title: peripheral EDTA blood, rLDH_12, rep1

description:
Library name: DS27
Column name in HTSeq_counts.xlsx: DS27


title: ATAC_TA3_Hauschka_Parent

status: Public on Mar 15 2026

type: SRA

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

country: USA

institute: Dana-Farber Cancer Institute

description:
10x Genomics
ATAC_TA3_Hauschka_Parent

library_source: genomic single cell

data_processing:
All procedures were made using Cell Ranger software
Assembly: mm10
Supplementary files format and content: h5 files, fragment.tsv and fragment.tsv.tbi files

molecule: genomic DNA

organism: Mus musculus

source_name: primary breast tumor

extract_protocol:
10X Chromium Single Cell Multiome ATAC + Gene Expression
DNA and RNA from indexed cells were extracted from following the 10X Chromium Nuclei Isolation Kitl.
Library preparation follows the 10X Chromium Single Cell Multiome ATAC + Gene Expression protocol.

tag: tissue

value: primary breast tumor

tag: cell line

tag: cell type

value: Murine mammary tumor

tag: genotype

value: WGD-

tag: treatment

value: In culture

tag: library type

value: Multiome ATAC


title: Mouse 5450, female, mock, 18mpi

city: New York

first: Brad

last: Rosenberg

state: New York

address: 1 Gustave L Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: cohort18mpi_J4

library_source: transcriptomic

data_processing:
Read quality was assessed using fastQC (v0.11.9) and reads were trimmed using fastp (v0.23.2)
For quantification of RNA expression, the Salmon (v1.4.0) package was used using the selective-alignment algorithm
Mapped reads to concatenated GRCm39 and B+4 NrHV transcriptome, where NrHV transcriptome was entire RNA genome of the virus (GenBank accession no. KX905133)
TPM normalized abundance output from Salmon read into R using tximport package (v1.18.0)
Assembly: Genome Reference Consortium Mouse Build 39
Supplementary files format and content: Salmon pseudoalignment output in .sf format is a quantification file that includes TPM (relative abundance) values and estimated number of reads mapping to each transcript, quantified for each sample

molecule: total RNA

source_name: normal liver

extract_protocol:
Liver slices previously flash-frozen and pulverized using liquid nitrogen were used for RNA and DNA isolation. Both nucleic acids were isolated from the same liver slice using Allprep Qiagen kit (QIAGEN) following manufacturer’s instructions with addition of RNase inhibitor and DNAseI to the original RNA isolation protocol. Samples were quality checked prior submission to bulk RNAseq. A RIN above 7 was accepted for downstream library preparation and sequencing. Samples that did not reach the criteria for downstream analysis were purified using either RNA mini kit (Zymo) or DNA purification kit (Zymo)
Total RNA previously isolated from livers were submitted to Novogene for bulk RNA sequencing. Samples were enriched for mRNA using polyA selection. Libraries were produced using directional mRNA preparation and submitted to Novaseq PE150, with about 20M depth per sample.

value: normal liver

value: NrHV viral infection


title: AJ_WGD+_Day8_Tumor1

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using cellranger v7.0.1.
Assembly: mm10
Supplementary files format and content: h5 files for each sample

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of Balb/c mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium. Immediately before library preparation, dead cells and debris was removed using percoll purification (50%/40%/20% layers).
About 26,000 single cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were generated using Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics).

value: MFP injection


title: F9R

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of A/J or NSG mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium.
Library was prepared following 10X Chromium Single Cell ATAC instruction

value: WGD+

value: MFP injection in NSG mice


title: Mouse 5428-T2, male, infected, 18mpi

description:
Library name: m2561_5428-T2
Base comparison, liver m2561

library_source: genomic

data_processing:
Processed FASTQ files were mapped to the mouse reference genome mm10 (GRCm38) using BWA-MEM.
Local realignment and quality score recalibration was performed using Genome Analysis Toolkit (GATK) according to GATK best practices.
Sample variant calling was performed on tumor samples and normal samples to identify point mutations/single nucleotide variants (SNVs) and small insertions/ deletion (indels).
MuTect (version 1.1.7) was used for SNV calling and SomaticIndelDetector, a tool in GATKv.2.3.9, was used for detecting indel events.
Variants were subsequently annotated using Annovar, and annotations relative to the canonical transcript for each gene (derived from a list of known canonical transcripts obtained from the UCSC genome browser) were reported. Variant allele frequency (VAF) was determined by calculating the fraction of variant reads for a specific out of the total reads at that location.
Assembly: mouse reference genome mm10 (GRCm38)
Supplementary files format and content: Processed data file provided is Mutation Annotation Format (MAF) is a tab-delimited text file/csv with aggregated mutation information from VCF Files.
Library strategy: DNA-Seq

source_name: tumor

extract_protocol:
For the detection of somatic genomic alterations in NrHV-elicited tumors, we extracted genomic DNA from tumor and normal uninfected liver samples and gDNA was enriched for targeted regions using a solution-phase hybridization-based exon capture as previously described (A. Zehir et al. 2017).
M-IMPACT_v2 (mouse version) assay covers more than 600 known cancer driver genes - library preparation and sequencing analysis was performed by the MSKCC Bioinformatics Core.

value: tumor


title: F8R

value: MFP injection in A/J mice


title: Mouse 2584-T, male, infected, 18 mo

description:
Library name: m2561_2584-T
Base comparison, liver m2561


title: PT_1R


title: Mouse 5477, female, infected, 18mpi

description: Library name: cohort18mpi_E5

source_name: adjacent liver

value: adjacent liver


title: Mouse 2575-T , male, infected, 18 mo

description:
Library name: m2561_2575-T
Base comparison, liver m2561


title: Mouse 5449, female, mock, 18mpi

description: Library name: cohort18mpi_J3


title: Mouse 5430-T2, male, infected, 18mpi

description:
Library name: m2561_5430-T2
Base comparison, liver m2561


title: F5L


title: Mouse 2554-T , male, infected, 12 mo

description:
Library name: m2561_2554-T
Base comparison, liver m2561


title: peripheral EDTA blood, CeAD_13, rep1

city: Moscow

first: Polina

middle: Sergeevna

last: Shlapakova

address: Volokolamskoye Shosse, 80

country: Russia

institute: Research Center of Neurology

description:
Library name: DS25
Column name in HTSeq_counts.xlsx: DS25

data_processing:
Paired-end reads were aligned to the human reference genome (GRCh38) using the STAR aligner, achieving an average unique alignment rate of 80% per sample
Gene-level read counting was performed with HTSeq in union mode, approximately 55% of total reads were uniquely mapped to annotated genes
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: peripheral EDTA blood

extract_protocol:
Total RNA was extracted from 1.5 mL of whole EDTA blood using the RNeasy Mini Kit (Qiagen, Germany). Residual genomic DNA was removed by treatment with DNase I (Monarch, NEB, USA).
Transcriptomic libraries were prepared from 1,000 ng of total RNA (RIN>8) using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, USA), which includes depletion of cytoplasmic and mitochondrial ribosomal RNA. Libraries were indexed using the IDT for Illumina – TruSeq RNA UD Indexes (Illumina, USA).

value: peripheral EDTA blood

tag: sample group

value: CeAD

value: 3-month anticoagulation post-dissection

tag: batch


title: peripheral EDTA blood, rLDH_8, rep1

description:
Library name: DS21
Column name in HTSeq_counts.xlsx: DS21

value: rLDH

value: Spinal disc surgery:L5-S1 (2 operations)


title: peripheral EDTA blood, rLDH_10, rep1

description:
Library name: DS23
Column name in HTSeq_counts.xlsx: DS23


title: Mouse 2540-T, female, infected, 18 mo

description:
Library name: m2561_2540-T
Base comparison, liver m2561


title: AJ_WGD+_Day14_Tumor3

description: 10x Genomics

value: primary breast tumor

value: Murine mammary tumor


title: peripheral EDTA blood, rLDH_9, rep1

description:
Library name: DS22
Column name in HTSeq_counts.xlsx: DS22

value: Spinal disc surgery:L4-L5, L5-S1 (2 operations)


title: Mouse 5438, male, mock, 18mpi

description: Library name: cohort18mpi_I9


title: Mouse 5437, male, mock, 18mpi

description: Library name: cohort18mpi_I8


title: AJ_WGD+_Day14_Tumor4

description: 10x Genomics


title: Mouse 5454, male, infected, 18mpi

description: Library name: cohort18mpi_E2


title: AJ_WGD-_Day14_Tumor4

description: 10x Genomics


title: Mouse 2582-T, female, infected, 18 mo

description:
Library name: m2561_2582-T
Base comparison, liver m2561


title: peripheral EDTA blood, rLDH_7, rep1

description:
Library name: DS20
Column name in HTSeq_counts.xlsx: DS20

value: Spinal disc surgery:L4-L5 (1 operation)


