce set should be autoclaved at 200˚C > 5 hr. Release nuclei by 40 strokes of loose Dounce pestle and 35 of tight Dounce pestle. Avoid bubbles. Filter 1 ml sample using 10 µm Flowmi (BelArt #H13680-0040) into a new 1.5 ml EP tube and keep the tube on ice. Centrifuge for 10 min at 600 g at 4˚C and discard the supernatant. Re-suspend the nuclei using desired amount of 1 x Nuclei Buffer with 1U/µL RNase inhibitor and 1mM DTT. Pipette mix 20 times to completely re-suspend the nuclei and keep the tube on ice.
Single cell multiome library were prepared as outlined by the 10x Genomics Single Cell Multiome ATAC + Gene Expression Reagent Kit user guides and as described previously (Mimitou et al., 2021). Standard protocols from 10x Genomics were followed to generate the dual index libraries. The quality and quantity of the libraries were confirmed using a Nanodrop (Thermo Scientific, Walthan, Massachusettes, USA) and Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). Libraries were sequenced on illumina NovaSeq 6000 at Berry Genomics using 150 cycle PE flowcell and 800 million paired reads were generated.

value: antenna


title: K215M_activated_repeat1

description:
Library name: K215M_RNAseq_activated_repeat1
K_A_1


title: H1755, MYCi, rep1


title: NE (scATAC-Seq)

source_name: New worker bees


title: E134G_naive_repeat1

description:
Library name: E134G_RNAseq__naive_repeat1
E_N_1


title: K215M_activated_repeat2

description:
Library name: K215M_RNAseq_activated_repeat2
K_A_2


title: H1755, Veh, rep1

value: Vehicle


title: E134G_naive_repeat2

description:
Library name: E134G_RNAseq__naive_repeat2
E_N_2


title: Forager (scRNA-Seq)

library_source: transcriptomic single cell

data_processing:
‘cellranger-arc mkref’ (version 2.0.0) from 10x Genomics was used to creating a reference package with Amel_HAv3.1 genome and the modified annotation gtf file. Raw sequencing scRNA- and scATAC-seq fastq files were aligned to the Amel_HAv3.1 reference genome by ‘cellranger -arc count’ to generate barcoded count matrices of gene expression and chromatin accessibility data. All ambiguous UMIs that mapped to multiple genes were removed from the BAM file with custom scripts using samtools and pysam to prevent double-counting UMIs. The gene expression matrix was then recalculated by counting the number of different UMIs per cell barcode for each gene(Tsukahara et al. 2021).
Assembly: Amel_HAv3.1 genome
Supplementary files format and content: tsv file include barcode, features and UMI for each sample

source_name: Forager bees


title: E134G_naive_repeat3

description:
Library name: E134G_RNAseq__naive_repeat3
E_N_3


title: H1703, Combo, rep1


title: Nurse (scRNA-Seq)


title: NE (scRNA-Seq)


title: H1703, TMP, rep1


title: CLBL-1, w36, p128, Ibr+AS, 72 h

city: Rostock

first: Hugo

middle: Murua

last: Escobar

address: Schillingallee 35

department: Clinic for Hematology, Oncology and Palliative Care

institute: Rostock University Medical Center

description: Library name: 3rd-72-IA

data_processing:
Reads were mapped to the soft masked Canine lupus familiaris reference genome assembly CamFam3.1 and transcript quantification were simultaneously done with STAR (v2.7.5a) according to gene annotation from Ensembl (https://ftp.ensembl.org/pub/release-101/gtf/canis_lupus_familiaris/Canis_lupus_familiaris.CanFam3.1.101.chr.gtf.gz, last accessed in June 2024). The resulting bam files were indexed and sorted with SAMtools.
Assembly: CamFam3.1
Supplementary files format and content: Tab-delimited tsv file includes raw counts for each sample. Each column refers to the library name

organism: Canis lupus familiaris

extract_protocol:
A total volume of 6 mL medium containing 2 x 106 cells was seeded into each well of 6-well plates, and then exposed to 1 μM Ibrutinib, 5 μM AS-605240, their combination, or DMSO, two wells per treatment. When reaching 24, 48, and 72 hours respectively, incubated cells were harvested and washed three times with cool PBS and centrifuged at 200x g for 8 min at 4° C. QIAzol® Lysis Reagent (QIAGEN, Venlo, Netherlands) of 700 μL was added into the pellet of 5 x 106 cells to lyse. Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN, Venlo, Netherlands) referring to the manufacturer’s Quick-Start Protocol. Genomic DNA contamination was prevented through the RNase-free DNase (QIAGEN, Venlo, Netherlands) digestion on the RNeasy® Mini column. Finally, the concentration and quality of RNA in each sample was evaluated by Nanodrop Spectrophotometer ND1000 (PEQLAB Biotechnologie GmbH, Erlangen, Germany).
A total RNA of 2 μg (with RNA integrity number > 8) was used to prepare the sequencing libraries. Referring to the manufacturer’s instruction, poly-A RNA was enriched and ligated to sequencing adapters with the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Ipswich, USA). Single-end sequencing was conducted on Illumina NextSeq500 sequencing platform (Illumina, San Diego, USA) to generate 75 bp-long reads.

value: canine b-cell lymphoma

value: Ibr 1 µM + AS 5 µM

tag: passage


title: CLBL-1, w35, p128, AS, 72 h

description: Library name: 3rd-72-A


title: K215M_naive_repeat1

description:
Library name: K215M_RNAseq_naive_repeat1
K_N_1


title: H1703, MYCi, rep1


title: CLBL-1, w33, p128, DMSO, 72 h

description: Library name: 3rd-72-D

value: DMSO


title: H1703, Veh, rep1


title: CLBL-1, w34, p128, Ibr, 72 h

description: Library name: 3rd-72-I

value: 1 µM Ibrutinib


title: K215M_naive_repeat2

description:
Library name: K215M_RNAseq_naive_repeat2
K_N_2


title: K215M_naive_repeat3

description:
Library name: K215M_RNAseq_naive_repeat3
K_N_3


title: Forager (scATAC-Seq)


title: CLBL-1, w29, p128, DMSO, 48 h

description: Library name: 3rd-48-D


title: H838, Combo, rep1

value: Combo


title: CLBL-1, w31, p128, AS, 48 h

description: Library name: 3rd-48-A


title: CLBL-1, w32, p128, Ibr+AS, 48 h

description: Library name: 3rd-48-IA


title: H838, MYCi975, rep1


title: CLBL-1, w28, p128, Ibr+AS, 24 h

description: Library name: 3rd-24-IA


title: CLBL-1, w27, p128, AS, 24 h

description: Library name: 3rd-24-A


title: K215M_Tex2

description:
Library name: K215M_Tex2
K215M_Tex2

data_processing:
The trimmed reads were mapped to the mouse reference genome (GRCm38.p6).
Assembly: GRCm38.p6
Supplementary files format and content: The narrowPeak file and bigwig file were provided for each sample

