title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, small RNA-seq, replicate 2

city: Tianjin

first: Shuangshuang

last: Pu

state: China

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases Institute of Hematology

description:
Library name: Sample 68
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-T2

data_processing:
Raw paired-end reads were processed using fastp v0.23.1. Read pairs were removed when either read contained adapter contamination, more than 10% undetermined bases, or more than 50% bases with Phred quality scores below 5. Clean reads were aligned to the Mus musculus GRCm38/mm10 reference genome using HISAT2. Alignment files were converted to BAM format, name-sorted, and filtered to remove unmapped reads using SAMtools. Gene-level unnormalized read counts were generated using HTSeq-count with the Ensembl Mus musculus GRCm38.101 annotation.
Raw single-end reads were processed to remove reads containing adapter contamination, poly-N sequences, homopolymeric sequences, low-quality bases, or reads lacking the expected 3′ adapter or insert sequence. Clean reads within the selected small-RNA length range were retained for downstream analysis. Clean reads were mapped to the Mus musculus GRCm38/mm10 reference genome using Bowtie. Seed-based alignment was performed using a 20-nt seed, allowing no more than one mismatch within the seed region. Mapped reads were annotated against known mouse miRNA sequences in miRGeneDB 2.1 and used to quantify known miRNAs.
Assembly: GRCm38/mm10
Supplementary files format and content: 32D_H19_Adar_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A.
Supplementary files format and content: ckit_h19_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for 12 bulk RNA-seq libraries generated from primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant.
Supplementary files format and content: AN_GN_TN_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles.
Supplementary files format and content: miRNA_pulldown_raw_counts.tsv.gz contains gene-level unnormalized read counts for 12 RNA-seq libraries generated from input and biotinylated miRNA pulldown fractions of 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics.
Supplementary files format and content: ki67_eGFP_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for six bulk RNA-seq libraries generated from steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs.
Supplementary files format and content: miRNA_RCadj_libraryRPM.tsv.gz contains reverse-complement-adjusted miRNA abundance values for 21 small RNA-seq libraries. The matrix includes 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A, and primary mouse c-Kit-positive cells expressing empty vector, H19-A, H19-G, or H19-T.

source_name: bone marrow

growth_protocol: 32D and 32D-LV-H19 mouse myeloid progenitor cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 10 ng/mL recombinant mouse interleukin-3, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Primary mouse c-Kit-positive hematopoietic progenitor cells were isolated from bone marrow by magnetic enrichment using CD117 MicroBeads (Miltenyi Biotec). Cells were cultured in serum-free expansion medium supplemented with 100 ng/mL stem cell factor, 100 ng/mL thrombopoietin, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Mice were maintained under specific-pathogen-free conditions. Bone marrow cells were collected from 8- to 10-week-old female mice. LT-HSCs were identified and purified by fluorescence-activated cell sorting using the Lin⁻Sca-1⁺c-Kit⁺CD34⁻Flt3⁻ phenotype. In Ki67-eGFP reporter mice, Ki67-eGFP-negative LT-HSCs were defined as quiescent cells, whereas Ki67-eGFP-positive LT-HSCs were defined as cycling cells.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. Samples were treated with DNase I to remove residual genomic DNA. For miRNA pulldown experiments, RNA was extracted separately from the input lysate and the streptavidin-enriched pulldown fraction using TRIzol reagent. RNA concentration was determined using a Qubit fluorometer or NanoDrop spectrophotometer. RNA integrity was evaluated using an Agilent RNA analysis system when sample yield permitted.
For conventional bulk RNA-seq, libraries were prepared from 200 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L). Poly(A)-positive RNA was enriched using poly-T oligo-attached magnetic beads, fragmented, reverse-transcribed, adapter-ligated, and PCR-amplified according to the manufacturer’s instructions. For miRNA pulldown RNA-seq, libraries were prepared from RNA recovered from the corresponding input and pulldown fractions using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were generated using the same poly(A) enrichment, fragmentation, reverse-transcription, adapter-ligation, and PCR-amplification workflow. Conventional bulk RNA-seq and miRNA pulldown RNA-seq libraries were sequenced using a paired-end 150-bp strategy on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform, as specified for each sample. For small RNA-seq, libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300L). Following sequential 3′- and 5′-adapter ligation, reverse transcription, and PCR amplification, library fragments containing 18–40-nt inserts were size-selected. Qualified libraries were sequenced using a single-end 50-bp strategy on an Illumina NovaSeq 6000.

treatment_protocol: For ADAR1-dependent experiments, 32D-LV-H19 cells were transduced with lentiviral vectors expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A. Cells were collected 48 h after transduction. For H19 allele-dependent experiments, primary mouse c-Kit-positive cells were transduced with lentiviral vectors expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant. GFP-positive transduced cells were purified by fluorescence-activated cell sorting before RNA extraction. For inflammatory-stress experiments, H19-A, H19-G, and H19-T mice carrying the Ki67-eGFP reporter were administered polyinosinic acid [poly(I)] at 10 mg/kg. Bone marrow was collected 24 h after treatment, and Ki67-eGFP-negative LT-HSCs were purified by fluorescence-activated cell sorting. For miRNA pulldown experiments, 32D cells were transfected with a biotinylated scrambled-control miRNA mimic, biotinylated unedited wild-type miR-675-3p mimic, or biotinylated edited miR-675-3p mimic. Cells were harvested 48 h after transfection. An aliquot of each cell lysate was retained as the input fraction, and biotinylated miRNA-associated RNA complexes were isolated using streptavidin-coated beads. Steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs were isolated without additional experimental treatment.

value: bone marrow

value: wild type

value: lentiviral transduction


title: Rh4 Clone, P3F1-FLAG Flow Screen, ARMS sgRNA Library, High Population, Rep1

status: Public on Aug 04 2026

type: SRA

city: Durham

first: Christopher

middle: David

last: Delaney

state: NC

address: 308 Research Drive, LSRC C131

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University School of Medicine

description:
Library name: Library 24
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_HighPopulation_Rep1

library_source: genomic

data_processing:
Raw FASTQ sequencing files were first quality tested with FastQC (RRID:SCR_014583). Read files were then merged across flow cell lanes when applicable.
The MAGeCK Count function from the MAGeCK pipeline (RRID:SCR_025016) was used to map sequences to sgRNA read counts.
In all MAGeCK analyses, read counts were normalized to a defined list of non-targeting control sgRNAs unique to each library using the Control normalization method. To obtain Beta (essentiality) scores, the MAGeCK maximum likelihood estimation (MLE) function from the MAGeCK VISPR pipeline was used.
For the Genome-scale screens, 2D and 3D Beta scores were obtained from MAGeCK MLE using Time Final samples compared to Plasmid Library samples. For the custom library essentiality screens, the four FP cell lines were merged and Beta scores were obtained from MAGeCK MLE using Time Final samples compared to Plasmid Library samples. The same analysis was performed separately for the two FN cell lines. For the PAX3::FOXO1-based flow screen, the P3F1 Depletion Score was equal to the Beta score from MAGeCK MLE using the sgRNA frequencies from bottom 10% population compared to the top 10% population. For the CKM-based flow screen, the four FP cell lines were merged and the CKM Depletion Score was equal to the Beta score from MAGeCK MLE using the sgRNA frequencies from bottom 10% population compared to the top 10% population. For the FANCM exon tiling screen, control normalized sgRNA counts were obtained from MAGeCK Count for the Rh4 Clone and RD cell lines and the Log10-Fold Change (LFC) of Rh4 Clone / RD normalized read counts was smoothened with a 0.1-weighted moving average in JMP Pro Version 17.0.0. This value was then standardized to compare relative depletion and plotted as Standardized Relative sgRNA Depletion (FP vs FN Cells).
Assembly: sgRNA reads were mapped to sgRNA library files
Supplementary files format and content: Tab-delimited texts files of  mapped sgRNA read counts
Supplementary files format and content: Included for each relevant screen are MACeCK-MLE output files with Beta (essentiality) scores and associated signficance
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: All cells were maintained in a humidified incubator at 37C with 5% CO2. Cells were grown in RPMI 1640 (Gibco) medium with 10% fetal bovine serum (FBS, VWR) and 1% penicillin-streptomycin (P/S, Gibco).

extract_protocol:
For flow-based screens, collected cells were subjected to reverse-crosslinking and genomic DNA extraction using the Arcturus PicoPure DNA Extraction Kit (ThermoFisher). For the growth-based screens, Genomic DNA was extracted from cell pellets using the Quick-DNA Midiprep Plus Kit (Zymo Research) or DNeasy Blood & Tissue Kit (Qiagen).
Amplification of the sgRNA barcodes and indexing of each sample was performed via 2-step PCR as previously described using the NEBNext Ultra II Q5 Master Mix (NEB) (12). Amplified libraries were run on a 2% agarose gel and purified by QIAquick Gel Extraction Kit (Qiagen). Each DNA sample was quantified using the Quant-iT dsDNA High Sensitivity Assay Kit (ThermoFisher).

treatment_protocol: Cells were grown as detailed in the manuscript and pellets were harvested for genomic DNA.

tag: tissue

value: cell line

tag: cell line

value: Rh4 Clone

tag: cell type

value: Rhabdomyosarcoma

tag: genotype

value: Fusion-Positive

tag: treatment

tag: screen

value: P3F1-FLAG Flow-Based Screen


title: RNA-seq_dTAG-MED26_HS_DMSO_rep3

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

description: Library name: Sample 18

library_source: transcriptomic

data_processing:
Raw paired-end sequence reads were subjected to quality control using FastQC (v0.12.1). For ChIP-seq data, Adapter sequences were trimmed and reads were quality filtered using fastp (fastp 0.23.2). Processed reads were mapped to the human genome (GRCh38) using Bowtie2 (version 2.4.2 64-bit) with default parameters. Mapped reads were converted to sorted BAM files and indexed using SAMtools (1.16.1). Normalized genome coverage tracks were generated using bamCoverage with CPM normalization. Peaks were identified using MACS2 (macs2 2.2.7.1), followed by peak annotation and motif analysis using HOMER.
For RNA-seq data, Raw paired-end RNA-seq reads were first subjected to quality control using FastQC (v0.12.1). Adapter trimming and quality filtering were performed with fastp, generating trimmed paired-end FASTQ files. Cleaned reads were aligned to the human reference genome (GRCh38) using STAR (2.7.8a) with default parameters. The STAR index was generated based on the Homo sapiens GRCh38 primary assembly and the corresponding Ensembl gene annotation (release 112). Aligned reads were output as coordinate-sorted BAM files, which were subsequently indexed using SAMtools (samtools 1.16.1). Genome-wide coverage tracks were generated from the sorted BAM files using bamCoverage with CPM normalizationto produce bigWig files for visualization. Transcript and gene expression levels were quantified using RSEM (v1.3.1) based on the STAR transcriptome-aligned BAM files.
Assembly: GRCh38
Supplementary files format and content: BigWig

molecule: total RNA

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovin serum (FBS) and penicillin/streptomycin under 5% CO2 at 37 °C.