title: Mouse 2576-T , male, infected, 18 mo

description:
Library name: m2561_2576-T
Base comparison, liver m2561


title: peripheral EDTA blood, CeAD_10, rep1

description:
Library name: DS17
Column name in HTSeq_counts.xlsx: DS17


title: Mouse 5452, male, infected, 18mpi

description: Library name: cohort18mpi_E1


title: Mouse 5475, female, infected, 18mpi

description: Library name: cohort18mpi_E4


title: AJ_WGD+_Day8_Tumor2

description: 10x Genomics

value: WGD-


title: Mouse 5429, male, infected, 18mpi

description: Library name: cohort18mpi_D6

value: NrHV viral infection


title: Mouse 5470, female, infected, 18mpi

description: Library name: cohort18mpi_E3


title: NSG_WGD+_Tumor3

description: 10x Genomics

value: MFP injection


title: Mouse 5430, male, infected, 18mpi

description: Library name: cohort18mpi_D7


title: Mouse 5470-T3, female, infected, 18mpi

description: Library name: cohort18mpi_C6


title: Mouse 5432, male, infected, 18mpi

description: Library name: cohort18mpi_D8


title: AJ_WGD-_Day14_Tumor3

description: 10x Genomics

value: WGD+


title: NSG_WGD+_Tumor2

description: 10x Genomics


title: peripheral EDTA blood, CeAD_7, rep1

description:
Library name: DS12
Column name in HTSeq_counts.xlsx: DS12


title: peripheral EDTA blood, CeAD_11, rep1

description:
Library name: DS18
Column name in HTSeq_counts.xlsx: DS18


title: peripheral EDTA blood, CeAD_8, rep1

description:
Library name: DS14
Column name in HTSeq_counts.xlsx: DS14


title: peripheral EDTA blood, rLDH_6, rep1

description:
Library name: DS15
Column name in HTSeq_counts.xlsx: DS15


title: peripheral EDTA blood, CeAD_12, rep1

description:
Library name: DS19
Column name in HTSeq_counts.xlsx: DS19


title: Mouse 5433, male, infected, 18mpi

description: Library name: cohort18mpi_D9


title: AJ_WGD-_Day8_Tumor1

description: 10x Genomics


title: Mouse 5428, male, infected, 18mpi

description: Library name: cohort18mpi_D5


title: Mouse 5422, male, infected, 18mpi

description: Library name: cohort18mpi_D3


title: NSG_WGD+_Tumor1

description: 10x Genomics


title: Mouse 5475-T2, female, infected, 18mpi

description: Library name: cohort18mpi_C8


title: Mouse 5423, male, infected, 18mpi

description: Library name: cohort18mpi_D4


title: Mouse 5477-T2, female, infected, 18mpi

description: Library name: cohort18mpi_D1


title: Mouse 5402, female, infected, 18mpi

description: Library name: cohort18mpi_D2


title: peripheral EDTA blood, CeAD_6, rep1

description:
Library name: DS11
Column name in HTSeq_counts.xlsx: DS11


title: AJ_WGD+_Tumor1

description: 10x Genomics


title: Mouse 5477-T1, female, infected, 18mpi

description: Library name: cohort18mpi_C9


title: Mouse 5475-T1, female, infected, 18mpi

description: Library name: cohort18mpi_C7


title: AJ_WGD-_Day8_Tumor2

description: 10x Genomics


title: peripheral EDTA blood, rLDH_4, rep1

description:
Library name: DS09
Column name in HTSeq_counts.xlsx: DS09

value: Spinal disc surgery:L5-S1 (1 operation)


title: Mouse 5454-T2, male, infected, 18mpi

description: Library name: cohort18mpi_C4

value: tumor


title: Mouse 5470-T1, female, infected, 18mpi

description: Library name: cohort18mpi_C5


title: NSG_WGD-_Tumor1

description: 10x Genomics


title: Mouse 5432-T1, male, infected, 18mpi

description: Library name: cohort18mpi_B7


title: AJ_WGD+_Tumor2

description: 10x Genomics


title: NSG_WGD-_Tumor2

description: 10x Genomics


title: Mouse 5432-T2, male, infected, 18mpi

description: Library name: cohort18mpi_B8


title: Mouse 5430-T1, male, infected, 18mpi

description: Library name: cohort18mpi_B5


title: Mouse 5454-T1, male, infected, 18mpi

description: Library name: cohort18mpi_C3


title: NSG_WGD-_Tumor3

description: 10x Genomics


title: AJ_WGD-_Tumor3

description: 10x Genomics


title: peripheral EDTA blood, CeAD_4, rep1

description:
Library name: DS07
Column name in HTSeq_counts.xlsx: DS07


title: AJ_WGD+_Day14_3

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Briefly, fastq files were aligned to the human reference mm10 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out. The gene-level counts from all studies were then normalized using TMM with edgeR  (Robinson et al., 2010). Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)] were used for analysis.
Assembly: mm10
Supplementary files format and content: Gene-level matrix table (in .csv format) with Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)]

source_name: Tumor

growth_protocol: Exponentially growing cells were resuspended in ice cold DMEM/F12 and 50% Matrigel (BD Biosciences) and injected orthotopically into the inguinal mammary fat pads of 6-week-old female NOD.Cg-Prkdcscid Il2rgtm1Wjl Tg(CMV-IL3,CSF2,KITLG)1Eav/MloySzJ or A/J mice. Tumor were collected either at day8 or day14 as indicated.

extract_protocol:
Total RNA were extracted following manufacturer's protocol pf Qiagen Rneasy Mini Kit. (Qiagen, #74106)
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

value: Tumor

value: Day14 collection


title: Mouse 5433-T, male, infected, 18mpi

description: Library name: cohort18mpi_B9


title: peripheral EDTA blood, CeAD_5, rep1

description:
Library name: DS08
Column name in HTSeq_counts.xlsx: DS08

value: peripheral EDTA blood


title: peripheral EDTA blood, rLDH_2, rep1

description:
Library name: DS05
Column name in HTSeq_counts.xlsx: DS05

value: Spinal disc surgery:L3-L4, L4-L5, L5-S1 (4 operations)


title: Mouse 5452-T3, male, infected, 18mpi

description: Library name: cohort18mpi_C2


title: peripheral EDTA blood, rLDH_1, rep1

description:
Library name: DS01
Column name in HTSeq_counts.xlsx: DS01


title: Mouse 5430-T2, male, infected, 18mpi

description: Library name: cohort18mpi_B6


title: peripheral EDTA blood, rLDH_5, rep1

description:
Library name: DS10
Column name in HTSeq_counts.xlsx: DS10


title: Mouse 5429-T3, male, infected, 18mpi

description: Library name: cohort18mpi_B4


title: Mouse 5425-T2, male, infected, 18mpi

description: Library name: cohort18mpi_A7


title: Mouse 2586-T , male, infected, 18 mo

source_name: liver

value: liver

tag: Sex

value: male

tag: agent

tag: age

value: 18 mo

tag: strain


title: Mouse 5429-T2, male, infected, 18mpi

description: Library name: cohort18mpi_B3


title: Mouse 5428-T2, male, infected, 18mpi

description: Library name: cohort18mpi_B1


title: Mouse 5429-T1, male, infected, 18mpi

description: Library name: cohort18mpi_B2


title: AJ_WGD+_Day14_2


title: AJ_WGD-_Tumor1

description: 10x Genomics

value: primary breast tumor


title: Mouse 5425-T3, male, infected, 18mpi

description: Library name: cohort18mpi_A8


title: Mouse 2576-T , male, infected, 18 mo


title: AJ_WGD+_Day14_1

value: Murine mammary tumor


title: Mouse 5428 - T1, male, infected, 18mpi

description: Library name: cohort18mpi_A9


title: peripheral EDTA blood, CeAD_3, rep1

description:
Library name: DS04
Column name in HTSeq_counts.xlsx: DS04

value: CeAD

value: 3-month anticoagulation post-dissection


title: Mouse 5423-T3, male, infected, 18mpi

description: Library name: cohort18mpi_A5


title: U251-NC-3

city: Wuhan

first: Lei

last: Shen

state: Hubei

address: Donghu Road No.169

country: China

institute: Department of Neurosurgery, Zhongnan Hospital of Wuhan University

description: Library name: UN3

data_processing:
Raw sequencing reads (FASTQ format) were first assessed using FastQC to evaluate base quality and composition. Adapter trimming and quality filtering were performed with fastp (Chen et al., 2018) using the following key settings: bases with Phred <10 were considered low quality (--qualified_quality_phred 10), reads containing more than 10% low-quality bases were discarded (--unqualified_percent_limit 10), and reads with more than 10 ambiguous nucleotides (N) were removed (--n_base_limit 10). High-quality clean reads were then aligned to the human reference genome GRCh38 using HISAT2 (Kim et al., 2019), allowing up to one mismatch. Alignment files (BAM) were generated for each sample, and gene-level raw counts were quantified using featureCounts from the Subread package. The resulting processed data include per-gene read count matrices for downstream differential expression analysis.
Assembly: All clean reads were aligned to the Homo sapiens reference genome GRCh38 using HISAT2.
Supplementary files format and content: Processed data provided in this submission include BAM alignment files (HISAT2-mapped reads) and a gene-level read count matrix generated by featureCounts, listing raw read counts for each annotated gene across all samples, suitable for differential expression analysis.

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove genomic DNA contamination. RNA concentration and purity were assessed by UV spectrophotometry (A260/A280, Bio-Rad SmartSpec Plus), and RNA integrity was verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for library preparation.
Polyadenylated mRNA was enriched using VAHTS mRNA Capture Beads (Vazyme, N401), followed by fragmentation and first- and second-strand cDNA synthesis with dUTP incorporation during second-strand synthesis to retain strand specificity. End repair, A-tailing, and adaptor ligation (Roche, KK8726) were performed, and ligated fragments (300–500 bp) were size-selected, PCR amplified, purified, and quantified. The final libraries were stored at -80°C prior to sequencing. Strand-specific libraries were generated using the KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544), following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 system to generate 150 bp paired-end reads.

