title: sh-hnRNP M#2 TGFbeta 3

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

description: Library name: LR21E26FV39

data_processing:
Using the 2-pass mapping function of the STAR software, the original data was aligned to the genome.
Assembly: hg19
Supplementary files format and content: Matrix of Percent Spliced In (PSI) values for alternative splicing events across samples,csv format

source_name: lung

extract_protocol:
A549 stably expressing either scramble or shRNAs targeting hnRNP M were treated with 5 ng/ml TGFbeta for 72h or not. Next, cells were harvest in 1ml TRIzol for RNAseq.
Total RNA was extracted and probed to generate Ribo-zero libraries using the Ribo-off rRNA Depletion Kit and Vazyme ssDNA Library Prep kit for Illumina. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: lung

value: NSCLC


title: L

status: Public on Aug 05 2026

type: SRA

city: Kunming

first: Ruixia

last: Tang

address: Jiaoling Road 935

country: China

institute: Chinese  Academy  of Medical Sciences & Peking Union Medical College

description: Library name: Sample7

library_source: transcriptomic

data_processing:
Raw sequencing data (fastq format) were processed using Seqtk to remove adapter sequences, trim low-quality bases (Q < 20) from the 3' end, filter reads shorter than 25 nt, and remove rRNA-derived reads. Clean reads were aligned to the human reference genome (hg38) using BWA-MEM with default parameters. Circular RNAs were predicted and annotated using CIRI (v2.0). circRNA expression levels were quantified using SRPBM (Spliced Reads Per Billion Mapping) based on back-splicing junction reads. Differential expression analysis between groups was performed using edgeR (v3.32) with the following criteria: |Fold-change| ≥ 2 and p-value ≤ 0.05. Functional enrichment analyses (GO and KEGG) of parental genes of differentially expressed circRNAs were carried out using hypergeometric test with q-value ≤ 0.05 as significance threshold.
Assembly: GRCh38.p12 (hg38)
Supplementary files format and content: Format: xls; Content: circRNA_expression.xls

molecule: total RNA

organism: Homo sapiens

source_name: healthy control

extract_protocol:
Total RNA was extracted from whole-blood samples using TRIzol reagent (Invitrogen, Catalog No. 10296028CN) per the manufacturer’s protocol. RNA concentration/purity was assessed via NanoDrop 1000 (A260/A280 ≥ 1.8, A260/A230 ≥ 2.0), and integrity via Agilent 2100 Bioanalyzer (RNA Integrity Number (RIN) ≥ 8.0). Only qualified RNA was used for subsequent sequencing.
Total RNA was subjected to ribosomal RNA (rRNA) removal using Ribo-Zero rRNA Removal Kit (Epicentre), followed by fragmentation at 94°C for 8 minutes. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) with random primers and Actinomycin D. Second-strand cDNA was synthesized using Second Strand Marking Master Mix. The double-stranded cDNA products were purified using AMPure XP beads (Beckman). After end repair and adenylation at the 3' ends, Illumina RNA adapters were ligated. Libraries were amplified by PCR (98°C for 30 sec; 10 cycles of 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; final extension 72°C for 5 min). The final libraries were validated on an Agilent 2100 Bioanalyzer and quantified by Qubit 2.0 Fluorometer.

tag: tissue

value: PBMC

tag: infected with


title: MAB-PD patient peripheral blood, biological replicate 2

status: Public on Aug 04 2026

city: Shanghai

first: Guoling

last: Yang

address: No. 507 Zhengmin Road

department: Department of Tuberculosis

institute: Shanghai Pulmonary Hospital

description:
Library name: MAB2
Bulk RNA-seq of peripheral blood from MAB subject

data_processing:
Raw sequencing reads were quality-controlled, adapters were trimmed, and clean reads were aligned to the human reference genome (GRCh38). Gene-level read counts were quantified.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: GSE_bulk_RNAseq_gene_counts_matrix.txt.gz: tab-delimited text file containing a gene-level raw read count matrix; rows are genes (Ensembl gene IDs), columns are samples. DGE_DGE-MAB_vs_HC.txt.gz, DGE_DGE-MAC_vs_HC.txt.gz and DGE_DGE-MA_vs_HC.txt.gz: tab-delimited text files of differential gene expression results (Gene_ID, Symbol, log2FoldChange, Pvalue, FDR) for each comparison.

source_name: peripheral blood

extract_protocol:
Total RNA was isolated from peripheral blood using the RNAmini kit (Qiagen, Germany). RNA quality was assessed by gel electrophoresis and Qubit fluorometry (Thermo, Waltham, MA, USA).
Strand-specific libraries were constructed with the Stranded mRNA-seq (NR602) kit (Vazyme, Nanjing, China) and sequenced on an Illumina NovaSeq 6000 in 150 bp paired-end mode to generate raw reads.

value: peripheral blood

tag: disease state

value: MAB-PD patient


title: L16

city: Hongkong

first: Xin

last: Deng

state: 九龍

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

department: BMS

country: Hong Kong

institute: City University of Hong Kong

description:
Library name: L16
DAP-seq

library_source: genomic

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

molecule: genomic DNA

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae

growth_protocol: LB at 37 °C

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

value: Klebsiella pneumoniae

tag: cell line

value: strain

tag: cell type

value: genotype

tag: genotype

value: WT

tag: treatment

value: ChIP antibody

tag: batch


title: RNASeq_144 05_48_T_d23

city: Cambridge

first: Richard

middle: Lee

last: Gieseck III

state: MA

address: 1 Portland St.

country: USA

institute: Pfizer, Inc.

description:
Library name: 05_48_T_d23
study day=23; RIN=6.2; tumor_volume_mm3=1177.5849460000002; sample_status=RNAlater

data_processing:
STAR Alignment v020201
bcl2fastq2 v2.20
RSEM v1.3.0
TPM and normalization using Data4Cure Biomedical Intelligence Cloud
Assembly: mm10
Supplementary files format and content: Tab-delimited matrix of log2(TPM) values by gene (HGNC filtered).

organism: Mus musculus

source_name: Tumor

growth_protocol: CT26 tumor-bearing BALB/c mouse study; tissue harvested at study day 16 or 23.

extract_protocol:
Total RNA extracted from collected tissues (spleen, tumor, TDLN) using study SOP.
Paired-end stranded mRNA-seq library prep with polyA enrichment.

treatment_protocol: Treatments include Isotype, PD1, CYTO, PD1/CYTO, TS/CYTO, and TS/PD1/CYTO per study design.