source_name: tumor microenvironment

extract_protocol:
Tumors were collected and incubated in serum-free RPMI medium containing 1mg/ml Collagenase D Type 4 (Gibco) and 0.02 mg/ml of DNase I (Sigma) for one hour at 37℃ under agitation. The cell suspension was filtered through a 70µm cell strainer and treated with RBC lysis buffer (eBioscience). Tumor-infiltrating CD8+ T cells were sorted based on CD8, Ly108 (SLAMF6), PD-1, and Viability Dye
Genomic DNA for ATAC-seq were prepared using Chromatin Profile Kit for Illumina following manufacturer's protocols

value: tumor microenvironment


title: CLBL-1, w26, p128, Ibr, 24 h

description: Library name: 3rd-24-I


title: K215M_Tex1

description:
Library name: K215M_Tex1
K215M_Tex1


title: WT_Tex2

description:
Library name: WT_Tex2
WT_Tex2


title: H838, Vehicle, rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to the hg38 (GENCODE GRCh38) using STAR
Read count extraction per gene was performed using featureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample


title: H460, Combo, rep1


title: CLBL-1, w25, p126, DMSO, 24 h

description: Library name: 3rd-24-D


title: CLBL-1, w24, p126, Ibr+AS, 72 h

description: Library name: 2nd-72-IA


title: CLBL-1, w22, p126, Ibr, 72 h

description: Library name: 2nd-72-I


title: CLBL-1, w23, p126, AS, 72 h

description: Library name: 2nd-72-A


title: WT_Tex1

description:
Library name: WT_Tex1
WT_Tex1


title: WT_Tprime2

description:
Library name: WT_Tprime2
WT_Tprime2


title: CLBL-1, w21, p126, DMSO, 72 h

description: Library name: 2nd-72-D


title: H460, TMP195, rep1


title: CLBL-1, w19, p126, AS, 48 h

description: Library name: 2nd-48-A


title: H460, MYCi975, rep1


title: CLBL-1, w18, p126, Ibr, 48 h

description: Library name: 2nd-48-I


title: CLBL-1, w20, p126, Ibr+AS, 48 h

description: Library name: 2nd-48-IA


title: CLBL-1, w30, p128, Ibr, 48 h

description: Library name: 3rd-48-I


title: CLBL-1, w17, p126, DMSO, 48 h

description: Library name: 2nd-48-D


title: Tumor

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Library name: Tumor

data_processing:
The snCUT&tAG sequencing files were preprocessed using the cellRanger arc pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0). All the samples were aligned against the mm10 reference transcriptome and only nuclei identified as "not doublets" by DoubletFinder included in the CellRanger count were kept. This pipeline generates fragment files used as raw input file. big wig files were used to construct genomic tracks.
Assembly: mm10
Supplementary files format and content: bigwig files; whereas fragment files were used as input by the ArchR software

source_name: Mammary Gland

extract_protocol:
control and tumor samples were roughly cut  with dissecting scissors  2 scalpels for approximately 10 min. Cell dissociation was performed by enzymatic digestion with 3mg/ml collagenase I (Roche, 11088793001) and 100U/ml hyaluronidase (Sigma-Aldrich, H3506) in complete media (HBSS (24020117), 5% SVF) during 1h30 under agitation at 170 rpm at 37°C. Thi step was followed by a second round dissociation under PBS 0,25% Trypsin-Versen (Thermo Fisher Scientific, 15040-033) prewarmed at 37°C for 1min30s with pipetting for 45s. The cell suspension was then treated with dispase 5 mg/ml (Sigma-Aldrich, D4693) and DNase 0,1 mg/ml (Roche, 11284932001) in complete media for 5 min at 37°C. A treatment with Red Blood cell lysis buffer (Thermo Fisher Scientific, 00-4333-57) was carried out then the suspension was filtered at 40µM before counting and FACS staining. Cell suspensions were stained 20 min in dark at 4°C with anti-CD45-APC 1:100 (BioLegend, 103112), anti-CD31-APC 1:100 (BioLegend, 102510), anti-CD24-BV421 1:50 (BioLegend, 101826), anti-CD49f-PE 1:50 (BioLegend, 313622). Cells were resuspended in cytometry media (PBS, BSA, EDTA). For the mammary gland samples, we either recovered the total epithelium or the luminal and basal cells populations separately.
If the sample did not show nuclei aggregates, nuclei were loaded on a 10x Chromium system using 10x Chromium Single Cell ATAC–Seq kit v2 (10X Genomics) as described16. Final library amplification with 15 PCR cycles was performed according to the Chromium Single Cell ATAC Library kit manual. snCUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE50 mode.

value: Mammary Gland

tag: cre status

value: positive

tag: histology

value: tumor

value: CreP Tp53 fl/fl Brca1 fl/fl

tag: number of_pooled_mice


title: CLBL-1, w15, p126, AS, 24 h

description: Library name: 2nd-24-A


title: CLBL-1, w16, p126, Ibr+AS, 24 h

description: Library name: 2nd-24-IA


title: USP7 uninfected replicate 2

city: Southampton

first: Rob

last: Ewing

state: Hampshire

address: University Rd, Southampton

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

description:
Medulloblastoma cell line (USP7) uninfected control
P7_ZC_2

data_processing:
Assembly: HISAT2
quality control checks on raw sequence data  was performed usingFastQC (V0.11.9-0)
Sequence reads were trimmed for low quality sequences and adapters using Trim galore (version 0.6.6-0)
Reads were aligned against the Homo Sapien GRCh38 and ZIKV BeH819966 genome using HISAT2 (V2.2.0)
Read counts were obtained using FeatureCounts via the Subread package (Version 2.0.6)
Supplementary files format and content: Tab-dellmited text files with raw counts for each sample

source_name: Cerebellum

growth_protocol: monolayer under standard conditions (5% CO2, 37°C)

extract_protocol:
High-quality total RNA was purified using the Monarch Total RNA Miniprep Kit (NEB #T2010S) as per the manufacturer’s protocol
mRNA library preparation (poly A enrichment)

treatment_protocol: Infected at multiplicity of infection (MOI) of 2 for 60 minutes

value: Cerebellum

value: Atypical teratoid rhabdoid tumor

value: WT


title: USP7 uninfected replicate 3

description:
Medulloblastoma cell line (USP7) uninfected control
P7_ZC_3


title: CLBL-1, w14, p126, Ibr, 24 h

description: Library name: 2nd-24-I


title: USP7 uninfected replicate 1

description:
Medulloblastoma cell line (USP7) uninfected control
P7_ZC_1


title: CreP_4

description: Library name: CreP_4

value: µlesions


title: CLBL-1, w13, p126, DMSO, 24 h

description: Library name: 2nd-24-D


title: CreP_3

description: Library name: CreP_3


title: CLBL-1, w11, p121, AS, 72 h

description: Library name: 1st-72-A


title: CLBL-1, w12, p121, Ibr+AS, 72 h

description: Library name: 1st-72-IA


title: USP7 ZIKV infected 24 hours post infection replicate 3

description:
Medulloblastoma cell line (USP7) infected for 24 hours with ZIKV (Strain KU365779.1)
P7_Z24_3