value: glioblastoma cell

value: NC


title: Mouse 5423-T2, male, infected, 18mpi

description: Library name: cohort18mpi_A4

value: NrHV viral infection


title: peripheral EDTA blood, CeAD_2, rep1

description:
Library name: DS03
Column name in HTSeq_counts.xlsx: DS03


title: U251-OE-2

description: Library name: UE2

value: PEPD-OE


title: peripheral EDTA blood, CeAD_1, rep1

description:
Library name: DS02
Column name in HTSeq_counts.xlsx: DS02


title: AJ_WGD+_Day8_2

value: WGD+

value: Day8 collection


title: Mouse 2582-T, female, infected, 18 mo

value: female


title: AJ_WGD-_Tumor2

description: 10x Genomics

value: WGD-

value: MFP injection


title: Mouse 5402-T1, female, infected, 18mpi

description: Library name: cohort18mpi_A1

value: tumor


title: Mouse 2554-T , male, infected, 12 mo

value: liver

value: 12 mo


title: AJ_WGD-_Day14_1

value: Tumor

value: Day14 collection


title: Mouse 2593, male, mock, 18 mo

value: male

value: mock

value: 18 mo


title: Mouse 2540-T, female, infected, 18 mo


title: U251-OE-3

description: Library name: UE3

value: glioblastoma cell


title: U251-NC-2

description: Library name: UN2

value: NC


title: AJ_WGD+_Day8_3

value: Murine mammary tumor


title: Mouse 5422-T1, male, infected, 18mpi

description: Library name: cohort18mpi_A2

value: NrHV viral infection


title: U251-OE-1

description: Library name: UE1

value: PEPD-OE


title: Mouse 5423-T1, male, infected, 18mpi

description: Library name: cohort18mpi_A3


title: T98G-NC-3

description: Library name: TN3


title: U251-NC-1

description: Library name: UN1


title: Mouse 5425-T1, male, infected, 18mpi

description: Library name: cohort18mpi_A6


title: Mouse 2575-T , male, infected, 18 mo


title: Mouse 2591, male, mock, 18 mo


title: AJ_WGD+_Day8_1

value: WGD+

value: Day8 collection


title: Mouse 2592, male, mock, 18 mo


title: T98G-OE-2

description: Library name: TE2


title: AJ_WGD-_Day8_3

value: WGD-


title: AJ_WGD+_aCD8_3


title: Mouse 2590, female, mock, 18 mo

value: female


title: Mouse 2584-T, male, infected, 18 mo


title: AJ_WGD-_Day14_3


title: Mouse 2567, male, mock, 18 mo


title: T98G-NC-2

description: Library name: TN2


title: AJ_WGD+_aCD8_2


title: Mouse ne1 -2526, male, mock, 18 mo


title: Mouse ne2 - 2596, male, mock, 18 mo


title: AS_mono

city: Chengdu

first: Xinpu

last: Tang

state: Sichuan

address: Guoxue Alley, Chengdu

institute: West China Hospital

description: Library name: Sample5

data_processing:
CLC Genomics Workbench V11.0.1
Assembly: GRCh38/hg38 for human and GRCm38/mm10 for mouse
Supplementary files format and content: tab-delimited text files containing gene expression matrices.
Supplementary files format and content: The content includes gene identifiers with corresponding FPKM values for each sample

source_name: Skin

extract_protocol:
Trizol-LS(for RNA extraction from liquid)
The library construction protocol in the file is a standard Illumina-compatible method involving mRNA purification from total RNA using poly-T magnetic beads, fragmentation with divalent cations, random hexamer-primed first-strand cDNA synthesis followed by RNaseH degradation and second-strand synthesis, end blunting and adenylation, hairpin adaptor ligation, size selection of 370-420 bp fragments with AMPure XP beads, PCR amplification, and quality assessment via Qubit fluorometry, Agilent 2100 insert size detection, and qRT-PCR effective concentration quantification.

value: Skin

value: Melanoma Cell

value: Monosome fractions


title: T98G-NC-1

description: Library name: TN1


title: Mouse 2594, male, mock, 18 mo

value: liver


title: AJ_WGD-_Day8_2

value: Tumor


title: Mouse 2582, female, infected, 18 mo


title: AJ_WGD-_Day14_2

value: Day14 collection


title: Mouse 2589, female, mock, 18 mo

value: mock


title: T98G-OE-1

description: Library name: TE1


title: AJ_WGD+_aPDL1_3


title: Mouse 2581, female, infected, 18 mo

value: 18 mo


title: Mouse 2584, male, infected, 18 mo

value: male


title: AJ_WGD+_aPDL1_2


title: Mouse 2560, female, mock, 18 mo


title: Mouse 2587, male, infected, 18 mo


title: Mouse 2575, male, infected, 18 mo


title: Mouse 2550, female, infected, 18 mo


title: Mouse 2541, female, infected, 18 mo


title: AJ_WGD-_Day8_1


title: Mouse 2586, male, infected, 18 mo


title: T98G-OE-3

description: Library name: TE3

value: glioblastoma cell


title: AS_poly

description: Library name: Sample6

value: Polysome  fractions


title: Mouse 2540, female, infected, 18 mo

value: NrHV viral infection


title: AS_input

description: Library name: Sample4

value: Polysome input


title: Mouse 2559, female, mock, 18 mo


title: Mouse 2576, male, infected, 18 mo


title: AJ_WGD+_aCD8_1

value: Murine mammary tumor

value: WGD+


title: Mouse 2561, female, mock, 18 mo


title: Mouse 2580, female, infected, 18 mo


title: Mouse 2571, female, infected, 18 mo


title: RNA-seq of MM-2 sample

city: Nanjing

first: XIAOXI

last: DAI

state: Jiangsu

address: 12 Jiangwangmiao Street

department: Department of Physiotherapy

institute: Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: LIB005

data_processing:
Raw sequencing reads were assessed for quality using FastQC
Adapters and low-quality bases were trimmed using Trimmomatic
Clean reads were aligned to the GRCh38 human reference genome using HISAT2
Gene-level expression quantification was performed using featureCounts
Differential expression analysis was conducted using DESeq2 in R.
Assembly: GRCh38
Supplementary files format and content: Processed data files include normalized gene expression values in FPKM format for each sample.
Supplementary files format and content: Each row represents a gene, and each column represents a sample. Gene IDs are based on GENCODE annotation.

source_name: foreskin

growth_protocol: Human dermal fibroblasts (HDFs) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells at passages 3–6 were used.

extract_protocol:
Total RNA was extracted using RNAiso Plus according to the manufacturer's protocol.
RNA libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.

treatment_protocol: RNA-seq profiling was performed in HDFs transfected with tRF-34 mimics or negative control. Cells were exposed to UVA1 (15 J/cm²) daily for three consecutive days. RNA was extracted 24 hours after the final irradiation.

value: foreskin

value: primary human dermal fibroblasts

value: HDFs transfected with tRF-34 mimics


title: AJ_WGD+_aPDL1_1


title: Mouse 2551, female, infected, 18 mo

value: female


title: AP_poly

description: Library name: Sample3

value: Skin

value: Melanoma Cell


title: RNA-seq of NCE-3 sample

description: Library name: LIB003

value: HDFs transfected with NC


title: AP_mono

description: Library name: Sample2

value: Monosome fractions


title: Mouse 2554, male, infected, 12 mo

value: liver

value: 12 mo


title: Mouse 2545, male, infected, 18 mo

value: male

value: 18 mo


title: AJ_WGD+_Isotype_1

value: Tumor

value: Isotype antibody


title: Mouse 2539, female, infected, 18 mo

value: NrHV viral infection


title: AP_input

description: Library name: Sample1

value: Polysome input


title: Mouse 2518, male, infected, 12 mo


title: Mouse 2583, male, infected, 12 mo


title: AJ_WGD-_aPDL1_1

value: Murine mammary tumor

value: WGD-


title: AJ_WGD+_Isotype_2

value: WGD+


title: FLS_IL1B_3

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: Library name: synf-il1b-3

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: FLS

growth_protocol: Cells were cultured under standard condistions.

extract_protocol:
Total RNA was extracted using RNA-easy mini klt.
Qiagen FastSelect

treatment_protocol: Cells were treated with IL-1b for 24 hours.

value: FLS

value: Fibroblasts


title: Mouse 2595, male, mock, 12 mo

value: mock


title: FLS_IL1B_2

description: Library name: synf-2-il1b


title: AJ_WGD-_aCD8_1


title: Mouse 2564, male, mock, 12 mo


title: AJ_WGD+_Isotype_3


title: RNA-seq of MM-3 sample

description: Library name: LIB006

value: foreskin

value: primary human dermal fibroblasts

value: HDFs transfected with tRF-34 mimics


title: RNA-seq of NCE-2 sample

description: Library name: LIB002

value: HDFs transfected with NC


title: Mouse 2519, male, infected, 12 mo

value: liver

value: 12 mo


title: RNA-seq of MM-1 sample

description: Library name: LIB004


title: AJ_WGD-_aPDL1_3


title: Mouse 2508, male, infected, 12 mo

value: male


title: Mouse 2566, male, mock, 12 mo


title: RNA-seq of NCE-1 sample

description: Library name: LIB001


title: Mouse 2529, male, mock, 12 mo


title: AJ_WGD-_Isotype_1

value: Tumor


title: Mouse 2555, male, infected, 12 mo


title: Mouse 2530, male, mock, 12 mo


title: Mouse 2536, female, mock, 12 mo

value: female


title: Mouse 2509, male, infected, 12 mo

value: NrHV viral infection


title: NSG_WGD+_YM155_3


title: Mouse 2535, female, mock, 12 mo


title: Mouse 2565, male, mock, 12 mo


title: AJ_WGD-_aCD8_2


title: AJ_WGD-_Isotype_3

value: Isotype antibody


title: FLS_control_1

description: Library name: synf-1

value: control


title: AJ_WGD-_aPDL1_2

value: Murine mammary tumor

value: WGD-


title: Mouse 2515, female, infected, 12 mo


title: Mouse 2579, female, infected, 12 mo


title: Mouse 2523, female, mock, 12 mo


title: NSG_WGD+_Vehicle_3

value: Vehicle


title: Mouse 2570, female, infected, 12 mo


title: FLS_IL1B_1

description: Library name: synf-il1b-1

value: FLS

value: Fibroblasts


title: FLS_control_2

description: Library name: synf-2


title: AJ_WGD-_Isotype_2


title: Mouse 2520, male, infected, 12 mo


title: Mouse 2503, female, infected, 12 mo


title: RNA-seq, CIS3

city: Hefei

first: Yuhang

last: Dong

address: Meishan Road NO.81

institute: Anhui Medical University

description: Library name: Sample3

data_processing:
RNA high throughput sequencing was performed by CloudSeq Biotech Inc.(Shanghai, China). Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on sequencer with 150bp paired end reads.
Assembly: hg38
Supplementary files format and content: CSV files include FPKM values for each sample.