value: Tumor

value: BALB/c

value: TS/CYTO


title: L2

description:
Library name: L2
DAP-seq


title: sh-hnRNP M#2 TGFbeta 2

institute: Sichuan University

description: Library name: LR21E26FV38


title: RNASeq_144 05_50_S_d23

description:
Library name: 05_50_S_d23
study day=23; RIN=8.6; tumor_volume_mm3=1170.59334; sample_status=RNAlater

source_name: Spleen

value: Spleen


title: MAB-PD patient peripheral blood, biological replicate 5

description:
Library name: MAB5
Bulk RNA-seq of peripheral blood from MAB subject


title: MAB-PD patient peripheral blood, biological replicate 1

description:
Library name: MAB1
Bulk RNA-seq of peripheral blood from MAB subject


title: sh-hnRNP M#2 TGFbeta 1

description: Library name: LR21E26FV37


title: RNASeq_144 05_48_TDLN_d23

description:
Library name: 05_48_TDLN_d23
study day=23; RIN=5.9; tumor_volume_mm3=1177.5849460000002; sample_status=RNAlater

source_name: Tumor draining lymph node

value: Tumor draining lymph node


title: Healthy control peripheral blood, biological replicate 10

description:
Library name: HC10
Bulk RNA-seq of peripheral blood from HC subject

value: healthy control


title: L14

description:
Library name: L14
DAP-seq


title: RNASeq_144 05_48_S_d23

description:
Library name: 05_48_S_d23
study day=23; RIN=7.7; tumor_volume_mm3=1177.5849460000002; sample_status=RNAlater


title: sh-hnRNP M#1 TGFbeta 3

description: Library name: LR21E26FV36


title: MAB-PD patient peripheral blood, biological replicate 3

description:
Library name: MAB3
Bulk RNA-seq of peripheral blood from MAB subject


title: Healthy control peripheral blood, biological replicate 9

description:
Library name: HC9
Bulk RNA-seq of peripheral blood from HC subject


title: L17

description:
Library name: L17
DAP-seq


title: RNASeq_144 05_49_S_d23

description:
Library name: 05_49_S_d23
study day=23; RIN=7.7; tumor_volume_mm3=1097.391456; sample_status=RNAlater


title: L13

description:
Library name: L13
DAP-seq


title: cCeO_aRG1_ATAC-seq

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

country: Germany

institute: TUD Dresden University of Technology

description:
Library name: 107334
GEO_chimp_ATAC_counts.tsv.gz
cCeO_aRG_consensusPeak.narrowPeak.gz

data_processing:
sequence data files were created with bcl2fastq2 v2.20.0
ATAC-seq libraries were mapped and processed using the ENCODE pipeline (Lee et al. 2016) with default settings. This includes that creating narrowPeak files with MACS2, conversion of bed files to bw files and count tables
consensusPeak.narrowPeak files represent IDR-filtered high-confidence ATAC-seq peaks representing reproducible chromatin accessibility regions across biological replicates.
Assembly: panTro6
Supplementary files format and content: bigWig: Normalized ATAC-seq signal tracks for genome browser visualization.
Supplementary files format and content: narrowPeak: Called accessible chromatin peaks with genomic coordinates and peak statistics.
Supplementary files format and content: GEO_chimp_ATAC_counts.tsv.gz: Raw counts per peak across samples with genomic/gene annotations and liftover to human (hg38) and gorilla (gorgor6)

organism: Pan troglodytes

source_name: cerebral organoid

growth_protocol: iPSC line grown under standard conditions (5 % CO2, 37 °C) on Matrigel-coated plates in mTeSR1. Cerebral organoids were generated as whole spheres using the STEMdiff Cerebral Organoid Kit or equivalent self-made medium based on previous publications with small modifications as described in detail (Lancaster & Knoblich, 2014; Giandomenico, Sutcliffe & Lancaster, 2021). Briefly, 9,000 cells were seeded into 96-well Ultra-Low Attachment plates and cultured in mTeSR1 containing 10 µM Y-27632 rho kinase inhibitor. Plates were spun for 3 min at 300x g to settle cells. After 48 hours, the medium was changed to mTeSR1 without Y-27632 rho kinase inhibitor (organoid formation medium). On day 4, the now-formed embryoid bodies (EBs) were changed to neural induction medium. EBs were embedded in Matrigel on day 8, transferred to differentiation medium containing B27 supplement without vitamin A (expansion medium), and henceforth cultured on an orbital shaker. Starting on day 14, young organoids were changed to, and then maintained in, differentiation medium containing B27 supplement with vitamin A (maturation medium), changed every 2–3 days until collection for experiments. All cerebral organoids were collected for experiments on w8 ± 3 days.

extract_protocol:
ATAC-seq was performed as previously described with minor alterations to the protocol (Corces et al. 2017). Briefly, sorted cells are pelleted at 500x g and 4 °C for 5 min. All supernatant was aspirated, cells were re-suspended in 50 µL ice-cold lysis buffer by pipetting up-and-down three times and incubated on ice for 3 min. Lysis was washed out with 1 mL ice-cold wash buffer, and the tubes were inverted to mix. Cells were again pelleted at 500x g and 4 °C for 10 min. Supernatant was fully aspirated and cells re-suspended in 50 µL transposition mix containing 100 mM transposase. Reactions were incubated at 37 °C and 1,000 rpm in a thermoshaker for 2 hours and then quenched by the addition of 40 mM EDTA. Reactions were pelleted at 500x g for 5 min, re-suspended in 200 µL reverse-crosslink solution and incubated O/N at 65 °C and 1,000 rpm in a thermoshaker as previously reported for ATAC-seq on fixed cells (Chen et al. 2020). The next day, the original protocol was continued, and reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit.
libraries were amplified with determination of amplification cycles by qPCR as described (Corces et al. 2017) and unique adapter combinations (i5 and i7), and final PCR reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit. Final libraries were size selected using SPRIselect Beads at 0.5x and 1.3x ratios, to retain fragments of 150–1,000 bp.

treatment_protocol: ATAC-seq was performed as previously described with minor alterations to the protocol95. Briefly, sorted cells are pelleted at 500x g and 4 °C for 5 min. All supernatant was aspirated, cells were re-suspended in 50 µL ice-cold lysis buffer by pipetting up-and-down three times and incubated on ice for 3 min. Lysis was washed out with 1 mL ice-cold wash buffer, and the tubes were inverted to mix. Cells were again pelleted at 500x g and 4 °C for 10 min. Supernatant was fully aspirated and cells re-suspended in 50 µL transposition mix containing 100 mM transposase. Reactions were incubated at 37 °C and 1,000 rpm in a thermoshaker for 2 hours and then quenched by the addition of 40 mM EDTA. Reactions were pelleted at 500x g for 5 min, re-suspended in 200 µL reverse-crosslink solution and incubated O/N at 65 °C and 1,000 rpm in a thermoshaker as previously reported for ATAC-seq on fixed cells96. The next day, the original protocol95 was continued, and reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit, libraries were amplified with determination of amplification cycles by qPCR as described95 and unique adapter combinations (i5 and i7), and final PCR reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit. Final libraries were size selected using SPRIselect Beads at 0.5x and 1.3x ratios, to retain fragments of 150–1,000 bp.

value: cerebral organoid

value: SandraA

value: apical radial glia


title: RNASeq_144 05_30_TDLN_d16

description:
Library name: 05_30_TDLN_d16
study day=16; RIN=7.7; tumor_volume_mm3=166.297536; sample_status=RNAlater


title: sh-hnRNP M#1 TGFbeta 2

description: Library name: LR21E26FV35

value: lung

value: NSCLC


title: A549 cells treated with 20 mM lactic acid for 24 h, biological replicate 3

city: chendu

first: lilan

last: he

address: yulin

description:
Library name: A549_LAC_3
Lactic-acid-treated biological replicate 3; 150-bp paired-end sequencing; matrix column: LAC-3 in All_gene_counts.txt and All_gene_fpkm.txt

data_processing:
Raw reads were filtered using in-house Perl scripts to remove adapter-containing reads, poly-N reads, and low-quality reads. Q20, Q30, and GC content were calculated.
Clean paired-end reads were aligned to the Homo sapiens reference genome Homo_sapiens.GRCh38_release95.genome.fa using HISAT2.
StringTie was used to assemble mapped reads and quantify gene and transcript expression as FPKM values.
Gene-level read counts were used for differential expression analysis between the lactic-acid and PBS-control groups with DESeq2. Genes with fold change ≥ 2 and FDR < 0.01 were considered differentially expressed.
Assembly: GRCh38, Ensembl Homo sapiens reference genome release 95
Supplementary files format and content: All_gene_counts.txt is a tab-delimited plain-text file containing gene-level raw read counts for NS-1, NS-2, NS-3, LAC-1, LAC-2, and LAC-3, together with gene identifiers.
Supplementary files format and content: All_gene_fpkm.txt is a tab-delimited plain-text file containing gene-level FPKM values for NS-1, NS-2, NS-3, LAC-1, LAC-2, and LAC-3, together with gene identifiers.