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: CLBL-1, w10, p121, Ibr, 72 h

description: Library name: 1st-72-I


title: CreP_2

description: Library name: CreP_2


title: USP7 ZIKV infected 24 hours post infection replicate 2

description:
Medulloblastoma cell line (USP7) infected for 24 hours with ZIKV (Strain KU365779.1)
P7_Z24_2


title: CLBL-1, w8, p121, Ibr+AS, 48 h

description: Library name: 1st-48-IA


title: CreP_1

description: Library name: CreP_1


title: CLBL-1, w7, p121, AS, 48 h

description: Library name: 1st-48-A


title: CreN_1

description: Library name: CreN_1

value: negative

value: normal

value: CreN Tp53 fl/fl Brca1 fl/fl


title: H460, Vehicle, rep1

value: Vehicle


title: WT_Tprime1

description:
Library name: WT_Tprime1
WT_Tprime1


title: USP7 ZIKV infected 24 hours post infection replicate 1

description:
Medulloblastoma cell line (USP7) infected for 24 hours with ZIKV (Strain KU365779.1)
P7_Z24_1


title: CLBL-1, w4, p121, Ibr+AS, 24 h

description: Library name: 1st-24-IA

value: canine b-cell lymphoma

value: Ibr 1 µM + AS 5 µM


title: KO_7 RNA-seq of mouse brain

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

country: Canada

institute: McGill University

description:
Library name: KO_7
RNA sequencing of KO mouse brain at P2 for differential expression analysis

data_processing:
Raw reads were quality-checked using FastQC and trimmed for adapter sequences using Trimmomatic.
Reads were aligned to the mouse genome (GRCm38) using STAR with default parameters.
Count matrices were generated using featureCounts (Subread package) with gene-level summarization.
Differential expression analysis was performed using edgeR with TMM normalization.
Normalized count data were used for downstream visualization and pathway analysis.
Assembly: GRCm38 (Ensembl release 98).
Supplementary files format and content: TSV files containing count matrices with rows as genes and columns as samples.
Supplementary files format and content: Gene annotations provided in TSV format with Ensembl gene IDs and gene symbols.

source_name: Brain

growth_protocol: P2 mouse brains were harvested and snap-frozen in liquid nitrogen immediately after dissection.

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by RNA cleanup with an RNeasy Mini Kit (Qiagen) per manufacturer instructions.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero for ribosomal RNA depletion.

treatment_protocol: No treatments were applied; mice were untreated and maintained under standard housing conditions.

value: Brain

value: Neurons

value: KO

value: Knockout

tag: batch


title: CLBL-1, w6, p121, Ibr, 48 h

description: Library name: 1st-48-I

tag: cell line

value: 1 µM Ibrutinib


title: USP7 ZIKV infected 18 hours post infection replicate 3

description:
Medulloblastoma cell line (USP7) infected for 18 hours with ZIKV (Strain KU365779.1)
P7_Z18_3

tag: treatment

value: Infection with ZIKV (Strain KU365779.1) for 18 hours


title: CLBL-1, w5, p121, DMSO, 48 h

description: Library name: 1st-48-D

value: DMSO


title: KO_6 RNA-seq of mouse brain

description:
Library name: KO_6
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: CLBL-1, w3, p121, AS, 24 h

description: Library name: 1st-24-A


title: USP7 ZIKV infected 18 hours post infection replicate 2

description:
Medulloblastoma cell line (USP7) infected for 18 hours with ZIKV (Strain KU365779.1)
P7_Z18_2

value: Cerebellum

value: Atypical teratoid rhabdoid tumor


title: CLBL-1, w2, p121, Ibr, 24 h

description: Library name: 1st-24-I


title: KO_5 RNA-seq of mouse brain

description:
Library name: KO_5
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: USP7 ZIKV infected 18 hours post infection replicate 1

description:
Medulloblastoma cell line (USP7) infected for 18 hours with ZIKV (Strain KU365779.1)
P7_Z18_1

value: WT


title: CLBL-1, w1, p121, DMSO, 24 h

description: Library name: 1st-24-D


title: Input 2.5 dpc

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

data_processing:
For scRNA-seq analysis, the computer was equipped with AMD Ryzen 9 5900X 12-Core Processor, 24 Threads and used as a server using Linux operating system. For PGR ChIP-seq: The model-based analysis of ChIP-sequencing (MACS) peak finding algorithm was used to normalize ChIP against the input control.
Assembly: mm10
Supplementary files format and content: Raw data were processed using CellRanger-6.0.1. Generated loom files were then read in scanpy v1.9.1 using JupyterLab33 for analyses and saved in an h5ad format. For PGR ChIP-seq: .bed file was used as processed file.

source_name: oviduct

extract_protocol:
For scRNA-seq analysis: Wild-type animals were ovariectomized and left for 14 days to recover and be rid of ovarian derived-steroid hormones. Sesame oil (100 μL) was used as a negative (Vehicle or Veh) control group. Progesterone (P4) at a dose of 1 mg was diluted in 100 μL of 10% ethanol and sesame oil. Ovariectomized females were subcutaneously injected with Veh or P4. Two or Twenty-four hours after injection, the oviduct was collected for scRNA-seq analysis. Wnt7aCre/+;Pgrf/f (cKO) mouse models were used in this study. Pgrf/f and PgrCre/+ mice were received from Drs. John Lydon (Baylor College of Medicine) and Francesco DeMayo (National Institute of Environmental Health Sciences). The generation of Wnt7aCre/+ mice is described previously. Genotyping protocols for each mouse strain are described in original publications. Oviducts were collected at 0.5 dpc from Pgrf/f and Wnt7aCre/+;Pgrf/f (n = 8 mice/group). In another group of experiments assessing the role of exogenous P4 in oviduct gene expression, oviducts were collected from ovariectomized females treated with Veh (n = 4 mice) and P4 for 2 h (n = 4 mice) or 24 h (n = 3 mice). Oviducts were pooled and collected in L15 media supplement with 1% fetal bovine serum (L15 + 1%FBS) and placed on ice. The oviduct was dissected into distal (infundibulum with ampulla, referred to as InfAmp) or proximal (isthmus with UTJ, referred to as IsthUTJ) regions. To isolate oviductal cells, oviducts were quickly uncoiled by trimming the mesosalpinx in order to locate the ampulla-isthmus junction (AIJ). Then, the tissues were dissected at the AIJ region for subsequent InfAmp and IsthUTJ cell isolation. After dissection, 0.25% trypsin-EDTA (Sigma, T4049) was injected into the oviduct using a blunted 30.5-gauge needle until the trypsin was visibly flushed out from the other end of the oviduct. The tissues were then placed in a tube containing 500 μL of trypsin and incubated on ice for 30 minutes and at 37°C for another 30 minutes. After the incubation, 500 μL of FBS was added to stop the enzymatic activity of trypsin. Oviductal cells were then flushed out from oviductal tubes with 4°C L15 + 10%FBS. At this stage, the epithelial, stromal, and parts of muscle cell layers were visibly flushed out. Only translucent longitudinal muscle cells were left intact. Cell clumps and tissue debris were strained twice through 40-μm cell strainers. Cells were then spun down and resuspended in 0.04% bovine serum albumin AlbuMax (ThermoFisher Scientific, 11020–021) in phosphate-buffered saline. The final cell concentration was targeted for 8,000 cells/run. For PGR ChIP-seq analysis: The oviducts were collected from C67BL6/J female mice at 2.5 dpc for ChIP-seq analysis (n=8 mice/treatment). The oviducts were flash frozen, and 16 oviducts were pooled per sample. ChIP was performed by Active Motif Inc. (Carlsbad, CA) using an antibody against PGR (sc7208, Santa Cruz Biotechnology, Dallas, TX). ChIP-seq libraries were prepared by Active Motif and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Facility using a NextSeq 500 NGS system.
For scRNA-seq analysis: scRNA-seq libraries were performed using the manufacturer’s protocol (10X Genomics Inc). Single Cell 3’ v2 chemistry was used. Briefly, individual cells (~8,000 cells/run) were separated into droplets by Gel bead in EMulsion (GEM) technology using 10X Chromium Controller. Emulsion beads were broken and barcoded cDNAs were pooled for amplification. Libraries generated were sequenced using an Illumina NovoSeq 6000.