source_name: HK2 cell

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HK2 cell


title: Mouse 2510, male, infected, 12 mo


title: Mouse 2563, male, mock, 7 mo

value: mock

value: 7 mo


title: Mouse 2562, male, mock, 7 mo


title: Mouse 2578, female, infected, 12 mo


title: NSG_WGD+_YM155_2

value: WGD+


title: Mouse 2549, female, infected, 12 mo

value: liver


title: RNA-seq, KD+CIS3

description: Library name: Sample6


title: FLS_control_3

description: Library name: synf-3


title: Mouse 2528, male, mock, 7 mo


title: NSG_WGD+_Vehicle_2


title: Mouse 2525, female, mock, 12 mo

value: 12 mo


title: Mouse 2524, female, mock, 12 mo


title: RNA-seq, KD+CIS1

description: Library name: Sample4


title: NSG_WGD-_YM155_1


title: Mouse 2543, male, infected, 7 mo

value: male


title: RNA-seq, KD+CIS2

description: Library name: Sample5


title: Mouse 2504, female, infected, 12 mo


title: Mouse 2505, female, infected, 12 mo


title: NSG_WGD-_YM155_3

value: Tumor


title: NSG_WGD+_Vehicle_1


title: NSUN7 KD+CIS1, input

description: Library name: Sample10

data_processing:
Briefly, Paired-end reads were harvested from sequencer, and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC hg38) by STAR software. Then clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: hg38
Supplementary files format and content: CSV files include FPKM values for each sample


title: Mouse 2517, male, infected, 7 mo


title: NSG_WGD-_YM155_2


title: Mouse 2514, female, infected, 12 mo

value: female


title: NSG_WGD+_YM155_1


title: NSUN7 KD+CIS3, input

description: Library name: Sample12


title: RNA-seq, CIS2

description: Library name: Sample2


title: Mouse 2513, female, infected, 12 mo

value: NrHV viral infection


title: Mouse 2507, male, infected, 7 mo


title: Mouse 2532, male, mock, 7 mo


title: Mouse 2552, male, infected, 7 mo


title: AJ_WGD+_YM155_2


title: Mouse 2542, male, infected, 7 mo


title: NSUN7 KD+CIS2, input

description: Library name: Sample11


title: Mouse 2558, female, mock, 7 mo


title: Mouse 2506, male, infected, 7 mo


title: NSG_WGD-_Vehicle_3


title: NSUN7 KD+CIS2

description: Library name: Sample5


title: Mouse 2553, male, infected, 7 mo


title: RNA-seq, CIS1

description: Library name: Sample1


title: CIS1, input

description: Library name: Sample7


title: Mouse 2588, female, mock, 7 mo


title: Mouse 2516, male, infected, 7 mo


title: Mouse 2521, female, mock, 7 mo


title: CIS2, input

description: Library name: Sample8


title: CIS3, input

description: Library name: Sample9


title: peripheral EDTA blood, rLDH_3, rep1

description:
Library name: DS06
Column name in HTSeq_counts.xlsx: DS06

value: peripheral EDTA blood

value: rLDH

value: Spinal disc surgery:L4-L5 (2 operations)


title: AJ_WGD+_Vehicle_2

value: Murine mammary tumor

value: WGD-


title: AJ_WGD+_YM155_3


title: Mouse 2533, male, mock, 7 mo


title: NSUN7 KD+CIS3

description: Library name: Sample6


title: AJ_WGD+_Vehicle_1

value: Vehicle


title: NSG_WGD-_Vehicle_1


title: P. aeruginosa PAO1, 22 °C, 7 days, biol rep 2

city: Hamburg

first: Tim

last: Hoffmann

state: Hamburg

address: Ohnhorststraße 18

country: Germany

institute: Universität Hamburg

description: Library name: Sample 12

data_processing:
Raw data in FASTQ format were first cleaned using fastp (Chen, 2023), removing adapter sequences, poly-N-containing reads and low-quality reads (Phred score < 20).
Gene-specific read counts were determined using FeatureCounts (2.0.6) (Liao et al., 2014).
To quantify gene expression, the FPKM value (fragments per kilobase of transcript per million mapped reads) was calculated for each gene to ensure comparability between genes and samples.
Differential expression analysis was performed using the DESeq2 R package (1.42.0) (Love et al., 2014)
The p-values were adjusted using the Benjamini-Hochberg correction for multiple testing.
Assembly: The cleaned reads were aligned using Bowtie2 (2.5.4) (Langmead et al., 2009) to the reference genome of P. aeruginosa PAO1 (NC_002516.2).
Supplementary files format and content: .xlsx file include differential gene expression data as well as fpkm values

organism: Pseudomonas aeruginosa PAO1

source_name: bacteria

growth_protocol: P. aeruginosa PAO1 was grown in LB broth as an over night culture. Cell were washed in PBS buffer. A viable count of 5 x 10e10 cfu/ mL was set up in PBS buffer. Cells were centrifuged and resuspended in 400 µL PBS buffer. 5 µL spots were pipetted on the surface of oak leaf lettuce leafes. After the spots had dried at ambient temperature for 30 to 60 min, the plants were incubated in the constant climate cabinet. The incubation took place at 18 °C and 22 °C for two, five, and seven days. To harvest the previously inoculated P. aeruginosa PAO1 biomass from the surface of the leaves, the leaves were cut off using sterile scissors and transferred to a stomacher bag with a filter insert (T256.2, Carl Roth, Karlsruhe, Germany). Fifty milliliters PBS were added and the leaves were treated with high-frequency vibration in the Pulsifier® (Microgen Bioproducts Ltd., Eastleigh, Great Britain) for 30 s. The cell suspension was transferred to sterile 50 mL tubes and centrifuged at 5,000 × g at 4 °C for 8 min. The supernatants were discarded and the pellets were resuspended in 800 μL RNA Shield (R1100-250, Zymo Research Europe, Freiburg, Germany) and stored at -80 °C until further processing.

extract_protocol:
To mechanically assist cell lysis, the samples were transferred to ZR BashingBead Lysis Tubes (0.1 mm and 0.5 mm, Zymo Research Europe, Freiburg, Germany) and homogenized for 10 min (Vortex-Genie 2, SI-0236, Scientific Industries, Inc., New York, USA). The samples were centrifuged at 10,000 × g at room temperature for 1 min and the supernatant was transferred to RNase-free tubes (AM12400, Thermo Fisher Scientific, Waltham, MA, USA). RNA was isolated and purified using the Direct-zol RNA Miniprep Kit (R2050, Zymo Research Europe, Freiburg, Germany) according to the manufacturer's instructions with subsequent quality and concentration check by the NanoPhotometer® NP80 (Implen, Munich, Germany). RNA was stored at -80 °C.
Library preparation, sequencing, and data analysis were performed by Novogene GmbH (Munich, Germany), ribosomal RNA was eliminated from the total RNA, accompanied by ethanol precipitation. For quantification of the library, Qubit and real-time PCR were used, and the Agilent 2100 Bioanalyzer for size distribution detection. The libraries were pooled according to their effective concentration and the required data volume and sequenced on an Illumina NovaSeq 6000 platform.

value: bacteria

value: 22 degrees celsius

tag: time

value: day 7


title: P. aeruginosa PAO1, 22 °C, 5 days, biol rep 2

description: Library name: Sample 10

value: day 5


title: Mouse 2527, male, mock, 7 mo

value: mock

value: 7 mo


title: Mouse 2534, female, mock, 7 mo

value: liver


title: P. aeruginosa PAO1, 22 °C, 7 days, biol rep 1

description: Library name: Sample 11


title: CIS2

description: Library name: Sample2

value: HK2 cell


title: NSUN7 KD+CIS1

description: Library name: Sample4


title: Mouse 2557, female, mock, 7 mo


title: NSG_WGD-_Vehicle_2

value: Tumor


title: CIS1

description: Library name: Sample1


title: AJ_WGD+_Vehicle_3


title: AJ_WGD-_YM155_1

value: WGD+


title: CIS3

description: Library name: Sample3


title: P. aeruginosa PAO1, 22 °C, 5 days, biol rep 1

description: Library name: Sample 9


title: Mouse 2522, female, mock, 7 mo

value: female


title: AJ_WGD-_YM155_3


title: Mouse 2569, female, infected, 7 mo

value: NrHV viral infection


title: AJ_WGD+_YM155_1


title: Mouse 2537, female, infected, 7 mo


title: A549 cell line,PQ_3

city: Harbin

first: Quankuan

last: Gu

state: Heilongjiang Province

address: Department of Critical Care Medicine

institute: the First Affiliated Hospital of Harbin Medical University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample.