growth_protocol: A549 cells were maintained under standard cell-culture conditions prior to treatment.

extract_protocol:
Total RNA was extracted from A549 cells using TRIzol reagent according to the manufacturer's instructions. RNA samples were submitted to a commercial sequencing service for quality assessment, library preparation, and sequencing.
Poly(A)+ mRNA was enriched using oligo(dT)-coupled magnetic beads. Sequencing libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, catalog no. 13533ES96) according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq X Plus platform to generate 150-bp paired-end reads (PE150).

treatment_protocol: A549 cells were treated with 20 mM lactic acid added directly to the culture medium for 24 h. Control cells received an equal volume of PBS for 24 h.

value: 20 mM lactic acid was added directly to the culture medium for 24 h


title: Healthy control peripheral blood, biological replicate 8

description:
Library name: HC8
Bulk RNA-seq of peripheral blood from HC subject

value: peripheral blood


title: L12

description:
Library name: L12
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: HepG2, control, rep2

city: Milan

first: Italia

last: Bongarzone

state: Milan

address: Via Amedeo, 42

department: Department of Diagnostic Innovation

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: CONTROL-3-2

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed using HTSeq-count.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each Sample

molecule: polyA RNA

extract_protocol:
RNA was extracted from untreated HepG2 cells and from HepG2 cells treated with Eliglustat (20 or 30 µM) for 72 h using the Maxwell® RSC RNA FFPE Kit (Cat. No. AS1440, Promega Corporation, Madison, WI, USA) on a semi-automated Maxwell® RSC instrument (Promega). RNA concentration was measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was assessed using the Agilent 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus Kit (Illumina, San Diego, CA, USA; Cat. No. 20040525), according to the manufacturer's instructions. Briefly, libraries were generated from 100 ng of total RNA. Ribosomal RNA (rRNA) was first depleted, and the remaining RNA was reverse-transcribed into cDNA. Adapter ligation and PCR amplification were subsequently performed to generate sequencing-ready libraries. Library concentrations were measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and library quality was assessed using the Agilent 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA). All libraries were purified, pooled, and diluted to a final concentration of 0.5 nM. Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) using a NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles) to generate paired-end 2 × 75 bp reads.

value: control


title: RNASeq_144 05_29_TDLN_d16

description:
Library name: 05_29_TDLN_d16
study day=16; RIN=8.1; tumor_volume_mm3=413.326012; sample_status=RNAlater


title: sh-hnRNP M#1 TGFbeta 1

description: Library name: LR21E26FV34


title: Healthy control peripheral blood, biological replicate 7

description:
Library name: HC7
Bulk RNA-seq of peripheral blood from HC subject


title: M14

description:
Library name: M14
DAP-seq

value: genotype

value: WT

value: ChIP antibody


title: A549 cells treated with PBS for 24 h, control biological replicate 3

description:
Library name: A549_NS_3
Control biological replicate 3; 150-bp paired-end sequencing; matrix column: WT-3 in All_gene_counts.txt and All_gene_fpkm.txt

value: An equal volume of PBS was added to the culture medium for 24 h


title: L11

description:
Library name: L11
DAP-seq


title: RNASeq_144 05_28_TDLN_d16

description:
Library name: 05_28_TDLN_d16
study day=16; RIN=7.7; tumor_volume_mm3=184.930552; sample_status=RNAlater

value: BALB/c

value: TS/CYTO


title: M12

description:
Library name: M12
DAP-seq


title: Healthy control peripheral blood, biological replicate 6

description:
Library name: HC6
Bulk RNA-seq of peripheral blood from HC subject

value: healthy control


title: L10

description:
Library name: L10
DAP-seq


title: RNASeq_144 04_40_TDLN_d23

description:
Library name: 04_40_TDLN_d23
study day=23; RIN=5.9; tumor_volume_mm3=29.179892; sample_status=RNAlater

value: Tumor draining lymph node


title: SCR_TGFbeta 2

description: Library name: LR21E26FV32


title: Healthy control peripheral blood, biological replicate 5

description:
Library name: HC5
Bulk RNA-seq of peripheral blood from HC subject


title: M10

description:
Library name: M10
DAP-seq


title: RNASeq_144 04_40_S_d23

description:
Library name: 04_40_S_d23
study day=23; RIN=7.1; tumor_volume_mm3=29.179892; sample_status=RNAlater

value: Spleen


title: Healthy control peripheral blood, biological replicate 4

description:
Library name: HC4
Bulk RNA-seq of peripheral blood from HC subject


title: L1

description:
Library name: L1
DAP-seq


title: k9

description:
Library name: k9
DAP-seq


title: SCR_TGFbeta 1

description: Library name: LR21E26FV31


title: M1

description:
Library name: M1
DAP-seq


title: RNASeq_144 04_39_T_d23

description:
Library name: 04_39_T_d23
study day=23; RIN=7.4; tumor_volume_mm3=701.652333; sample_status=RNAlater

value: Tumor


title: k8

description:
Library name: k8
DAP-seq


title: sh-hnRNP M#2 Untreated 2

description: Library name: LR21E26FV26

value: lung


title: RNASeq_144 04_39_TDLN_d23

description:
Library name: 04_39_TDLN_d23
study day=23; RIN=6.5; tumor_volume_mm3=701.652333; sample_status=RNAlater


title: Healthy control peripheral blood, biological replicate 2

description:
Library name: HC2
Bulk RNA-seq of peripheral blood from HC subject


title: k7

description:
Library name: k7
DAP-seq


title: Healthy control peripheral blood, biological replicate 1

description:
Library name: HC1
Bulk RNA-seq of peripheral blood from HC subject


title: k6

description:
Library name: k6
DAP-seq


title: k5

description:
Library name: k5
DAP-seq


title: BE63_NON_CF_IFNa

city: Pozzuoli

first: Michele

last: Genovese

address: Via Campi Flegrei 34

institute: Tigem

description:
Library name: BE63_NON_CF_IFNa
Non-cystic fibrosis human bronchial epithelial preparation treated with IFNα.