extract_protocol:
Total RNA was harvested using sepasol Sepasol-RNA I Super G and purified by phenol-chloroform extraction and ethanol precipitation method.
For ChIP, Cells were fixed with DSG for 30min and 1%PFA for 15min, after quenching and cell lysis, chromatin was sonimated using a Bioruptor Sonicator (30×30 s at maximum power, Diagenode, Denville, NJ).
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (rRNA Depletion Kit v2) (NEB#E7400L). 1µg of total RNA was used for the construction of sequencing libraries.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB#E7645L).

treatment_protocol: HCT116 cells were incubated at 43℃, 1hr for the HS treatment

value: colon cancer cells

value: WT

value: HS


title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, small RNA-seq, replicate 1

country: China

description:
Library name: Sample 67
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-T1

organism: Mus musculus

value: c-Kit-positive hematopoietic progenitor cells

tag: batch


title: Rh4 Clone, P3F1-FLAG Flow Screen, ARMS sgRNA Library, Low Population, Rep3

description:
Library name: Library 23
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_LowPopulation_Rep3


title: RNA-seq_dTAG-MED26_HS_DMSO_rep2

description: Library name: Sample 17


title: RNA-seq_dTAG-MED26_HS_DMSO_rep1

description: Library name: Sample 16


title: Rh4 Clone, P3F1-FLAG Flow Screen, ARMS sgRNA Library, Low Population, Rep2

description:
Library name: Library 22
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_LowPopulation_Rep2


title: H1

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

description:
Library name: H1
DAP-seq

data_processing:
Quality-filtered paired reads were mapped to the reference genome, and gene-level quantification was performed using featureCounts (Subread v2.0.1) against annotated features. The resulting count matrix was analyzed using DESeq2 (v1.40.2).
Assembly: Genome assembly ASM585424v1
Supplementary files format and content: The bed file for each DAP-seq displayed the TF binding sites. The counts txt files contained the gene expression counts for each RNA-seq.

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae

growth_protocol: LB at 37 °C

extract_protocol:
Total RNA was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen, # Gdp430) and depleted of rRNA using NEBNext® rRNA Depletion Kit (Bacteria) (NEB, #E7850).
Libraries were constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, #E7770L) and sequenced on the Illumina Xten platform.

value: Klebsiella pneumoniae

value: strain

value: genotype

value: ChIP antibody


title: RNA-seq_dTAG-MED26_NT_DMSO_rep3

description: Library name: Sample 15

value: NT


title: Rh4 Clone, P3F1-FLAG Flow Screen, ARMS sgRNA Library, Low Population, Rep1

description:
Library name: Library 21
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_LowPopulation_Rep1


title: G9

description:
Library name: G9
DAP-seq


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, small RNA-seq, replicate 1

description:
Library name: Sample 64
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-G1

value: bone marrow


title: SMS_CTR, ARMS sgRNA Library, Tf Sample, Rep2

description:
Library name: Library 20
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: SMS_CTR_ARMS_Tfinal_Rep2

value: Fusion-Negative

value: Custom sgRNA Essentiality


title: G8

description:
Library name: G8
DAP-seq


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, small RNA-seq, replicate 3

description:
Library name: Sample 63
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-A3

value: wild type

value: lentiviral transduction


title: RNA-seq_dTAG-MED26_NT_DMSO_rep1

description: Library name: Sample 13


title: SMS_CTR, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 19
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: SMS_CTR_ARMS_Tfinal_Rep1

value: cell line

value: Rhabdomyosarcoma


title: G7

description:
Library name: G7
DAP-seq


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, small RNA-seq, replicate 2

description:
Library name: Sample 62
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-A2


title: RNA-seq_HSF1-SA_HS_rep3

description: Library name: Sample 12

value: SA


title: RNA-seq_HSF1-SA_HS_rep2

description: Library name: Sample 11

value: colon cancer cells


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, small RNA-seq, replicate 1

description:
Library name: Sample 61
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-A1


title: RD, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 17
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: RD_ARMS_Tfinal_Rep1

value: RD


title: G5

description:
Library name: G5
DAP-seq

value: WT


title: Primary mouse c-Kit-positive cells expressing empty vector, small RNA-seq, replicate 3

description:
Library name: Sample 60
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EV3

value: c-Kit-positive hematopoietic progenitor cells


title: RNA-seq_HSF1-SA_HS_rep1

description: Library name: Sample 10

value: HS


title: G4

description:
Library name: G4
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Primary mouse c-Kit-positive cells expressing empty vector, small RNA-seq, replicate 2

description:
Library name: Sample 59
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EV2


title: RNA-seq_HSF1-SA_NT_rep3

description: Library name: Sample 9


title: Rh30, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 15
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh30_ARMS_Tfinal_Rep1

value: Fusion-Positive


title: G3

description:
Library name: G3
DAP-seq

value: genotype

value: ChIP antibody


title: Primary mouse c-Kit-positive cells expressing empty vector, small RNA-seq, replicate 1

description:
Library name: Sample 58
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EV1

value: bone marrow


title: RNA-seq_HSF1-SA_NT_rep2

description: Library name: Sample 8

value: NT


title: Rh28, ARMS sgRNA Library, Tf Sample, Rep2

description:
Library name: Library 14
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh28_ARMS_Tfinal_Rep2

value: Custom sgRNA Essentiality


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, small RNA-seq, replicate 3

description:
Library name: Sample 57
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EA-3

value: myeloid progenitor cell line

value: wild type

value: lentiviral transduction


title: Rh28, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 13
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh28_ARMS_Tfinal_Rep1

value: cell line

value: Rhabdomyosarcoma


title: G2

description:
Library name: G2
DAP-seq


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, small RNA-seq, replicate 2

description:
Library name: Sample 56
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EA-2


title: RNA-seq_HSF1-WT_HS_rep3

description: Library name: Sample 6

value: colon cancer cells


title: Rh4 Native, ARMS sgRNA Library, Tf Sample, Rep2

description:
Library name: Library 12
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh4Native_ARMS_Tfinal_Rep2

value: Rh4 Native


title: G19

description:
Library name: G19
DAP-seq

value: WT


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, small RNA-seq, replicate 1

description:
Library name: Sample 55
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-EA-1


title: RNA-seq_HSF1-WT_HS_rep2

description: Library name: Sample 5

value: HS


title: Rh4 Native, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 11
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh4Native_ARMS_Tfinal_Rep1


title: G20

description:
Library name: G20
DAP-seq

value: Klebsiella pneumoniae


title: RNA-seq_HSF1-SA_NT_rep1

description: Library name: Sample 7

value: SA


title: G18

description:
Library name: G18
DAP-seq

value: strain


title: 32D-LV-H19 cells expressing ADAR1 p110, small RNA-seq, replicate 3

description:
Library name: Sample 54
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-WT-3


title: RNA-seq_HSF1-WT_HS_rep1

description: Library name: Sample 4


title: Rh4 Clone, ARMS sgRNA Library, Tf Sample, Rep2

description:
Library name: Library 10
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh4Clone_ARMS_Tfinal_Rep2

value: Rh4 Clone

value: Fusion-Positive


title: G17

description:
Library name: G17
DAP-seq

value: genotype

value: ChIP antibody


title: 32D-LV-H19 cells expressing ADAR1 p110, small RNA-seq, replicate 2

description:
Library name: Sample 53
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-WT-2


title: RNA-seq_HSF1-WT_NT_rep3

description: Library name: Sample 3

value: NT


title: Rh4 Clone, ARMS sgRNA Library, Tf Sample, Rep1

description:
Library name: Library 9
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh4Clone_ARMS_Tfinal_Rep1

value: Custom sgRNA Essentiality


title: Rh4 Clone, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep2

description:
Library name: Library 28
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Clone_CKMScreen_LowPopulation_Rep2

value: CKM Flow-Based Screen


title: G16

description:
Library name: G16
DAP-seq


title: H15

description:
Library name: H15
DAP-seq


title: 32D-LV-H19 cells expressing ADAR1 p110, small RNA-seq, replicate 1

description:
Library name: Sample 52
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-WT-1

value: myeloid progenitor cell line

value: wild type

value: lentiviral transduction


title: Rh4 Clone, P3F1-FLAG Flow Screen, ARMS sgRNA Library, High Population, Rep3

description:
Library name: Library 26
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_HighPopulation_Rep3

value: cell line

value: Rhabdomyosarcoma

value: P3F1-FLAG Flow-Based Screen


title: RNA-seq_HSF1-WT_NT_rep2

description: Library name: Sample 2

value: colon cancer cells

value: WT


title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, small RNA-seq, replicate 3

description:
Library name: Sample 69
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-T3