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Total RNA was used as input material for the RNA sample preparations.

value: Human alveolar epithelial cells line


title: A549 cell line,PQ+SS-31_1


title: P. aeruginosa PAO1, 22 °C, 2 days, biol rep 1

description: Library name: Sample 7

value: day 2


title: Mouse 2512, female, infected, 7 mo


title: sample_2

city: Jinan

first: Zhengfang

last: Liu

address: 107 Wenhua Xilu

department: Urology

institute: Qilu Hospital of Shandong University

description: 10× Genomics

data_processing:
Cellranger v7.1.0;10X barcode recognition and genome alignment with UMI, ultimately generating expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated vaule Mes and  matrix file

source_name: Renal cancer

extract_protocol:
Freshly collected RENCA tumors from BALB/c mice were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent(0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min(repeated twice). The candidate cells were obtained after tissue dissociation,lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl.
Libraries were generated using the 10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3. Briefly, cells were loaded into the Chromium Controller (10x Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion. Reverse transcription was performed, and the resulting cDNA was amplified following the manufacturer’s instructions. The full-length amplified cDNA was used to generate gene expression libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters. The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200, and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. Final libraries were then pooled, denatured, and diluted to 300 p.m. with 1% PhiX control library added. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: Renal cancer

value: RENCA

value: Epithelial cell

value: WT


title: P. aeruginosa PAO1, 18 °C, 7 days, biol rep 2

description: Library name: Sample 6

value: bacteria

value: 18 degrees celsius


title: AJ_WGD+_Tumor3

description: 10x Genomics

value: primary breast tumor

value: Murine mammary tumor

value: MFP injection


title: Mouse 2568, female, infected, 7 mo

value: liver

value: 7 mo


title: sample_1

description: 10× Genomics

value: SMYD3 knockdown


title: A549 cell line,PQ+SS-31_2


title: AJ_WGD-_Vehicle_2

value: Tumor

value: WGD-

value: Vehicle


title: Mouse 2548, female, infected, 7 mo

value: female

value: NrHV viral infection


title: P. aeruginosa PAO1, 22 °C, 2 days, biol rep 2

description: Library name: Sample 8

value: 22 degrees celsius

value: day 2


title: Mouse 2547, female, infected, 7 mo


title: P. aeruginosa PAO1, 18 °C, 7 days, biol rep 1

description: Library name: Sample 5

value: day 7


title: WT_Male_SD_Control

type: RNA

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 725 North Wolfe St

department: The Solomon H. Snyder Department of Neuroscience

institute: Johns Hopkins University School of Medicine

description: Wildtype C57BL/6J

hyb_protocol: Custom probe hybridization, ligation, amplification, cell segmentation staining, and autofluorescence quenching was performed according to manufacturer protocols “Xenium In Situ Gene Expression with Cell Segmentation Staining - User Guide CG000749 Rev A.

scan_protocol: Xenium In Situ Analyzer

data_processing: The Xenium Onboard Analysis platform was used to generate cell segmentaion, gene transcript-by-cell, and transcript-by-tissue location data matrics.

label: Xenium probe set

source_name: Hypothalamus

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Fresh Frozen brain samples were coronally sliced onto Xenium capture areas according to “Xenium In Situ for FFPE - Tissue Preparation Guide CG000578 Rev C” before delivering slides to the Spatial Technology Platform.

treatment_protocol: Mouse was housed in a climate-controlled pathogen-free facility and allowed food, water, and sleep ad libitum during lights on (6:30am-12:30pm). Euthanized after 6 hours (12:30pm).

value: Hypothalamus

tag: tissue preservation method

value: Fresh Frozen

value: Male


title: AJ_WGD-_Vehicle_3


title: AJ_WGD-_Vehicle_1


title: A549 cell line,PQ_2

value: Human alveolar epithelial cells line


title: AJ_WGD-_YM155_2

value: Murine mammary tumor

value: WGD+


title: P. aeruginosa PAO1, 18 °C, 5 days, biol rep 1

description: Library name: Sample 3

value: bacteria

value: 18 degrees celsius

value: day 5


title: P. aeruginosa PAO1, 18 °C, 5 days, biol rep 2

description: Library name: Sample 4


title: A549 cell line,PQ+SS-31_3


title: Mouse 2538, female, infected, 7 mo

value: liver

value: 7 mo


title: H520, SOX2, CUT&Run

status: Public on Mar 14 2026

city: GuangZhou

first: Wen

last: Yulin

state: Guangdong

address: No.190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS)

description: Library name: H520_SOX2

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the hg38 genome using bowtie2 version 2.3.2.
Read coverage normalized by RPKM
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

growth_protocol: The lung squamous cell carcinoma cell lines NCI-H520 was cultured in RPMI-1640 medium containing 15% fetal bovine serum (FBS).

extract_protocol:
1 × 105 cells were harvested and bound to Concanavalin A-coated beads, then incubated with individual primary antibody at 4°C overnight. pAG-MNase enzyme was added to each sample followed by incubation 1 hour at 4°C. Targeted digestion was done by 30 minutes incubation on ice block (0°C) under low salt conditions.The DNA released into the supernatant were purified and subjected to library preparation and next-generation sequencing.
The sequencing libraries were prepared through VAHTS Universal DNA Library Prep Kit (Vazyme, ND607).

value: lung squamous cell carcinoma cells

value: WT


title: Cd11b-P2X4mCherryIN KI female mouse, number 549

city: Leioa

first: Maria

last: Domercq

state: Bizkaia

address: Barrio Sarriena, s/n

department: Neurosciences

country: Spain

institute: Achucarro Basque Center for Neuroscience

description:
Library name: cd11b_549
Column name in counts.txt: cd11b_549

data_processing:
Aligned to the reference with STAR(version 2.7.5c)
Pre-processing and manipulation of BAMfiles with samtools(version 1.9) and STAR(version 2.7.5c)
Read counts using FeatureCounts (version 2.0.3) from the SubReadpackage
Analysis using a custom R(version 3.6.0) pipeline based on EdgeR, Limma, WGCNAand others
Assembly: mm10
Supplementary files format and content: Tab-delimited text file

source_name: spinal cord

growth_protocol: Spinal cords were mechanically dissociated and nuclear cells were isolated from debris using a Percoll gradient. Single cell suspensions were incubated with TruStain FcX™ antibodies for 15 minutes to block unspecific bindings, and then stained for 30 minutes with CD11b-FITC, CD45-PE, Ly6C-PE/Cy7 and SYTOX AADvanced™ Ready Flow™, a viability marker. We identified microglial population as SYTOX-/CD11b+/CD45low/Ly6C-.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit (Qiagen)
NEBNext® Low Input RNA Library Prep

value: spinal cord

value: microglia cells

value: KI


title: Cd11b-P2X4mCherryIN KI female mouse, number 513

description:
Library name: cd11b_513
Column name in counts.txt: cd11b_513


title: H520_Vehicle_rep2, RNA-seq

description: Library name: H520_Vehicle_rep2_RNA-seq

data_processing:
Clean reads were aligned to human reference genome (hg38/GRCh38) using STAR version 2.7.9. Only unique mapped reads were used in further analysis.
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text files include TPM values for each sample.

extract_protocol:
Total RNAs were extracted with TRIzol.1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed by using a Fast RNA-seq Lib Prep Kit V2 (ABclonal, RK20306) according to the manufacturer’s instructions.

treatment_protocol: NCI-H520 cells were treated with ultrapure water and 10 μM Hx1R8  for 12 hours, respectively.

value: ultrapure water


title: A549 cell line,PQ_1


title: Mouse 2501, female, infected, 7 mo

data_processing:
Read quality was assessed using fastQC (v0.11.9) and reads were trimmed using fastp (v0.23.2)
For quantification of RNA expression, the Salmon (v1.4.0) package was used using the selective-alignment algorithm
Mapped reads to concatenated GRCm39 and B+4 NrHV transcriptome, where NrHV transcriptome was entire RNA genome of the virus (GenBank accession no. KX905133)
TPM normalized abundance output from Salmon read into R using tximport package (v1.18.0)
Assembly: Genome Reference Consortium Mouse Build 39
Supplementary files format and content: Salmon pseudoalignment output in .sf format is a quantification file that includes TPM (relative abundance) values and estimated number of reads mapping to each transcript, quantified for each sample

extract_protocol:
Liver slices previously flash-frozen and pulverized using liquid nitrogen were used for RNA and DNA isolation. Both nucleic acids were isolated from the same liver slice using Allprep Qiagen kit (QIAGEN) following manufacturer’s instructions with addition of RNase inhibitor and DNAseI to the original RNA isolation protocol. Samples were quality checked prior submission to bulk RNAseq. A RIN above 7 was accepted for downstream library preparation and sequencing. Samples that did not reach the criteria for downstream analysis were purified using either RNA mini kit (Zymo) or DNA purification kit (Zymo)
Total RNA previously isolated from livers were submitted to Novogene for bulk RNA sequencing. Samples were enriched for mRNA using polyA selection. Libraries were produced using directional mRNA preparation and submitted to Novaseq PE150, with about 20M depth per sample.

value: female

value: NrHV viral infection


title: Cd11b-P2X4mCherryIN KI female mouse, number 526

description:
Library name: cd11b_526
Column name in counts.txt: cd11b_526


title: P. aeruginosa PAO1, 18 °C, 2 days, biol rep 2

description: Library name: Sample 2

value: day 2


title: WildType female mouse, number 506

description:
Library name: WT_506
Column name in counts.txt: WT_506


title: H520, Vehicle,SOX2, CUT&Run

description: Library name: H520_Vehicle_SOX2


title: H520_CDDP_rep3, RNA-seq

description: Library name: H520_CDDP_rep3_RNA-seq

treatment_protocol: NCI-H520 cells were treated with PBS and 2 μM cisplatin for 48 hours, respectively.

value: cisplatin


title: H520_Vehicle_rep1, RNA-seq

description: Library name: H520_Vehicle_rep1_RNA-seq


title: H520, Hx1,SOX2, CUT&Run

description: Library name: H520_Hx1_SOX2


title: H520_Hx1_rep1, RNA-seq

description: Library name: H520_Hx1_rep1_RNA-seq


title: H520_Hx1_rep2, RNA-seq

description: Library name: H520_Hx1_rep2_RNA-seq


title: P. aeruginosa PAO1, 18 °C, 2 days, biol rep 1

description: Library name: Sample 1


title: H520_CDDP_rep1, RNA-seq

description: Library name: H520_CDDP_rep1_RNA-seq


title: H520_CDDP_rep2, RNA-seq

description: Library name: H520_CDDP_rep2_RNA-seq


title: Cd11b-P2X4mCherryIN KI female mouse, number 528

description:
Library name: cd11b_528
Column name in counts.txt: cd11b_528


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), muscle-3

city: Changsha

first: xiao

middle: qiao

last: ni

address: No. 87, Xiangya Road

institute: Xiangya hospital central south university

description: Library name: LCJ-DD3-muscle

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope v1.9.0 pipeline.
Assembly: GRCm38 (ensemble version 92 annotation)
Supplementary files format and content: gene expression matrices

molecule: nuclear RNA

source_name: muscle

extract_protocol:
Single-cell suspensions (2×10^5 cells/mL) with PBS were loaded onto microwell chip.Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE protocol by GEXSCOPE Single-Cell RNA Library Kit.

