title: GinB_Run3

city: Rochester

first: Neil

middle: Alistair

last: Robertson

state: MN

address: 200 1st Street

department: Quantitative Health Sciences

institute: MAYO CLINIC ROCHESTER

description: Library name: GinB_Run3

data_processing:
Reads were quality-filtered with a ‘phred’ score threshold of ≥30, and adapter sequences were removed using Trimmomatic (version 0.27) (Bolger et al. 2014). Afterward, guided alignment to the human genome assembly hg19 was performed using both bwa-mem (version 0.7.17) and bowtie2 (version 2.2.1) (Langmead & Salzberg 2012; Li & Durbin 2009). Unique molecular barcodes, introduced before PCR amplification, were utilized for deduplication to enable accurate multiplexed quantification and reliable mutation detection. Variant calling within targeted regions was conducted using three different tools: Lofreq (version 2.1.0) (Wilm et al. 2012), Freebayes (Garrison & Marth 2012), and Vision (ArcherDX version 6.2.7, unpublished). A consensus was generated by combining the results and selecting for agreement from all three variant callers (see Supplementary Table 3).
All filtered variants with a variant allele frequency (VAF) of 1% or 2% satisfied the following conditions: (1) the number of reads supporting the alternative allele exceeded the minimum coverage requirement without displaying directional bias (AO ≥ 5, UAO ≥ 3); (2) the variants were significantly underrepresented in the Genome Aggregation Database (gnomAD; P ≤ 0.05); (3) the variants were unlikely to be germline, as indicated by a stable VAF (50% or 100%) across all sequencing waves, which could have been underrepresented in gnomAD due to the limited geographic diversity of the LBC cohort; and (4) the variants included events, such as frameshift duplications and deletions, that were overrepresented in the dataset, likely reflecting misaligned artifacts from the capture method (see Supplementary Table 3) (Karczewski et al. 2020). Additionally, the list was manually curated, cross-referencing variants previously reported in COSMIC, Jaiswal et al., or other published studies (Tate et al. 2019). Finally, for any variant that met the above criteria with a VAF of ≥ 1% or 2% at any time point, all participant-matched data points were included, regardless of baseline VAF.
Assembly: hg19
Supplementary files format and content: tsv - custom variant file format - somatic and synonymous variant calls for 1% and 2% VAF

source_name: Other

extract_protocol:
Our expanded cohort longitudinally sampled from the LBC1936 was processed as per our previous work. Briefly, DNA was extracted from whole blood with Ethylenediaminetetraacetic acid (EDTA) using the Nucleon BACC3 kit (Sigma-Aldrich, GERPN8512), according to the manufacturer’s protocol.
Libraries were generated from 200 ng of each DNA sample using the Invitea/Archer VariantPlex® 75 Myeloid gene panel and the VariantPlex® Somatic Protocol for Illumina sequencing (Invitae, AB0108, and the VariantPlex®-HCG Myeloid Kit; see Supplementary Table 2), with adaptations for detecting low variant allele frequencies. Sequencing was performed on the NextSeq 550 platform (Illumina) using the NextSeq 500/550 High-Output version 2.5 kit (300 cycles). Two ‘Genome in a Bottle’ (GIAB) DNA samples (NA12878, Coriell Institute) were included in each sequencing batch to ensure reproducibility and support background error modeling and batch correction.

value: Other


title: WT_OPT_STAT_B3_vs_WT_OPT_LATELOG_B3

status: Public on Mar 26 2025

type: RNA

city: Helsinki

first: Miia

last: Lindström

address: Agnes Sjöbergin katu 2

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

hyb_protocol: 300 ng of Cy3-labeled and of 300 ng of Cy5-labeld cDNA samples were mixed with 2.3 μg of salmon sperm DNA (Invitrogen), denaturized for 2 min at 95°C, then mixed with 5 μl 10x blocking agent and 26 μl 2x RPMI hybridization buffer (Agilent) and hybridized for 16 h at 65°C. After hybridization the slides were washed according to the manufacturer’s instructions.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing:
A custom R-script was used for background subtraction and LOWESS normalization.
normalized log2 ratio (Cy3/Cy5) representing test/reference

molecule: total RNA

organism: Clostridium botulinum

source_name: C. botulinum harvested cells from batch culture

label_protocol: 2 μg total RNA was reverse transcribed and labeled directly with fluorescent dye for 3 h at 46˚C. The mixture contained 5 μg of random primers, 40 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, 6 μl 5x first-strand buffer, 3 μl of 100 mM DTT, 400 U SuperScript™ III Reverse Transcriptase (all Invitrogen, Life Technologies Ltd, Paisley, UK), 0.6 μl dNTP mix (25 mM dATP, 25 mM dGTP, 25 mM dTTP, 10 mM dCTP [Promega Corporation, Madison, WI, USA]), and 2 nmol Cy3-dCTP or Cy5-dCTP (GE Healthcare, Buckinghamshire, UK). The labeled cDNA was purified using a DNA purification column (QIAquick PCR purification kit; Qiagen).

growth_protocol: C. botulinum strain ATCC 19397 or derivatives were cultured in TPGY broth at 37 °C anaerobically.

extract_protocol: Total RNA extracted using Qiagen's RNeasy Midi Kit (Qiagen, Hilden, Germany), with on-column DNase treatment, following manufacturer's instructions. Additional DNase treatment using the Ambion DNA-free kit (Applied Biosystems, Life Technologies Corporation, Carlsbad, CA) according to the manufacturer’s instructions.

tag: strain

tag: genotype

value: wild-type

tag: timepoint

value: STAT

value: LATELOG


title: Donor36, control, Ap-, scRNA-seq

type: SRA

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

country: USA

institute: University of Pittsburgh

description: 10x Genomics Single Cell 3ʹ Kit v3.1

library_source: transcriptomic single cell

data_processing:
scMultiome-seq data were processed by Cell Ranger ARC software, and scRNA-seq data were processed by Cell Ranger software.
The BCL files generated by Illumina sequencing were demultiplexed by cellranger-arc mkfastq or cellranger mkfastq. We generated feature (GEX, ATAC)-barcode count matrix using cellranger-arc count or cellranger count (mapped to GRCh38 human reference genome) for each sample separately. The outputs of the samples from the same donor were aggregated using cellranger-arc aggr or cellranger aggr.
Assembly: GRCh38
Supplementary files format and content: UMI matrix

organism: Homo sapiens

source_name: PBMCs, in vitro culture

extract_protocol:
Cells were harvested from dishes. Accutase 37C incubation for 10 min was used to harvest adherent cells. After CD33 beads enrichment (scMultiome) or flow sorting enrich (scRNA-seq), cells were subjected to 10x Genomics library preparation.
We followed Chromium Next GEM Single Cell Nultiome ATAC + Gene Expression protocol (CG000338 Rev C) and Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index, CG000315) to prepare the corresponding libraries.
scMultiome-seq or scRNA-seq

treatment_protocol: MDSCs were generated by treating PBMCs with GM-CSF (10ng/mL) + IL-6 (10ng/mL) at 5x10^5 cell/mL in full media at 37C with 5%CO2. Cytokines were added daily for 3 days. PBMCs cultured in full media alone were used as control. Serum starvation was performed using serum-free media.

tag: tissue

value: PBMCs, in vitro culture

tag: treatment

value: control


title: hippocampus,  Mr1+/+ P301S mice 3

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

description: Library name: Tau3

data_processing:
Raw data were processed by Cellranger. The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
Assembly: Reference genome mouse (mm10) was used for read alignment.
Supplementary files format and content: Processed data are in the formats of mtx and tsv for processed data

molecule: nuclear RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Nuclei were extracted from the hippocampus of mice.
Libraries were prepared using 3’ GEM gene expression kit (10xgenomics) following the manufacturer’s instructions.

value: hippocampus

tag: cell type

value: hippocampus cells

tag: batch


title: Donor36, control, Ap+, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: HC3529, GMCSF+IL6, scMultiome_ATAC

description: 10x Genomics Multiome ATAC + Gene Expression kit

library_source: genomic

molecule: genomic DNA


title: hippocampus,  Mr1+/+ P301S mice 2

description: Library name: Tau2


title: hippocampus,  Mr1+/+ P301S mice 1

description: Library name: Tau1


title: GinB_Run1

description: Library name: GinB_Run1


title: MsigD_OPT_T1_B2_vs_WT_OPT_T1_B2

value: ATCC 3502 cbo2641_sigD::intron-erm-


title: WT_OPT_MIDLOG_B3_vs_WT_OPT_EARLYLOG_B3

value: MIDLOG

value: EARLYLOG


title: CHIP2024_407_Wave3

description: Library name: CHIP2024_407_Wave3

source_name: PBMCs

value: PBMCs


title: HC3524, GMCSF+IL6, scMultiome_ATAC


title: MsigD_OPT_T4_B1_vs_WT_OPT_T4_B2


title: hippocampus,  Mr1-/- P301S mice 2

description: Library name: TauMR2


title: HC3533, GMCSF+IL6, scMultiome_ATAC


title: An.dirus Control rep1

city: Chongqing

first: Shasha

last: Yu

address: 30 Gaotanyan street

country: China

institute: Army medical university

library_source: transcriptomic

data_processing:
Paired-end sequencing of the library was performed on the Illumina Novaseq 6000 sequencers (Illumina, San Diego, CA).
Fastp (version 0.19.5) was used for evaluating the quality of sequenced data.
Clean reads were mapped to the reference genome by HISAT2 (version 2.1.0) with default parameters.
DESeq2 (version 1.24.0) was used to determine differentially expressed genes (DEGs) between two samples.
Assembly: The reference genome downloaded from VectorBase (Anopheles dirus WRAIR2 Genome).
Supplementary files format and content: Processed data with gene expression level was provided in file " gene_expression_processed_data.txt".

organism: Anopheles dirus

source_name: whole mosquito

growth_protocol: An.dirus (Hainan strain) larvae were fed on powder mix of dry degreased pork liver and yeast in a ratio of 1:4 at 28℃ with a 12h light/dark cycle, , while the adult mosquitoes were fed on 10.0% sugar solution with the same environment conditions.

extract_protocol:
Total RNA was extracted using the Trizol Reagent (Invitrogen, Carlsbad, USA) from a pool of 30 mosquitoes treated with or without Bs.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Illumina TruseqTM RNA sample prep Kit following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Sublethal dose of Bs 2362 strain was administrated to the early 4th instar larvae of An.dirus to simulate shortage use of Bs in field circumstance. When the surviving larvae developed to pupae, they were collected and further emerged to adults in cages. The adult mosquitoes were then routinely maintained under the same environmental and rearing conditions as the group without Bs treatment.

value: whole mosquito

tag: cell line

value: strain:Hainan strain

value: hours past blood feeding:24h

value: untreated


title: LLC_KD

city: Beijing

first: yufeng

last: guo

address: No. 17 Panjiayuan Nanli, Chaoyang District

institute: Cancer Hospital Chinese Academy of Medical Sciences

description:
Library name: Sample 2
kd_filtered_feature_bc_matrix

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse lung orthotopic xenograft

extract_protocol:
Implants of the indicated synergic mouse tumor cell lines were dissected from mice at ~500 mm3 and measured for total weight. Biopsies were minced using scalpels and digested with 500 U/mL collagenase IV (Sigma‒Aldrich) and 200 mg/mL DNAse I (Roche) per 0.3 g tumor weight for 30 min at 37 °C. After incubation, the cell suspensions were passed through a 70-μm cell filter to remove large pieces of undigested tissue. Erythrocytes were lysed using Red Blood Cell Lysis Solution (Solarbio).
The protoplast suspension was loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with illumina Novaseq 6000 according to the manufacturer’s instructions (Illumina).