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells


title: Rh4 Clone, 3D Culture, TKOv3 sgRNA Library, Tfinal Sample, Rep2

description:
Library name: Library 5
Column name in Rh4Clone_GenomeScaleScreen_sgRNA_ReadCounts.txt: Rh4Clone_3D_Tfinal_Rep2

value: Rh4 Clone

value: 3D Culture

value: Genome-Scale Essentiality


title: G15

description:
Library name: G15
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: ChIP antibody


title: 32D-LV-H19 cells expressing empty vector, small RNA-seq, replicate 3

description:
Library name: Sample 51
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-Ctrl-3

value: myeloid progenitor cell line


title: H11

description:
Library name: H11
DAP-seq


title: RNA-seq_HSF1-WT_NT_rep1

description: Library name: Sample 1

value: NT


title: H10

description:
Library name: H10
DAP-seq


title: Rh4 Clone, 3D Culture, TKOv3 sgRNA Library, Tfinal Sample, Rep1

description:
Library name: Library 4
Column name in Rh4Clone_GenomeScaleScreen_sgRNA_ReadCounts.txt: Rh4Clone_3D_Tfinal_Rep1

value: Fusion-Positive


title: G14

description:
Library name: G14
DAP-seq


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, small RNA-seq, replicate 3

description:
Library name: Sample 66
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-G3

value: wild type

value: lentiviral transduction


title: 32D-LV-H19 cells expressing empty vector, small RNA-seq, replicate 2

description:
Library name: Sample 50
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-Ctrl-2


title: Ribo_Cell_3

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: Ribo_Cell_3

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts
Library strategy: Ribo-Seq

source_name: HeLa

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

value: HeLa

tag: lab

value: Iwasaki


title: 32D-LV-H19 cells expressing empty vector, small RNA-seq, replicate 1

description:
Library name: Sample 49
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-Ctrl-1


title: Rh4 Clone, 2D Culture, TKOv3 sgRNA Library, Tfinal Sample, Rep2

description:
Library name: Library 3
Column name in Rh4Clone_GenomeScaleScreen_sgRNA_ReadCounts.txt: Rh4Clone_2D_Tfinal_Rep2

value: cell line

value: Rhabdomyosarcoma

value: 2D Culture


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, small RNA-seq, replicate 2

description:
Library name: Sample 65
Column name in miRNA_RCadj_libraryRPM.tsv.gz: miRNA-G2

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells


title: G13

description:
Library name: G13
DAP-seq

value: WT


title: Ribo_Cell_2

description: Library name: Ribo_Cell_2


title: Rh4 Clone, 2D Culture, TKOv3 sgRNA Library, Tfinal Sample, Rep1

description:
Library name: Library 2
Column name in Rh4Clone_GenomeScaleScreen_sgRNA_ReadCounts.txt: Rh4Clone_2D_Tfinal_Rep1

value: Rh4 Clone

value: Genome-Scale Essentiality


title: RNA-seq_dTAG-MED26_NT_DMSO_rep2

description: Library name: Sample 14

value: colon cancer cells


title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, replicate 3

description:
Library name: Sample 21
Column name in ckit_h19_gene_count_matrix.tsv.gz: T3


title: Ribo_Cell_1

description: Library name: Ribo_Cell_1


title: G12

description:
Library name: G12
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: ChIP antibody


title: DD1130

type: genomic

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: genomic DNA was hybridized to Agilent 244K or 1M oligonucleotide arrays per manufacturer's instructions in the presence of a DNA reference set (Human Genomic DNA from blood (buffy coat); Roche Applied Science)

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C at 3 microns per pixel resolution in two-color mode. Images were extracted using Agilent Feature Extraction software version 10.2.1.3.

data_processing:
Array comparative genomic hybridization (aCGH) was performed using Agilent 244K or 1M arrays and analyzed using the RAE pipeline as previously reported.(14, 28).
progV2aCGHMatrixTable_260619_v2__final.csv: Log2 ratio of Cy5 (sample) to Cy3 (reference) signal intensities, background-corrected and dye-normalized by Agilent Feature Extraction software.

source_name: Human Genomic DNA, blood (buffy coat), Roche Applied Science

label_protocol: per Agilent protocols

growth_protocol: not applicable

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

treatment_protocol: not applicable

value: blood (buffy coat)

source_name: surgical specimen

tag: tumor class

value: Dedifferentiated

value: retroperitoneal


title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, replicate 2

description:
Library name: Sample 20
Column name in ckit_h19_gene_count_matrix.tsv.gz: T2

value: wild type

value: lentiviral transduction


title: Rh4 Clone Cells, ishP3F1, Day 7, Rep 3

description:
Library name: Sample 6
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishP3F1_D7_Rep3

data_processing:
Raw FASTQ files were first validated and trimmed with TrimGalore (RRID:SCR_011847).
Preprocessed FASTQ files were indexed against the GRCh38 human genome assembly using HISAT2 (RRID:SCR_015530).
Output SAM files were converted to BAM files, indexed, and sorted using SAMtools (RRID:SCR_002105).
FeatureCounts (RRID:SCR_012919) was used to get raw gene read counts, which are presented here as processed data files.
Processed data files were then normalized and processed for differential gene expression using the DESeq2 (RRID:SCR_015687) pipeline in R version 4.4.2.. Log-fold change values from DESeq2 were analyzed with gene set enrichment analysis (GSEA) via ClusterProfiler (RRID:SCR_016884) or FGSEA (RRID:SCR_020938) in R version 4.4.2.
Assembly: GRCh38 human genome assembly
Supplementary files format and content: tab-delimited text files include raw counts for each sample from FeatureCounts output

molecule: polyA RNA

growth_protocol: Rh4 Clone cell lines were maintained in a humidified incubator at 37C with 5% CO2. Cells were grown in RPMI 1640 (Gibco) medium with 10% fetal bovine serum (FBS, VWR) and 1% penicillin-streptomycin (P/S, Gibco). FBS was switched to tetracycline-free (tet-free) FBS (Cytiva) for doxycycline induction.

extract_protocol:
Cell pellets were thawed on ice, and RNA was homogenized and purified using the Qiashredder and RNeasy Kits (Qiagen). For Rh4 Clone parental and IR-treated samples, cell pellets were suspended in Zymo DNA/RNA shield.
Purified RNA was submitted for poly(A) enrichment and library preparation using the KAPA mRNA HyperPrep Kit (Roche), or lysed cell pellets were submitted to Plasmidsaurus for sequencing.

treatment_protocol: Rh4 Clone cells were made to stably express inducible shRNA constructs as indicated. Cells were prepared in triplicate for each condition, treated with Dox at 100 ng/mL for 7 days, or 150 ng/mL for 2 days, and then were pelleted and frozen at -80C. For irradiation, treated cells were exposed to 5 Gy of irradiation and harvested 24 hrs afterwards.

value: cell line

value: Rhabdomyosarcoma

value: PAX3::FOXO1 knockdown

value: 100 ng/mL Doxycycline

tag: time

value: Day 7


title: G11

description:
Library name: G11
DAP-seq

value: WT


title: Ribo_mBR_3

description: Library name: Ribo_mBR_3

value: HeLa

value: Iwasaki


title: Rh4 Clone Cells, ishP3F1, Day 7, Rep 2

description:
Library name: Sample 5
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishP3F1_D7_Rep2

value: Rh4 Clone


title: G10

description:
Library name: G10
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Ribo_mBR_2

description: Library name: Ribo_mBR_2


title: Primary mouse c-Kit-positive cells expressing H19-T editing-resistant, replicate 1

description:
Library name: Sample 19
Column name in ckit_h19_gene_count_matrix.tsv.gz: T1

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells


title: Ribo_mBR_1

description: Library name: Ribo_mBR_1


title: Rh4 Clone Cells, ishP3F1, Day 7, Rep 1

description:
Library name: Sample 4
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishP3F1_D7_Rep1


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, replicate 3

description:
Library name: Sample 18
Column name in ckit_h19_gene_count_matrix.tsv.gz: G3


title: Rh4 Clone Cells, ishNTC, Day 7, Rep 3

description:
Library name: Sample 3
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D7_Rep3


title: G1

description:
Library name: G1
DAP-seq

value: genotype

value: ChIP antibody


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, replicate 2

description:
Library name: Sample 17
Column name in ckit_h19_gene_count_matrix.tsv.gz: G2

value: wild type


title: Rh4 Native Cells, ishFANCM, pRPA32 (WCE), Rep3

description:
Library name: Library 18
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

data_processing:
Raw FASTQ sequencing files were first quality tested with FastQC (RRID:SCR_014583) and reads were then merged across flow cell lanes. Merged FASTQ files were aligned to the GRCh38 human genome assembly using BWA (RRID:SCR_010910).
Output SAM files were converted to BAM files, indexed, and sorted using SAMtools (RRID:SCR_002105).
Duplicates reads were marked and removed with PICARD (RRID:SCR_006525) and bigWig (bW) files were generated from the bamCoverage function in Deeptools (RRID:SCR_016366) with the following settings: bin size of 20, RPKM normalization, smooth length of 60, extend reads to 150, and center reads.
For visualized tracks, bW sample files were normalized by ratio to respective WCE bW files using the bigwigCompare function in Deeptools, and representative replicate files were depicted using the Integrative Genomics Viewer (IGV, (RRID:SCR_011793)).
For pRPA32 samples, MACS2 (RRID:SCR_013291) was used to call peaks relative to WCE samples and to generate narrowPeak files. To obtain the genomic loci enriched in pRPA32 for ishFANCM samples relative to ishFANCM-SMS controls, DiffBind (RRID:SCR_012918) was used. Genomic loci enriched in pRPA32 signal were mapped to genes and gene Over Representation Analysis (ORA) was performed with ClusterProfiler (RRID:SCR_016884).
Assembly: GRCh38 human genome assembly
Supplementary files format and content: BigWig files normalized to WCE, or Input

source_name: Rh4 Native

growth_protocol: Rh4 Native cells were maintained in a humidified incubator at 37C with 5% CO2. Cells were grown in RPMI 1640 (Gibco) medium with 10% fetal bovine serum (FBS, VWR) and 1% penicillin-streptomycin (P/S, Gibco). FBS was switched to tetracycline-free (tet-free) FBS (Cytiva) for doxycycline induction.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. After quenching and cell lysis, chromatin was sheared with a Covaris ME220 machine. Sheared chromatin was incubated with anti-H3K29Ac antibody (Active Motif, #39133) or anti-pRPA32-S33 antibody (Bethyl, #A300-246A).
For each replicate, DNA libraries were end prepared and adapter ligated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and indexed using the NEBNext Multiplex Oligos for Illumina (NEB) according to manufacturer recommendations. Amplified indexed libraries were quantified using the using the Quant-iT dsDNA High Sensitivity Assay Kit (ThermoFisher) and mixed in equimolar ratios for pooled library sequencing. Pooled library was sequenced at the Duke University Sequencing and Genomic Technologies Core Facility on a NovaSeq X Plus (Illumina) 1.5B flow cell with 150 bp paired-end sequencing.