value: oviduct

tag: region

value: whole oviduct

tag: strain

tag: timepoint

value: 2.5 days post coitus (dpc)


title: PGRChIP-seq 2.5 dpc

tag: tissue


title: KO_4 RNA-seq of mouse brain

description:
Library name: KO_4
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: CLBL-1, w9, p121, DMSO 72 h

description: Library name: 1st-72-D


title: USP7 ZIKV infected 12 hours post infection replicate 3

description:
Medulloblastoma cell line (USP7) infected for 12 hours with ZIKV (Strain KU365779.1)
P7_Z12_3

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: KO_3 RNA-seq of mouse brain

description:
Library name: KO_3
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: nuclei from peri-infarct

city: Los Angeles

first: Ruslan

last: Rust

address: 1501 San Pablo Street

institute: University of Southern California

data_processing:
For the clustering and annotation of cell types, single-nucleus RNA sequencing (snRNAseq) data alignment and gene quantification were performed using Cellranger v3.1.0, which followed default settings and referenced the mm10 2020-A dataset. Cells were screened, excluding any with greater than 5% mitochondrial gene expression or with less than 500 nFeature_RNA. Normalization and scaling of gene counts were performed using Seurat v5.0.192, to adjust for total unique molecular identifier counts per cell.
Assembly: mm10
Supplementary files format and content: mtx, tsv

source_name: brain

extract_protocol:
cortical brain tissue was removed and flash frozen using liquid nitrogen. Cortices were then homogenized using a Dounce homogenizer in lysis buffer (10mM Tris-HCl, ph 7.5, 10mM NaCl, 3mM MgCl2, and 0.1% Nonidet P40 in nucleuase-free water). Homogenized tissue was incubated for 15 minutes and subsequently filtered through a 30 μm cell strainer. The filtered cell suspension was centrifuged (to pellet the nuclei. Nuclei were washed and filtered twice through a 40 μm cell strainer using 2% BSA in sterile PBS with 0.2 U/μl RNase inhibitor (nuclei wash). After resuspension in 500 μl nuclei wash and 900 μl 1.8M sucrose, nuclei were carefully layered on top of 500 μl of 1.8M sucrose and centrifuged (13000g, 45 min, 4°C) to remove myelin debris. The pellet was resuspended in nuclei wash and filtered again through a 40 μm Cell Strainer.
According to manufacturers instructions (Single Cell 3' Reagent Kits v3, 10x Genomics)

value: brain


title: KO_2 RNA-seq of mouse brain

description:
Library name: KO_2
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: KO_1 RNA-seq of mouse brain

description:
Library name: KO_1
RNA sequencing of KO mouse brain at P2 for differential expression analysis


title: USP7 ZIKV infected 12 hours post infection replicate 2 batch 2

description:
Medulloblastoma cell line (USP7) infected for 12 hours with ZIKV (Strain KU365779.1)- second batch
P7_Z12_2_B2


title: nuclei from contralaesional intact brain


title: mES cells Dis3L WT_1

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
Reads were mapped to the reference mouse genome (GRCm38) using the STAR short read aligner (version STAR 2.4.0b)
Quality control, read processing and filtering, visualization of the results was performed using custom scripts and elements of the RSeQC, BEDtools and SAMtools packages.
Reads were counted of reads for the Genecode v M6 basic annotation using featureCounts of the subread package (v2.0.1).
Differential expression analyses were performed using the DESeq2 (version 1.34.0) Bioconductor R package
Assembly: GRCm38
Supplementary files format and content: tab separated format. Contais count tables as well as DESeq2 differential annalisis output

source_name: Embryonic stem cell

growth_protocol: Ovulation was artificially stimulated in females by intraperitoneal injection of 10 units of PMSG and hCG in 48h interval. Stimulated females were mated with males in the evening and terminated by cervical dislocation and dissected 96h after hCG injection to obtain blastocysts. ransferred to single wells of gelatin-coated culture plates with feeder layer of inactivated MEFs. After 3-4 days of culture blastocysts formed outgrowths which were disaggregated by 5 min incubation in 0.25% trypsin-EDTA followed by mechanical pipetting. Resulting cell suspension was transferred into a separate culture plate well onto fresh layer of inactivated MEFs and inspected daily for appearance of primary colonies. Established ESC lines were cultured in medium composed of KnockOut Dulbecco's modified Eagle's Medium supplemented with 15% heat inactivated FBS with addition of nonessential amino acids, L-glutamine, β-mercaptoethanol, penicillin and streptomycin, and 500 IU/ml LIF.

extract_protocol:
RNA from ES cells was extracted by lysis of 1 million cells using TRI Reagent, following manufacturers protocol. RNA from blastocysts was extracted using PicoPure RNA Isolation Kit following manufacturers protocol.
For ES cells’ RNA sequencing, total DNA-free RNA was ribodepleted using Ribo-Zero Gold rRNA-removal kit (Illumina). rRNA-free RNA samples were clean-up by precipitation with 3M NaAc. Sequencing libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems). Between each step samples were cleaned up using AMPure XP Reagent magnetics beads. Library quality and fragment size distribution was verified by electrophoresis in Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).     RNA-seq libraries from single blastocysts DNA-free RNA samples were prepared by tagmentation reaction following published protocols (24,25) with various steps and amount of enzyme optimized for use of homemade batch of Tn5 transposase produced in our laboratory. Briefly: Tn5 (0,25 mg/ml) was loaded with linker oliguncleotides Tn5ME-A/Tn5Merev and Tn5ME-B/Tn5Merev by mixing of 10 ul Tn5 with 0,5 ul of both linkers (0,35 uM) and incubating for 45 min in 23oC with shaking at 350 rpm. Right before the reaction setup loaded Tn5 was diluted 10 times with nuclease-free water. 10 ul of freshly prepared tagmentation buffer (20 mM Tris-HCl ph 7,5; 20 mM MgCl2; 50% dimethylformamide (Sigma-Aldritch)  were mixed with 5 ul of diluted Tn5 and 5 ul od cDNA, incubated for 3 min at 55oC in preheated thermocycler and cooled to 10oC for 1 min. Reaction was inactivated by addition of 5 ul 0,2% SDS (Sigma-Aldrich and incubation for 5 min at RT. Tagmented cDNA was purified in 1,25 volume of AMPure XP Reagent magnetic beads.     For library amplification (15 cycles) KAPA HiFi HotStart ReadyMix PCR Kit (Roche) with addition of 5% DMSO was used. Number of cycles yielding best results was determined experimentally and was further individually adjusted for each batch of prepared cDNA. Library quality and fragment size distribution was verified by electrophoresis in Agilent 2100 Bioanalyzer.  Illumina NovaSeq or NextSeq sequencing platform in the 100-nt or 75-nt pair-end mode was used for sequencing.