value: Mouse lung orthotopic xenograft

value: LLC

value: S100a1 shRNA


title: WT_OPT_T1_B1_vs_MsigD_OPT_T1_B1

value: wild-type


title: HC3531, GMCSF+IL6, scMultiome_ATAC


title: CHIP2024_406_Wave5

description: Library name: CHIP2024_406_Wave5


title: hippocampus,  Mr1+/+ P301S mice 4

description: Library name: Tau4


title: HC3514, GMCSF+IL6, scMultiome_ATAC


title: MsigD_OPT_T3_B1_vs_WT_OPT_T3_B1


title: GinB_Run2

description: Library name: GinB_Run2

value: Other


title: CHIP2024_406_Wave3

description: Library name: CHIP2024_406_Wave3


title: Day40, replicate2, scRNAseq

city: Sapporo

first: Tomoki

last: Kamatani

address: Kita-15, Nishi-7, Kita-ku

country: Japan

institute: Hokkaido University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Teratoma

extract_protocol:
Teratomas from each mouse were collected at 10 (n = 33), 20 (n = 20), and 40 days (n = 20) after subcutaneous administration of CBA/N iPS into B6C3F1 mice and processed collectively at each time point. Single-cell suspensions were obtained using BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences), and infiltrated immune cells were collected through sorting of CD45-positive cells by FACSAria II (BD Biosciences). We followed the 10x Genomics protocol for Next GEM Single Cell 3′ Gene Expression v3.1 (CG000315 Rev C) and used cell suspensions with ≥70% viability to generate complementary DNA and prepare scRNA-seq libraries
Library was perfomed according to the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics).

value: Teratoma

value: CD45+ cells

tag: Sex

value: Male

tag: time

value: Day 40


title: WT_OPT_EARLYLOG_B3_vs_M365_CS_POST_5h_B2

value: ATCC 3502 cbo0365::intron-erm-sense


title: CHIP2024_407_Wave5

description: Library name: CHIP2024_407_Wave5


title: Day40, replicate1, scRNAseq

description: 10x Genomics


title: WT_OPT_T4_B2_vs_MsigD_OPT_T4_B2

value: ATCC 3502 cbo2641_sigD::intron-erm-


title: HC3523, GMCSF+IL6, scMultiome_ATAC

value: PBMCs, in vitro culture


title: WT_OPT_T1_B3_vs_MsigD_OPT_T1_B3


title: HC3529, control, scMultiome_ATAC

value: control


title: CHIP2024_405_Wave5

description: Library name: CHIP2024_405_Wave5

value: PBMCs


title: WT_OPT_T3_B2_vs_MflgE_OPT_T3_B2

value: ATCC 3502 cbo2654_flgE::intron-erm-


title: CHIP2024_405_Wave3

description: Library name: CHIP2024_405_Wave3


title: CHIP2024_407_Wave1

description: Library name: CHIP2024_407_Wave1


title: Day20, replicate2, scRNAseq

description: 10x Genomics

value: Day 20


title: CHIP2024_406_Wave1

description: Library name: CHIP2024_406_Wave1


title: LLC_Scramble

description:
Library name: Sample 1
nc_filtered_feature_bc_matrix

value: scramble control


title: MflgE_OPT_T1_B3_vs_WT_OPT_T1_B3


title: HC3533, control, scMultiome_ATAC


title: CHIP2024_405_Wave1

description: Library name: CHIP2024_405_Wave1


title: Day10, replicate2, scRNAseq

description: 10x Genomics

value: Day 10


title: Day10, replicate1, scRNAseq

description: 10x Genomics


title: HC3531, control, scMultiome_ATAC


title: MsigD_OPT_T4_B3_WT_OPT_T4_B3


title: CHIP2024_463_Wave5

description: Library name: CHIP2024_463_Wave5


title: KPC cells, NA-Chd4-Rep2

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

description: 10 × Genomics

data_processing:
FASTQ files were trimmed with Fastp software (Fastp version 0.12.4), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2(Bowtie2 version 2.3.5.1)
Peaks were called over input using MACS2 (version 2.2.7.1)84 and only peaks with a q-value < 0.05 were kept , and then annotated by HOMER(version 4.11.1)
The Diffbind R package (version 3.8.4) was used to generate the count matrix for each consensus peak. DARs(differentially accessible regions) were identified between conditions using the limma R package with P < 0.05 and |fold change|>0.58. To visualize peaks , we use “plotHeatmap” commamd to plot Heatmap and "bamCoverage" command, adding the parameter "--normalizeUsingRPKM" to convert bam files to bw format with Deeptools (version 1.9). CUT&Tag signals of H3K27ac and Chd4 were calculated by BEDTools
Visualization of the depositions along genomic regions was using IGV (2.6.3)
Assembly: mm10
Supplementary files format and content: BigWig

source_name: KPC cell

growth_protocol: RPMI 1640,15% fetal bovine serum, 2mM glutamine, 1x pen:illin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Genomic DNA was extracted using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
Sequencing libraries were prepared according to the manufacturer's protocol and cleaned-up using XP beads (Beckman Coulter). Sequencing was conducted on the Illumina NovaSeq 6000 platform using PE150.

treatment_protocol: Vehicle or NA treatment (10 μM)

value: KPC cell

value: Mouse pancreatic cancer cell line

value: WT

tag: chip antibody


title: HC3514, control, scMultiome_ATAC


title: WT_OPT_T4_B2_vs_MflgE_OPT_T4_B1

value: wild-type


title: MsigD_OPT_T3_B2_vs_WT_OPT_T3_B2


title: KPC cells, NA-Chd4-Rep1

description: 10 × Genomics


title: CHIP2024_463_Wave3

description: Library name: CHIP2024_463_Wave3


title: CHIP2024_463_Wave1

description: Library name: CHIP2024_463_Wave1


title: HC3523, control, scMultiome_ATAC


title: KPC cells, Vehicle-Chd4-Rep2

description: 10 × Genomics

value: Vehicle


title: Day20, replicate1, scRNAseq

description: 10x Genomics

value: Teratoma

value: CD45+ cells


title: HC3524, control, scMultiome_ATAC


title: CHIP2024_404_Wave5

description: Library name: CHIP2024_404_Wave5


title: MflgE_OPT_T4_B2_vs_WT_OPT_T4_B2


title: HC3533, GMCSF+IL6, scMultiome_GEX


title: CHIP2024_404_Wave3

description: Library name: CHIP2024_404_Wave3


title: KPC cells, NA-H3K27ac-Rep2

description: 10 × Genomics


title: WT_OPT_T3_B3_vs_MflgE_OPT_T3_B3


title: CHIP2024_404_Wave1

description: Library name: CHIP2024_404_Wave1


title: MflgE_OPT_T2_B1_vs_WT_OPT_T2_B1


title: HC3531, GMCSF+IL6, scMultiome_GEX


title: KPC cells, NA-H3K27ac-Rep1

description: 10 × Genomics


title: KPC cells, Vehicle-H3K27ac-Rep2

description: 10 × Genomics


title: CHIP2024_403_Wave3

description: Library name: CHIP2024_403_Wave3


title: HC3514, GMCSF+IL6, scMultiome_GEX


title: HC3529, GMCSF+IL6, scMultiome_GEX


title: KPC cells, Vehicle-H3K27ac-Rep1

description: 10 × Genomics


title: KPC cells, Vehicle-Chd4-Rep1

description: 10 × Genomics


title: HC3523, GMCSF+IL6, scMultiome_GEX


title: WT_OPT_T2_B1_vs_M1120_OPT_T2_B1


title: Gli1creERT-Hhipflox_TamP14

city: Zhongshan

first: Chaoqun

last: Wang

state: Guangdong province

address: Xiangshan Street

institute: Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
10X Genomics Cell Ranger software (version3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: mm10
Supplementary files format and content: Matrix table with rwa gene for every gene and every cell

source_name: lung

extract_protocol:
Cell viability was assessed by trypan blue staining and the sam ples (cell viability >90%) were prepared using a 10x Genomics Single Cell 30 v2 Reagent Kit according to the manufacturer’s instructions.
R1 (read1primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence)were added during library construction via End Repair,A-tailing, Adaptor Ligation,and PCR.The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: lung


title: HC3524, GMCSF+IL6, scMultiome_GEX


title: Gli1creERT-Hhipflox_OilP14

description: 10x Genomics


title: CHIP2024_462_Wave5

description: Library name: CHIP2024_462_Wave5


title: WT_OPT_T4_B3_vs_M0780_OPT_T4_B3

value: ATCC 3502 cbo0780::intron-erm-


title: CHIP2024_403_Wave1

description: Library name: CHIP2024_403_Wave1


title: HC3529, control, scMultiome_GEX


title: WT_OPT_T6_B1_vs_Mspo0A_OPT_T6_B1

value: ATCC 3502 cbo1872_spo0A::intron-erm-


title: CHIP2024_462_Wave3

description: Library name: CHIP2024_462_Wave3


title: HC3524, control, scMultiome_GEX

value: PBMCs, in vitro culture


title: CHIP2024_403_Wave5

description: Library name: CHIP2024_403_Wave5


title: WT_OPT_T2_B2_vs_M0780_OPT_T2_B2


title: HC3533, control, scMultiome_GEX

value: control


title: CHIP2024_462_Wave1

description: Library name: CHIP2024_462_Wave1

value: PBMCs


title: M0780_OPT_T4_B1_vs_WT_OPT_T4_B1_1


title: Control_HSPC

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

description: 10x Genomics

data_processing:
Gene counts were generated by running cellranger count (6.1.2) with mm10-2020A as the transcriptome dataset.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Lineage-cKit+ cells were collected in PBS with 2% FBS and centrifuged, and the pellet was resuspended in Cellbanker and frozen for storage. After thawing the cells, the number of viable cells was counted before use in experiments.
Libraries were prepared according to the manufacturer’s protocol using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3.1 and Dual Index Kit.

treatment_protocol: Mice received 500 µg/mouse polyinosine-polycyticylic acid (pI-pC) injection every other day for a total of 3 doses.

value: Bone marrow

value: Lineage- cKit+ bone marrow cells in femora and tibiae

value: Trsp f/f

value: pI-pC


title: Trsp_KO_CD11b_2

description:
CD11b_4
NORcount_CD11b.txt

data_processing:
RNA-seq raw-data was cleaned by FastP(PE mode) and aligned to GRCm38/mm10 by Hisat2(2.2.1)
Data were filtered using Samtools(1.9) and converted to BAM files
Read counted by FeatureCount from Subreads Packages(R)
Counts data was normalized by Deseq2 with significant difference genes were screened out
Assembly: GRCm38/mm10
Supplementary files format and content: raw counts, Differentially expressed gene Excel