treatment_protocol: Rh4 Native cells were made to stably express inducible shRNA constructs as indicated. Cells were prepared in triplicate for each condition, treated with Dox at 150 ng/mL for 2 days, and then crosslinked and frozen at -80C prior to chromain shearing.

value: Rh4 Native

value: FANCM knockdown

value: Doxycycline 150 ng/mL for 2 days

tag: chip antibody


title: Rh4 Clone Cells, ishNTC, Day 7, Rep 2

description:
Library name: Sample 2
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D7_Rep2

value: cell line

value: Rhabdomyosarcoma


title: RD, ARMS sgRNA Library, Tf Sample, Rep2

description:
Library name: Library 18
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: RD_ARMS_Tfinal_Rep2

value: RD

value: Fusion-Negative

value: Custom sgRNA Essentiality


title: G6

description:
Library name: G6
DAP-seq

value: WT


title: F9

description:
Library name: F9
DAP-seq


title: F8

description:
Library name: F8
DAP-seq


title: Primary mouse c-Kit-positive cells expressing H19-G edited-mimic, replicate 1

description:
Library name: Sample 16
Column name in ckit_h19_gene_count_matrix.tsv.gz: G1

value: lentiviral transduction


title: Rh4 Native Cells, ishFANCM, pRPA32 (ChIP), Rep3

description:
Library name: Library 17
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: Rh4 Clone Cells, ishNTC, Day 7, Rep 1

description:
Library name: Sample 1
Column name in Rh4Clone_P3F1_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D7_Rep1

value: Rh4 Clone

value: 100 ng/mL Doxycycline

value: Day 7


title: F7

description:
Library name: F7
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Rh4 Native Cells, ishFANCM, pRPA32 (WCE), Rep2

description:
Library name: Library 16
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, replicate 3

description:
Library name: Sample 15
Column name in ckit_h19_gene_count_matrix.tsv.gz: A3

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells


title: ND33947, HD, DMSO replicate 1

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and coefficients for conditions, sex, age, and BMI were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.1.
Assembly: Ensemble release 76
Supplementary files format and content: Tab delimited .txt file contains CPM for each sample

source_name: cell culture

extract_protocol:
Trizol extraction and total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 10ng of total RNA. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were treated from PID14 to PID30 with Raphin1 or DMSO.

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons

value: HTT CAG expansion

value: DMSO


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, replicate 2

description:
Library name: Sample 14
Column name in ckit_h19_gene_count_matrix.tsv.gz: A2

value: wild type


title: F6

description:
Library name: F6
DAP-seq

value: genotype

value: ChIP antibody


title: ND33947, HD, DMSO replicate 3


title: F5

description:
Library name: F5
DAP-seq


title: Rh4 Native Cells, ishFANCM, pRPA32 (WCE), Rep1

description:
Library name: Library 14
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Rhabdomyosarcoma

value: FANCM knockdown

value: Doxycycline 150 ng/mL for 2 days


title: Rh4 Native Cells, ishFANCM, pRPA32 (ChIP), Rep2

description:
Library name: Library 15
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: Primary mouse c-Kit-positive cells expressing wild-type editable H19-A, replicate 1

description:
Library name: Sample 13
Column name in ckit_h19_gene_count_matrix.tsv.gz: A1

value: lentiviral transduction


title: ND33947, HD, DMSO replicate 2


title: F4

description:
Library name: F4
DAP-seq

value: WT


title: Primary mouse c-Kit-positive cells expressing empty vector, replicate 3

description:
Library name: Sample 12
Column name in ckit_h19_gene_count_matrix.tsv.gz: EV3


title: Rh4 Native Cells, ishFANCM, pRPA32 (ChIP), Rep1

description:
Library name: Library 13
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: Control A3 (CA3)

city: Nakhon Ratchasima

first: Yongcai

last: Zhu

address: School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand

country: Thailand

institute: Suranaree University of Technology

description: Library name: CA3

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Low-quality and technical sequences were removed from the raw sequencing reads using Cutadapt version 1.9.1
Hisat2 version 2.0.1 was used to align the clean reads against the chicken reference genome, GRCg6a (GenBank Assembly ID: GCF_000002315.6).
Gene expression levels were estimated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using HTSeq version 0.6.1. The DESeq2 Bioconductor package was used for differential expression analysis between control and heat stress groups.
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: Column 1, gene_symbol; Column 2 - 7,   Sample_FPKM: FPKM of each gene; Column 8-13, Sample: read_count, count of each gene.

organism: Gallus gallus

source_name: Jejunal mucosa

extract_protocol:
Total RNA was harvested using  an RNeasy Mini Kit (Qiagen, Hilden, Germany). Three RNA pools were generated for each treatment from 12 hens, with each pool consisting of four individual jejunal mucosa samples. The pooled samples were utilized to create an RNA-seq library.
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Jejunal mucosa

value: Leuang Hang Kao breeder hen

value: Control (TN)


title: Primary mouse c-Kit-positive cells expressing empty vector, replicate 2

description:
Library name: Sample 11
Column name in ckit_h19_gene_count_matrix.tsv.gz: EV2

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells


title: Control A2 (CA2)

description: Library name: CA2


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (ChIP), Rep3

description:
Library name: Library 11
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: FANCM Seed-Matched-Control knockdown


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (WCE), Rep2

description:
Library name: Library 10
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, replicate 3

description:
Library name: Sample 9
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_EA-3

value: myeloid progenitor cell line


title: F2

description:
Library name: F2
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Control A1 (CA1)

description: Library name: CA1


title: Heat-sensitive3 (HS3)

description: Library name: HS3

value: SUT breeder hen

value: HS under heat stress


title: F19

description:
Library name: F19
DAP-seq

value: genotype

value: ChIP antibody


title: Heat-sensitive2 (HS2)

description: Library name: HS2


title: F18

description:
Library name: F18
DAP-seq


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (WCE), Rep1

description:
Library name: Library 8
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Rhabdomyosarcoma


title: Heat-sensitive1 (HS1)

description: Library name: HS1


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (ChIP), Rep1

description:
Library name: Library 7
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Doxycycline 150 ng/mL for 2 days


title: Heat-adopted3 (HA3)

description: Library name: HA3

value: HA under heat stress


title: F16

description:
Library name: F16
DAP-seq

value: WT


title: 32D-LV-H19 cells expressing ADAR1 p110, replicate 2

description:
Library name: Sample 5
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_WT-2

value: wild type

value: lentiviral transduction


title: Rh4 Native Cells, H3K27Ac (WCE), Rep3

description:
Library name: Library 6
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: Heat-adopted2 (HA2)

description: Library name: HA2

value: Jejunal mucosa

value: Leuang Hang Kao breeder hen


title: Rh4 Native Cells, H3K27Ac (ChIP), Rep3

description:
Library name: Library 5
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: H3K27Ac (Active Motif, #39133)


title: Heat-adopted1 (HA1)

description: Library name: HA1


title: 32D-LV-H19 cells expressing ADAR1 p110, replicate 1

description:
Library name: Sample 4
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_WT-1

value: myeloid progenitor cell line


title: 32D-LV-H19 cells expressing empty vector, replicate 3

description:
Library name: Sample 3
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_Ctrl-3


title: ND33947, HD, Raphin1 replicate 3

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons

value: HTT CAG expansion


title: F13

description:
Library name: F13
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Rh4 Native Cells, H3K27Ac (ChIP), Rep2

description:
Library name: Library 3
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.


title: ND33947, HD, Raphin1 replicate 1


title: F12

description:
Library name: F12
DAP-seq

value: genotype

value: ChIP antibody


title: 32D-LV-H19 cells expressing empty vector, replicate 1

description:
Library name: Sample 1
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_Ctrl-1


title: Rh4 Native Cells, H3K27Ac (WCE), Rep1

description:
Library name: Library 2
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Rhabdomyosarcoma


title: ND33947, HD, Raphin1 replicate 2


title: F11

description:
Library name: F11
DAP-seq


title: SH-3

city: Nanchang

first: Jing

last: Mao

address: No. 566, Xuefu Avenue

institute: The Second Affiliated Hospital of Nanchang University

description: Library name: sample6

data_processing:
QC (RseQC,v4.0.0) → Alignment (HISAT2,v2.1.0) → Quantification (htseq-count,v0.11.2).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to thed manufacturer's protocol.
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions.

value: cancer cells


title: Rh4 Native Cells, H3K27Ac (ChIP), Rep1

description:
Library name: Library 1
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: WT


title: GM04198, HD, DMSO replicate 2

value: DMSO


title: F10

description:
Library name: F10
DAP-seq


title: SH-2

description: Library name: sample5


title: Rh4 Clone Cells, ishFANCM, Day 2, Rep 3

description:
Library name: Sample 15
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_D2_Rep3

value: cell line

value: Rh4 Clone

value: FANCM knockdown

value: 150 ng/mL Doxycycline

value: Day 2


title: GM04198, HD, DMSO replicate 1

value: cell culture


title: F1

description:
Library name: F1
DAP-seq


title: SH-1

description: Library name: sample4


title: Rh4 Clone Cells, ishFANCM, Day 2, Rep 2

description:
Library name: Sample 14
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_D2_Rep2


title: GM04198, HD, DMSO replicate 3

value: Directly reprogrammed Medium Spiny Neurons


title: E8

description:
Library name: E8
DAP-seq


title: NC-3

description: Library name: sample3


title: Rh4 Clone Cells, ishFANCM, Day 2, Rep 1

description:
Library name: Sample 13
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_D2_Rep1


title: GM04198, HD, Raphin1 replicate 2

value: HTT CAG expansion


title: E7

description:
Library name: E7
DAP-seq

value: Klebsiella pneumoniae


title: Rh4 Clone Cells, ishFANCM_SMC, Day 2, Rep 3

description:
Library name: Sample 12
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_SMC_D2_Rep3

value: FANCM Seed-Matched-Control knockdown


title: NC-2

description: Library name: sample2


title: GM04198, HD, Raphin1 replicate 3


title: lncRNA_iPEDV_exo_1

status: Public on Aug 05 2026

city: nanjing

first: qiu

last: zhong

address: No. 1 Weigang, Xuanwu District

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
Library name: sample 4
iPEDV group, lncRNA-SEQ, replicate biosample 1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Sscrofa11.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