value: Embryonic stem cell

value: Dis3L WT


title: USP7 ZIKV infected 12 hours post infection replicate 1

description:
Medulloblastoma cell line (USP7) infected for 12 hours with ZIKV (Strain KU365779.1)
P7_Z12_1


title: USP7 ZIKV infected 12 hours post infection replicate 2 batch 1 (outlier sample)

description:
Medulloblastoma cell line (USP7) infected for 12 hours with ZIKV (Strain KU365779.1)- potential outlier
P7_Z12_2_B1


title: mES cells Dis3L WT_2


title: nuclei from stroke core


title: mES cells Dis3L WT_3


title: WT_7 RNA-seq of mouse brain

description:
Library name: WT_7
RNA sequencing of WT mouse brain at P2 for differential expression analysis

value: Brain

value: Wild type


title: USP13 uninfected replicate 3

description:
Medulloblastoma cell line (USP13) uninfected control
P13_ZC_3

value: Medulloblastoma


title: mES cells Dis3L KO_1

value: Dis3L KO


title: mES cells Dis3L KO_2


title: mES cells Dis3L KO_3


title: C61A_aCD8_rep2

city: San Diego

first: John

middle: R

last: Teijaro

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

data_processing:
Illumina’s bcl2fastq Conversion Software (version 2.17.1.14) was used to de-multiplex reads and convert BCL files generated by the Illumina NextSeq 500 to FASTQ.
Quality of raw RNA-sequencing reads was checked using FastQC version 0.11.9 (Barbaham Institute, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (GRCm38 assembly with Ensembl v95 transcriptome annotations) and gene counts calculated using STAR version 2.7.1a (Dobin et al., 2013) using the following parameters: --quantMode GeneCounts –outSAMtype None –sjdbGTfile /Ensembl/Mus_musculus.GRCm38.95.gtf –sjdbOverhang 74
Library size normalization was performed using DESeq2 version 1.26.0 in R version 3.5.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene counts normalized for library size

source_name: lung CD11b+ cells

growth_protocol: Wild type C57BL/6J mice and Usp18-C61A mice were maintained under specific pathogen free conditions

extract_protocol:
RNA was isolated using Rneasy Mini kit (Qiagen)
Total RNA was quality-checked using RNA Bioanalyzer (Agilent) Nano chip and subjected to ribosomal RNA depletion using TruSeq (Illumina, San Diego, CA). Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) and sequenced using the NextSeq 500 system (Illumina, San Diego, CA) at a minimum depth of 20 million single-end 75 bp reads per sample.

treatment_protocol: Mice received intravenous dose of LCMV Clone 13 (2x10^6 pfu).

tag: infection

value: LCMV Clone 13

value: CD45.2+ CD3- CD19- CD11c- CD8- CD11b+ lung cells


title: WT_6 RNA-seq of mouse brain

description:
Library name: WT_6
RNA sequencing of WT mouse brain at P2 for differential expression analysis

value: Neurons

tag: genotype


title: USP13 uninfected replicate 1

description:
Medulloblastoma cell line (USP13) uninfected control
P13_ZC_1

value: Cerebellum

tag: cell type


title: wt_aCD8_rep1

value: wild type


title: wt_aCD8_rep2


title: C61A_iso_rep2

value: isotype


title: USP13 ZIKV infection 24 hours post infection replicate 3

description:
Medulloblastoma cell line (USP13) infected for 24 hours with ZIKV (Strain KU365779.1)
P13_Z24_3

value: WT

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: C61A_iso_rep1


title: WT_4 RNA-seq of mouse brain

description:
Library name: WT_4
RNA sequencing of WT mouse brain at P2 for differential expression analysis

tag: developmental stage


title: WT_3 RNA-seq of mouse brain

description:
Library name: WT_3
RNA sequencing of WT mouse brain at P2 for differential expression analysis


title: C61A_aCD8_rep1


title: WT_2 RNA-seq of mouse brain

description:
Library name: WT_2
RNA sequencing of WT mouse brain at P2 for differential expression analysis


title: USP13 ZIKV infection 24 hours post infection replicate 1

description:
Medulloblastoma cell line (USP13) infected for 24 hours with ZIKV (Strain KU365779.1)
P13_Z24_1


title: BJAB cells 3

city: Beijing

first: Cuifeng

address: Qinghua Yuan Street

institute: Tsinghua University

description: Library name: AD_6_3

data_processing:
Then these libraries were sequenced on the Illumina sequencing platform ( Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.
Assembly: GrCh38
Supplementary files format and content: fpkm_anno.xls
Supplementary files format and content: AD_3-vs-AD_5-all.gene.xls
Supplementary files format and content: AD_3-vs-AD_6-all.gene.xls
Supplementary files format and content: AD_5-vs-AD_6-all.gene.xls
Supplementary files format and content: counts_anno.xls
Supplementary files format and content: DEG_combinded_nofiltered.xls

source_name: BJAB

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’ s instructions.

value: BJAB


title: WT_1 RNA-seq of mouse brain

description:
Library name: WT_1
RNA sequencing of WT mouse brain at P2 for differential expression analysis


title: BJAB cells 1

description: Library name: AD_6_1


title: BJAB cells BAFF and RS47 3

description: Library name: AD_5_3


title: BJAB cells BAFF and RS47 1

description: Library name: AD_5_1


title: BJAB cells BAFF 3

description: Library name: AD_3_3


title: USP13 ZIKV infection 18 hours post infection replicate 1

description:
Medulloblastoma cell line (USP13) infected for 18 hours with ZIKV (Strain KU365779.1)
P13_Z18_1

value: Infection with ZIKV (Strain KU365779.1) for 18 hours


title: USP13 ZIKV infection 18 hours post infection replicate 3

description:
Medulloblastoma cell line (USP13) infected for 18 hours with ZIKV (Strain KU365779.1)
P13_Z18_3


title: BJAB cells 2

description: Library name: AD_6_2


title: BJAB cells BAFF 2

description: Library name: AD_3_2


title: BJAB cells BAFF 1

description: Library name: AD_3_1


title: USP13 uninfected replicate 2

description:
Medulloblastoma cell line (USP13) uninfected control
P13_ZC_2


title: BJAB cells BAFF and RS47 2

description: Library name: AD_5_2


title: USP13 ZIKV infection 24 hours post infection replicate 2

description:
Medulloblastoma cell line (USP13) infected for 24 hours with ZIKV (Strain KU365779.1)
P13_Z24_2


title: AC16, 10 nM doxorubicin, 30 min

first: Yuan

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts and transcript counts for every gene and every sample

source_name: AC16 cells

growth_protocol: About 5×10^7 AC16 cells were treated with 10 nM doxorubicin for 0 min, 10 min, 30 min, 360 min.