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD11b+ bone marrow cells in femora and tibiae

value: Trsp f/f:Mx1-Cre


title: WT_OPT_T2_B1_vs_MsigD_OPT_T2_B1

value: ATCC 3502 cbo2641_sigD::intron-erm-


title: MflgE_OPT_T2_B2_vs_WT_OPT_T2_B2

value: ATCC 3502 cbo2654_flgE::intron-erm-

value: wild-type


title: CHIP2024_491_Wave5

description: Library name: CHIP2024_491_Wave5


title: HC3514, control, scMultiome_GEX


title: CHIP2024_491_Wave3

description: Library name: CHIP2024_491_Wave3


title: Trsp_KO_CD11b_1

description:
CD11b_3
NORcount_CD11b.txt


title: Mspo0A_OPT_T6_B3_vs_WT_OPT_T6_B3


title: Trsp_KO_HSPC

description: 10x Genomics


title: HC3523, control, scMultiome_GEX


title: Control_CD11b_2

description:
CD11b_2
NORcount_CD11b.txt


title: WT_OPT_T6_B1_vs_M0780_OPT_T6_B1


title: WT_OPT_T4_B2_vs_Mspo0A_OPT_T4_B2


title: CHIP2024_491_Wave1

description: Library name: CHIP2024_491_Wave1


title: SLX-22619.B5_Ven_res_3_hs

city: Cambridge

first: Sarah

middle: J

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

country: United Kingdom

institute: University of Cambridge

description: RNA-seq

data_processing:
Paired end RNA-seq reads were quality filtered and adapter sequences were trimmed using TrimGalore package.
Trimmed sequence reads were mapped using STAR version=2.7.10a against the human genome (Hg38). Uniquely-mapping, high confidence reads were retained using the following flags (NH:i:1 and MAPQ=255).
Read counts were quantified with featureCounts version 2.0.1
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: tab-delimited text files containing read counts for each gene (in ENSEMBL IDs)

source_name: B-ALL cell line 697

extract_protocol:
697WT and 697KI were harvested, washed and RNA was extracted from 4×106 cells using the RNeasy kit (Qiagen).
Libraries were prepared using NEBNext Poly(A) mRNA magnetic Isolation module (NEB, E7490) starting with 1µg DNA-free RNA, as per manufacturer’s instructions. RNA fragmentation, double-strand cDNA synthesis, end repair, adapter ligation and PCR amplification (9 cycles) was performed using NEBNext Ultra II directional RNA library prep kit for Illumina protocol (NEB, E7760) according to manufacturer’s protocol. Library quality and molarity was measured by Qubit (ThermoFisher) and TapeStation (Agilent). Samples were 50-bp paired-end sequenced on the NovaSeq (Illumina) instrument (CRUK CI Genomics Core Facility).

treatment_protocol: B-ALL cell line 697 (697WT & 697KI) were treated with 20nM Venetoclax or DMSO vehicle for 24h, then harvested and RNA was extracted from 4×106 cells. All experiments were performed in triplicate.

value: B-ALL cell line 697


title: CHIP2024_490_Wave3

description: Library name: CHIP2024_490_Wave3


title: Trsp_KO_Pre-B_4

description:
PreB_8
NORcount_PreB.txt

value: CD3-CD11b-Gr-1-Ter-119-IgM-CD19+CD43- bone marrow cells in femora and tibiae


title: CHIP2024_490_Wave5

description: Library name: CHIP2024_490_Wave5


title: SLX-22619.4B7_Ven_res_3_hs

description: RNA-seq


title: Control_CD11b_1

description:
CD11b_1
NORcount_CD11b.txt


title: WT_OPT_T4_B2_vs_M0780_OPT_T4_B2


title: HC3531, control, scMultiome_GEX


title: Mspo0A_OPT_T4_B1_vs_WT_OPT_T4_B1


title: SLX-22619.4B7_Ven_res_2_hs

description: RNA-seq


title: CHIP2024_490_Wave1

description: Library name: CHIP2024_490_Wave1


title: SLX-22619.B5_Ven_res_2_hs

description: RNA-seq


title: M0780_OPT_T6_B2_vs_WT_OPT_T6_B2


title: Trsp_KO_Pre-B_3

description:
PreB_7
NORcount_PreB.txt


title: WT_OPT_T2_B3_vs_Mspo0A_OPT_T2_B3


title: CHIP2024_489_Wave5

description: Library name: CHIP2024_489_Wave5


title: Trsp_KO_Pre-B_2

description:
PreB_4
NORcount_PreB.txt


title: SLX-22619.4B7_Ven_res_1_hs

description: RNA-seq


title: Trsp_KO_Pre-B_1

description:
PreB_3
NORcount_PreB.txt


title: CHIP2024_489_Wave3

description: Library name: CHIP2024_489_Wave3


title: CHIP2024_489_Wave1

description: Library name: CHIP2024_489_Wave1


title: SLX-22619.B5_Ven_res_1_hs

description: RNA-seq


title: WT_OPT_T4_B2_vs_M1120_OPT_T4_B2

value: ATCC 3502 cbo1120::intron-erm-


title: CHIP2024_401_Wave5

description: Library name: CHIP2024_401_Wave5


title: Control_Pre-B_4

description:
PreB_6
NORcount_PreB.txt


title: SLX-22619.4B7_DMSO_3_hs

description: RNA-seq


title: Mspo0A_OPT_T2_B2_vs_WT_OPT_T2_B2


title: Control_Pre-B_3

description:
PreB_5
NORcount_PreB.txt


title: SLX-22619.B5_DMSO_3_hs

description: RNA-seq


title: CHIP2024_401_Wave3

description: Library name: CHIP2024_401_Wave3


title: Mspo0A_OPT_T2_B1_vs_WT_OPT_T2_B1


title: SLX-22619.B5_DMSO_2_hs

description: RNA-seq


title: Control_Pre-B_2

description:
PreB_2
NORcount_PreB.txt


title: WT_OPT_T3_B3_vs_MsigD_OPT_T3_B3


title: Control_Pre-B_1

description:
PreB_1
NORcount_PreB.txt


title: CHIP2024_401_Wave1

description: Library name: CHIP2024_401_Wave1


title: Trsp_KO_Prepro-B_4

description:
PreproB_8
NORcount_PreproB.txt

value: CD3-CD11b-Gr-1-Ter-119-IgM-CD19-CD43+ bone marrow cells in femora and tibiae


title: SLX-22619.4B7_DMSO_2_hs

description: RNA-seq


title: SLX-22619.4B7_DMSO_1_hs

description: RNA-seq


title: CHIP2024_460_Wave5

description: Library name: CHIP2024_460_Wave5


title: MflgE_OPT_T4_B3_vs_WT_OPT_T4_B3


title: SLX-22619.B5_DMSO_1_hs

description: RNA-seq


title: Trsp_KO_Prepro-B_3

description:
PreproB_7
NORcount_PreproB.txt


title: CHIP2024_460_Wave1

description: Library name: CHIP2024_460_Wave1


title: Trsp_KO_Prepro-B_2

description:
PreproB_4
NORcount_PreproB.txt


title: CHIP2024_460_Wave3

description: Library name: CHIP2024_460_Wave3


title: WT_OPT_T2_B2_vs_MsigD_OPT_T2_B2


title: Mspo0A_OPT_T6_B2_vs_WT_OPT_T6_B2_1

value: ATCC 3502 cbo1872_spo0A::intron-erm-


title: SLX-22618.4B7_Ven_20nm_3_hs

description: RNA-seq


title: CHIP2024_459_Wave5

description: Library name: CHIP2024_459_Wave5


title: CHIP2024_459_Wave3

description: Library name: CHIP2024_459_Wave3


title: WT_OPT_T1_B2_vs_MflgE_OPT_T1_B2


title: Control_Prepro-B_4

description:
PreproB_6
NORcount_PreproB.txt


title: WT_OPT_T1_B1_vs_MflgE_OPT_T1_B1


title: MflgE_OPT_T3_B1_vs_WT_OPT_T3_B1


title: SLX-22618.4B7_Ven_20nm_2_hs

description: RNA-seq


title: CHIP2024_459_Wave1

description: Library name: CHIP2024_459_Wave1


title: Control_Prepro-B_2

description:
PreproB_2
NORcount_PreproB.txt


title: M0780_OPT_T4_B1_vs_WT_OPT_T4_B1

value: ATCC 3502 cbo0780::intron-erm-


title: SLX-22618.B5_Ven_20nm_2_hs

description: RNA-seq


title: SLX-22618.4B7_Ven_20nm_1_hs

description: RNA-seq


title: CHIP2024_488_Wave5

description: Library name: CHIP2024_488_Wave5


title: M1120_OPT_T2_B2_vs_WT_OPT_T2_B2


title: SLX-22618.B5_Ven_20nm_1_hs

description: RNA-seq


title: MsigD_OPT_T2_B3_vs_WT_OPT_T2_B3


title: Mspo0A_OPT_T6_B2_vs_WT_OPT_T6_B2


title: Trsp_KO_HSPC_3

description:
Trsp_169
NORcount_HSPC.txt


title: CHIP2024_488_Wave1

description: Library name: CHIP2024_488_Wave1


title: Control_Prepro-B_1

description:
PreproB_1
NORcount_PreproB.txt


title: Trsp_KO_HSPC_4

description:
Trsp_172
NORcount_HSPC.txt


title: CHIP2024_488_Wave3

description: Library name: CHIP2024_488_Wave3


title: CHIP2024_399_Wave3

description: Library name: CHIP2024_399_Wave3


title: SLX-22618.4B7_DMSO_3_hs

description: RNA-seq


title: SLX-22618.B5_DMSO_3_hs

description: RNA-seq


title: CHIP2024_399_Wave5

description: Library name: CHIP2024_399_Wave5


title: M1120_OPT_T4_B3_vs_WT_OPT_T4_B3


title: SLX-22618.B5_Ven_20nm_3_hs

description: RNA-seq


title: Trsp_KO_Prepro-B_1

description:
PreproB_3
NORcount_PreproB.txt


title: Control_Prepro-B_3

description:
PreproB_5
NORcount_PreproB.txt


title: WT_OPT_T2_B3_vs_M1120_OPT_T2_B3


title: SLX-22618.4B7_DMSO_2_hs

description: RNA-seq


title: CHIP2024_399_Wave1

description: Library name: CHIP2024_399_Wave1


title: Trsp_KO_HSPC_2

description:
Trsp_162
NORcount_HSPC.txt


title: SLX-22618.B5_DMSO_2_hs

description: RNA-seq


title: Trsp_KO_HSPC_1

description:
Trsp_158
NORcount_HSPC.txt


title: M0780_OPT_T2_B1_vs_WT_OPT_T2_B1


title: CHIP2024_458_Wave5

description: Library name: CHIP2024_458_Wave5


title: Control_HSPC_4

description:
Trsp_171
NORcount_HSPC.txt


title: SLX-22618.4B7_DMSO_1_hs

description: RNA-seq


title: Mspo0A_OPT_T4_B3_vs_WT_OPT_T4_B3


title: CHIP2024_458_Wave3

description: Library name: CHIP2024_458_Wave3


title: Control_HSPC_3

description:
Trsp_170
NORcount_HSPC.txt


title: M1120_OPT_T6_B3_vs_WT_OPT_T6_B3


title: CHIP2024_458_Wave1

description: Library name: CHIP2024_458_Wave1


title: SLX-22618.B5_DMSO_1_hs

description: RNA-seq


title: CHIP2024_457_Wave5

description: Library name: CHIP2024_457_Wave5


title: SUP-B15, shIKZF1, rep 2 (rna)

city: Palo Alto

first: Pablo

last: Domizi

state: CA

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

data_processing:
Sequence reads were mapped to GrCh38.p13/hg38 using SALMON (version 1.2.0)
Reads aligning to annotated regions were summarized as counts using R package tximport (version 1.18.0).
Read counts were normalized using variance-stabilizing transformation (vst) build into the DESeq2 package (version 1.30.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include vst values for each sample

growth_protocol: NALM6 and REH cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. SUP-B15 cells were maintained in IMDM supplemeted with 20% FBS under same conditions.

extract_protocol:
RNA was harvested using Rneasy mini kit, with Dnase I treatment (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocols.

treatment_protocol: Cells were transduced with lentivirus expressing IKZF1 specific or scramble shRNA, and maintained in culture for additionnal 72 hours.