data_processing:
FASTQ demultiplexing was performed using the mkfastq command from 10x Genomics Cell Ranger v6.0.1. Gene-cell count matrices were generated using the count command from 10x Genomics Cell Ranger v6.0.0. All samples were processed using the 10x Genomics human reference transcriptome refdata-gex-GRCh38-2020-A.
Cell-level quality control was performed in Python using Scanpy v1.11.5. Cells with mitochondrial count percentages >=20%, fewer than 500 detected genes, fewer than 1,000 total counts, or more than 6,000 detected genes were excluded from downstream analyses. After quality control filtering, the final dataset contained 51,088 cells and 36,601 genes.
Raw counts were normalized using total-count normalization by scaling each cell to a target library size of 10,000 counts, followed by log1p transformation. Highly variable genes were identified using the Seurat v3 method implemented in Scanpy. The top 3,000 highly variable genes were selected using the raw count layer while accounting for sample-specific effects by specifying sample_id as the batch variable.
For downstream dimensionality reduction and graph-based analyses, the dataset was restricted to highly variable genes. The expression matrix was scaled with a maximum value of 10. Principal component analysis was performed using the ARPACK solver. A nearest-neighbor graph was constructed using 30 nearest neighbors and the first 20 principal components. UMAP was used for visualization, and clusters were identified using the Leiden community detection algorithm at a resolution of 0.5. Random seeds were fixed to 0 for PCA, UMAP, and Leiden clustering
Cell-type annotation was performed manually based on the expression of canonical marker genes. Marker expression was assessed using dotplots grouped by Leiden cluster. Final cell-type labels were assigned by evaluating the coordinated expression of curated marker panels derived from publicly available marker resources and relevant single-cell studies of the human airway and lung epithelium.
Assembly: GRCh38
Supplementary files format and content: Processed data are provided for each sample as Cell Ranger filtered feature-barcode matrices in Matrix Market format, including matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files. Filtered feature-barcode matrix H5 files are also provided for each sample.
Supplementary files format and content: adata_GEO.h5ad contains normalized/log-normalized expression in .X, raw counts in layers['counts'], and curated annotations in obs['curated_coarse_cell_type'] and obs['curated_cell_type'].

source_name: bronchial epithelium

growth_protocol: Human bronchial epithelial cells from cystic fibrosis patients homozygous for the F508del mutation and non-CF individuals were provided by the Servizio Colture Primarie of the Italian Cystic Fibrosis Research Foundation. Basal airway stem cells (p63+/KRT5+) were isolated and expanded in serum-free medium. To promote cell proliferation, the medium was supplemented with the BMP antagonist DMH-1 (1 μM), the TGF-β antagonist A 83-01 (1 μM), and the ROCK1 inhibitor Y-27632 (10 μM). After 5–6 passages, cells were seeded at high density on Snapwell or Transwell porous inserts. After 24 hours from seeding, the proliferative medium on the basolateral side was switched to PneumaCult ALI differentiation medium, and the medium on the apical side was removed to establish air-liquid interface conditions. Epithelia were maintained for at least 2–3 weeks to achieve full mucociliary differentiation.

extract_protocol:
Bronchial epithelial cells were detached from Snapwell inserts as single cells. Both apical and basolateral sides were washed with PBS without Ca2+ and Mg2+, incubated for 30 minutes with Versene, and then incubated for an additional 15 minutes in 10x concentrated trypsin solution at 37°C. Cells were collected directly in New Zealand serum plus 10% DMSO, frozen for 24 hours at -80°C, and then stored in liquid nitrogen. For sequencing, single cells were suspended in phosphate-buffered saline containing 0.04% BSA, filtered using a 40 μm cell strainer, and counted with a LUNA-II Automated Cell Counter.
The cell suspension was loaded onto the Chromium Single Cell G Chip Kit and run on the Chromium Single Cell Controller according to the manufacturer's protocol. Single-cell 3' libraries were generated using the Chromium Single Cell 3' Library and Gel Bead Kit v3.1. cDNA quality was assessed using High Sensitivity D5000 ScreenTape on an Agilent 4200 TapeStation system. Library quality was assessed using High Sensitivity DNA D1000 ScreenTape. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer according to the manufacturer's specifications.

treatment_protocol: Differentiated bronchial epithelial cells were treated basolaterally for 72 hours. BE63_NON_CF_TNFa_IL17 cells were treated with IL-17A (20 ng/mL, SRP3080, Sigma-Aldrich) and TNF-α (10 ng/mL, T6674, Sigma-Aldrich). BE63_NON_CF_IFNa cells were treated with IFN-α (10 ng/mL, H6041, Sigma-Aldrich). Untreated samples were maintained under the same culture conditions without cytokine stimulation.

value: bronchial epithelium

value: bronchial epithelial cells

value: non-CF

value: IFNα


title: sh-hnRNP M#1 Untreated 2

description: Library name: LR21E26FV23

value: NSCLC


title: RNASeq_144 04_38_TDLN_d23

description:
Library name: 04_38_TDLN_d23
study day=23; RIN=7.1; tumor_volume_mm3=294.39590400000003; sample_status=RNAlater


title: k4

description:
Library name: k4
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: BE63_NON_CF_TNFa_IL17

description:
Library name: BE63_NON_CF_TNFa_IL17
Non-cystic fibrosis human bronchial epithelial preparation treated with TNFα + IL-17.

value: TNFα + IL-17


title: RNASeq_144 04_38_S_d23

description:
Library name: 04_38_S_d23
study day=23; RIN=8.4; tumor_volume_mm3=294.39590400000003; sample_status=RNAlater


title: sh-hnRNP M#1 Untreated 1

description: Library name: LR21E26FV22


title: BE73_NT

description:
Library name: BE73_NT
Cystic fibrosis human bronchial epithelial preparation, untreated.

value: cystic fibrosis

value: untreated


title: HepG2, control, rep1

description: Library name: CONTROL-3-1

value: control


title: RNASeq_144 04_32_T_d23

description:
Library name: 04_32_T_d23
study day=23; RIN=6.6; tumor_volume_mm3=1390.253725; sample_status=Fresh-frozen

value: BALB/c


title: SCR_Untreated 3

description: Library name: LR21E26FV21


title: k20

description:
Library name: k20
DAP-seq

value: genotype

value: WT

value: ChIP antibody


title: BE63_NON_CF_NT

description:
Library name: BE63_NON_CF_NT
Non-cystic fibrosis human bronchial epithelial preparation, untreated.


title: Organoid_ATAC

city: New York City

first: Jaymin

middle: J

last: Kathiriya

state: NY

address: 1425 Madison Ave

department: Pulmonary

institute: Icahn School fo Medicine at Mount Sinai

description: Library name: aBasal_ATAC

library_source: transcriptomic single cell

data_processing:
CellRanger
Assembly: hg38
Supplementary files format and content: Feature Matrices, Barcodes, and Counts Data

source_name: AT2 and Fibroblast

extract_protocol:
Single cell suspension of all cells prior to library prepration
10X Genomics Multiome Library Prep
Active Motif CUT&RUN kit

value: AT2 and Fibroblast


title: SCR_Untreated 1

description: Library name: LR21E26FV19

value: lung


title: Donor Lung 2_ATAC

description: Library name: AJJW168_ATAC

source_name: Lung

value: Lung


title: RNASeq_144 04_22_TDLN_d16

description:
Library name: 04_22_TDLN_d16
study day=16; RIN=8.2; tumor_volume_mm3=680.8265205; sample_status=RNAlater

value: Tumor draining lymph node


title: A549-MASCOT-mhM-TGFbeta #3

description: Library name: GJW174

extract_protocol:
A549 stably expressing either wildtype or hnRNP M-interaction deficient mhM variant were treated with 5 ng/ml TGFbeta for 72h or not. Next, cells were harvest in 1ml TRIzol for RNAseq.
Total RNA was extracted and probed to generate Ribo-zero libraries using the Ribo-off rRNA Depletion Kit and Vazyme ssDNA Library Prep kit for Illumina. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: lung cancer


title: Donor Lung 1_ATAC

description: Library name: AJJO420_ATAC


title: RNASeq_144 03_30_T_d23

description:
Library name: 03_30_T_d23
study day=23; RIN=5.2; tumor_volume_mm3=1615.584092; sample_status=RNAlater

value: Tumor


title: A549-MASCOT-mhM-TGFbeta #2

description: Library name: GJW173


title: IPF Lung 1_ATAC

description: Library name: IPF_epi_227788_ATAC


title: k17

description:
Library name: k17
DAP-seq


title: NAC103-GFP, input, rep2

city: Jinan

first: Pengcheng

last: Li

address: 23788 Gongye North Road

institute: Shandong Academy of Agricultural Sciences

description: Library name: NAC103-GFP, input, rep2

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.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the BWA program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: TAIR10
Supplementary files format and content: bw, narrowPeak