organism: Sus scrofa

source_name: IPEC-DQ

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: IPEC-DQ


title: NC-1

description: Library name: sample1


title: E6

description:
Library name: E6
DAP-seq

value: strain

value: genotype

value: ChIP antibody


title: Rh4 Clone Cells, ishFANCM_SMC, Day 2, Rep 2

description:
Library name: Sample 11
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_SMC_D2_Rep2

value: Rhabdomyosarcoma


title: GM04198, HD, Raphin1 replicate 1


title: E5

description:
Library name: E5
DAP-seq

value: WT


title: Naive3

city: Columbia

first: Rajiv

middle: R

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

description:
Library name: Sample 6
Gene count

data_processing:
Standard protocol using R-Programming
Quality check using FastQC
Read alignment using HISAT2
Gene counts using StringTie and StringTie Merge
Differential gene expression using DESeq2
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt files

source_name: Cornea

extract_protocol:
Total RNA was isolated from mouse corneas via RNeasy Mini Kit according to the manufacturer’s instructions (QIAGEN, Hilden, Germany). For each sample, a total of 2 μg of RNA was taken for RNA-seq library preparation.
RNA-seq library preparation via a KAPA Stranded RNA-Seq Library Prep Kit (Roche) using manufacturer's protocol

value: Cornea

tag: Sex

value: Male

tag: strain

value: Naïve


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (WCE), Rep3

description:
Library name: Library 12
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Doxycycline 150 ng/mL for 2 days


title: F3

description:
Library name: F3
DAP-seq


title: F20

description:
Library name: F20
DAP-seq


title: Primary mouse c-Kit-positive cells expressing empty vector, replicate 1

description:
Library name: Sample 10
Column name in ckit_h19_gene_count_matrix.tsv.gz: EV1

value: bone marrow

value: c-Kit-positive hematopoietic progenitor cells

value: wild type

value: lentiviral transduction


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, replicate 2

description:
Library name: Sample 8
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_EA-2

value: myeloid progenitor cell line


title: Rh4 Clone Cells, ishFANCM_SMC, Day 2, Rep 1

description:
Library name: Sample 10
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishFANCM_SMC_D2_Rep1

value: cell line

value: Rh4 Clone

value: FANCM Seed-Matched-Control knockdown

value: 150 ng/mL Doxycycline

value: Day 2


title: GM04196, HD, DMSO replicate 3

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons

value: HTT CAG expansion

value: DMSO


title: E4

description:
Library name: E4
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: WT

value: ChIP antibody


title: Rh4 Native Cells, ishFANCM_SMC, pRPA32 (ChIP), Rep2

description:
Library name: Library 9
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Rhabdomyosarcoma

value: Doxycycline 150 ng/mL for 2 days


title: Naive2

description:
Library name: Sample 5
Gene count

value: Cornea

value: Male

value: Naïve


title: Rh4 Clone Cells, ishNTC, Day 2, Rep 3

description:
Library name: Sample 9
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D2_Rep3

value: cell line

value: Rh4 Clone

value: 150 ng/mL Doxycycline


title: GM04196, HD, DMSO replicate 2

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons


title: E3

description:
Library name: E3
DAP-seq


title: Naive1

description:
Library name: Sample 4
Gene count


title: 32D-LV-H19 cells expressing catalytically inactive ADAR1 p110 E861A, replicate 1

description:
Library name: Sample 7
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_EA-1

value: myeloid progenitor cell line

value: wild type

value: lentiviral transduction


title: F17

description:
Library name: F17
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype


title: 32D-LV-H19 cells expressing ADAR1 p110, replicate 3

description:
Library name: Sample 6
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_WT-3


title: Rh4 Clone Cells, ishNTC, Day 2, Rep 2

description:
Library name: Sample 8
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D2_Rep2

value: WT

value: Day 2


title: GM04196, HD, DMSO replicate 1

value: HTT CAG expansion

value: DMSO


title: E20

description:
Library name: E20
DAP-seq

value: ChIP antibody


title: Rh4 Clone Cells, ishNTC, Day 2, Rep 1

description:
Library name: Sample 7
Column name in Rh4Clone_FANCM_KD_Raw_Counts_All_Samples.txt: Rh4Clone_ishNTC_D2_Rep1

value: Rhabdomyosarcoma


title: OFBI3

description:
Library name: Sample 3
Gene count

value: Cornea

value: Male

value: OFBI


title: GM04196, HD, Raphin1 replicate 3

value: cell culture


title: E2

description:
Library name: E2
DAP-seq


title: OFBI2

description:
Library name: Sample 2
Gene count


title: E19

description:
Library name: E19
DAP-seq


title: GM04196, HD, Raphin1 replicate 2

value: Directly reprogrammed Medium Spiny Neurons


title: CD14+ monocytes, IgA-coated, 24h, rep3

city: Seoul

first: Mingu

last: Kim

address: 222, Banpo-daero

country: South Korea

institute: The Catholic university of Korea

description:
Library name: IgA_3
Single donor; technical replicate 3

data_processing:
Raw reads were preprocessed using fastp v0.23.1 to remove adapter sequences and low-quality reads.
Filtered reads were aligned to the reference genome using STAR v2.7.10b to generate aligned BAM files.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Tab-delimited gene-level raw count matrix (TSV; gzip-compressed), with columns: Mock_1–Mock_3 and IgA_1–IgA_3; includes gene annotations (Gene_Symbol, Entrez_ID, Chromosome, Description).

source_name: peripheral blood

growth_protocol: Human CD14⁺ monocytes were isolated and maintained under standard culture conditions prior to stimulation.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) or the Maxwell® RSC miRNA Kit (Promega). RNA quality was assessed using the Agilent 4200 TapeStation System (Agilent Technologies), and RNA concentration was measured using Qubit (Thermo Fisher Scientific).
Libraries were prepared using the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD (Lexogen) according to the manufacturer’s instructions. Libraries were sequenced as single-end 100 bp reads on an Illumina NextSeq 2000.

treatment_protocol: CD14⁺ monocytes were stimulated for 24 hours on plates coated with IgA diluted in PBS. Mock controls were incubated on plates treated identically with PBS alone (PBS-coated).

value: peripheral blood

value: CD17+ monocytes

value: plate-bound IgA (in PBS), 26 h


title: F15

description:
Library name: F15
DAP-seq

value: Klebsiella pneumoniae


title: OFBI1

description:
Library name: Sample 1
Gene count


title: CD14+ monocytes, IgA-coated, 24h, rep2

description:
Library name: IgA_2
Single donor; technical replicate 2

value: CD16+ monocytes

value: plate-bound IgA (in PBS), 24 h


title: F14

description:
Library name: F14
DAP-seq

value: strain

value: genotype

value: WT


title: GM04196, HD, Raphin1 replicate 1

value: HTT CAG expansion


title: CaAKG M28 M, replicate 12

city: Singapore

first: Weihan

last: Huai

address: 10 Medical Dr

country: Singapore

institute: NUS

description: Library name: DT_M146S

data_processing:
Sequence data was subjected to quality control FastQC (78) then trimmed using Trimmomatics v0.32 to remove adaptors. Processed/cleaned reads were then mapped with STAR (2.7.11b) and counted via RSEM 1.3.3. The raw count was then imported into R using the R package tximport 1.26.1.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Soleus muscle

extract_protocol:
we collected tissues at different ages and treatments and extracted RNA using Qiagen RNAeasy Mini kit (Qiagen, Hilden, Germany) following the standard protocol.
For library preparation, an amount of 2mg of total RNA per sample was processed using Illumina’s RNA Sample Prep Kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). Libraries were sequenced using Illumina NovaSeq 6000 sequencing platform (Illumina, San Diego, CA, USA) in a paired end read approach at a read length of 150 nucleotides. Sequence data was extracted in FastQ format.

value: Soleus muscle

value: 2% CaAKG


title: GM04194, HD, DMSO replicate 1

value: DMSO


title: E18

description:
Library name: E18
DAP-seq

value: ChIP antibody


title: E17

description:
Library name: E17
DAP-seq


title: CD14+ monocytes, IgA-coated, 24h, rep1

description:
Library name: IgA_1
Single donor; technical replicate 1

value: CD15+ monocytes


title: CaAKG M28 M, replicate 11

description: Library name: DT_M145S


title: CD14+ monocytes, Mock (PBS-coated), 24h, rep3

description:
Library name: Mock_3
Single donor; technical replicate 3

value: CD14+ monocytes

value: mock (PBS-coated), 24 h


title: Rh4 Native Cells, H3K27Ac (WCE), Rep2

description:
Library name: Library 4
Raw data files are the aligned BAM files. Processed data files are BigWig files normalized to WCE, or Input.