extract_protocol:
After the culture medium with doxorubicin was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Doxorubicin was dissolved in DMEM. Further dilutions were made with serum-free DMEM. At the time of DOX exposure, after the FBS-DMEM culture medium was removed, AC16 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing 10nM DOX for 3 time points.

value: AC16 cells

value: cardiomyocyte

value: 10 nM doxorubicin for 30 min


title: USP13 ZIKV infection 12 hours post infection replicate 1

description:
Medulloblastoma cell line (USP13) infected for 12 hours with ZIKV (Strain KU365779.1)
P13_Z12_1

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: Tex_CITE-seq_r1_ADT

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

description: Library name: Tex_CITE-seq_r1_ADT

library_source: other

data_processing:
The CITE-seq data were pre-processed with 10x "cellranger multi" pipeline with default parameter, with the help of 10x cloud analysis platform. Processed expression matrix (RNA part) and multiplexing assignment (ADT part) were provided as processed data. Individual cells with high quality on both RNA and ADT parts were kept for downstream analysis (RNA: ≥1000 covered genes. ADT: quality filtered by cellranger multi pipeline).
Assembly: mm10
Supplementary files format and content: For CITE-seq data, processed expression matrix (RNA part) and  cell multiplexing  assignment(ADT part) were provided as processed data.
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on WT and Hdac1KO GP33-tetramer+ CD8+ T cells sorted on day 8 post-infection with LCMV- clone 13.
Construction of gene expression libraries and cell surface protein libraries was performed using the 10X Genomics Chromium Next GEM Single Cell 3’ library kit (PN-1000269), following the manufacturer's instructions. The resulting gene expression and cell multiplexing libraries  were combined at a molecular ratio of 9:1. Libraries were quantified using a KAPA Library Quantification Kit (KK4835), assessed for quality using an Agilent Tapestation, and then sequenced on Illumina’s NovaSeq X plus in paired-end read mode with the read length of 150 nucleotides at the Admera Health.

treatment_protocol: Sorted cells were used directly for downstream analyses without further treatment.

value: spleen

value: Cd11a high, GFP+, GP33-tetramer+, CD8+ T cells

value: WT and Hdac1 KO with Gzmb-Cre

value: day 8 post-infection with LCMV Cl13


title: USP13 ZIKV infection 18 hours post infection replicate 2

description:
Medulloblastoma cell line (USP13) infected for 18 hours with ZIKV (Strain KU365779.1)
P13_Z18_2

value: Medulloblastoma


title: Tex_CITE-seq_r1_RNA

description: Library name: Tex_CITE-seq_r1_RNA


title: Neural precursor cell 788-1 uninfected replicate 3

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N7_ZC_3

value: hiPSC-derived NPC from CZS-affected twin


title: sh-Hmgb1-2

first: Ji

last: Wu

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: SAMPLES5

data_processing:
Briefly, Hi-C clean sequencing reads were processed using the HiC-Pro. The reads were mapped against the mouse genome (mm9), and experimental artifacts, such as circularized reads and re‐ligations, were filtered out, and duplicate reads were removed. Aligned Hi-C data were normalized using iterative correction (ICE) method and visualized with Juicer tools v0.7.5. Using binned Hi-C data, we generated 500 kb, 40kb, 20 kb resolutions normalized Hi-C matrices.
Assembly: mm9

source_name: FGSCs

extract_protocol:
Briefly, cells were cross-linked, lysed, and digested with the restriction enzyme MboI(R0147, NEB). Biotin was incorporated into the cohesive ends of DNA fragments prior to proximity ligation using T4 DNA ligase. After ligation, the DNA was purified and sheared into smaller fragments. Subsequent steps, including end repair, adenylation, and adapter ligation, were conducted using the NEBNext End Repair Kit (E6050, NEB). Biotin-labeled DNA fragments were captured using MyOne Streptavidin T1 beads (65602, Invitrogen).
The Hi-C libraries were amplified using the KAPA HiFi Library Amplification Kit (KK2620, KAPA Biosystems), and size selection of the DNA fragments was performed using AMPure XP beads (A63880, Beckman Coulter).

value: FGSCs

value: female germline stem cells


title: WT_5 RNA-seq of mouse brain

description:
Library name: WT_5
RNA sequencing of WT mouse brain at P2 for differential expression analysis

value: Brain

value: Neurons

value: Wild type


title: USP13 ZIKV infection 12 hours post infection replicate 3

description:
Medulloblastoma cell line (USP13) infected for 12 hours with ZIKV (Strain KU365779.1)
P13_Z12_3

value: Cerebellum

value: WT


title: Neural precursor cell 788-1 uninfected replicate 1

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N7_ZC_1


title: sh-Hmgb1-1

description: Library name: SAMPLES4

data_processing:
For ATAC pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters. PCR duplicates were removed using Samtools (version 2.0.1)  and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Assembly: mm9

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, and 0.1% IGEPAL CA-630). Nuclei were isolated by centrifugation at 500 × g for 10 minutes at 4°C, and the supernatant was discarded. The nuclei pellet was resuspended in a transposition mix containing 25 μL of 2x TD buffer, 2.5 μL of transposase (S604-02, Vazyme), and 22.5 μL of nuclease-free water, followed by a transposition reaction at 37°C for 30 minutes.After transposition, the sample was purified using the MinElute PCR Purification Kit (28006, Qiagen).
Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute, last extension at 72℃ for 5min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library.


title: wt_iso_rep2

value: wild type

value: isotype

value: LCMV Clone 13

value: CD45.2+ CD3- CD19- CD11c- CD8- CD11b+ lung cells


title: AC16, 10 nM doxorubicin, 360 min

value: AC16 cells

value: cardiomyocyte

value: 10 nM doxorubicin for 360 min


title: sh-Hmgb1-1

description: Library name: SAMPLES4


title: USP13 ZIKV infection 12 hours post infection replicate 2

description:
Medulloblastoma cell line (USP13) infected for 12 hours with ZIKV (Strain KU365779.1)
P13_Z12_2

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: H096_9_Hut78_18_6uM_HuGene-2_0-st

type: RNA

city: Duarte

first: Hannah

last: Zhang

address: 1500 E Duarte Rd

department: Research-Rosen, Steven - MC

institute: City of Hope National Medical Center

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Hut78 cells

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

growth_protocol: Hut78 cells cultured as previously described in our published paper (2018), in 10% serum IMDM medium 37oC incubation.

extract_protocol: Using Qiagene mini RNA Isolation kit, we extracted RNAs from cell pellets (30mg, each) of cultured Hut78 cells -  CSH18 (250nM, 30h) treated and untreated Hut78 cells, respectively (each sample in duplicates). We then provided to the core facility of COH for microarray analysis.

treatment_protocol: CSH18 (250nM, for 30h) treated and untreated Hut78 cells (each sample in duplicates).