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium in a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
About 5 g of materials were collected from the liquid 1/2 MS medium and fixed with 1% formaldehyde. After nuclei extraction, the chromatin was sonicated using a Bioruptor (on, 30s; off, 30s; 15 cycles).
For ChIP-seq, the DNA library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. For DAP-seq, the DNA library was prepared using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme, China).

treatment_protocol: For ChIP-seq, 35S:NAC103-GFP seedlings were treated with 20 µM MG132 for 24 h before collection.

value: Whole seedlings


title: NAC103-Halo, DAP, rep1

description: Library name: NAC103-Halo, DAP, rep1

value: Col


title: Liver, control, rep1

city: Jefferson

first: Li

last: Xia

state: AR

address: 3900 NCTR Rd

institute: National Center for Toxicological Research

description: Library name: Sample 1

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform, using 100 nt single end reads, with 5 million reads on average per sample. Data analysis was processed via aligning sequencing reads to a reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner, which enables fast and accurate mapping through a pre-built genome index. Following alignment, the number of RNA molecules per gene was quantified to assess gene expression levels, and differentially expressed genes (DEGs) were identified for downstream analysis. DESeq2 was used to perform differential expression analysis with the adjusted p-value < 0.05. Downstream analyses include pathway enrichment and data visualization to interpret biological relevance were performed via Ingenuity Pathway analysis (IPA, Qiagen).
Assembly: The STAR aligner (Spliced Transcripts Alignment to a Reference) is Lexogen’s preferred tool for aligning reads from its products. It aligns sequencing reads directly to a reference genome using a pre-built genome index.
Supplementary files format and content: txt. file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Six-week-old female Big Blue rats obtained from Gentronix (Alderley Edge, UK) were housed at 24 °C with a 12-hour light/dark cycle. The rats had ad libitum access to water and an NIH-41 irradiated pelleted diet. After one week of acclimation, they were randomly assigned to different treatment groups, with 3 rats per cage.

extract_protocol:
Total RNA was isolated from liver and bone marrow using the Mini RNeasy Kit (Qiagen, Hilden, Germany). The quality and concentration of the RNA samples were assessed using the Qubit RNA Broad Range Assay Kits (Invitrogen, Waltham, MA).
Library preparation, sequencing, and initial data processing were subsequently performed by Lexogen GmbH, Austria. Briefly, RNA samples were characterized using UV-Vis spectrophotometry (NanoDrop 2000c, Thermo Fisher), and RNA integrity was assessed on a Fragment Analyzer System with the DNF-471 RNA Kit (15 nt) (Agilent). Libraries were constructed using Lexogen’s QuantSeq 3' mRNA-Seq Library Prep Kit FWD, incorporating the BC1-block add-on, following UG version 191UG444V0111. The quality of the prepared libraries was verified on a Fragment Analyzer System with the DNF-474 HS-DNA Kit (1-6000 bp) (Agilent).

treatment_protocol: All rats were gavaged with NDEA at doses of 0, 5 and 10 mg/kg/day with a volume of 2 ml/kg for 28 consecutive days. Dose volumes were calculated individually based on the animal’s most recent body weight. Six rats per dose group were treated, except for the positive control group that consisted of three rats. Positive control animals received B(a)P at a dose of 75 mg/kg/day for the same duration.

value: Liver

tag: strain

value: Big Blue

tag: Sex

value: female

value: Transgenic for vector carrying cII and lacI reporter genes

value: Treated with Control


title: NAC103-GFP, input, rep3

description: Library name: NAC103-GFP, input, rep3


title: RNASeq_144 03_30_TDLN_d23

description:
Library name: 03_30_TDLN_d23
study day=23; RIN=6.5; tumor_volume_mm3=1615.584092; sample_status=RNAlater

value: BALB/c


title: A549-MASCOT-mhM-TGFbeta #1

description: Library name: GJW172


title: A549-MASCOT-mhM-Untreated #3

description: Library name: GJW170


title: k16

description:
Library name: k16
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype


title: RNASeq_144 03_30_S_d23

description:
Library name: 03_30_S_d23
study day=23; RIN=9.0; tumor_volume_mm3=1615.584092; sample_status=RNAlater

value: Spleen


title: k15

description:
Library name: k15
DAP-seq

value: WT

value: ChIP antibody


title: RNASeq_144 03_29_T_d23

description:
Library name: 03_29_T_d23
study day=23; RIN=6.9; tumor_volume_mm3=412.514946; sample_status=RNAlater


title: A549-MASCOT-mhM-Untreated #2

description: Library name: GJW169

value: Lung


title: Donor Lung 2_GEX

description: Library name: AJJW168_GEX


title: k14

description:
Library name: k14
DAP-seq


title: Whole rosette tissue, wild type, 17 day, RNA, rep1

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

description: Library name: WT_1

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using hisat2 (v 2.2.1)
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The gene feature was counted in DESeq2 and limma packages in Bioconductor
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Whole rosette tissue

growth_protocol: Plants used for RNA-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
Total RNA was extracted from 17-day-old shoot tissue of 5 plants that had not bolted and that were randomly selected from 5 individual pots using a RNeasy Plant Mini Kit (Qiagen; catalog no. 74904) following with the DNase I digestion and RNA clean up included in an RNA Clean & Concentrator kit (Zymo Research; catalog no. 1014). Three biological replicates were collected for each indicated genotype.
1 μg of total RNA of each sample was used for cDNA library construction. cDNA library construction was performed using an NEBNext Ultra II Directional RNA Library Prep C (NEB; catalog no. E7760S) combined with an NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; catalog no. E7490S) according to the manufacturer’s manual.