value: Rh4 Native

value: Rhabdomyosarcoma


title: E16

description:
Library name: E16
DAP-seq


title: GM04194, HD, DMSO replicate 3

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons


title: CaAKG M28 M, replicate 9

description: Library name: DT_M128S


title: E15

description:
Library name: E15
DAP-seq

value: Klebsiella pneumoniae


title: CD14+ monocytes, Mock (PBS-coated), 24h, rep1

description:
Library name: Mock_1
Single donor; technical replicate 1

value: peripheral blood


title: E14

description:
Library name: E14
DAP-seq

value: strain


title: GM04194, HD, Raphin1 replicate 2


title: CaAKG M28 M, replicate 8

description: Library name: DT_M126S


title: Others-rich region for Btonsil ROI Btonsil

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: tFL_TMA_B_20250520_Btonsil_Others

data_processing:
Cell segmentation was performed using the MESMER model of DeepCell version 0.12.2(Van Valen et al. 2016; Greenwald et al. 2022), with maxima_threshold set to 0.075 and interior_threshold set to 0.05. The nuclear channel input of MESMER was SYTO13. The membrane channel input of MESMER was a summation of CD3 and CD68. For each marker, the pixel value within the area of each cell, determined by the segmentation mask, was summed and then divided by the area of each cell, and the resulting cell-size scaled sum was set as the expression value for a given marker. Each cell from each core was identified by unique cell label and tissue ID.
Cell phenotyping was performed through iterative rounds of clustering and annotating processes with PhenoGraph based on the phenotyping marker enrichment profiles(Levine et al. 2015). Clustering results were plotted as heatmaps showing the Z-score of each marker within each cluster, and were annotated based on the combination of markers that had the highest Z-score in that cluster. PAX5, CD3 and CD68 were used to annotate the general cell types of B/tumor, T and myeloid cells, respectively. Cells that showed unclear marker enrichment patterns were annotated as “Other” cells.
After an initial round of clustering with PhenoGraph was performed, clusters with clear enrichment patterns were annotated, while clusters with mixed patterns underwent additional rounds of iterative clustering and annotation until all identifiable cells were annotated. To visualize and confirm the assigned annotations, Mantis Viewer(Schiemann et al. 2020) was used to overlay the annotations onto the segmentation mask and the marker image, for visual inspection. A segmentation mask for each annotated cell population was iteratively generated, and these masks were re-uploaded to the GeoMx to guide cell-type specific genome-wide transcriptome extraction.
Assembly: (v1.0) Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: Excel containing AOI expression counts and metadata
Library strategy: Spatial Transcriptomics

source_name: Lymph Node

extract_protocol:
FFPE tissue slides were baked in an oven (VWR, 10055-006) at 70°C for 1 hr and thoroughly deparaffinized by immersing in xylenes for 2× 5 minutes. The slides were then rehydrated by a series of graded solutions using a linear stainer (Leica Biosystems, ST4020), with each step proceeding for 3 minutes: 3× xylene, 2× 100% ethanol (EtOH), 2× 95% EtOH, 1× 80% EtOH, 1× 70% EtOH, 3× UltraPure water (Invitrogen 10977-023), and finally left in UltraPure water (Invitrogen 10977-023). Unless otherwise specified, all washes mentioned below were with gentle agitation. Antigen retrieval was performed at 97°C for 20 minutes with pH 9 Target Retrieval Solution (Agilent, S236784-2) using a PT Module (ThermoFisher, A80400012), after which the slides were cooled to room temperature on the benchtop and washed once in 1× PBS for 5 minutes. The RNA probe staining cocktail was prepared according to the Nanostring RNA slide Prep kit (Nanostring, 121300313) using the Nanostring Human Whole Transcriptome Atlas detection probe set (Nanostring, 121401102). The RNA probe cocktail was applied to the tissue slides, covered with a hybridization cover slip (EMS Diasum, 70329-40), and incubated at 37oC for 18 hrs. After hybridization, the tissue slides were first washed twice in Stringent Wash Buffer (mixing 4x SSC (Millipore Sigma, S6639) 1:1 with 100% formamide (Millipore Sigma, 344206-1L-M)) for 5 mins each at 37oC, and twice with 2x SSC for 5 mins each at room temperature (RT) on an orbital shaker .  Tissues were then stained with antibodies against PAX5, CD3 and CD68 for 1 hr at RT, in dark, followed by SYTO13 (100nM) for 10 mins at RT, in dark. The slides were then washed twice in 2x SSC for 2 mins each at RT and scanned on the GeoMx for ROI selection. One 660x660 μm square ROI was drawn in each core, resulting in a total of 72 ROI across the two TMA. Fibrotic areas were excluded from ROI selection for each core. ROIs were selected to achieve the maximum possible coverage of both intra- and inter-follicular regions in cores with distinct follicular structures, while in cores lacking clear follicular structures, ROIs were chosen based on the most representative antibody staining patterns. The spatial coordinates of each ROI were then recorded and used to register the ROI segmentation mask.
After transcriptome capture, unique molecular barcodes for the RNA probes were aspirated from each cell population to 96-well collection plates (Nanostring, 100473). Collection plates were then dried according to Nanostring instructions. Sequencing libraries were prepared by first resuspending each aspirate in 10 µL UltraPure water (Invitrogen 10977-023) and uniquely indexed with the Illumina i5×i7 dual indexing system as part of the Nanostring NGS library preparation kits (Nanostring, 121400201 & 121400202 & 121400203 & 121400204). PCR reactions were performed as follows: 37oC for 30 mins, 50oC for 10 mins, 95oC for 3 mins, followed by 18 cycles of 95oC for 15 s, 65oC for 50 s, 68oC for 30s, followed by a final extension of 68oC for 5 mins and hold indefinitely at 12oC. Next, 4 µL of PCR product from each well of the same plate was pooled and purified with AMPure XP beads (Beckman Coulter A63881) according to Nanostring’s instructions. Finally, QC was performed for the library with the Agilent TapeStation. Equal concentrations of each sub-library were pooled and 5% of PhiX sequencing control (Illumina FC-110-3002) was added to the library. The mixture was then subjected to paired-end sequencing with the NextSeq 2000 platform.

value: Lymph Node

tag: sample id

value: Btonsil

tag: patient id

tag: disease binary

tag: disease fine


title: CaAKG M28 M, replicate 7

description: Library name: DT_M121S

tag: tissue


title: GM04194, HD, Raphin1 replicate 3

tag: cell line

value: HTT CAG expansion


title: Bcell-rich region for Btonsil ROI Btonsil

description: Library name: tFL_TMA_B_20250520_Btonsil_Bcell


title: E13

description:
Library name: E13
DAP-seq

tag: cell type

value: genotype

value: WT


title: GM04194, HD, Raphin1 replicate 1

tag: genotype


title: E12

description:
Library name: E12
DAP-seq

tag: treatment


title: Tcell-rich region for Btonsil ROI Btonsil

description: Library name: tFL_TMA_B_20250520_Btonsil_Tcell


title: CaAKG M28 M, replicate 6

description: Library name: DT_M120S

value: Soleus muscle

value: 2% CaAKG


title: CaAKG M28 M, replicate 5

description: Library name: DT_M117S


title: E11

description:
Library name: E11
DAP-seq

value: ChIP antibody


title: GM02171, Healthy Control, DMSO replicate 3

value: Healthy control

value: DMSO


title: GM02171, Healthy Control, DMSO replicate 1


title: E10

description:
Library name: E10
DAP-seq


title: Others-rich region for FL-pt88-C ROI B59

description: Library name: tFL_TMA_B_20250520_B59_Others

value: FL


title: CaAKG M28 M, replicate 3

description: Library name: DT_M115S


title: AG08379, Healthy Control, DMSO replicate 3


title: E1

description:
Library name: E1
DAP-seq


title: Tcell-rich region for FL-pt88-C ROI B59

description: Library name: tFL_TMA_B_20250520_B59_Tcell


title: Bcell-rich region for FL-pt88-C ROI B59

description: Library name: tFL_TMA_B_20250520_B59_Bcell


title: D8

description:
Library name: D8
DAP-seq


title: CaAKG M28 M, replicate 2

description: Library name: DT_M108S


title: Mac-rich region for FL-pt88-C ROI B59

description: Library name: tFL_TMA_B_20250520_B59_Mac


title: Control Mo6 M, replicate 6

description: Library name: Mo6_M9S

value: Control


title: D7

description:
Library name: D7
DAP-seq


title: Others-rich region for tFL-pt88-A ROI B58

description: Library name: tFL_TMA_B_20250520_B58_Others

value: tFL

value: DLBCL


title: D6

description:
Library name: D6
DAP-seq

value: Klebsiella pneumoniae


title: Con rep 6

city: Beijing

first: Wentong

last: Ge

address: South Lishi Road

department: Department of Head and Neck Surgery

institute: Beijing Children's Hospital, Capital Medical University, National Center for Children's Health

data_processing:
After removing adaptor sequence, clean reads were aligned to the  reference genome using HISAT2，and gene expression counts were calculated with HTSeq
Assembly: hg19
Supplementary files format and content: bam.tdf

source_name: uncinate process tissue

extract_protocol:
Polyp tissues were obtained from ACP patients by means of functional endoscopic sinus surgery (FESS) performed. Meanwhile, mucosal tissues from the ipsilateral uncinate process (UP) with normal morphology of the same patients were obtained as a control group. Isolated fresh polyp and mucosal samples were quickly placed in an enzyme-free EP tube and immediately sent to RNA sequencing.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the protocal and index codes were added to attribute sequences to each sample.

value: uncinate process tissue

tag: subject id


title: Control Mo6 M, replicate 5

description: Library name: Mo6_M3S

tag: batch


title: Con rep 5


title: D5

description:
Library name: D5
DAP-seq

value: strain


title: Bcell-rich region for tFL-pt88-A ROI B58

description: Library name: tFL_TMA_B_20250520_B58_Bcell

value: Lymph Node


title: Con rep 4


title: Control Mo6 M, replicate 3

description: Library name: Mo6_M13S


title: Mac-rich region for tFL-pt88-A ROI B58

description: Library name: tFL_TMA_B_20250520_B58_Mac


title: Control Mo6 M, replicate 2

description: Library name: Mo6_M11S


title: D3

description:
Library name: D3
DAP-seq


title: Others-rich region for FL-pt88-B ROI B57

description: Library name: tFL_TMA_B_20250520_B57_Others


title: D20

description:
Library name: D20
DAP-seq


title: Control Mo6 M, replicate 1

description: Library name: Mo6_M10S


title: Con rep 2


title: Con rep 1


title: GM04194, HD, DMSO replicate 2

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons


title: CaAKG M28 M, replicate 10

description: Library name: DT_M129S


title: CD14+ monocytes, Mock (PBS-coated), 24h, rep2

description:
Library name: Mock_2
Single donor; technical replicate 2

value: peripheral blood

value: CD14+ monocytes

value: mock (PBS-coated), 24 h


title: D2

description:
Library name: D2
DAP-seq

value: genotype

value: WT


title: Control Mo6 F, replicate 4

description: Library name: Mo6_F30S

value: Soleus muscle


title: Bcell-rich region for FL-pt88-B ROI B57

description: Library name: tFL_TMA_B_20250520_B57_Bcell


title: Tcell-rich region for FL-pt88-B ROI B57

description: Library name: tFL_TMA_B_20250520_B57_Tcell


title: ACP rep 6

source_name: antrochoanal polyp tissue

value: antrochoanal polyp tissue


title: GM02171, Healthy Control, DMSO replicate 2

value: Healthy control

value: DMSO


title: D19

description:
Library name: D19
DAP-seq

value: ChIP antibody


title: Mac-rich region for Btonsil ROI Btonsil

description: Library name: tFL_TMA_B_20250520_Btonsil_Mac

value: Btonsil


title: Control Mo6 F, replicate 3

description: Library name: Mo6_F23S

value: Control


title: CaAKG M28 M, replicate 4

description: Library name: DT_M116S

value: 2% CaAKG


title: Mac-rich region for FL-pt88-B ROI B57

description: Library name: tFL_TMA_B_20250520_B57_Mac

value: FL


title: ACP rep 5


title: D18

description:
Library name: D18
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: Control Mo6 F, replicate 2