value: muscle


title: H520_PBS_rep2, RNA-seq

description: Library name: H520_PBS_rep2_RNA-seq

value: PBS


title: WildType female mouse, number 527

description:
Library name: WT_527
Column name in counts.txt: WT_527


title: H520_PBS_rep3, RNA-seq

description: Library name: H520_PBS_rep3_RNA-seq


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), muscle-3

description: Library name: LCJ-Veh3-muscle


title: H520, input, CUT&Run

description: Library name: H520_input


title: WildType female mouse, number 504

description:
Library name: WT_504
Column name in counts.txt: WT_504


title: WildType female mouse, number 503

description:
Library name: WT_503
Column name in counts.txt: WT_503


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), muscle-2

description: Library name: LCJ-Veh2-muscle


title: peripheral EDTA blood, CeAD_9, rep1

description:
Library name: DS16
Column name in HTSeq_counts.xlsx: DS16

data_processing:
Paired-end reads were aligned to the human reference genome (GRCh38) using the STAR aligner, achieving an average unique alignment rate of 80% per sample
Gene-level read counting was performed with HTSeq in union mode, approximately 55% of total reads were uniquely mapped to annotated genes
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

value: peripheral EDTA blood

value: CeAD

value: 3-month anticoagulation post-dissection


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), muscle

description: Library name: LCJ-Veh1-muscle


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), bone-2

description: Library name: LCJ-Veh2-bone

source_name: bone

value: bone


title: H520_PBS_rep1, RNA-seq

description: Library name: H520_PBS_rep1_RNA-seq


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), adipose

description: Library name: LCJ-DD1-adipose

source_name: adipose

value: adipose


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), muscle-2

description: Library name: LCJ-DD2-muscle


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), adipose-2

description: Library name: LCJ-DD2-adipose

source_name: adipsoe

value: adipsoe


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), adipose

description: Library name: LCJ-Veh1-adipose


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), bone

description: Library name: LCJ-Veh1-bone


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), muscle

description: Library name: LCJ-DD1-muscle


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), adipose-2

description: Library name: LCJ-Veh2-adipose


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), bone-2

description: Library name: LCJ-DD2-bone


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), thymus-1

description: Library name: LCJ-Veh1-thymus-1

source_name: thymus

value: thymus


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), liver-2

description: Library name: LCJ-Veh2-liver

value: liver


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), thymus-2

description: Library name: LCJ-Veh2-thymus-2


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), liver-2

description: Library name: LCJ-DD2-liver


title: PS19,10month,rep1

city: Xiamen

first: Boxin

last: Zhang

address: 良渚实验室1369号

institute: 良渚实验室

description: Library name: Sample4

data_processing:
FASTQ files was filtered using the Trim_Galore (v.0.6.5)
Filtered Sequences were aligned with STAR (v.2.5.3a) to the mm39 assembly
Gene expression and TE expression were quantified from uniquely aligned reads using Featurecounts (v.2.0.4) with -f parameters and their annotations from the UCSC
For repeat analysis, alignment positions were mapped with repeats annotated in UCSC with RepeatMasker (rmsk table from mm39)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: All mice were on a C57BL/6 genetic background and housed in a constant temperature of 23℃ in a 12-h light/dark cycle at the Laboratory Animal Center of Zhejiang University and Xiamen University.

extract_protocol:
RNA was extracted with the TRIzol method, and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit following manufacturer's protocols.

value: Hippocampus


title: Single-cell sequencing data, aged male mice, Vehicle (CMC-Na), liver

description: Library name: LCJ-Veh1-liver


title: PS19,10month,rep3

description: Library name: Sample6


title: WT,10month,rep3

description: Library name: Sample3

source_name: WT

value: WT


title: PS19, Zbp1+-,10month,rep3

description:
Library name: Sample9
zbp1ps19

source_name: Hippocampus

value: PS19, Zbp1+-,10month,rep3


title: PS19, Zbp1+-,10month,rep1

description: Library name: Sample7


title: PS19-K9,rep2

description: Library name: Sample11

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
Clean reads were then aligned to the mouse mm10 reference genome via Bowtie v.1.2.21.
SAMtools was applied for the BAM file conversion and duplicates removal. Peak calling was conducted with MACS2 v2.2.7.13 using following key parameters:  -f BAMPE --keep-dup all --nomodel --extsize 200. We obtained the peaks based on P-value < 0.05 (two-sided t-test). Differential peaks for the PS19 vs. WT comparisons were selected using the threshold of P-value (two-sided t-test) < 0.05 and log2 fold change in reads per million of mapped reads (RPM) < -1.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Approximately 1× 10^7 cells from hippocampus as above was fixed in 1% formaldehyde for 10 min at room temperature (RT), followed by quenching in 125 nM glycine for 5 min. Cell nuclei were collected and lysed in lysing buffer (50 mM HEPES/KOH pH 7.6, 1 mM EDTA, 140 nM NaCl, 10% v/v Glycerol, 0.5% NP-40, 0.25% v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with 1.5 μg H3K9me3 antibody (Abcam, #ab232324) overnight at 4°C, followed with collection using 30 μl protein A/G plus agarose beads (Millipore). After elute and purify the chromatin, the ChIP-seq library was constructed using a KAPA HyperPrep Kits (Roche, 07962347001) according to the manufacturer’s instructions，and then run on the Illumina sequencer Hiseq-Xten PE150.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

value: H3K9me3 antibody (Abcam, #ab232324)


title: PS19-K9,rep3

description: Library name: Sample12


title: PS19, Zbp1+-,10month,rep2

description: Library name: Sample8


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), bone

description: Library name: LCJ-DD1-bone


title: WT,10month,rep1

description:
Library name: Sample1
WT


title: PS19, Zbp1+-,10month,rep3

description: Library name: Sample9


title: PS19, Zbp1+-,10month,rep2

description:
Library name: Sample8
zbp1ps19

value: PS19, Zbp1+-,10month,rep2


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), thymus-2

description: Library name: LCJ-DD2-Thymus-2


title: WT,10month,rep1

description: Library name: Sample1


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), thymus-1

description: Library name: LCJ-DD1-Thymus-1


title: PS19,10month,rep2

description: Library name: Sample5


title: WT,10month,rep2

description: Library name: Sample2


title: WT-K9,rep1

description: Library name: Sample7


title: PS19-K9,rep1

description: Library name: Sample10


title: Single-cell sequencing data, aged male mice, Dasatinib plus Quercetin (DQ), liver

description: Library name: LCJ-DD1-liver


title: WT-input,rep2

description: Library name: Sample2


title: PS19,10month,rep3

description:
Library name: Sample6
ps19


title: PS19,10month,rep2

description:
Library name: Sample5
ps19


title: WT-K9,rep3

description: Library name: Sample9


title: WT,10month,rep3

description:
Library name: Sample3
WT


title: S24K0858_rep1_1_miRNA

description: Library name: Sample7

data_processing:
The adapter sequences of raw reads were initially removed using cutadapt  v4.0
The processed reads were aligned to the mouse genome mm10 using Hisat2 v2.2.1  with default parameters
Peak calling was done using macs2 v 2.2.7.1  with these key parameters: -f BED –nolambda --nomodel --extsize 50. Peak distribution across genomic regions was calculated using HOMER  v4.11 annotatePeaks
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
The immunoprecipitated RNA was extracted with the TRIzol method and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

value: WT zbp1

tag: fraction

value: input


title: S24K0860_rep1_1_miRNA

description: Library name: Sample9


title: S24K0853_rep1_1_miRNA

description: Library name: Sample2

value: IP


title: PS19-input,rep3

description: Library name: Sample6


title: PS19-input,rep2

description: Library name: Sample5


title: WT-K9,rep2

description: Library name: Sample8


title: 20-month-old mice treated with Dasatinib plus Quercetin (DQ), liver

description: Library name: Sample6

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope v1.9.0 pipeline.
raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.
used STAR v2.6.1a to map reads to the reference genome GRCm38 (ensembl version 92 annotation)
UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS were loaded onto microwell chip.Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE protocol by GEXSCOPE Single-Cell RNA Library Kit.

value: male


title: 20-month-old mice treated with Vehicle, liver

description: Library name: Sample5


title: 20-month-old mice treated with Dasatinib plus Quercetin (DQ), adipose

description: Library name: Sample2


title: WT,10month,rep2

description:
Library name: Sample2
WT


title: S24K0857_rep1_1_miRNA

description: Library name: Sample6

value: PS19 zbp1


title: PS19, Zbp1+-,10month,rep1

description:
Library name: Sample7
zbp1ps19

value: PS19, Zbp1+-,10month,rep1


title: PS19,10month,rep1

description:
Library name: Sample4
ps19


title: PS19-input,rep1

description: Library name: Sample4


title: WT-input,rep3

description: Library name: Sample3


title: S24K0862_rep1_1_miRNA

description: Library name: Sample11


title: S24K0859_rep1_1_miRNA

description: Library name: Sample8


title: Iγ3-PS-Cα_sti_3

city: Beijing

first: Xuefei

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description:
Library name: Sample 27
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells

data_processing:
Reads were aligned using bowtie 2.2.8 with --local flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Assembly: mm9
Supplementary files format and content: wig files contain peak information for samples

source_name: CH12F3 murine lymphoma cells

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with permeabilization buffer. The permeabilized cells were resuspended in 100 ml of storage buffer for nuclear run-on with 2X run-on mix at 37℃ for 5 min. RNA was extracted by Trizol and followed by hybrolyzation. The RNA was incubated with streptavidin C1 beads (Thermo Fisher Scientific, #65001) and the enriched run-on samples were incubated with hydroxyl repair with T4 PNK (NEB, M0201S) and RppH (NEB, M0356S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA.
The cDNA was subjected to making PRO-seq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318). PRO-seq libraries were sequenced via single end 50bp or paired end 150bp sequencing on a Nova-seq 6000 (Illumina) sequencer and normalized to a coverage of 10 million 100nt reads for display.