value: IKAROS  KD

tag: replicate

value: rep 2


title: WT_OPT_T6_B3_vs_M0780_OPT_T6_B3


title: SUP-B15, shIKZF1, rep 1 (rna)

value: rep 1


title: Control_HSPC_1

description:
Trsp_157
NORcount_HSPC.txt

value: Bone marrow

value: Lineage- cKit+ bone marrow cells in femora and tibiae


title: SUP-B15, shCTRL, rep 2 (rna)

value: WT


title: MEF_33_Prrx1_KO_rep2

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameter: )
Trimmed sequence reads were mapped to mm10 genome
The gene expression level was calculated by Cufflinks and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count and FPKM values for each Sample

source_name: primary MEF

growth_protocol: E14.5 primary MEFs were generated from wild‑type，Prrx1+/‑ or Prrx1‑/‑ C57BL/6 littermates and were cultured in DMEM medium containing 10% fetal bovine serum and 1% penicillin–streptomycin (10,000 U/mL)at 37°C in 5% (v/v) CO2.

extract_protocol:
Total RNA isolation of MEFs was performed using RNAiso Plus (TAKARA) according to manufacturer’s instructions. Total RNA was converted to cDNA using HiScript II Q RT SuperMix (Vazyme).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: primary MEF

value: embryonic fibroblast


title: MEF_32_Prrx1_KO_rep1


title: WT_OPT_T6_B2_vs_M1120_OPT_T6_B2


title: WT_OPT_T6_B1_vs_M1120_OPT_T6_B1


title: Control_HSPC_2

description:
Trsp_161
NORcount_HSPC.txt

value: Trsp f/f

value: pI-pC


title: M0780_OPT_T2_B3_vs_WT_OPT_T2_B3

value: wild-type


title: CHIP2024_457_Wave1

description: Library name: CHIP2024_457_Wave1

value: PBMCs


title: MEF_24_Prrx1_Het_rep2


title: SUP-B15, shCTRL, rep 1 (rna)


title: WT_OPT_T4_B2_vs_WT_OPT_T1_B2


title: CHIP2024_456_Wave5

description: Library name: CHIP2024_456_Wave5


title: CHIP2024_456_Wave3

description: Library name: CHIP2024_456_Wave3


title: M1120_OPT_T4_B1_vs_WT_OPT_T4_B1


title: REH, shIKZF1, rep 1 (rna)

source_name: REH

value: REH


title: CHIP2024_456_Wave1

description: Library name: CHIP2024_456_Wave1


title: MEF_25_WT_rep2


title: WT_OPT_T5_B2_vs_WT_OPT_T1_B2


title: CHIP2024_487_Wave5

description: Library name: CHIP2024_487_Wave5


title: CHIP2024_457_Wave3

description: Library name: CHIP2024_457_Wave3


title: REH, shCTRL, rep 2 (rna)


title: WT_OPT_T2_B2_vs_WT_OPT_T1_B2


title: MEF_23_WT_rep1


title: REH, shCTRL, rep 1 (rna)


title: CHIP2024_487_Wave3

description: Library name: CHIP2024_487_Wave3


title: WT_OPT_T3_B2_vs_WT_OPT_T1_B2


title: REH, shIKZF1, rep 2 (rna)


title: NALM6, shIKZF1, rep 1 (rna)


title: epithelial cells, RY_07

city: San Diego

first: Sunyoung

last: Lee

address: 9500 Gilman Drive

institute: University of California, San Diego

description: 10X Genomics

data_processing:
Using the software package Cell Ranger v3.0.2(10x Genomics), sequenced reads were demultiplexed (cellranger mkfastq) into FASTQ files and aligned (cellranger count) to the mouse reference genome mm10.
The resulting raw gene-by-cell count matrices were filtered using the software package CellBender59 to remove ambient RNA (cellbender remove-background) from the count matrix. Default CellBender parameters were used with the exception of --expected-cells and --total-droplets-included, which were individually determined for each single cell library based on UMI curves generated by Cell Ranger. The filtered count matrices were then loaded into Seurat60
Genes present in at least 3 cells and cells with a minimum of 200 detected genes were included in downstream analysis. Doublets were removed using the scDblFinder v1.13.1 R package61. Furthermore, cells with greater than 10% mitochondrial gene content were removed from the dataset. UMI counts were normalized, scaled, and top variable features were identified using the SCTransform62 function. UMI matrices were integrated utilizing anchors determined by reciprocal PCA.
Assembly: mouse mm10
Supplementary files format and content: h5 files from Cell Ranger

source_name: Lung

extract_protocol:
Immune cells and endothelial cells were excluded by depletion and epithelial cells were selected for by EPCAM expression and then sorted into GFP+ and GFP- populations. For the club cell mutant lungs (Scgb1a1creERT; Cdh1CKO;Sun1GFP/+), GFP+ and GFP- populations were used to make separate 10X scRNA-seq libraries. Due to limited number of GFP+ cells in the control lungs (Scgb1a1creERT; Cdh1flox/+;Sun1GFP/+), GFP+ and GFP- cells were combined into the same library at equal proportions.
For scRNA, single cell libraries were generated by using Chromium Single Cell 3’ v3 kit (10X Genomics).

value: Lung

value: Epithelial cell

tag: age

value: 8-12 weeks

value: Scgb1a1creERT/+; Cdh1F/F; Sun1GFP/+


title: MEF_22_Prrx1_Het_rep1


title: WT_OPT_T1_B1_vs_WT_OPT_T4_B1


title: CHIP2024_486_Wave5

description: Library name: CHIP2024_486_Wave5


title: CHIP2024_486_Wave3

description: Library name: CHIP2024_486_Wave3


title: NALM6, shIKZF1, rep 2 (rna)

value: IKAROS  KD


title: WT_OPT_T1_B1_vs_WT_OPT_T5_B1


title: CHIP2024_487_Wave1

description: Library name: CHIP2024_487_Wave1


title: WT_OPT_T1_B1_vs_WT_OPT_T2_B1


title: epithelial cells, RY_06

description: 10X Genomics


title: OVA5

city: Nanjing

first: shan

last: zhang

state: Jiangsu

address: 12 Jiangwangmiao St

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

data_processing:
quality control
reads mapping to the reference genome
quantification of gene expression level
differential expression analysis
enrichment analysis of differentially expressed genes, gene set enrichment analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep Kit (Cat#FC-122-1001) was used to total RNA extraction.
Total RNA was used as input material for the RNA sample preparations.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magneticbeads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase HRemaining overhangs were converted into blunt ends via exonuclease/polymerase activities.After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-FidelityDNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products werepurified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: skin

value: OVA


title: epithelial cells, RY_05

description: 10X Genomics

value: Scgb1a1creERT/+; Cdh1F/+; Sun1GFP/+


title: NALM6, shCTRL, rep 2 (rna)

value: rep 2


title: OVA4


title: CHIP2024_486_Wave1

description: Library name: CHIP2024_486_Wave1


title: NALM6, shCTRL, rep 1 (rna)

value: WT

value: rep 1


title: WT_OPT_T1_B1_vs_WT_OPT_T3_B1


title: CHIP2024_485_Wave5

description: Library name: CHIP2024_485_Wave5


title: OVA3


title: OVA2


title: SUP-B15, shIKZF1, rep 1 (atac)

data_processing:
ENCODE ATAC-seq piipeline
Sequenced reads were trimmed for adaptor and low-quality sequences using cutadapt.
Trimmed sequence were aligned to hg38 using bowtie2. We filtered for non-mithocondrial reads, mapq > 20 and properly paired reads.
Duplicates were removed using Picard tools.
Peaks were called using macs2 with the following parameters on Tn5 insertion sites: --shift -75 –extsize 150 –nomodel –call-summits –nolambda -p 0.01 -B –SPMR.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Nuclei were prepared from 50,000 sorted cells prior to transposition. Following transposition, DNA was extracted and 10 cycles of PCR was performed.
According to the ATAC-seq protocol (Buenrostro JD, PMID: 24097267)


title: SUP-B15, shIKZF1, rep 2 (atac)


title: CHIP2024_485_Wave3

description: Library name: CHIP2024_485_Wave3

data_processing:
Reads were quality-filtered with a ‘phred’ score threshold of ≥30, and adapter sequences were removed using Trimmomatic (version 0.27) (Bolger et al. 2014). Afterward, guided alignment to the human genome assembly hg19 was performed using both bwa-mem (version 0.7.17) and bowtie2 (version 2.2.1) (Langmead & Salzberg 2012; Li & Durbin 2009). Unique molecular barcodes, introduced before PCR amplification, were utilized for deduplication to enable accurate multiplexed quantification and reliable mutation detection. Variant calling within targeted regions was conducted using three different tools: Lofreq (version 2.1.0) (Wilm et al. 2012), Freebayes (Garrison & Marth 2012), and Vision (ArcherDX version 6.2.7, unpublished). A consensus was generated by combining the results and selecting for agreement from all three variant callers (see Supplementary Table 3).
All filtered variants with a variant allele frequency (VAF) of 1% or 2% satisfied the following conditions: (1) the number of reads supporting the alternative allele exceeded the minimum coverage requirement without displaying directional bias (AO ≥ 5, UAO ≥ 3); (2) the variants were significantly underrepresented in the Genome Aggregation Database (gnomAD; P ≤ 0.05); (3) the variants were unlikely to be germline, as indicated by a stable VAF (50% or 100%) across all sequencing waves, which could have been underrepresented in gnomAD due to the limited geographic diversity of the LBC cohort; and (4) the variants included events, such as frameshift duplications and deletions, that were overrepresented in the dataset, likely reflecting misaligned artifacts from the capture method (see Supplementary Table 3) (Karczewski et al. 2020). Additionally, the list was manually curated, cross-referencing variants previously reported in COSMIC, Jaiswal et al., or other published studies (Tate et al. 2019). Finally, for any variant that met the above criteria with a VAF of ≥ 1% or 2% at any time point, all participant-matched data points were included, regardless of baseline VAF.
Assembly: hg19
Supplementary files format and content: tsv - custom variant file format - somatic and synonymous variant calls for 1% and 2% VAF

extract_protocol:
Our expanded cohort longitudinally sampled from the LBC1936 was processed as per our previous work. Briefly, DNA was extracted from whole blood with Ethylenediaminetetraacetic acid (EDTA) using the Nucleon BACC3 kit (Sigma-Aldrich, GERPN8512), according to the manufacturer’s protocol.
Libraries were generated from 200 ng of each DNA sample using the Invitea/Archer VariantPlex® 75 Myeloid gene panel and the VariantPlex® Somatic Protocol for Illumina sequencing (Invitae, AB0108, and the VariantPlex®-HCG Myeloid Kit; see Supplementary Table 2), with adaptations for detecting low variant allele frequencies. Sequencing was performed on the NextSeq 550 platform (Illumina) using the NextSeq 500/550 High-Output version 2.5 kit (300 cycles). Two ‘Genome in a Bottle’ (GIAB) DNA samples (NA12878, Coriell Institute) were included in each sequencing batch to ensure reproducibility and support background error modeling and batch correction.