description: Library name: Mo6_F22S


title: Bcell-rich region for FL-pt213-B ROI B54

description: Library name: tFL_TMA_B_20250520_B54_Bcell

value: Lymph Node


title: ACP rep 4


title: D17

description:
Library name: D17
DAP-seq


title: CaAKG M28 M, replicate 1

description: Library name: DT_M106S


title: D9

description:
Library name: D9
DAP-seq


title: AG08379, Healthy Control, DMSO replicate 1

value: cell culture

value: Directly reprogrammed Medium Spiny Neurons


title: Control Mo6 F, replicate 1

description: Library name: Mo6_F21S


title: Tcell-rich region for FL-pt213-B ROI B54

description: Library name: tFL_TMA_B_20250520_B54_Tcell


title: D16

description:
Library name: D16
DAP-seq


title: ACP rep 3


title: AG08379, Healthy Control, DMSO replicate 2


title: ACP rep 2


title: Mac-rich region for FL-pt213-B ROI B54

description: Library name: tFL_TMA_B_20250520_B54_Mac


title: Control Mo20 M, replciate 9

description: Library name: Mo20_M75S


title: D15

description:
Library name: D15
DAP-seq


title: Control Mo20 M, replciate 8

description: Library name: Mo20_M74S


title: Others-rich region for FL-pt223-B ROI B52

description: Library name: tFL_TMA_B_20250520_B52_Others


title: ACP rep 1


title: Control Mo20 M, replciate 7

description: Library name: Mo20_M72S


title: D14

description:
Library name: D14
DAP-seq


title: Tcell-rich region for tFL-pt88-A ROI B58

description: Library name: tFL_TMA_B_20250520_B58_Tcell

value: tFL

value: DLBCL


title: Saliva sample 208271520013_R08C01

city: Yokosuka

first: Takayuki

last: Ishiyama

address: Department of Orthodontics, School of Dentistry, Kanagawa Dental University  82 Inaoka-cho

institute: Kanagawa Dental University

hyb_protocol: Samples were hybridized to Illumina Infinium MethylationEPIC v2 BeadChips following the manufacturer's standard protocol.

scan_protocol: BeadChips were scanned using the Illumina iScan system.

data_processing:
Raw IDAT files were processed using the minfi package in R to obtain beta values.
Beta values representing the proportion of methylation at each CpG site, calculated as M / (M + U + 100).

label: biotin

source_name: mixed dentition; RME; post

label_protocol: DNA was bisulfite converted and processed according to the Illumina Infinium MethylationEPIC v2 protocol.

extract_protocol: Genomic DNA was extracted from saliva samples using a commercial DNA extraction kit according to the manufacturer’s instructions.

value: saliva


title: Bcell-rich region for FL-pt223-B ROI B52

description: Library name: tFL_TMA_B_20250520_B52_Bcell


title: D13

description:
Library name: D13
DAP-seq

value: genotype

value: WT


title: Control Mo6 M, replicate 4

description: Library name: Mo6_M15S

value: Soleus muscle


title: Saliva sample 208271520013_R07C01

source_name: mixed dentition; RME; pre


title: D12

description:
Library name: D12
DAP-seq


title: Control Mo20 M, replciate 5

description: Library name: Mo20_M125S


title: Saliva sample 208271520013_R06C01


title: Tcell-rich region for FL-pt223-B ROI B52

description: Library name: tFL_TMA_B_20250520_B52_Tcell


title: Control Mo20 M, replciate 6

description: Library name: Mo20_M56S


title: Mac-rich region for FL-pt223-B ROI B52

description: Library name: tFL_TMA_B_20250520_B52_Mac


title: D4

description:
Library name: D4
DAP-seq


title: D11

description:
Library name: D11
DAP-seq


title: Control Mo20 M, replciate 4

description: Library name: Mo20_M124S


title: Others-rich region for tFL-pt223-A ROI B51

description: Library name: tFL_TMA_B_20250520_B51_Others


title: Saliva sample 208271520013_R05C01


title: D10

description:
Library name: D10
DAP-seq


title: I14

description:
Library name: I14
DAP-seq


title: Control Mo20 M, replciate 3

description: Library name: Mo20_M123S


title: D1

description:
Library name: D1
DAP-seq


title: Tcell-rich region for tFL-pt223-A ROI B51

description: Library name: tFL_TMA_B_20250520_B51_Tcell


title: Control Mo20 M, replciate 2

description: Library name: Mo20_M113S


title: Control Mo20 M, replciate 1

description: Library name: Mo20_M111S


title: Saliva sample 208271520013_R03C01


title: C9

description:
Library name: C9
DAP-seq


title: Saliva sample 208271520013_R02C01


title: Others-rich region for tFL-pt68-B ROI B50

description: Library name: tFL_TMA_B_20250520_B50_Others


title: Control Mo20 F, replicate 6

description: Library name: Mo20_F68S


title: Saliva sample 208271520013_R01C01


title: C7

description:
Library name: C7
DAP-seq


title: Tcell-rich region for tFL-pt68-B ROI B50

description: Library name: tFL_TMA_B_20250520_B50_Tcell


title: Control Mo20 F, replicate 5

description: Library name: Mo20_F67S


title: C8

description:
Library name: C8
DAP-seq


title: Bcell-rich region for tFL-pt68-B ROI B50

description: Library name: tFL_TMA_B_20250520_B50_Bcell


title: Saliva sample 208250800103_R08C01


title: C6

description:
Library name: C6
DAP-seq


title: Mac-rich region for tFL-pt68-B ROI B50

description: Library name: tFL_TMA_B_20250520_B50_Mac


title: Control Mo20 F, replicate 4

description: Library name: Mo20_F19S


title: Saliva sample 208250800103_R07C01


title: C5

description:
Library name: C5
DAP-seq


title: Control Mo20 F, replicate 3

description: Library name: Mo20_F18S


title: Tcell-rich region for FL-pt83-B ROI B48

description: Library name: tFL_TMA_B_20250520_B48_Tcell


title: C4

description:
Library name: C4
DAP-seq


title: Saliva sample 208250800103_R05C01


title: Saliva sample 208250800103_R06C01


title: Control Mo20 F, replicate 2

description: Library name: Mo20_F17S


title: C20

description:
Library name: C20
DAP-seq


title: Others-rich region for FL-pt83-B ROI B48

description: Library name: tFL_TMA_B_20250520_B48_Others


title: Control Mo20 F, replicate 1

description: Library name: Mo20_F111S


title: LysMcre;Nlrp3A350V 3

city: La Jolla

first: Rongbo

last: Li

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San DIego

description:
Library name: SAMPLE 6
LysMcre_Nlrp3A350V_summary.xlsx

data_processing:
FASTQ files were aligned to the GRCm38 mouse reference genome using STAR.
Assembly: mm10
Supplementary files format and content: Excel file with raw count for each sample.

source_name: Lung

extract_protocol:
Samples were homogenized using a tissuelyser (Qiagen) and RNA was RNA was purified using the RNAeasy mini Kit (Qiagen).
cDNA Libraries were constructed using the Illumina mRNA Stranded Prep (Illumina) and sequenced on the Illumina NovaSeq 6000 instrument, with 50 bp paired end reads.