value: Cancer cell line (CTCL)

value: CSH18_treated sample


title: AC16, 10 nM doxorubicin, 10 min

value: 10 nM doxorubicin for 10 min


title: H820 siCtrl 8gy RNA-seq C

city: Morgantown

first: Emily

last: Westemeier-Rice

state: WV

address: 1 Medical Center Drive

institute: West Virginia University

description:
21112R-04-02_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

data_processing:
Reads were processed by WVU's Bioinformatics Core
Trimming and alignment (SubRead) and filtering, differential expression checked with DESeq2 (p <0.01)
Assembly: hg38
Supplementary files format and content: text files containing RPKM and counts
Supplementary files format and content: text files containing RPKM and RPKMs with matched Entrez.ID

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, and antibiotics in a humidified atmosphere at 5% CO2

extract_protocol:
RNA was extracted using Trizol/chloroform according to manufacturers instructions.
Libraries were prepared with Stranded Total RNA Prep with Ribo-Zero Plus by Admera.

treatment_protocol: Cells were treated with 300 pmol siRNA scramble or 100pmol each of 3 siRNAs designed against lnc-RAINY (designated siPool), 24 hours later, cells were treated with 8gy radiation, then left to recover for 72 hours before RNA extraction

value: Male Lung Cancer Lymph Node Metastasis

tag: sample group

value: siCtrl 8gy


title: H820 siCtrl NR RNA-seq C

description:
21112R-04-01_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: siCtrl NR


title: Neural precursor cell 788-1 ZIKV infection 24 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N7_Z24_2

value: hiPSC-derived NPC from CZS-affected twin

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: sh-Hmgb1-3

description: Library name: SAMPLES6

value: FGSCs

value: female germline stem cells


title: wt_iso_rep1

value: wild type

value: isotype


title: sh-Control-2

description: Library name: SAMPLES2

value: WT

value: Control


title: H820 siPool NR RNA-seq B

description:
21112R-06-03_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: siPool NR


title: sh-Control-1

description: Library name: SAMPLES1


title: Neural precursor cell 788-1 ZIKV infection 24 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N7_Z24_1

value: Cerebellum


title: Neural precursor cell 788-1 uninfected replicate 2

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N7_ZC_2


title: Neural precursor cell 788-1 ZIKV infection 18 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N7_Z18_3

value: Infection with ZIKV (Strain KU365779.1) for 18 hours


title: sh-Control-3

description: Library name: SAMPLES3


title: sh-Hmgb1-2

description: Library name: SAMPLES5


title: H820 siPool 8gy RNA-seq A

description:
21112R-01-16V1_S252
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: siPool 8gy


title: H820 siCtrl NR RNA-seq B

description:
21112R-06-01_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt


title: Neural precursor cell 788-1 ZIKV infection 18 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N7_Z18_2


title: Neural precursor cell 788-1 ZIKV infection 18 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N7_Z18_1


title: H095_8_Hut78_18_2uM_HuGene-2_0-st

value: Cancer cell line (CTCL)

value: CSH18_treated sample


title: H460 siPool 8gy RNA-seq C

description:
21112R-01-12V1_S30
H460.RPKM.txt
H460.counts.txt

value: NSCLC Male Lung Epithelial


title: H820 siPool 8gy RNA-seq C

description:
21112R-04-04_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: Male Lung Cancer Lymph Node Metastasis


title: H097_10_Hut78_18_6uM_HuGene-2_0-st


title: H094_7_Hut78_Ctr_HuGene-2_0-st

value: untreated sample


title: H820 siPool NR RNA-seq C

description:
21112R-04-03_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt


title: AC16, 10 nM doxorubicin, 0 min

value: AC16 cells

value: cardiomyocyte

value: untreated


title: H089_2_Hut78_Ctr_HuGene-2_0-st


title: H460 siPool 8gy RNA-seq B

description:
21112R-01-08V1_S27
H460.RPKM.txt
H460.counts.txt


title: Neural precursor cell 788-1 ZIKV infection 24 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N7_Z24_3

value: hiPSC-derived NPC from CZS-affected twin

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: H820 siPool 8gy RNA-seq B

description:
21112R-06-04_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt


title: Remye3+Ctrl IgG2a

city: Hangzhou

first: Jinchao

last: Hou

state: Zhejiang

address: Binsheng Road

department: Anesthesiology

institute: Zhejiang University

description: Library name: B6

data_processing:
Sample demultiplexing, barcode processing and single-cell counting were performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). A custom reference genome was constructed by incorporating Clec7a cDNA into the pre-existing mouse reference genome (mm10). The Cellranger count (v.3.0.2) pipeline was used to align the reads to the custom reference genome, quantify the reads, and filter out those with a quality score below 30.
Assembly: To include Clec7a gene, we built a custom reference genome by adding Clec7a cDNA to the pre-built mouse reference genome (mm10)
Supplementary files format and content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: cortex and white matter

extract_protocol:
Isolation of nuclei from the frozen brain tissue of the aforementioned groups was performed similarly as previously described. In brief, the flash frozen cortex and white matter were Dounce homogenized in 5 ml of ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40) for 15 min. The homogenates was filtered through a 30-μm cell filter and pelleted at 500g for 5 min at 4 °C. Nuclei pellet was then washed and filtered twice with Nuclei Wash buffer (1% BSA in PBS with 0.2 U/μl RNasin (Promega)), and were resuspended in 500 μl nuclei wash buffer and 900 µl 1.8 M sucrose. The total 1400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 ℃ to separate the nuclei from myelin debris. Finally, the nuclei pellet was resuspended in nuclei wash buffer at 1,200 nuclei/μl and filtered through a 40-μm FlowMi Cell Strainer.
The isolated mouse brain nuclei were subjected to droplet-based single-nucleus RNA sequencing (snRNA-seq) using the Chromium Single Cell 5′ Reagent Kits (v1) according to the manufacturer's instructions (10x Genomics).

treatment_protocol: WT C57BL/6J mice were purchased from Jackson Laboratory (#000664) and housed under specific-pathogen-free conditions. All experimental protocols were approved by the Institutional Animal Care and Use Committee at Washington University in St. Louis. 8-week-old male mice were fed with 0.2% (w/w) cuprizone (bis-cyclohexanone oxaldihydrazone) (Sigma, #c9012) in ground breeder chow for 5 weeks to induce demyelination, followed by a 2-week period on regular chow to promote remyelination. For snRNA-seq dataset, brain cortex and white matter tissues from 3 in demyelination with control IgG2a treatment, 3 in demyelination with anti-TREM2 treatment, 3 in remyelination with control IgG treatment, and 3 in remyelination with anti-TREM2 treatment were processed.