title: SUP-B15, shCTRL, rep 2 (atac)


title: Knockout rep1

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

description:
Library name: K1
Column name K1

data_processing:
Bulk RNA seq workflow
Trimming: Trim data using Trimmomatic with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 CROP:150
Alignment: Align reads using STAR with parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 2
Counting: Generate raw counts using featureCounts with parameters: -t exon -g gene_id -s 1
Assembly: GRCm39 version 112
Supplementary files format and content: csv file includes raw counts for all Samples
Supplementary files format and content: csv file include TPM values for all Samples

source_name: Whole Uterus

growth_protocol: Gestational Day 4 mouse uteri

extract_protocol:
RNeasyÒ Plus Mini Kit protocol (Qiagen 74134)
Libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina

treatment_protocol: Control and conditional knockout mice were collected on gestational day 4

value: Whole Uterus

value: Prss29Cre/Cre;Pgrf/f (Pgr gecKO)


title: Knockout rep2

description:
Library name: K2
Column name K2


title: OVA1


title: CHIP2024_485_Wave1

description: Library name: CHIP2024_485_Wave1


title: CHIP2024_432_Wave3

description: Library name: CHIP2024_432_Wave3


title: TSB3

value: TSB


title: SUP-B15, shCTRL, rep 1 (atac)


title: Control rep2

description:
Library name: C2
Column name C2

value: Control WT


title: Control rep1

description:
Library name: C1
Column name C1


title: TSB2


title: CHIP2024_432_Wave4

description: Library name: CHIP2024_432_Wave4

value: PBMCs


title: REH, shIKZF1, rep 1 (atac)

value: REH


title: NR_7d_Amp.73_M00.07232015.Left

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
FASTQ files were generated by CASAVA.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized
Assembly: mm10
Supplementary files format and content: The gene expected read counts and TPMs were estimated by RSEM (v1.2.3).

source_name: mouse distal terminal phalanx

extract_protocol:
Total RNAs were isolated from tissues using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
One hundred nanograms of total RNA was used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol(Hou et al., 2015).
RNAs was selected using the NEB Next Poly A+ Isolation Kit (NEB #E7490S/L).

value: mouse distal terminal phalanx

value: A mixture cell types around wound bed


title: REH, shCTRL, rep 2 (atac)


title: NR_7d_Amp.75_M00.11182015.Left


title: REH, shIKZF1, rep 2 (atac)


title: S.aureus4


title: TSB1


title: NR_7d_Amp.72_R2.11182015.Right


title: CHIP2024_484_Wave4

city: Rochester

first: Neil

last: Robertson

address: 200 1st Street

institute: MAYO CLINIC ROCHESTER

description: Library name: CHIP2024_484_Wave4


title: S.aureus3


title: NALM6, shIKZF1, rep 2 (atac)


title: CHIP2024_484_Wave1

description: Library name: CHIP2024_484_Wave1


title: NR_7d_Amp.63_L1.07232015.Left


title: NR_7d_Amp.65_R1.11182015.Right


title: S.aureus2


title: S.aureus1


title: CHIP2024_429_Wave4

description: Library name: CHIP2024_429_Wave4


title: NR_6h_Amp.76_M00.11192015.Left


title: CHIP2024_432_Wave1

description: Library name: CHIP2024_432_Wave1


title: NALM6, shCTRL, rep 2 (atac)


title: NR_6h_Amp.74_M00.07152015.Left.P3


title: CHIP2024_429_Wave3

description: Library name: CHIP2024_429_Wave3


title: Acetone Olive oil2

value: Acetone Olive oil


title: Acetone Olive oil3


title: NALM6, shCTRL, rep 1 (atac)


title: CHIP2024_429_Wave1

description: Library name: CHIP2024_429_Wave1


title: NR_6h_Amp.60_R1.07152015.Left


title: CHIP2024_483_Wave3

description: Library name: CHIP2024_483_Wave3


title: REH, shCTRL, rep 1 (atac)


title: CHIP2024_483_Wave4

description: Library name: CHIP2024_483_Wave4


title: PANC-1_sh-NAT10_acRIP_Rep 3

first: Leyi

last: Huang

state: Guangdong

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

description:
acRIP-seq
T1_peak.txt

data_processing:
For RNA-seq, total RNA in cells was extracted by using TRIzol™ Reagent (Invitrogen™, Cat# 15596018) and detected by Bioptic Qseq100 Bio-Fragment Analyzer (Bioptic lnc.). DNase I (Invitrogen™, Cat# EN0525) treatment was adopted to remove DNA contamination. Additional phenol-chloroform isolation and ethanol precipitation treatments were performed to remove enzyme contamination. The library preparation was performed according
Breifly, adaptor and primer sequences from the library were trimmed. Following trimming, sequence reads were then aligned to the human genome genome (version hg38) using Hisat2(version 2 2.1.0) followed by a post-alignment quality check to assess the performance of the alignment. After alignment, HTseq (version 0.11.0) were used to calculate the counts of the Reads mapped the genome. FPKM（Fragments Per Kilo base Million Reads）was used to standardize the expression data. which allowed the comparison of expression levels between mRNAs. We applied DESeq2 (version 1.22.2) algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i)log2FC>1; ii) FDR < 0.05. Volcano Plots were drawn by the R based on the differentially gene analysis and the color was determined by the filtering criteria.
For acRIP-Seq, total RNA in cells was extracted by using TRIzol™ Reagent (Invitrogen™, Cat# 15596018) and detected by Bioptic Qseq100 Bio-Fragment Analyzer (Bioptic lnc.). DNase I (Invitrogen™, Cat# EN0525) treatment was adopted to remove DNA contamination. Additional phenol-chloroform isolation and ethanol precipitation treatments were performed to remove enzyme contamination.
Peaks were called using exomePeak.
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: For acRIP-seq, tab-delimited text files include peak calling values.

source_name: Pancreatic tumor cells

extract_protocol:
The PANC-1 cells were divided in two groups: 1.PANC-1 transfected with short hairpin RNA (shRNA) empty vector; 2.PANC-1 transfected with shRNA vector which could knockdown the expression of NAT10. Lentivirus was used to carry shRNAs, respectively.
For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols. For acRIP-seq, fragmented total RNA (Input) and immunoprecipitated RNA (IP) were subjected to library construction by using EpiTM mini longRNA-seq kit(Epibiotek, Cat# E1802) according to the manufacturer’s protocols. Breifly, reverse transcription was performed using random primers and the ribosome cDNA (cDNA fragments originating from rRNA molecules) was removed after cDNA synthesis using probes specific to mammalian rRNA. The directionality of the template-switching reaction not only preserves the 5’ end sequence information of RNA but the strand orientation of the original RNA. Libraries for immunoprecipitated RNA were PCR amplified for 18 cycles. Libraries quality were determined on Qseq100 Bio-Fragment Analyzer（Bioptic lnc.）.The strand-specific libraries were sequenced on Illumina Novaseq 6000 system with paired-end 2×150 bp read length.

tag: disease

value: Pancreatic cancer

tag: shRNA


title: PANC-1_sh-NAT10_acRIP_Rep 2

description:
acRIP-seq
T1_peak.txt


title: DNFB+OVA4

value: DNFB+OVA


title: CHIP2024_484_Wave3

description: Library name: CHIP2024_484_Wave3


title: NR_3h_Amp.75_M00.07142015.Left


title: CHIP2024_483_Wave1

description: Library name: CHIP2024_483_Wave1


title: PANC-1_sh-NAT10_acRIP_Rep 1

description:
acRIP-seq
T1_peak.txt


title: NR_3h_Amp.64_L1.07142015.Left


title: DNFB+OVA3

value: skin


title: NALM6, shIKZF1, rep 1 (atac)

value: IKAROS  KD


title: PANC-1_sh-NAT10_Input_Rep 3

description:
acRIP-seq
T1_peak.txt


title: CHIP2024_482_Wave5

description: Library name: CHIP2024_482_Wave5


title: NR_3h_Amp.63_R1.07142015.Left


title: DNFB+OVA2


title: PANC-1_sh-NAT10_Input_Rep 2

description:
acRIP-seq
T1_peak.txt


title: NR_3d_Amp.70_L1.07232015.Left


title: DNFB+OVA1


title: Acetone Olive oil1


title: CHIP2024_482_Wave3

description: Library name: CHIP2024_482_Wave3


title: PANC-1_sh-NAT10_Input_Rep 1

description:
acRIP-seq
T1_peak.txt


title: CHIP2024_482_Wave1

description: Library name: CHIP2024_482_Wave1


title: NR_3d_Amp.69_L1.11192015.Left


title: DNFB4

value: DNFB


title: PANC-1_sh-Ctrl_acRIP_Rep 3

description:
acRIP-seq
NC_peak.txt

value: sh-Ctrl


title: CHIP2024_468_Wave5

description: Library name: CHIP2024_468_Wave5


title: NR_3d_Amp.68_R1.07232015.Left


title: NR_24h_Amp.68_M00.12032015.Left


title: PANC-1_sh-Ctrl_acRIP_Rep 1

description:
acRIP-seq
NC_peak.txt


title: NR_24h_Amp.73_L1.08132015.Left


title: PANC-1_sh-Ctrl_acRIP_Rep 2

description:
acRIP-seq
NC_peak.txt


title: DNFB1


title: CHIP2024_427_Wave5

description: Library name: CHIP2024_427_Wave5


title: CHIP2024_468_Wave1

description: Library name: CHIP2024_468_Wave1


title: NR_21d_Amp.79_R1.12022015.Left


title: ETOH3

value: ETOH


title: CHIP2024_427_Wave3

description: Library name: CHIP2024_427_Wave3


title: PANC-1_sh-Ctrl_Input_Rep 3

description:
acRIP-seq
NC_peak.txt


title: NR_21d_Amp.79_L1.01082016.Left


title: ETOH1


title: NR_21d_Amp.71_L2.01082016.Left


title: PANC-1_sh-NAT10_Rep 3

description: All.HTSeq.fpkm.anno.txt


title: DNFB3


title: MC903+OVA4


title: DNFB2


title: CHIP2024_426_Wave5

description: Library name: CHIP2024_426_Wave5


title: NR_14d_Amp.77_L2.12012015.Left


title: NR_14d_Amp.80_L1.12012015.Left


title: CHIP2024_426_Wave3

description: Library name: CHIP2024_426_Wave3


title: PANC-1_sh-NAT10_Rep 1

description: All.HTSeq.fpkm.anno.txt


title: NR_24h_Amp.63_R1.08132015.Left


title: CHIP2024_468_Wave3

description: Library name: CHIP2024_468_Wave3


title: CHIP2024_426_Wave1

description: Library name: CHIP2024_426_Wave1


title: NR_14d_Amp.63_R1.07292015.Left


title: MC903+OVA3


title: CHIP2024_425_Wave5

description: Library name: CHIP2024_425_Wave5


title: CHIP2024_427_Wave1

description: Library name: CHIP2024_427_Wave1


title: MC903+OVA2


title: PANC-1_sh-Ctrl_Rep 3

description: All.HTSeq.fpkm.anno.txt


title: PANC-1_sh-Ctrl_Input_Rep 1

description:
acRIP-seq
NC_peak.txt


title: MC903+OVA1


title: MC9034


title: CHIP2024_425_Wave3

description: Library name: CHIP2024_425_Wave3


title: PANC-1_sh-Ctrl_Input_Rep 2

description:
acRIP-seq
NC_peak.txt


title: PANC-1_sh-Ctrl_Rep 1

description: All.HTSeq.fpkm.anno.txt


title: NR_12h_Amp.67_R1.07202015.Left


title: NR_12h_Amp.64_M00.07202015.Left


title: ETOH2


title: PANC-1_sh-NAT10_Rep 2

description: All.HTSeq.fpkm.anno.txt


title: CHIP2024_425_Wave1

description: Library name: CHIP2024_425_Wave1


title: MC9033


title: NR_12h_Amp.64_L1.07202015.Left


title: MC9032


title: PANC-1_sh-Ctrl_Rep 2

description: All.HTSeq.fpkm.anno.txt


title: A549 xenograft, HIF1A-AS3 overexpression, rep2

city: Linz

first: Yong

state: Upper-Austria

address: Altenberger Straße 69

country: Austria

institute: Johannes Keppler University Linz

description: Library name: A549 OE 2

data_processing:
RNAseq reads were cleaned by Trimmomatic (0.39) to trim low-quality sequences and remove adapter sequences, ensuring high-quality reads for downstream analysis. Following the trimming, genomic alignment was performed by Hisat2 (2.2.1) using the mm10 (mouse) reference genome to accurately map the reads to their respective genomes. After alignment, featureCounts (v2.0.6) to quantify gene expression by counting the number of reads that overlapped to each gene. For differential expression analysis, two robust statistical tools based on R (4.3.3) languague, DESeq2 and edgeR, were used to identify genes with significant differences in expression between conditions, ensuring comprehensive and reliable results through cross-validation of the findings from both methods.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: A549 xenograft tumor

growth_protocol: A549 cells were cultured in DMEM containing 10% FBS and 1% P/S in an incubator with 37 ℃, 5% CO2, and 5 million cells were subcutaneously transplantated into nude mice to form xenografts.