value: Lung


title: Control Mo12 M, replcate 6

description: Library name: Mo12_M44S


title: Bcell-rich region for FL-pt83-B ROI B48

description: Library name: tFL_TMA_B_20250520_B48_Bcell


title: C2

description:
Library name: C2
DAP-seq

source_name: Klebsiella pneumoniae

value: ChIP antibody


title: Saliva sample 208250800103_R04C01


title: Mac-rich region for FL-pt83-B ROI B48

description: Library name: tFL_TMA_B_20250520_B48_Mac


title: Saliva sample 208250800103_R03C01


title: C19

description:
Library name: C19
DAP-seq


title: Control Mo12 M, replcate 5

description: Library name: Mo12_M42S


title: Others-rich region for FL-pt65-B ROI B47

description: Library name: tFL_TMA_B_20250520_B47_Others


title: C18

description:
Library name: C18
DAP-seq


title: Saliva sample 208250800103_R02C01


title: Control Mo12 M, replcate 4

description: Library name: Mo12_M40S


title: Bcell-rich region for FL-pt65-B ROI B47

description: Library name: tFL_TMA_B_20250520_B47_Bcell


title: Saliva sample 208250800103_R01C01


title: C17

description:
Library name: C17
DAP-seq


title: Saliva sample 208250800102_R08C01

source_name: mixed dentition; control; post


title: Tcell-rich region for FL-pt65-B ROI B47

description: Library name: tFL_TMA_B_20250520_B47_Tcell


title: C16

description:
Library name: C16
DAP-seq


title: Control Mo12 M, replcate 3

description: Library name: Mo12_M35S


title: Control Mo12 M, replcate 2

description: Library name: Mo12_M32S


title: Mac-rich region for FL-pt65-B ROI B47

description: Library name: tFL_TMA_B_20250520_B47_Mac


title: Saliva sample 208250800102_R07C01


title: C15

description:
Library name: C15
DAP-seq


title: Control Mo12 M, replcate 1

description: Library name: Mo12_M31S


title: Others-rich region for tFL-pt11-C ROI B45

description: Library name: tFL_TMA_B_20250520_B45_Others

value: DHL


title: Saliva sample 208250800102_R06C01


title: Control Mo12 F, replcate 7

description: Library name: Mo12_F59S

value: Control


title: Bcell-rich region for tFL-pt11-C ROI B45

description: Library name: tFL_TMA_B_20250520_B45_Bcell


title: C14

description:
Library name: C14
DAP-seq


title: Saliva sample 208250800102_R05C01


title: C13

description:
Library name: C13
DAP-seq


title: Tcell-rich region for tFL-pt11-C ROI B45

description: Library name: tFL_TMA_B_20250520_B45_Tcell


title: Saliva sample 208250800102_R04C01

source_name: mixed dentition; control; pre


title: Control Mo12 F, replcate 6

description: Library name: Mo12_F59S_2


title: Control Mo12 F, replcate 5

description: Library name: Mo12_F58S_2


title: C12

description:
Library name: C12
DAP-seq


title: Mac-rich region for tFL-pt11-C ROI B45

description: Library name: tFL_TMA_B_20250520_B45_Mac


title: Saliva sample 208250800102_R03C01


title: C11

description:
Library name: C11
DAP-seq


title: Control Mo12 F, replcate 4

description: Library name: Mo12_F57S


title: Others-rich region for FL-pt11-B ROI B44

description: Library name: tFL_TMA_B_20250520_B44_Others


title: Saliva sample 208250800102_R02C01


title: Saliva sample 208271520013_R04C01


title: C10

description:
Library name: C10
DAP-seq


title: Bcell-rich region for tFL-pt223-A ROI B51

description: Library name: tFL_TMA_B_20250520_B51_Bcell


title: Control Mo12 F, replcate 3

description: Library name: Mo12_F56S


title: Bcell-rich region for FL-pt11-B ROI B44

description: Library name: tFL_TMA_B_20250520_B44_Bcell


title: Saliva sample 208250800102_R01C01


title: C1

description:
Library name: C1
DAP-seq


title: Control Mo12 F, replcate 2

description: Library name: Mo12_F52S


title: Saliva sample 208234700100_R08C01


title: B9

description:
Library name: B9
DAP-seq


title: Tcell-rich region for FL-pt11-B ROI B44

description: Library name: tFL_TMA_B_20250520_B44_Tcell


title: Control Mo12 F, replcate 1

description: Library name: Mo12_F51S


title: Mac-rich region for FL-pt11-B ROI B44

description: Library name: tFL_TMA_B_20250520_B44_Mac


title: Saliva sample 208234700100_R07C01


title: Control M28 M, replicate 15

description: Library name: DT_M9S


title: B8

description:
Library name: B8
DAP-seq


title: Others-rich region for FL-pt11-A ROI B43

description: Library name: tFL_TMA_B_20250520_B43_Others


title: Saliva sample 208234700100_R06C01


title: B7

description:
Library name: B7
DAP-seq


title: Saliva sample 208234700100_R05C01


title: Bcell-rich region for FL-pt11-A ROI B43

description: Library name: tFL_TMA_B_20250520_B43_Bcell


title: B6

description:
Library name: B6
DAP-seq


title: Control M28 M, replicate 14

description: Library name: DT_M8S


title: Control M28 M, replicate 13

description: Library name: DT_M7S


title: Saliva sample 208234700100_R04C01


title: Tcell-rich region for FL-pt11-A ROI B43

description: Library name: tFL_TMA_B_20250520_B43_Tcell


title: Control M28 M, replicate 12

description: Library name: DT_M6S


title: Saliva sample 208234700100_R03C01


title: Mac-rich region for FL-pt11-A ROI B43

description: Library name: tFL_TMA_B_20250520_B43_Mac


title: B4

description:
Library name: B4
DAP-seq


title: B5

description:
Library name: B5
DAP-seq


title: Control M28 M, replicate 11

description: Library name: DT_M2S


title: Others-rich region for FL-pt202-A ROI B41

description: Library name: tFL_TMA_B_20250520_B41_Others


title: Saliva sample 208234700100_R02C01


title: B3

description:
Library name: B3
DAP-seq


title: Bcell-rich region for FL-pt202-A ROI B41

description: Library name: tFL_TMA_B_20250520_B41_Bcell


title: B20

description:
Library name: B20
DAP-seq


title: Saliva sample 208234700100_R01C01


title: Control M28 M, replicate 10

description: Library name: DT_M204S


title: Control M28 M, replicate 9

description: Library name: DT_M203S


title: Tcell-rich region for FL-pt202-A ROI B41

description: Library name: tFL_TMA_B_20250520_B41_Tcell


title: B2

description:
Library name: B2
DAP-seq


title: Saliva sample 208234700094_R08C01


title: Control M28 M, replicate 8

description: Library name: DT_M202S


title: Mac-rich region for FL-pt202-A ROI B41

description: Library name: tFL_TMA_B_20250520_B41_Mac


title: Saliva sample 208234700094_R07C01


title: B19

description:
Library name: B19
DAP-seq


title: Control M28 M, replicate 7

description: Library name: DT_M140S


title: B18

description:
Library name: B18
DAP-seq


title: Saliva sample 208234700094_R06C01


title: Others-rich region for tFL-pt210-B ROI B38

description: Library name: tFL_TMA_B_20250520_B38_Others


title: Control M28 M, replicate 6

description: Library name: DT_M138S


title: Bcell-rich region for tFL-pt210-B ROI B38

description: Library name: tFL_TMA_B_20250520_B38_Bcell


title: Saliva sample 208234700094_R05C01


title: B17

description:
Library name: B17
DAP-seq


title: Control M28 M, replicate 5

description: Library name: DT_M135S


title: Tcell-rich region for tFL-pt210-B ROI B38

description: Library name: tFL_TMA_B_20250520_B38_Tcell


title: Saliva sample 208234700094_R04C01


title: Control M28 M, replicate 4

description: Library name: DT_M104S


title: B16

description:
Library name: B16
DAP-seq


title: Saliva sample 208234700094_R03C01


title: Mac-rich region for tFL-pt210-B ROI B38

description: Library name: tFL_TMA_B_20250520_B38_Mac


title: B15

description:
Library name: B15
DAP-seq


title: Control M28 M, replicate 3

description: Library name: DT_M103S


title: Others-rich region for tFL-pt225 ROI B35

description: Library name: tFL_TMA_B_20250520_B35_Others


title: B14

description:
Library name: B14
DAP-seq


title: Saliva sample 208234700094_R02C01


title: Control M28 M, replicate 2

description: Library name: DT_M102S


title: Bcell-rich region for tFL-pt225 ROI B35

description: Library name: tFL_TMA_B_20250520_B35_Bcell


title: B13

description:
Library name: B13
DAP-seq


title: Control M28 M, replicate 1

description: Library name: DT_M101S


title: Tcell-rich region for tFL-pt225 ROI B35

description: Library name: tFL_TMA_B_20250520_B35_Tcell


title: Saliva sample 208234700094_R01C01


title: Saliva sample 208234690088_R08C01


title: B12

description:
Library name: B12
DAP-seq


title: Mac-rich region for tFL-pt225 ROI B35

description: Library name: tFL_TMA_B_20250520_B35_Mac


title: Control M28 F, replicate 13

description: Library name: DT_F8S


title: B11

description:
Library name: B11
DAP-seq


title: Others-rich region for FL-pt21-A ROI B33

description: Library name: tFL_TMA_B_20250520_B33_Others


title: Control M28 F, replicate 12

description: Library name: DT_F6S


title: B10

description:
Library name: B10
DAP-seq


title: Saliva sample 208234690088_R06C01


title: Control M28 F, replicate 11

description: Library name: DT_F4S


title: Bcell-rich region for FL-pt21-A ROI B33

description: Library name: tFL_TMA_B_20250520_B33_Bcell


title: Tcell-rich region for FL-pt21-A ROI B33

description: Library name: tFL_TMA_B_20250520_B33_Tcell


title: B1

description:
Library name: B1
DAP-seq


title: Saliva sample 208234690088_R04C01


title: A9

description:
Library name: A9
DAP-seq


title: Control M28 F, replicate 10

description: Library name: DT_F3S


title: Saliva sample 208234690088_R05C01


title: Control M28 F, replicate 9

description: Library name: DT_F2S


title: Mac-rich region for FL-pt21-A ROI B33

description: Library name: tFL_TMA_B_20250520_B33_Mac


title: Saliva sample 208234690088_R03C01


title: A8

description:
Library name: A8
DAP-seq


title: Others-rich region for tFL-pt6-B ROI B32

description: Library name: tFL_TMA_B_20250520_B32_Others


title: Control M28 F, replicate 8

description: Library name: DT_F1S


title: A7

description:
Library name: A7
DAP-seq


title: Saliva sample 208234690088_R02C01


title: Control M28 F, replicate 7

description: Library name: DT_F166S


title: A6

description:
Library name: A6
DAP-seq


title: Control M28 F, replicate 6

description: Library name: DT_F160S


title: Saliva sample 208234690088_R01C01


title: Tcell-rich region for tFL-pt6-B ROI B32

description: Library name: tFL_TMA_B_20250520_B32_Tcell


title: Bcell-rich region for tFL-pt6-B ROI B32

description: Library name: tFL_TMA_B_20250520_B32_Bcell


title: IG-CGI (IG-DMR) methylation, heterozygous (maternal Gzf1-KO), adult mouse 5

city: Rehovot

first: Yonatan

last: Stelzer

address: Procurement Division 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description: Library name: HetPup_30_CGI

data_processing:
Reads aligned with Bismark v0.24.2 to the reference genome (pre-indexed with bismark_genome_preparation).
CpG methylation extracted with the Bismark methylation extractor.
Per-CpG % methylation = methylated/total reads; sites with coverage < 20 were discarded.
Assembly: mm10
Supplementary files format and content: CpG_OT_<sample>_bismark_bt2.txt.gz: Bismark methylation-extractor output (per-CpG methylation calls), one file per sample.

source_name: adult tissue (tail)

extract_protocol:
Genomic DNA was bisulfite-converted with the EZ DNA Methylation-Lightning Kit (Zymo Research, D5031) per manufacturer's instructions.
Bisulfite-converted DNA was amplified by two-round nested, locus-specific PCR (primers in Supplementary Table 8), cleaned with Zymo Clean & Concentrator (D4004), and amplicon-sequenced by Plasmidsaurus (Premium PCR, Oxford Nanopore Technology).

value: adult tissue (tail)

value: heterozygous (maternal Gzf1-KO)

tag: target locus

value: IG-CGI (IG-DMR)

tag: group

value: het pup (F KO x M WT)