treatment_protocol: CH12F3 cell lines were cultured in R15 medium and stimulated with anti-CD40+IL4+TGF-β for 72 hrs.

value: CH12F3 murine lymphoma cells

value: aCD40/IL4/TGFb stimulation


title: WT-input,rep1

description: Library name: Sample1


title: S24K0863_rep1_1_miRNA

description: Library name: Sample12


title: Iγ3-FS-Cα_sti_3

description:
Library name: Sample 21
AID-/-;Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: S24K0861_rep1_1_miRNA

description: Library name: Sample10


title: Iγ3-FS-Cα_sti_1

description:
Library name: Sample 19
AID-/-; Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-FS-Iα_sti_1

description:
Library name: Sample 22
AID-/-; Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: S24K0856_rep1_1_miRNA

description: Library name: Sample5


title: Iγ3-PS-Iα_sti_1

description:
Library name: Sample 28
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells


title: α_3CBEInv_sti_6

description:
Library name: Sample 15
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: α_3CBEInv_sti_5

description:
Library name: Sample 14
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: 20-month-old mice treated with Vehicle, adipose

description: Library name: Sample1

value: adipose


title: Iγ3-PS-Iα_sti_3

description:
Library name: Sample 30
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells


title: S24K0855_rep1_1_miRNA

description: Library name: Sample4


title: S24K0854_rep1_1_miRNA

description: Library name: Sample3


title: Iγ3-PS-Cα_sti_2

description:
Library name: Sample 26
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: S24K0852_rep1_1_miRNA

description: Library name: Sample1


title: Iγ3-PS-Iα_sti_2

description:
Library name: Sample 29
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells


title: Iγ3-FS-Iα_sti_3

description:
Library name: Sample 24
AID-/-; Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: α_3CBEInv_αΔ_sti_2

description:
Library name: Sample 17
AID-/-; Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: α_3CBEInv_αΔ_sti_1

description:
Library name: Sample 16
AID-/-; Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: 20-month-old mice treated with Dasatinib plus Quercetin (DQ), bone marrow

description: Library name: Sample4

value: bone


title: Iγ3-FS-Cα_sti_2

description:
Library name: Sample 20
AID-/-; Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-PS-Cα_sti_1

description:
Library name: Sample 25
AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-FS-Iα_sti_2

description:
Library name: Sample 23
AID-/-; Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: 20-month-old mice treated with Vehicle, bone marrow

description: Library name: Sample3


title: α_3CBEInv_sti_4

description:
Library name: Sample 13
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: α_3CBEInv_αΔ_sti_3

description:
Library name: Sample 18
AID-/-; Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: αInv_sti_3

description:
Library name: Sample 9
AID-/-; Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells

value: aInv-AID-/-


title: γ3_αInv_sti_3

description:
Library name: Sample 6
AID-/-; γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-PS-Iα_sti_iEμ_2

description: Library name: Sample 39

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: bedgraph files were generated for displaying (Jane et al., 2018)

source_name: AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

value: cytokine stimulation


title: CH12F3PO_sti_3

description:
Library name: Sample 3
AID-/-; non-coding IgH VH-3'BCEs deletion


title: Iγ3-PS-Iα_sti_iEμ_3

description: Library name: Sample 40


title: CH12F3PO_sti_2

description:
Library name: Sample 2
AID-/-; non-coding IgH VH-3'BCEs deletion


title: αInv_sti_2

description:
Library name: Sample 8
AID-/-; Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-PS-Iα_sti_iEμ_1

description: Library name: Sample 38


title: Iγ3-FS-Cα_sti_iEμ_2

description: Library name: Sample 30

source_name: AID-/-; Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-PS-Cα_sti_iEμ_3

description: Library name: Sample 37

source_name: AID-/-; Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: α_3CBEInv_sti_3

description:
Library name: Sample 12
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: Iγ3-PS-Cα_sti_iEμ_1

description: Library name: Sample 35


title: γ3_αInv_sti_2

description:
Library name: Sample 5
AID-/-; γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3-FS-Iα_sti_iEμ_2

description: Library name: Sample 33

source_name: AID-/-; Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: Iγ3-PS-Cα_sti_iEμ_2

description: Library name: Sample 36


title: Iγ3-FS-Cα_sti_iEμ_1

description: Library name: Sample 29


title: α_3CBEInv_sti_2

description:
Library name: Sample 11
AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: Iγ3-FS-Iα_sti_iEμ_3

description: Library name: Sample 34


title: Iγ3-FS-Iα_sti_iEμ_1

description: Library name: Sample 32


title: Iγ3-FS-Cα_sti_iEμ_3

description: Library name: Sample 31

source_name: AID-/-;Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: α_3CBEInv_sti_3CBE_2

description: Library name: Sample 27

source_name: AID-/-; Cα-3'CBE inversion in Iα-Cα inversion cells


title: α_3CBEInv_sti_3RR_2

description: Library name: Sample 21


title: α_3CBEInv_sti_3CBE_1

description: Library name: Sample 26


title: αInv_sti_3CBE_3

description: Library name: Sample 25

source_name: AID-/-; Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: αInv_sti_3CBE_2

description: Library name: Sample 24


title: α_3CBEInv_sti_3RR_1

description: Library name: Sample 20


title: α_3CBEInv_sti_3CBE_3

description: Library name: Sample 28


title: αInv_sti_3CBE_1

description: Library name: Sample 23


title: α_3CBEInv_sti_3RR_3

description: Library name: Sample 22


title: αInv_sti_3RR_1

description: Library name: Sample 17


title: αInv_sti_3RR_3

description: Library name: Sample 19


title: αInv_sti_iEμ_3

description: Library name: Sample 13


title: αInv_sti_iEμ_2

description: Library name: Sample 12


title: α_3CBEInv_sti_iEμ_1

description: Library name: Sample 14


title: α_3CBEInv_sti_iEμ_3

description: Library name: Sample 16


title: αInv_sti_iEμ_1

description: Library name: Sample 11


title: CH12F3PO_sti_3RR_1

description: Library name: Sample 7

source_name: AID-/-; non-coding IgH VH-3'BCEs deletion


title: γ3_αInv_sti_iEμ_3

description: Library name: Sample 6

source_name: AID-/-; γ3-α inversion in non-coding IgH VH-3'BCEs deletion cells


title: γ3_αInv_sti_iEμ_2

description: Library name: Sample 5


title: CH12F3PO_sti_3RR_2

description: Library name: Sample 8


title: αInv_sti_3RR_2

description: Library name: Sample 18


title: α_3CBEInv_sti_iEμ_2

description: Library name: Sample 15


title: γ3_αInv_sti_iEμ_1

description: Library name: Sample 4


title: CH12F3PO_sti_iEμ_3

description: Library name: Sample 3


title: CH12F3PO_sti_iEμ_1

description: Library name: Sample 1


title: γ3_αInv_sti_3RR_1

description: Library name: Sample 9


title: testicular cells, wind control at 30 hrs, biol rep 8

city: Ottawa

first: Jeffrey

last: Ethier

state: Ontario

address: 75 Laurier Ave E

department: Biology

country: Canada

institute: University of Ottawa

description: Library name: W_30_8

data_processing:
De novo assembly was produced by LC Sciences. Cutadapt 45 and custom Perl scripts (https://www.perl.org/about.html) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was then verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
De novo assembly of the transcriptome was performed with Trinity 2.4.0 46. Trinity groups transcripts into clusters, loosely defined as a ‘gene’, based on shared sequence content.
Assembly: De novo assembly
Supplementary files format and content: xlsx files include raw counts and TPM each all samples

organism: Pseudacris maculata

source_name: testicular cells

extract_protocol:
total RNA was purified from the homogenates using NucleoZOL reagents with NucleoSpin RNA columns (Macherey-Nagel, Germany). RNA concentrations were measured with a Qubit 4 Fluorometer (Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity (RIN) was assessed using an Agilent 4150 TapeStation system (Agilent Technologies, Inc., Santa Clara, CA, USA).
RNA sequencing library was performed by LC Sciences Inc. (https://lcsciences.com, Houston, TX, USA) and was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

value: testicular cells

value: wind


title: ZH11-BM-H3K27me3-2

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: Library name: ZH11-BM-H3K27me3-2

data_processing:
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Library strategy: CUT&Tag

organism: Oryza sativa Japonica Group

source_name: Bicellular microspore

growth_protocol: For field cultivation, the plants were grown in Wuhan during summer seasons under standard agricultural practices. Seedlings were transplanted to the field in early May and harvested in October. For greenhouse experiments, germinated rice seedlings were planted in soil-filled containers and grown under controlled conditions with a 14-h light/10-h dark cycle at 32°C (light) and 26°C (dark). Tillers of rice plants at an appropriate developmental stage were harvested for collection of spikelets. The collected spikelets were used for phenotypic analysis and isolation of male germ cells.

extract_protocol:
For collection of tetrads and microspores, when tillers flag leaf collar and penultimate leaf collar aligned spikelets of 0.4-0.6 cm length were taken. Like extracting meiocytes, anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with tetrad shapes were collected as tetrads. Cells with single, free-floating state and have not formed cell walls were collected as microspores.For collection of mature unicellular microspores, when tillers flag leaf auricle was about 5 cm above the auricle of the penultimate leaf, fresh spikelets > 0.6 cm were collected. At this stage the color of the spikelets is still white. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct germination pores and having formed cell walls are collected as unicellular microspores.For collection of bicellular microspores, spikelets turning greener in color were taken. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct large vacuoles, two nuclei, and thickened pollen walls are collected as bicellular microspores.For collection of mature pollen, tillers green spikelets were taken. At this point, the anthers have developed into yellow color. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. The cells that are distinctly filled with starch are collected as pollen.A differential centrifugation isolation method was used to separate sperm from whole rice anthers.
Isolation and purification of mRNA from different types of cells were performed using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat. # N712). The RNA-seq libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. # TD502) and sequenced on Illumina HiSeq 6000. For rice in SY63 backgrounds, we used single male germ cell to construct the transcriptome library. We used approximately 100-200 male germ cells to construct the transcriptome library.BS-seq libraries were constructed using reported protocol Clark et al (2017). About 400–500 male germ cells were pooled for each replicate bisulfite seq library construction.The CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat. # TD903) and sequenced on Illumina HiSeq 6000. We used approximately 10,000 male germ cells to construct the CUT&Tag library by male germ cell isolation technology. The male germ cells were lysed with 200 µL Nuclear extraction buffer 2 (NEB2) (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1× protease inhibitor), and the nuclei pellet was resuspended in 100 µL wash buffer (from the TD903 kit) for library construction. About 100,000 sperm cells were pooled for each replicate CUT&Tag library construction. About 100,000–200,000 seedling cell nuclei were pooled for each replicate CUT&Tag library construction.For ATAC-seq library construction, the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat. # TD711) was used to prepare libraries for different types of cells. Using the same number of cells as for CUT&Tag, we isolated approximately 10,000 male germ cells to construct the ATAC-seq library. Approximately 100,000 sperm cells and 100,000–200,000 seedling cell nuclei were pooled for each replicate ATAC-seq library construction.