extract_protocol:
Xenograft were isolated for total RNA extraction using TRIzol reagent. 1ug total RNA was used for library preparation.
RNA-seq libraries were prepared using Optimal Dual-mode mRNA library prep kit (BGI-Shenzhen)

treatment_protocol: Stable A549 cell lines were established by infecting cells with lentiviral pLV-CMV-EGFP-Neo, or pLV-CMV-HIF1A-AS3-EGFP-Neo, before transplanted into nude mice.

value: A549 xenograft tumor

value: Lung adenocarcinoma

value: HIF1A-AS3 overexpression


title: Isolated_tumor_cell-Control-RNA-seq-Rep3

data_processing:
Fastp software (version 0.12.4)87 was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. We used STAR (version 2.7.1a)88 to map reads to the reference genome of mm10. Read counts were calculated using RSEM (version 1.2.28-0)89. The differentially expressed mRNAs were calculated by R package DESeq290.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Isolated tumor cell from Orthotopic tumor tisssue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
The library preparation was performed on an Illumina Novaseq 6000 sequencing platform (LC-Bio Technology).

value: Control


title: A549 xenograft,vector control, rep2

description: Library name: A549 ctr.2

value: vector control


title: A549 xenograft, HIF1A-AS3 overexpression, rep1

description: Library name: A549 OE 1


title: NR_0h_Amp.75_L1.11302015.Left


title: NR_0h_Amp.62_R1.07202015.Left


title: MC9031


title: CHIP2024_467_Wave5

description: Library name: CHIP2024_467_Wave5

source_name: PBMCs

value: PBMCs


title: Isolated_tumor_cell-Control-RNA-seq-Rep1

value: Isolated tumor cell from Orthotopic tumor tisssue


title: A549 xenograft, vector control, rep3

description: Library name: A549 ctr.3


title: A549 xenograft, vector control, rep1

description: Library name: A549 ctr.1


title: NR_0h_Amp.62_R1.11302015.Left

value: mouse distal terminal phalanx


title: CHIP2024_424_Wave3

description: Library name: CHIP2024_424_Wave3


title: CHIP2024_424_Wave1

description: Library name: CHIP2024_424_Wave1


title: CHIP2024_467_Wave3

description: Library name: CHIP2024_467_Wave3


title: Isolated_tumor_cell-Stress-RNA-seq-Rep3

value: GDA mice were exposed to nociception-induced stress


title: Medium_24h_Amp.41_M00.08132015.Left

value: A mixture cell types around wound bed


title: CHIP2024_467_Wave1

description: Library name: CHIP2024_467_Wave1


title: H1299, HIF1A-AS3 overexpression, rep3

description: Library name: H1299 OE 3

data_processing:
RNAseq reads were cleaned by Trimmomatic (0.39) to trim low-quality sequences and remove adapter sequences, ensuring high-quality reads for downstream analysis. Following the trimming, genomic alignment was performed by Hisat2 (2.2.1) using the hg38 (human) reference genome to accurately map the reads to their respective genomes. After alignment, featureCounts (v2.0.6) to quantify gene expression by counting the number of reads that overlapped to each gene. For differential expression analysis, two robust statistical tools based on R (4.3.3) languague, DESeq2 and edgeR, were used to identify genes with significant differences in expression between conditions, ensuring comprehensive and reliable results through cross-validation of the findings from both methods.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: A549 and H1299 cells were cultured in DMEM containing 10% FBS and 1% P/S in an incubator with 37 ℃, 5% CO2.

extract_protocol:
Cells were harvested to isolate total RNA using TRIzol reagent. 1ug total RNA was used for library preparation.
RNA-seq libraries were prepared using Optimal Dual-mode mRNA library prep kit (BGI-Shenzhen)

treatment_protocol: Cells were infected with lentiviral pLV-CMV-EGFP-Neo, or pLV-CMV-HIF1A-AS3-EGFP-Neo to stably overexpress HIF1A-AS3


title: CHIP2024_481_Wave5

description: Library name: CHIP2024_481_Wave5


title: H1299, HIF1A-AS3 overexpression, rep2

description: Library name: H1299 OE 2


title: Isolated_tumor_cell-Stress-RNA-seq-Rep2


title: Medium_24h_Amp.52_L2.12032015.Left


title: Medium_24h_Amp.50_R2.12032015.Right


title: Isolated_tumor_cell-Control-RNA-seq-Rep2


title: A549 xenograft, HIF1A-AS3 overexpression, rep3

description: Library name: A549 OE 3


title: Isolated_tumor_cell-Stress-RNA-seq-Rep1


title: Isolated_tumor_cell-Control-ATAC-seq-Rep3

data_processing:
The Diffbind R package (version 3.8.4)92 was used to generate the count matrix of Tn5 insertion site numbers for each consensus peak (peaks that were present in at least two samples). DARs (differentially accessible regions) were identified between conditions using the limma R package (version3.54.2)93 with P < 0.05 and |Log2FC| > 0.58. To visualize ATAC peaks, we use "plotHeatmap" commamd to plot Heatmap and "bamCoverage" command, adding the parameter "normalizeUsingRPKM" to convert bam files to bw format with Deeptools (version 1.9)94.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
The transposition was assessed using the Nextera DNA Library Preparation Kit (Illumina). The nuclei (5 x 104) were pelleted and resuspended with transposase for 30 min at 37 °C. The transposed DNA fragments were then purified instantly with a MinElute PCR Purification Kit (Qiagen) and PCR-amplified using 1 × NEB Next High-Fidelity PCR Master Mix (New England Biolabs).
Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.


title: H1299, vector control, rep3

description: Library name: H1299 ctr.3


title: Medium_21d_Amp.48_M00.08122015.Left


title: Isolated_tumor_cell-Control-ATAC-seq-Rep2


title: CHIP2024_417_Wave3

description: Library name: CHIP2024_417_Wave3


title: Medium_21d_Amp.52_R1.08122015.Left


title: H1299, HIF1A-AS3 overexpression, rep1

description: Library name: H1299 OE 1


title: CHIP2024_417_Wave5

description: Library name: CHIP2024_417_Wave5


title: CHIP2024_414_Wave5

description: Library name: CHIP2024_414_Wave5


title: H1299, vector control, rep1

description: Library name: H1299 ctr.1


title: CHIP2024_481_Wave1

description: Library name: CHIP2024_481_Wave1


title: A549, HIF1A-AS3 overexpression, rep3

description: Library name: A549 OE 3


title: Isolated_tumor_cell-Stress-ATAC-seq-Rep3


title: CHIP2024_417_Wave1

description: Library name: CHIP2024_417_Wave1


title: H1299, vector control, rep2

description: Library name: H1299 ctr.2


title: Medium_14d_Amp.54_M00.07292015.Left


title: Medium_0h_Amp.55_M00.07202015.Left


title: Isolated_tumor_cell-Control-ATAC-seq-Rep1


title: A549, HIF1A-AS3 overexpression, rep2

description: Library name: A549 OE 2


title: Isolated_tumor_cell-Stress-ATAC-seq-Rep2


title: Medium_0h_Amp.53_L1.07202015.Left


title: Medium_14d_Amp.52_L1.07292015.Left


title: Isolated_tumor_cell-Stress-ATAC-seq-Rep1


title: Medium_14d_Amp.42_L1.12012015.Left


title: A549, HIF1A-AS3 overexpression, rep1

description: Library name: A549 OE 1


title: CHIP2024_414_Wave3

description: Library name: CHIP2024_414_Wave3


title: Medium_21d_Amp.49_L1.08122015.Left


title: A549, vector control, rep3

description: Library name: A549 ctr.3


title: Scgb1a1cre, Day10, Cdh1_Mutant_3

data_processing:
Sequence reads were mapped to GrCM38 using STAR
Read count extraction and normalization were performed using featureCounts
For bulk RNA-seq, FASTQ files were aligned to the mouse reference genome (mm10) by using Bowtie2 (Langmead and Salzberg, 2012) with default settings. Differential gene expression analysis was performed using Cufflinks (Trapnell et al., 2010). Heatmaps were generated by ggplot2 (version 3.3.2).
GrCM38
tab-delimited text files include RPKM values for each Sample
Assembly: mouse mm10
Supplementary files format and content: For bulk RNA-seq, bam files from alignment to the mouse genome. Gene expression matrix.

source_name: airway cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA
For bulk RNAseq, cDNA libraries were constructed by using Illumina TruSeq RNA Library Prep Kit V2 (Illumina).

value: airway cells

value: Scgb1a1cre; Cdh1F/F

value: 10 days post tamoxifen

value: Day 10


title: Scgb1a1cre, Day10, Cdh1_Mutant_4


title: Medium_0h_Amp.52_R1.12182015.Right


title: CHIP2024_414_Wave1

description: Library name: CHIP2024_414_Wave1


title: CHIP2024_480_Wave5

description: Library name: CHIP2024_480_Wave5


title: A549, vector control, rep1

description: Library name: A549 ctr.1


title: MO_Baseline_3

source_name: Macrophage

value: Macrophage


title: Scgb1a1cre, Day10, Cdh1_Mutant_1


title: MO_Baseline_2


title: CHIP2024_480_Wave1

description: Library name: CHIP2024_480_Wave1


title: A549, vector control, rep2

description: Library name: A549 ctr.2


title: MO_Baseline_1


title: Scgb1a1cre, Day10, Cdh1_Mutant_2


title: CHIP2024_480_Wave3

description: Library name: CHIP2024_480_Wave3


title: Scgb1a1cre, Day10, Cdh1_Cre-control_4

value: Scgb1a1cre; Cdh1F/+


title: CHIP2024_411_Wave5

description: Library name: CHIP2024_411_Wave5


title: S15_12_MIX

city: Herlev

first: Joachim

last: Størling

address: Borgmester Ib Juuls Vej 83,

country: Denmark

institute: Steno Diabetes Center Copenhagen

data_processing:
RNA-seq libraries were sequenced on DNBseq platform to produce 100 bp long paired-end reads. An average of 46 million paired reads per sample were obtained after pre-processing and QC (removal of low-quality reads and adapter sequences) using SOAPnuke software with following parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim". Reads were aligned using TopHat (version 2.1.1) to GRCh38 genome with default parameters. Afterwards, reads were assigned to Ensembl version 107 gene annotation using HTSeq-count (version 0.9.1) with default parameters.
Assembly: GRCh38
Supplementary files format and content: txt file with normalized read counts produced by DESeq2 (pre-filtering/removal of low count reads with a cut-off of 10 read counts in at least 4 samples).