value: cortex and white matter

value: wild type

value: 5-week cuprizone, followed by 2-week regular chow+ Ctrl IgG2a


title: sh-Control-2

description: Library name: SAMPLES2

value: FGSCs

value: female germline stem cells

value: WT

value: Control


title: H820 siCtrl 8gy RNA-seq B

description:
21112R-06-02_S0
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: siCtrl 8gy


title: H460 siPool NR RNA-seq B

description:
21112R-01-07V1_S26
H460.RPKM.txt
H460.counts.txt

value: siPool NR


title: sh-Control-1

description: Library name: SAMPLES1


title: H820 siPool NR RNA-seq A

description:
21112R-01-15V1_S32
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt


title: H088_1_Hut78_Ctr_HuGene-2_0-st

value: Cancer cell line (CTCL)


title: Remye1+ anti-TREM2

description: Library name: B1

value: 5-week cuprizone, followed by 2-week regular chow+ anti-TREM2


title: H460 siCtrl NR RNA-seq B

description:
21112R-01-05V1_S35
H460.RPKM.txt
H460.counts.txt

value: NSCLC Male Lung Epithelial

value: siCtrl NR


title: Neural precursor cell 763-1 uninfected replicate 3

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N3_ZC_3

value: Cerebellum


title: H820 siCtrl 8gy RNA-seq A

description:
21112R-01-14V1_S31
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt

value: Male Lung Cancer Lymph Node Metastasis


title: H820 siCtrl NR RNA-seq A

description:
21112R-01-13V1_S37
all.rpkm.filtered.txt
all.rpkm.entrz.filtered.txt


title: Demye3+ anti-TREM2

description: Library name: A11

value: 5-week cuprizone+ anti-TREM2


title: H460 siPool NR RNA-seq C

description:
21112R-01-11V1_S36
H460.RPKM.txt
H460.counts.txt


title: H460 siCtrl 8gy RNA-seq C

description:
21112R-01-10V1_S29
H460.RPKM.txt
H460.counts.txt


title: H460 siCtrl NR RNA-seq C

description:
21112R-01-09V1_S28
H460.RPKM.txt
H460.counts.txt


title: Neural precursor cell 788-1 ZIKV infection 12 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N7_Z12_3

value: hiPSC-derived NPC from CZS-affected twin

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: Remye3+ anti-TREM2

description: Library name: B3

value: cortex and white matter

value: wild type


title: Remye2+ anti-TREM2

description: Library name: B2


title: Neural precursor cell 788-1 ZIKV infection 12 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N7_Z12_1


title: Neural precursor cell 788-1 ZIKV infection 12 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N7_Z12_2


title: H460 siCtrl 8gy RNA-seq B

description:
21112R-01-06V1_S25
H460.RPKM.txt
H460.counts.txt


title: Neural precursor cell 763-1 uninfected replicate 2

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N3_ZC_2


title: H460 siCtrl 8gy RNA-seq A

description:
21112R-01-02_S34
H460.RPKM.txt
H460.counts.txt


title: H460 siPool 8gy RNA-seq A

description:
21112R-01-04_S24
H460.RPKM.txt
H460.counts.txt

value: siPool 8gy


title: H460 siPool NR RNA-seq A

description:
21112R-01-03_S23
H460.RPKM.txt
H460.counts.txt


title: Remye2+Ctrl IgG2a

description: Library name: B5

value: 5-week cuprizone, followed by 2-week regular chow+ Ctrl IgG2a


title: Demye2+ anti-TREM2

description: Library name: A10


title: H820 siPool NR ATAC-seq B

data_processing:
Reads were processed by WVU's Bioinformatics Core
Trimming (Bowtie2), alignment (SubRead) and filtering, Peak calling and visualization (featureCounts)
Assembly: hg38
Supplementary files format and content: NarrowPeak Files containing peak locations, summit, p-value and q-value

extract_protocol:
DNA was .
After irradiation, 50,000 cells were removed for ATAC-Seq library preparation, the rest for further analysis to ensure effective knockdown of lnc-RAINY. The ATAC-Seq library was prepared as follows. Cells were centrifuged at 500xg at 4C for 5 min and supernatant was removed. Pellet was resuspended in RSB Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL each of Digitonin, Tween 20 and NP40) and incubated on ice 3 min. RSB-without (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL Tween 20) was added and the cells were centrifuged at 500xg for 10 min. Cells were resuspended in Transposition Mix (2x TD buffer 2.5uL transposase (Illumina cat#20043196), 1uL/100uL each of Digitonin and Tween 20, water and PBS). Tubes were then incubated at 37C shaking at 1000rpm for 30 min. Reaction was cleaned using Qiagen PCR Purification Kit with 3M sodium acetate. Sample was eluted in an elution buffer and prepped for PCR Amplification. Barcoded Primers were added to each sample with 2x NEBNext Master mix (NEB cat#M0541S). Samples were PCR amplified for 12 cycles and purified using Qiagen PCR Purification Kit, eluted in water. Samples were loaded on a 2% agarose e-gel and ran 3 minutes. Each lane was cut from the gel and the DNA extracted via Qiagen gel Purification kit.


title: H460 siCtrl NR RNA-seq A

description:
21112R-01-01_S33
H460.RPKM.txt
H460.counts.txt


title: Neural precursor cell 763-1 ZIKV infection 24 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N3_Z24_2

value: WT

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: H820 siPool 8gy ATAC-seq B


title: Demye3+Ctrl IgG2a

description: Library name: A8

value: 5-week cuprizone+ Ctrl IgG2a


title: Demye1+ anti-TREM2

description: Library name: A9


title: Remye1+Ctrl IgG2a

description: Library name: B4


title: H820 siCtrl NR ATAC-seq B


title: H820 siPool 8gy ATAC-seq A


title: H820 siCtrl 8gy ATAC-seq B

value: siCtrl 8gy


title: Neural precursor cell 763-1 ZIKV infection 24 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N3_Z24_1


title: H820 siPool NR ATAC-seq A

value: siPool NR


title: Neural precursor cell 763-1 ZIKV infection 24 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 24 hours with ZIKV (Strain KU365779.1)
N3_Z24_3


title: Demye1+Ctrl IgG2a

description: Library name: A6


title: H820 siCtrl 8gy ATAC-seq A


title: H820 siCtrl NR ATAC-seq A


title: Neural precursor cell 763-1 ZIKV infection 18 hours post infection replicate 3

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N3_Z18_3

value: Infection with ZIKV (Strain KU365779.1) for 18 hours


title: Demye2+Ctrl IgG2a

description: Library name: A7


title: H460 siPool 8gy ATAC-seq B

value: NSCLC Male Lung Epithelial


title: Neural precursor cell 763-1 ZIKV infection 18 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N3_Z18_2


title: H460 siPool NR ATAC-seq B


title: Neural precursor cell 763-1 uninfected replicate 1

description:
Control uninfected Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC)
N3_ZC_1


title: Neo_CM, replicate 1, Day3

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

description: Library name: NeoCM_1

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using hisat2 software with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: Primary cell

value: cardiac fibroblast

tag: age

value: NeoCF


title: Neo_CM, replicate 2, Day3

description: Library name: NeoCM_2


title: H460 siCtrl NR ATAC-seq B

value: siCtrl NR


title: Neural precursor cell 763-1 ZIKV infection 18 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 18 hours with ZIKV (Strain KU365779.1)
N3_Z18_1

value: Cerebellum

value: hiPSC-derived NPC from CZS-affected twin


title: H460 siPool 8gy ATAC-seq A