value: Bicellular microspore


title: sdg723-Me-H3K4me3-2

description: Library name: sdg723-Me-H3K4me3-2

source_name: Meiocyte

value: Meiocyte


title: Iγ3_PS_Iα_1

description:
Library name: Sample 71
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)


title: Iγ3_PS_Iα_2

description:
Library name: Sample 72
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells


title: sdg723-Me-H3K4me3-1

description: Library name: sdg723-Me-H3K4me3-1


title: Iγ3_FS_Iα_1

description:
Library name: Sample 65
Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: γ3_αInv_sti_3RR_2

description: Library name: Sample 10


title: Iγ3_PS_Cα_2

description:
Library name: Sample 69
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3_FS_Iα_2

description:
Library name: Sample 66
Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: testicular cells, wind control at 30 hrs, biol rep 5

description: Library name: W_30_5

value: WT


title: Iγ3_FS_Cα_3

description:
Library name: Sample 64
Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3_PS_Cα_1

description:
Library name: Sample 68
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: testicular cells, wind control at 30 hrs, biol rep 3

description: Library name: W_30_3


title: Iγ3_PS_Iα_3

description:
Library name: Sample 73
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions  in αInv cells


title: testicular cells, wind control at 30 hrs, biol rep 4

description: Library name: W_30_4


title: Iγ3_FS_Iα_3

description:
Library name: Sample 67
Cγ3-Cα deletion while retaining the full-length Sγ3 and Sα regions in αInv cells


title: Iγ3_FS_Cα_2

description:
Library name: Sample 63
Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: sdg701-Me-H3K4me3-1

description: Library name: sdg701-Me-H3K4me3-1


title: Iγ3_FS_Cα_1

description:
Library name: Sample 62
Cγ3-Iα deletion while retaining the full-length Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: Iγ3_PS_Cα_3

description:
Library name: Sample 70
Sγ3-Sα deletion while retaining partial Sγ3 and Sα regions in non-coding IgH VH-3'BCEs deletion cells


title: testicular cells, wind control at 30 hrs, biol rep 7

description: Library name: W_30_7


title: α_3CBEInv_αΔ_6

description:
Library name: Sample 61
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: α_3CBEInv_αΔ_5

description:
Library name: Sample 60
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: testicular cells, wind control at 30 hrs, biol rep 6

description: Library name: W_30_6


title: α_3CBEInv_αΔ_4

description:
Library name: Sample 59
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: sdg701-Me-H3K4me3-2

description: Library name: sdg701-Me-H3K4me3-2


title: α_3CBEInv_αΔ_3

description:
Library name: Sample 58
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: testicular cells, wind control at 30 hrs, biol rep 2

description: Library name: W_30_2


title: testicular cells, wind control at 30 hrs, biol rep 1

description: Library name: W_30_1


title: testicular cells, wind control at 24 hrs, biol rep 8

description: Library name: W_24_8


title: α_3CBEInv_6

description:
Library name: Sample 55
Cα-3'CBE inversion in Iα-Cα inversion cells


title: CH12F3PO_sti_iEμ_2

description: Library name: Sample 2


title: CBFA2T2-KD_3

city: Ube

first: MITSUKAI

last: FUJIMOTO

state: Yamaguchi

address: 1-1-1 Minami-Kogushi

department: Graduate School of Medicine

country: Japan

institute: Yamaguchi University

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S Array  human. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Human melanoma MeWo cells

label_protocol: Biotinylated cDNA were prepared from 100 ng total RNA with WT PLUS Reagent Kit (Thermo Fisher).

growth_protocol: DMEM containing 10% fetal boviine serum at 37C

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: No

value: Human melanoma MeWo cells


title: α_3CBEInv_αΔ_1

description:
Library name: Sample 56
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: testicular cells, wind control at 24 hrs, biol rep 6

description: Library name: W_24_6


title: testicular cells, wind control at 24 hrs, biol rep 7

description: Library name: W_24_7


title: α_3CBEInv_4

description:
Library name: Sample 53
Cα-3'CBE inversion in Iα-Cα inversion cells


title: α_3CBEInv_5

description:
Library name: Sample 54
Cα-3'CBE inversion in Iα-Cα inversion cells


title: testicular cells, wind control at 24 hrs, biol rep 5

description: Library name: W_24_5


title: α_3CBEInv_3

description:
Library name: Sample 52
Cα-3'CBE inversion in Iα-Cα inversion cells


title: α_3CBEInv_αΔ_2

description:
Library name: Sample 57
Iα-Cα deletion in Cα-3'CBE inversion and Iα-Cα inversion cells


title: αInv_7

description:
Library name: Sample 48
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells

value: aInv


title: αInv_8

description:
Library name: Sample 49
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: γ3IRD_3

description:
Library name: Sample 46
intergenic regions deletion between Cγ3 and Cμ  in Iα deletion cells


title: CBFA2T2-KD_2


title: α_3CBEInv_2

description:
Library name: Sample 51
Cα-3'CBE inversion in Iα-Cα inversion cells


title: testicular cells, wind control at 24 hrs, biol rep 4

description: Library name: W_24_4


title: HSF1-KD_2

description: Gene expression data from MeWo cells treated with shRNA-mediated knockdown of HSF1


title: α_3CBEInv_1

description:
Library name: Sample 50
Cα-3'CBE inversion in Iα-Cα inversion cells


title: testicular cells, wind control at 24 hrs, biol rep 3

description: Library name: W_24_3


title: γ3Inv_γ3Inv_2

description:
Library name: Sample 42
γ3 local inversion in γ3 inversion to next to Cμ cells


title: γ3IRD_2

description:
Library name: Sample 45
intergenic regions deletion between Cγ3 and Cμ  in Iα deletion cells


title: testicular cells, wind control at 24 hrs, biol rep 2

description: Library name: W_24_2


title: γ3Inv_3

description:
Library name: Sample 40
γ3 inversion to next to Cμ in Iα deletion cells


title: CBFA2T2-KD_1


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, female - rep3

first: Adam

last: Davidovich

state: Maryland

address: 855 N. Wolfe Street

institute: Johns Hopkins University

description: Library name: 3719-116M

data_processing:
ONT reads were canonical and modified base (5mCG_5hmCG) called using the super high accuracy model of Dorado (v0.8.3).
Basecalled reads were aligned to the CC019 and CC037 reference genomes separately using MiniMap2 (v2.28) and reads with a MAPQ of < 20 were filtered.
Aligned reads were phased separately with CC019 and CC037 as the reference genomes using WhatsHap (v2.3) with SNPs between CC019 and CC037 identified via MUMmer4 (v4.0.0rc1).
Methylation data was extracted from the phased BAM files using the modkit (v0.4.1) pileup command with strain-specific reference genomes provided.
Assembly: CC019 and CC037 reference genomes from the Collaborative Cross Graphical Genome (v2.0).
Supplementary files format and content: Modkit bedMethyl file with phased CC019 allele-specific methylation information for each CpG in each sample (zero-based, half-open).
Supplementary files format and content: Modkit bedMethyl file with phased CC037 allele-specific methylation information for each CpG in each sample (zero-based, half-open).

source_name: Muscle

extract_protocol:
High molecular weight (HMW) DNA was extracted from ~35mg of flash-frozen right femoral muscle using the Nanobind PanDNA Kit (PacBio SKU 103-260-000) following to the manufacturer’s instructions. Homogenization was performed using the TissueRuptor II (Qiagen Cat. 9002755) at maximum speed for 10s.
DNA was sheared to 20-30kb. Libraries were prepared using Ligation Sequencing Kit LSK114 and sequenced on R10.4.1 flow cells.

value: Muscle

value: F1:CC037/TauUnc x CC019/TauUnc

value: female

value: 4 months


title: testicular cells, wind control at 24 hrs, biol rep 1

description: Library name: W_24_1


title: SCR_3

description: Gene expression data from MeWo cells treated with scrambled shRNA (SCR)

value: SCR (Control)


title: γ3Inv_γ3Inv_3

description:
Library name: Sample 43
γ3 local inversion in γ3 inversion to next to Cμ cells

value: aCD40/IL4/TGFb stimulation


title: γ3Inv_γ3Inv_1

description:
Library name: Sample 41
γ3 local inversion in γ3 inversion to next to Cμ cells


title: testicular cells, low chorus at 30 hrs, biol rep 8

description: Library name: L_30_8

value: low chorus


title: γ3Inv_2

description:
Library name: Sample 39
γ3 inversion to next to Cμ in Iα deletion cells


title: HSF1-KD_3


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, female - rep2

description: Library name: 3719-115M


title: Muscle, F1: CC037/TauUnc x CC019/TauUnc, female - rep1

description: Library name: 3719-112M

value: 5 months


title: αInv_6

description:
Library name: Sample 47
Iα-Cα inversion in non-coding IgH VH-3'BCEs deletion cells


title: HSF1-KD_1