source_name: Pancreatic islet

growth_protocol: Human pancreatic islets from cadaveric donors were obtained from Prodo Labs, Inc.

extract_protocol:
Total RNA was extracted using Direct-zol™ RNA Miniprep kit (Zymo Research, USA).
Libraries were prepared according to DNBSEQ Eukaryotic Strand-specific mRNA library kit

treatment_protocol: 100-150 islets were incubated for 24 hours ± recombinant human IL-1β (R&D systems, USA) and recombinant human IFN-γ (PeproTech, USA) ± recombinant human GIP (Caslo, Denmark).

value: Pancreatic islet

value: Human pancreatic islet cells (alpha, beta, delta, etc)

value: Treated with IL-1β and IFN-γ for 24 hours


title: M2_24h_3


title: S14_12_GIP

value: Treated with GIP for 24 hours


title: S16_12_MIX_GIP

value: Treated with GIP, IL-1β, and IFN-γ for 24 hours


title: CHIP2024_411_Wave3

description: Library name: CHIP2024_411_Wave3


title: Scgb1a1cre, Day10, Cdh1_Cre-control_3


title: S13_12_CTRL

value: Control


title: CHIP2024_411_Wave1

description: Library name: CHIP2024_411_Wave1

value: PBMCs


title: CHIP2024_424_Wave4

description: Library name: CHIP2024_424_Wave4


title: M2_24h_2


title: Scgb1a1cre, Day10, Cdh1_Cre-control_2


title: M2_24h_1


title: CHIP2024_409_Wave5

description: Library name: CHIP2024_409_Wave5


title: Scgb1a1cre, Day10, Cdh1_Cre-control_1


title: M1_24h_3


title: S12_11_MIX_GIP


title: CHIP2024_409_Wave3

description: Library name: CHIP2024_409_Wave3


title: M1_24h_2


title: S11_11_MIX


title: FGF23_12h, scRNAseq

city: Indianapolis

first: Kenneth

last: White

state: IN

address: 635 Barnhill Drive

institute: Indiana University School of Medicine

data_processing:
CellRanger 3.1.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
The FASTQ files were then aligned to the mouse reference genome mm10 with RNAseq aligner STAR. The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes identification, visualization, and differential analysis.
Assembly: mm10
Supplementary files format and content: single cell barcode/feature/matrix file

source_name: Kidney

extract_protocol:
Murine kidneys were transported in RPMI1640 (Corning), on ice immediately after surgical procurement. Kidneys were rinsed with PBS and minced into eight sections. Each sample was then enzymatically and mechanically digested for 30 min (Multi-Tissue Dissociation Kit two and GentleMACS dissociator/tube rotator, Miltenyi Biotec). The samples were prepared per protocol ‘Dissociation of mouse kidney using the Multi Tissue Dissociation Kit 2’ with the following modifications: After termination of the program ‘Multi_E_2’, we added 10 mL RPMI1640 (Corning) and 10% BSA (Sigma-Aldrich) to the mixture, filtered and homogenate was centrifuged (300 g for 5 min at 4°C). The cell pellet was resuspended in 1 mL of RBC lysis buffer (Sigma), incubated on ice for 3 min, and cell pellet washed three times (300 g for 5 min at 4°C). Annexin V dead cell removal (Stem Cell Technologies) was performed using magnetic bead separation after final wash, and the pellet resuspended in RPMI1640/BSA 0.04%. Viability and counts were assessed using Trypan blue (Gibco) and brought to a final concentration of 1 million cells/mL, exceeding 80% viability as specified by 10x Genomics processing platform.
10x Genomics protocol for chromium single cell 3' reagent kits V3

treatment_protocol: C57BL/6J male and female mice were purchased from the Jackson Laboratory at 9-weeks of age and housed in the IUSM Laboratory Animal Resource Center (LARC) for 1 week prior to the start of the experiments. At 10-weeks of age, mice were treated with a single intraperitoneal injection of 10 μg/mouse body weight of rhFGF23 (R&D Systems, Inc.) and euthanized at baseline (0h), 1, 4, 12, or 24h. For scRNAseq experiment, male-female kidney pairs were digested, and cells were isolated as previously described.

value: 10 weeks old

value: Kidney

value: kidney cells

value: FGF23 10ug/mouse


title: CHIP2024_409_Wave1

description: Library name: CHIP2024_409_Wave1


title: S10_11_GIP


title: M1_24h_1


title: Asscending aorta, mgR+Vehicle_4

city: Atlanta

first: Qian

last: Xu

state: GA

address: 101 Woodruff Circle

institute: Emory University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Asscending aorta

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100-400ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Asscending aorta

value: Vascular cells

value: Vehicle


title: S9_11_CTRL


title: CHIP2024_461_Wave5

description: Library name: CHIP2024_461_Wave5


title: FGF23_1h, scRNAseq


title: CHIP2024_461_Wave3

description: Library name: CHIP2024_461_Wave3


title: Asscending aorta, mgR+Vehicle_3


title: FGF23_0h, scRNAseq

value: FGF23 0ug/mouse


title: Neurons_m6A-unmodified-RNAs_RNA-seq_Rep3

data_processing:
Sequenced reads were cleaned for adaptor and low-quality sequence, then m6A-seq and PAR CLIP-seq reads were mapped to mm10 using Bowtie 2, RNA-seq reads using STAR.
For RNS-seq, read counts were calculated using RSEM and the differentially expressed mRNAs were calculated by the R package DESeq2.
The m6A-enriched regions (peaks) in each sample were detected by exomePeak2. The m6A peaks were retained and merged using BEDTools and then annotated using HOMER. The read coverage of each peak in m6A-IP and input were calculated using Multicov from BEDTools.
For PAR CLIP-seq, peaks were calculated and selected with P < 0.0001 by using Piranha software (version 1.2.1) and then annotated by homer
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Primary neurons

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
For RNA-seq, the clustering of the indexed samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). For RNA m6A-seq, sequencing libraries for m6A-IP and input samples were prepared and sequenced on an Illumina HiSeqX Ten PE150 platform. For PAR-CLIP, library construction was performed by employing the NEBNext small RNA library prep kit (E7330S) and then sequenced on an Illumina HiSeq 4000.
PARCLIP-seq, RNA-seq, RNA m6A-seq

value: Primary neurons

value: Dorsal root ganglion neurons

value: WT

value: Transfection with scrambledRNAs


title: Asscending aorta, mgR+Vehicle_2


title: S7_10_MIX

value: Pancreatic islet

value: Human pancreatic islet cells (alpha, beta, delta, etc)

value: Treated with IL-1β and IFN-γ for 24 hours


title: Neurons_m6A-unmodified-RNAs_RNA-seq_Rep2


title: Asscending aorta, mgR+Vehicle_1


title: S8_10_MIX_GIP

value: Treated with GIP, IL-1β, and IFN-γ for 24 hours


title: CHIP2024_479_Wave5

description: Library name: CHIP2024_479_Wave5

value: PBMCs


title: S6_10_GIP

value: Treated with GIP for 24 hours


title: CHIP2024_479_Wave3

description: Library name: CHIP2024_479_Wave3


title: FGF23_4h, scRNAseq

value: 10 weeks old

value: Kidney


title: Neurons_m6A-unmodified-RNAs_RNA-seq_Rep1


title: S5_10_CTRL

value: Control


title: S4_9_MIX_GIP


title: Asscending aorta, mgR+DT-061_3

value: Asscending aorta


title: Neurons_m6A-modified-RNAs_RNA-seq_Rep3

value: Transfection with mixedRNAs


title: CHIP2024_397_Wave5

description: Library name: CHIP2024_397_Wave5


title: Neurons_m6A-modified-RNAs_RNA-seq_Rep2


title: Asscending aorta, mgR+DT-061_2

value: Vascular cells


title: Asscending aorta, mgR+DT-061_4


title: CHIP2024_461_Wave1

description: Library name: CHIP2024_461_Wave1


title: Asscending aorta, mgR+DT-061_1


title: S2_9_GIP


title: Neurons_SgCtrl_EVRNAs_RNA-seq_Rep3

value: Transfection with EV-RNAs from control cells


title: S1_9_CTRL


title: CHIP2024_396_Wave5

description: Library name: CHIP2024_396_Wave5


title: Neurons_m6A-modified-RNAs_RNA-seq_Rep1

value: Primary neurons


title: Ptprd+/-3

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences using cutadapt version 1.10. Reads shorter than 40 bases were discarded.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a
Gene expression quantication was performed from uniquely aligned reads using htseq-count version 0.6.1p1 with annotations from Ensembl version 91 and in “union” mode.
Read counts were normalized across samples with the median-of-ratios method.
Differential expression analysis was performed using DESeq2 version1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: TSV files providing raw read counts and normalized read counts for each gene together with gene annotations and the p-value, adjusted p-value and log2 fold-change for each performed comparison.

source_name: liver

extract_protocol:
Liver samples from C57BL/6J mice were lysed using TRI reagent (Sigma-Aldrich) and RNA was extracted using the Direct-zol kit (Zymo Research).
RNA-Seq libraries were generated from 145ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 14 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Liver

value: Ptprd heterozygous


title: S3_9_MIX


title: Ptprd+/-2


title: Neurons_SgCtrl_EVRNAs_RNA-seq_Rep2

first: Zhou

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

value: Dorsal root ganglion neurons

value: WT


title: C. briggsae scRNA-seq: AF16 whole embryo 500 minutes

city: Seattle

first: Robert

middle: H

last: Waterston

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

description: Library name: Cb_EMB_500

data_processing:
The single-cell RNA-seq reads were mapped using the 10X genomics CellRanger pipeline (8.0.0) to a modified version of the WormBase WS290 C. elegans and C. briggsae reference genomes (available through SRA BioProject PRJNA1201888). As was previously done for the C. elegans reference genome, the C. briggsae 3’ UTR annotations were similarly extended to improve gene expression quantification. After alignment, the C. briggsae and new/mutant C. elegans datasets were filtered for cells that were likely doublets between two different cell types. Within all cells, the percentages of reads coming from the background ambient RNA profile was determined and subtracted.
To jointly project the two species data into the same reduced dimensional space, we used Reciprocal Principle Components Analysis (RPCA), implemented in Seurat V5 (5.1.0). Both species gene by cell matrix were first subsetted to the 1:1 orthologs. The cells of both species were then jointly split by collection batch and each batch was run through a standard pipeline of normalization and finding the 2,000 most variable features. Subsequently, the datasets were integrated by batch.  After integration, the data were further reduced to 2 dimensions using UMAP implemented in Seurat. Clusters were then identified inside of the integrated space using louvain clustering and matched to tissue classes using known marker genes. Cells belonging to these tissue classes were further subsetted, reintegrated using RPCA on 50 principal components, and re-projected for subsequent cell type annotation. Additional cell subsets based on the inferred embryo time were similarly reintegrated using RPCA and re-projected for subsequent progenitor annotation.  The terminal cell types were annotated using markers, trajectory relationships, and embryo time. The progenitor cell types from C. briggsae were similarly annotated using markers with known progenitor-specific expression in C. elegans. We used multiple markers per lineage branch.
To generate an aggregated quantification of each cell type's gene expression, we calculated a relative expression metric, the Transcripts Per Million (TPM) for each cell type. As 10x single-cell RNA-seq data is 3’ biased, there is no requirement for gene size correction of the TPM values. First, the background corrected gene by cell matrix was normalized for library sequencing depth and complexity by dividing by a per-cell size factor (calculated in Monocle3). Second, the matrix was subsetted to the cells corresponding to a single cell type in one species. Next, the mean expression of every gene was calculated. Finally, each cell type's expression vector was scaled to 1,000,000 using each species' full gene set. The process was repeated for every cell type from either species.
Assembly: WormBase WS290 (C. elegans and C. briggsae)
Supplementary files format and content: Supplementary_files_format_and_content: expression_matrix.mtx contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, lineage, etc.) for each cell. Columns in gene_annotations.csv: elegans_gene_short_name,elegans_gene_long_name,elegans_id,briggsae_id,briggsae_gene_short_name,briggsae_gene_long_name,gene.type.  Columns in cell_annotations.csv: cell_type,lineage_broad,species,n.umi,barcode,packer_cell.type,packer_cell.subtype,packer_plot.cell.type,packer_lineage,smoothed.embryo.time,embryo.time.bin,germline_pseudotime,time.point,batch,genotype,filter,mt.frac,cel_lineage_broad,cbr_lineage_broad,cel_lineage_complete,cbr_lineage_complete,lineage_complete