value: Whole rosette tissue

tag: ecotype

value: Wild type

tag: development stage


title: Whole rosette tissue, wild type, 17 day, RNA, rep2

description: Library name: WT_2


title: Whole rosette tissue, hta9 hta11, 17 day, H3K27me3, ChIP, rep1

description: Library name: HTA_H3K27me3_1

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using Bowtie2 (v 2.2.1) in very-sensitive-end-to-end mode
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The reads of individual biological replicate were merged into one BAM file using SAMtools (v 1.17)
The BAM files of individual replicate and the merged sample were converted to paired-end BED files using BEDTools
ChIP-seq quantification was conducted using the annotated code was deposited on GitHub (https://github.com/BradleyDickson/Arabidopsis_H2AZ_H3K27me3_siQ-ChIP).
Assembly: TAIR10
Supplementary files format and content: TXT files include the quantification of the normalized distribution at indicated genomic regions in all included samples with a p-value < 0.05 threshold (-pv)
Supplementary files format and content: TXT files include the quantification of the normalized distribution at indicated genomic regions in all included samples (-DB)
Supplementary files format and content: BED files include the normalized distribution (NC) at the indicated genomic regions
Supplementary files format and content: BED files include the number of ChIP DNA fragemtents (NA) at the indicated genomic regions

source_name: Whole Rosette tissue

growth_protocol: Plants used for ChIP-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
4 g of 17-day-old whole rosette tissue were collected for each biological replicate. Nuclear lysis buffer was replaced with 1.7 mL of ChIP Lysis Buffer (50 mM HEPES-NaOH (pH =7.4), 16.7 mM Tris-HCl (pH = 8), 1 mM EDTA (pH = 8), 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 0.1% Sodium deoxycholate, 1 cOmpleteTM mini tablet / 10 mL solution). The total chromatin samples were sonicated using Bioruptor Pico. Sheared chromatin samples were stored at -80 °C overnight prior to the immunoprecipitation. The following antibodies were used in the analysis: Anti-H3 (ab1791, Abcam) (1:200 dilution), Anti-H3K27me3 (07-449, Millipore) (1:100 dilution), and Anti-H2A.Z (1.5 µg for a 500 µL IP sample) (Deal et al., 2007). The QIAquick MinElute PCR purification kit was replaced with ChIP DNA Clean & Concentrator purification kit (D5205, Zymo research) for elution of the ChIP DNA. The eluted ChIP DNA was quantified us a Qubit 2.0 Fluorometer and used immediately in library construction.
0.5 ng eluted ChIP DNA was used for each library construction. ChIP DNA libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit (NEB; catalog no. E7645L) according to the manufacturer’s manual. Illumina Multiplexing adapter was used for indexing. Pair-ended,150-bp sequencing was performed using an Illumina Novaseq S4 lane.

value: Whole Rosette tissue

value: hta9 hta11


title: Whole rosette tissue, hta9 hta11, 17 day, H3K27me3, ChIP, rep2

description: Library name: HTA_H3K27me3_2


title: L15

description:
Library name: L15
DAP-seq


title: RNASeq_144 03_29_TDLN_d23

description:
Library name: 03_29_TDLN_d23
study day=23; RIN=6.9; tumor_volume_mm3=412.514946; sample_status=RNAlater

value: Tumor draining lymph node


title: Donor Lung 1_GEX

description: Library name: AJJO420_GEX


title: A549-MASCOT-mhM-Untreated #1

description: Library name: GJW167

value: lung cancer


title: k13

description:
Library name: k13
DAP-seq


title: A549-MASCOT-WT-TGFbeta #3

description: Library name: GJW166


title: RNASeq_144 03_29_S_d23

description:
Library name: 03_29_S_d23
study day=23; RIN=8.4; tumor_volume_mm3=412.514946; sample_status=RNAlater


title: k12

description:
Library name: k12
DAP-seq


title: RNASeq_144 03_28_T_d23

description:
Library name: 03_28_T_d23
study day=23; RIN=7.8; tumor_volume_mm3=835.320096; sample_status=RNAlater

value: Tumor


title: IPF Lung 2_GEX

description: Library name: IPF_epi_22794_GEX


title: A549-MASCOT-WT-TGFbeta #2

description: Library name: GJW165


title: k11

description:
Library name: k11
DAP-seq


title: RNASeq_144 03_28_TDLN_d23

description:
Library name: 03_28_TDLN_d23
study day=23; RIN=7.9; tumor_volume_mm3=835.320096; sample_status=RNAlater


title: A549-MASCOT-WT-TGFbeta #1

description: Library name: GJW164


title: SCR252,SCR253,SCR254 reads with undetermined index pair to sample mapping, for additional barcode detection

city: Seattle

first: Thomas

middle: A.

last: Reh

state: WA

address: 1959 NE Pacific Street

department: Neurobiology and Biophysics

institute: University of Washington

description: Library name: SCR252-SCR253-SCR254_Undetermined_reads

data_processing:
Cellranger count was used for read alignment and counting. All analyses of the resulting count matrices and plotting of results was done in R  using the Seurat package .
Assembly: GRCh38
Supplementary files format and content: h5 file containing sparse count matrix

source_name: retina

growth_protocol: Human fetal eyes of gestational ages between 70 to 150 days were received from the Birth Defects Research Laboratory at the University of Washington following the approved protocol. After the removal of cornea, lens and retina, the remaining tissue consisting of sclera, choroid and RPE was incubated in 0.1 U/µl Collagenase IV (Gibco, 17104019) in HBSS (Gibco, 14025134) at 37 °C for 10 min. RPE was carefully peeled away in coherent sheets from the choroid making sure to avoid carryover of vasculature. RPE sheets were incubated for 15 min in 0.2 U/µl Collagenase IV in HBSS at 37 °C for 10-15 min and subsequently titruated with a P1000 pipette until a suspension of small clumps of ~ 20 cells was achieved. Cells were spun down for 5 min. at 300g, supernatant was removed and pellet resuspended in prewarmed retinal differentiation medium (RDM). Cells were seeded into wells of a 24 well plate (1 ml/well) containing Matrigel (Corning, 354234) coated coverslips. RDM consisted in general of 50% DMEM (Gibco, 12430062), 50% DMEM/F12 (Gibco, 11330032), 1% antibiotic/antimycotic (Millipore Sigma, A5955-100ML), 1% NEAA (Gibco, 11140050), 1-10% FBS (Corning, 35-011-CV), 2% B27 (Gibco, 17504044). For the first experiment cells were isolated from a donor of gestational day 137 (D137) and cultured in RDM with 10% FBS until processing for scRNAseq or staining. For all following experiments we used RDM with 5 % dialyzed FBS (Gibco, 26400044) and B27 without Vitamin A (Gibco, 12587010) from plating until the day of infection when we reduced the FBS concentration to 1%.

extract_protocol:
Single cell RNAseq libraries were prepared using 10x Genomics’ Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics, PN-1000268) according to manufacturer’s protocol.
Single cell RNAseq libraries were prepared using 10x Genomics’ Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics, PN-1000268) according to manufacturer’s protocol.

treatment_protocol: CMV-ASCL1-NEUROD1 overexpression was performed on a D115 sample, which was infected at DIV8 and harvested for scRNAseq or immunostaining on DIV28. After infection, half the wells were treated with 50 ng/ml bFGF (R&D Systems, 3718-FB-025) and 10 µM Activin A inhibitor (SB431542 Gibco, 120-14E-10UG).