organism: Caenorhabditis briggsae

source_name: embryonic cells

extract_protocol: see experimental design

value: embryonic cells


title: CHIP2024_396_Wave3

state: MN

description: Library name: CHIP2024_396_Wave3


title: Neurons_SgCtrl_EVRNAs_RNA-seq_Rep1

city: Guangzhou

last: yifan


title: Ptprd+/-1


title: C. briggsae scRNA-seq: AF16 whole embryo 400 minutes

description: Library name: Cb_EMB_400


title: CHIP2024_479_Wave1

description: Library name: CHIP2024_479_Wave1


title: Neurons_Alkbh5KO_EVRNAs_RNA-seq_Rep3

value: Transfection with EV-RNAs from Alkbh5-KO KPC cells


title: CHIP2024_396_Wave1

description: Library name: CHIP2024_396_Wave1


title: C. briggsae scRNA-seq: AF16 whole embryo 360 minutes

description: Library name: Cb_EMB_360


title: CHIP2024_397_Wave3

description: Library name: CHIP2024_397_Wave3


title: CHIP2024_469_Wave5

description: Library name: CHIP2024_469_Wave5


title: C. briggsae scRNA-seq: AF16 whole embryo 300 minutes

description: Library name: Cb_EMB_300


title: Neurons_Alkbh5KO_EVRNAs_RNA-seq_Rep2


title: CHIP2024_397_Wave1

description: Library name: CHIP2024_397_Wave1


title: Ptprd+/+2

value: Ptprd wild type


title: Ptprd+/+3


title: Neurons_Alkbh5KO_EVRNAs_RNA-seq_Rep1


title: C. briggsae scRNA-seq: AF16 whole embryo 240 minutes

description: Library name: Cb_EMB_240


title: CHIP2024_469_Wave3

description: Library name: CHIP2024_469_Wave3

value: PBMCs


title: Ptprd+/+1


title: CHIP2024_469_Wave1

description: Library name: CHIP2024_469_Wave1


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 8

city: Irvine

first: Pavan

last: Nayak

address: 4462 Natural Sciences 2

institute: UC Irvine

description: Library name: P57

data_processing:
Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1
Assembly: GRCz10
Supplementary files format and content: DESeq2 normalized counts

organism: Danio rerio

source_name: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos

extract_protocol:
For 48 hpf bulk RNA-seq alone transgenic Tg(scxa:mCherry) embryos, BTX-injected or un-injected siblings, were dissociated using Subtilisin A cold-active protease in a stock solution consisting of: 5 ul of 1M CaCl2, 100 ul of protease stock solution (100mg of Bacillus licheniformis protease (Sigma P5380) solubilized in 1 ml of Ca and Mg free PBS), 889ul of PBS, 1 ul of 0.5M EDTA (Sigma E5134) and 5ul of DNAse I  (Roche 10104159001) stock (25U/ul in PBS, stored at -80C) adapted from (O’Flanagan et al., 2019). Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min, tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took ~30 min per samples, and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA (0.01% BSA in PBS, made fresh on the day of dissociation) and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C, supernatant is discarded, and cells are resuspended in 1 ml of ice-cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio-Rad FACS Aria II cell sorter.
Clontech SMARTer Stranded Total RNA-Seq v3 Kit

value: mCherry+ tenocytes

value: WT Tg(scxa:mCherry) background

value: 48 hpf embryos uninjected control


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep9

source_name: KPC cells

value: KPC cells

value: Murine pancreatic cancer cell line

value: Alkbh5 KO


title: CHIP2024_478_Wave4

description: Library name: CHIP2024_478_Wave4


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep8


title: C. briggsae scRNA-seq: AF16 whole embryo 180 minutes

description: Library name: Cb_EMB_180


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 7

description: Library name: P56

value: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos


title: C. briggsae scRNA-seq: AF16 whole embryo 120 minutes

description: Library name: Cb_EMB_120


title: cPIIRS+Ruxolitinib Mouse 4

city: Bethesda

first: Jessica

middle: Caroline

last: Hargarten

state: MD

address: 10 Center Drive

department: LCIM

institute: NIAID/NIH

hyb_protocol: At time of hybridization, every sample was spiked in with the positive and negative controls provided with the panel. This technique utilizes capture and reporter probes specific for each gene labelled with a unique fluorescent barcode. Signals generated from these barcodes are automatically detected and quantified by the nCounter Pro Analysis System. The generated data were compiled as resource compiler (RCC) files.

data_processing:
RCC files were imported into nSolver 4.0 analysis software (NanoString), and quality control steps were performed following the manufacturer’s guidelines. Raw data were processed sequentially: first background subtraction was performed using the formula: read count of each gene − 2 × (mean + 2 × SD) of all negative controls. Next, the positive control normalization factor was calculated according to the manufacturer’s instructions using positive controls that were spiked into every sample. Then, the CodeSet content normalization factor (housekeeping normalization factor) was calculated using all reference genes to adjust for differences in analyte abundance and/or analyte quality across samples. The most stably expressed housekeeping genes (10 out of 14 for human data and 7 out of 14 for mouse data) were selected using the geNorm algorithm (PMID: 19531210). Normalization was performed per the default settings. The selection criteria for the positive control normalization factor were 0.3–3.0. Pathway scores were calculated as the first principal component of the pathway genes’ normalized expression. The software will orient the scores such that increased score corresponds with increased expression in a majority of the pathway genes. Scores of the cell type characteristic genes were analyzed using the default settings from the cell type profiling algorithm in the nSolver analysis software.
Normalized log2 count data

source_name: Mouse Brain

extract_protocol: RNA was extracted from whole brain homogenates using the Qiagen RNeasy Kit according to manufacturers' recommendations.

value: Female


title: CHIP2024_478_Wave3

description: Library name: CHIP2024_478_Wave3

data_processing:
Reads were quality-filtered with a ‘phred’ score threshold of ≥30, and adapter sequences were removed using Trimmomatic (version 0.27) (Bolger et al. 2014). Afterward, guided alignment to the human genome assembly hg19 was performed using both bwa-mem (version 0.7.17) and bowtie2 (version 2.2.1) (Langmead & Salzberg 2012; Li & Durbin 2009). Unique molecular barcodes, introduced before PCR amplification, were utilized for deduplication to enable accurate multiplexed quantification and reliable mutation detection. Variant calling within targeted regions was conducted using three different tools: Lofreq (version 2.1.0) (Wilm et al. 2012), Freebayes (Garrison & Marth 2012), and Vision (ArcherDX version 6.2.7, unpublished). A consensus was generated by combining the results and selecting for agreement from all three variant callers (see Supplementary Table 3).
All filtered variants with a variant allele frequency (VAF) of 1% or 2% satisfied the following conditions: (1) the number of reads supporting the alternative allele exceeded the minimum coverage requirement without displaying directional bias (AO ≥ 5, UAO ≥ 3); (2) the variants were significantly underrepresented in the Genome Aggregation Database (gnomAD; P ≤ 0.05); (3) the variants were unlikely to be germline, as indicated by a stable VAF (50% or 100%) across all sequencing waves, which could have been underrepresented in gnomAD due to the limited geographic diversity of the LBC cohort; and (4) the variants included events, such as frameshift duplications and deletions, that were overrepresented in the dataset, likely reflecting misaligned artifacts from the capture method (see Supplementary Table 3) (Karczewski et al. 2020). Additionally, the list was manually curated, cross-referencing variants previously reported in COSMIC, Jaiswal et al., or other published studies (Tate et al. 2019). Finally, for any variant that met the above criteria with a VAF of ≥ 1% or 2% at any time point, all participant-matched data points were included, regardless of baseline VAF.
Assembly: hg19
Supplementary files format and content: tsv - custom variant file format - somatic and synonymous variant calls for 1% and 2% VAF

extract_protocol:
Our expanded cohort longitudinally sampled from the LBC1936 was processed as per our previous work. Briefly, DNA was extracted from whole blood with Ethylenediaminetetraacetic acid (EDTA) using the Nucleon BACC3 kit (Sigma-Aldrich, GERPN8512), according to the manufacturer’s protocol.
Libraries were generated from 200 ng of each DNA sample using the Invitea/Archer VariantPlex® 75 Myeloid gene panel and the VariantPlex® Somatic Protocol for Illumina sequencing (Invitae, AB0108, and the VariantPlex®-HCG Myeloid Kit; see Supplementary Table 2), with adaptations for detecting low variant allele frequencies. Sequencing was performed on the NextSeq 550 platform (Illumina) using the NextSeq 500/550 High-Output version 2.5 kit (300 cycles). Two ‘Genome in a Bottle’ (GIAB) DNA samples (NA12878, Coriell Institute) were included in each sequencing batch to ensure reproducibility and support background error modeling and batch correction.


title: CHIP2024_478_Wave1

description: Library name: CHIP2024_478_Wave1


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 6

description: Library name: P55


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep7


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep6


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 5

description: Library name: P54


title: cPIIRS+Ruxolitinib Mouse 2


title: CHIP2024_423_Wave5

description: Library name: CHIP2024_423_Wave5


title: CHIP2024_423_Wave3

description: Library name: CHIP2024_423_Wave3


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 4

description: Library name: P53


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep4


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep5


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 3

description: Library name: P52


title: CHIP2024_423_Wave1

description: Library name: CHIP2024_423_Wave1


title: cPIIRS+Ruxolitinib Mouse 1


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 2

description: Library name: P51


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep3


title: cPIIRS Mouse 4


title: CHIP2024_420_Wave5

description: Library name: CHIP2024_420_Wave5


title: sorted mCherry+ tenocytes from uninjected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 1

description: Library name: P50


title: CHIP2024_420_Wave3

description: Library name: CHIP2024_420_Wave3


title: cPIIRS Mouse 3


title: cPIIRS Mouse 2


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 6

description: Library name: P49

value: 48 hpf embryos aBTX injected at single cell stage


title: cPIIRS Mouse 1


title: CHIP2024_477_Wave4

description: Library name: CHIP2024_477_Wave4


title: CHIP2024_420_Wave1

description: Library name: CHIP2024_420_Wave1


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 3_IP

library_source: other

molecule: other

tag: fraction

value: EV-packaged total RNA


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 5

description: Library name: P48


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep1


title: Naïve Mouse 4


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 4

description: Library name: P47


title: cPIIRS+Ruxolitinib Mouse 3


title: CHIP2024_477_Wave3

description: Library name: CHIP2024_477_Wave3


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 1_IP


title: Naïve Mouse 3


title: CHIP2024_477_Wave1

description: Library name: CHIP2024_477_Wave1


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 3

description: Library name: P46