value: retina

value: retinal pigment epithelium


title: k10

description:
Library name: k10
DAP-seq


title: RNASeq_144 03_28_S_d23

description:
Library name: 03_28_S_d23
study day=23; RIN=8.9; tumor_volume_mm3=835.320096; sample_status=RNAlater

value: BALB/c


title: A549-MASCOT-WT-Untreated #3

description: Library name: GJW162


title: D115 RPE, CMV>ASCL1-NEUROD1-mScarlet, FGF, AAI

description: Library name: SCR269_CMV-AN-FA


title: k1

description:
Library name: k1
DAP-seq

value: Klebsiella pneumoniae


title: RNASeq_144 03_18_TDLN_d16

description:
Library name: 03_18_TDLN_d16
study day=16; RIN=6.2; tumor_volume_mm3=314.94015; sample_status=RNAlater


title: A549-MASCOT-WT-Untreated #2

description: Library name: GJW161


title: J9

description:
Library name: J9
DAP-seq

value: strain


title: D115 RPE, CMV>ASCL1-NEUROD1-mScarlet

description: Library name: SCR268_CMV-AN


title: IPF Lung 2_ATAC

description: Library name: IPF_epi_22794_ATAC


title: RNASeq_144 03_17_TDLN_d16

description:
Library name: 03_17_TDLN_d16
study day=16; RIN=7.6; tumor_volume_mm3=314.146326; sample_status=RNAlater


title: A549-MASCOT-WT-Untreated #1

description: Library name: GJW159


title: D115 RPE, CMV>mScarlet

description: Library name: SCR267_ctrl


title: J8

description:
Library name: J8
DAP-seq

value: genotype


title: SCR_TGFbeta 3

description: Library name: LR21E26FV33

value: lung

value: NSCLC


title: Organoid_GEX

description: Library name: aBasal_GEX

value: AT2 and Fibroblast


title: RNASeq_144 03_16_TDLN_d16

description:
Library name: 03_16_TDLN_d16
study day=16; RIN=5.1; tumor_volume_mm3=169.979504; sample_status=RNAlater


title: D147 RPE, Ef1a>library; CMV>mScarlet

description: Library name: SCR254_lib2


title: Rh4 Clone Cells, Treated IR24hrs, Rep3

city: Durham

first: Christopher

middle: David

last: Delaney

state: NC

address: 308 Research Drive, LSRC C131

department: Pharmacology and Cancer Biology

institute: Duke University School of Medicine

description:
Library name: Sample 6
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalTreated_IR24hr_Rep3

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

source_name: Rh4 Clone

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

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

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

value: Rh4 Clone

value: Rhabdomyosarcoma

value: WT


title: J7

description:
Library name: J7
DAP-seq

value: ChIP antibody


title: RNASeq_144 02_20_T_d23

description:
Library name: 02_20_T_d23
study day=23; RIN=6.9; tumor_volume_mm3=611.286153; sample_status=RNAlater

value: CYTO


title: D91 RPE, Ef1a>library; CMV>mScarlet

description: Library name: SCR253_lib


title: Rh4 Clone Cells, Treated IR24hrs, Rep2

description:
Library name: Sample 5
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalTreated_IR24hr_Rep2


title: J6

description:
Library name: J6
DAP-seq


title: D91 RPE, Ef1a>mScarlet

description: Library name: SCR252_ctrl


title: RNASeq_144 02_20_TDLN_d23

description:
Library name: 02_20_TDLN_d23
study day=23; RIN=5.7; tumor_volume_mm3=611.286153; sample_status=RNAlater

value: Tumor draining lymph node


title: Rh4 Clone Cells, Treated IR24hrs, Rep1

description:
Library name: Sample 4
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalTreated_IR24hr_Rep1


title: J5

description:
Library name: J5
DAP-seq


title: sh-hnRNP M#2 Untreated 3

description: Library name: LR21E26FV27

source_name: lung

extract_protocol:
A549 stably expressing either scramble or shRNAs targeting hnRNP M were treated with 5 ng/ml TGFbeta for 72h or not. Next, cells were harvest in 1ml TRIzol for RNAseq.
Total RNA was extracted and probed to generate Ribo-zero libraries using the Ribo-off rRNA Depletion Kit and Vazyme ssDNA Library Prep kit for Illumina. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: Healthy control peripheral blood, biological replicate 3

description:
Library name: HC3
Bulk RNA-seq of peripheral blood from HC subject

value: peripheral blood

value: healthy control


title: RNASeq_144 02_20_S_d23

description:
Library name: 02_20_S_d23
study day=23; RIN=8.5; tumor_volume_mm3=611.286153; sample_status=RNAlater

value: Spleen


title: Rh4 Clone Cells, Parental, Rep3

description:
Library name: Sample 3
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalControl_Rep3


title: J4

description:
Library name: J4
DAP-seq


title: The poor group,age 51,male,temporal muscle,P1

city: Fuzhou

first: Jingyi

last: Chen

address: xinquan road

institute: Fujian Medical University Union Hospital

description: Library name: P1

data_processing:
1. Quality Control: Raw data filtered using Cutadapt to remove adapter sequences at 3' end and reads with average quality score < Q20
2. Alignment: Clean reads mapped to reference genome using HISAT2 v2.0.5
3. Quantification: Gene-level read counts generated with HTSeq v0.9.1
4. Normalization: Expression levels calculated as FPKM
5. Differential Analysis: DEGs identified using DESeq v1.20.0 (p<0.05, |log2FC|>1)
6. Functional Enrichment:  - GO analysis using topGO (hypergeometric test, p<0.05)  - KEGG pathway analysis using ClusterProfiler v3.4.4 (p<0.05)
Assembly: GRCh38
Supplementary files format and content: Expression Matrices

source_name: temporal muscle

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies). RNA concentration, quality and integrity were determined using NanoDrop spectrophotometer (Thermo Scientific).
Sequencing libraries were prepared with 3 μg total RNA input. mRNA was purified using poly-T oligo-attached magnetic beads. Fragmentation performed with divalent cations in Illumina fragmentation buffer at elevated temperature. First-strand cDNA synthesized with random oligonucleotides and SuperScript II. Second-strand cDNA synthesized using DNA Polymerase I and RNase H. Blunt ends generated via exonuclease/polymerase treatment. After adenylation of 3' ends, Illumina PE adapters were ligated. Library fragments (400-500 bp) were selected using AMPure XP system (Beckman Coulter). Adapter-ligated fragments were enriched with Illumina PCR Primer Cocktail in 15-cycle PCR. Final library purification used AMPure XP system. Library quantification performed with Agilent High Sensitivity DNA assay on Bioanalyzer 2100 system (Agilent). Libraries sequenced on NovaSeq 6000 platform (Illumina) by Suzhou PANOMIX Biomedical Tech Co., Ltd.

value: temporal muscle

tag: age

value: age 51

value: male

tag: group

value: angiogenesis-deficient cohort


title: RNASeq_144 02_19_TDLN_d23

description:
Library name: 02_19_TDLN_d23
study day=23; RIN=4.7; tumor_volume_mm3=1147.146875; sample_status=RNAlater

value: BALB/c


title: Rh4 Clone Cells, Parental, Rep2

description:
Library name: Sample 2
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalControl_Rep2


title: RNASeq_144 04_39_S_d23

description:
Library name: 04_39_S_d23
study day=23; RIN=8.8; tumor_volume_mm3=701.652333; sample_status=RNAlater


title: RNASeq_144 04_38_T_d23

description:
Library name: 04_38_T_d23
study day=23; RIN=5.1; tumor_volume_mm3=294.39590400000003; sample_status=RNAlater

value: Tumor


title: J3

description:
Library name: J3
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype


title: sh-hnRNP M#1 Untreated 3

description: Library name: LR21E26FV24

data_processing:
Using the 2-pass mapping function of the STAR software, the original data was aligned to the genome.
Assembly: hg19
Supplementary files format and content: Matrix of Percent Spliced In (PSI) values for alternative splicing events across samples,csv format

value: lung

value: NSCLC


title: The poor group,age 45,female,temporal muscle,P2

description: Library name: P2

value: age 45

value: female


title: Rh4 Clone Cells, Parental, Rep1

description:
Library name: Sample 1
Column name in Rh4clone_TreatedIR24hrs_Raw_Counts_All_Samples.txt: Rh4Clone_ParentalControl_Rep1

value: Rh4 Clone

value: Rhabdomyosarcoma

value: WT


title: The poor group,age 51,male,temporal muscle,P3

description: Library name: P3


title: sh-hnRNP M#2 Untreated 1

description: Library name: LR21E26FV25


title: J20

description:
Library name: J20
DAP-seq

value: ChIP antibody


title: RNASeq_144 02_19_S_d23

description:
Library name: 02_19_S_d23
study day=23; RIN=7.5; tumor_volume_mm3=1147.146875; sample_status=RNAlater

value: Spleen

value: CYTO


title: IPF Lung 1_GEX

description: Library name: IPF_epi_227788_GEX

value: Lung


title: RNASeq_144 02_18_T_d23

description:
Library name: 02_18_T_d23
study day=23; RIN=4.6; tumor_volume_mm3=1416.6649710000002; sample_status=RNAlater


title: TGFB SMAD3

description: Library name: TGFB SMAD3

library_source: other

data_processing:
CellRanger
Assembly: hg38
Supplementary files format and content: Feature Matrices, Barcodes, and Counts Data
Library strategy: CUT&Run

molecule: protein


title: J2

description:
Library name: J2
DAP-seq


title: RNASeq_144 02_18_TDLN_d23

description:
Library name: 02_18_TDLN_d23
study day=23; RIN=7.2; tumor_volume_mm3=1416.6649710000002; sample_status=RNAlater

value: Tumor draining lymph node


title: The poor group,age 51,female,temporal muscle,P4

description: Library name: P4

value: temporal muscle

value: age 51

value: angiogenesis-deficient cohort


title: TGFB IgG

description: Library name: TGFB IgG


title: The poor group,age 56,female,temporal muscle,P5

description: Library name: P5

value: age 56


title: J19

description:
Library name: J19
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype


title: The poor group,age 18,male,temporal muscle,P6

description: Library name: P6

value: age 18

value: male


title: RNASeq_144 02_18_S_d23

description:
Library name: 02_18_S_d23
study day=23; RIN=6.7; tumor_volume_mm3=1416.6649710000002; sample_status=RNAlater

value: BALB/c


title: CTL SMAD3

description: Library name: CTL SMAD3


title: J18

description:
Library name: J18
DAP-seq


title: CTL IgG

description: Library name: CTL IgG


title: RNASeq_144 02_12_T_d23

description:
Library name: 02_12_T_d23
study day=23; RIN=7.4; tumor_volume_mm3=1211.71875; sample_status=Fresh-frozen

value: Tumor


title: The poor group,age 55,male,temporal muscle,P7

description: Library name: P7

value: age 55


title: J17

description:
Library name: J17
DAP-seq

value: WT

value: ChIP antibody


title: The poor group,age 53,male,temporal muscle,P8

description: Library name: P8

value: age 53


title: P2-ChIP-seq_dTAG-MED26_HS_dTAG_rep2 (ChIP)

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

description: Library name: Sample 63, ChIP

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

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

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

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

value: colon cancer cells

value: KD

value: HS

tag: chip antibody

value: Pol II CTD (MBL, #MABI0601)


title: RNASeq_144 02_11_TDLN_d16

description:
Library name: 02_11_TDLN_d16
study day=16; RIN=6.7; tumor_volume_mm3=290.416608; sample_status=RNAlater

value: Tumor draining lymph node

value: CYTO


title: RNASeq_144 02_12_TDLN_d16

description:
Library name: 02_12_TDLN_d16
study day=16; RIN=6.4; tumor_volume_mm3=583.1650080000001; sample_status=RNAlater


title: J16

description:
Library name: J16
DAP-seq

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

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

value: Klebsiella pneumoniae


title: P2-ChIP-seq_dTAG-MED26_HS_dTAG_rep1 (ChIP)

description: Library name: Sample 62, ChIP


title: k3

description:
Library name: k3
DAP-seq

value: strain


title: The poor group,age 42,female,temporal muscle,P9

description: Library name: P9

value: temporal muscle

value: age 42

value: female

value: angiogenesis-deficient cohort


title: P2-ChIP-seq_dTAG-MED26_HS_DMSO_rep2 (ChIP)

description: Library name: Sample 61, ChIP


title: J15

description:
Library name: J15
DAP-seq

value: genotype


title: RNASeq_144 02_10_TDLN_d16

description:
Library name: 02_10_TDLN_d16
study day=16; RIN=7.5; tumor_volume_mm3=247.25106; sample_status=RNAlater

data_processing:
STAR Alignment v020201
bcl2fastq2 v2.20
RSEM v1.3.0
TPM and normalization using Data4Cure Biomedical Intelligence Cloud
Assembly: mm10
Supplementary files format and content: Tab-delimited matrix of log2(TPM) values by gene (HGNC filtered).

extract_protocol:
Total RNA extracted from collected tissues (spleen, tumor, TDLN) using study SOP.
Paired-end stranded mRNA-seq library prep with polyA enrichment.

value: BALB/c


title: The poor group,age 48,male,temporal muscle,P10

description: Library name: P10

value: age 48

value: male


title: J14

description:
Library name: J14
DAP-seq

value: WT

value: ChIP antibody


title: RNASeq_144 01_10_T_d23

description:
Library name: 01_10_T_d23
study day=23; RIN=4.8; tumor_volume_mm3=1772.3052; sample_status=RNAlater

value: Tumor

value: Isotype


title: P2-ChIP-seq_dTAG-MED26_HS_DMSO_rep1 (ChIP)

description: Library name: Sample 60, ChIP

value: colon cancer cells

value: HS

value: Pol II CTD (MBL, #MABI0601)


title: The poor group,age 51,female,temporal muscle,P11

description: Library name: P11

value: age 51


title: J13

description:
Library name: J13
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: RNASeq_144 01_10_TDLN_d23

description:
Library name: 01_10_TDLN_d23
study day=23; RIN=7.8; tumor_volume_mm3=1772.3052; sample_status=RNAlater

value: Tumor draining lymph node


title: P2-ChIP-seq_dTAG-MED26_NT_DMSO_rep2 (ChIP)

description: Library name: Sample 59, ChIP

value: NT


title: The poor group,age 51,male,temporal muscle,P12

description: Library name: P12

value: temporal muscle

value: angiogenesis-deficient cohort


title: J12

description:
Library name: J12
DAP-seq

value: genotype


title: RNASeq_144 01_10_S_d23

description:
Library name: 01_10_S_d23
study day=23; RIN=7.5; tumor_volume_mm3=1772.3052; sample_status=RNAlater

value: Spleen

value: BALB/c


title: P2-ChIP-seq_dTAG-MED26_NT_DMSO_rep1 (ChIP)

description: Library name: Sample 58, ChIP

value: WT


title: The poor group,age 46,female,temporal muscle,P13

description: Library name: P13

value: age 46

value: female


title: J11

description:
Library name: J11
DAP-seq

value: ChIP antibody


title: M1-ChIP-seq_dTAG-MED26_HS_dTAG_rep2 (ChIP)

description: Library name: Sample 57, ChIP

value: colon cancer cells

value: KD

value: MED1 (Abcam, #Ab64965)


title: The good group,age 5,female,temporal muscle,G1

description: Library name: G1

value: age 5

value: angiogenesis-competent cohort


title: RNASeq_144 01_09_TDLN_d23

description:
Library name: 01_09_TDLN_d23
study day=23; RIN=7.9; tumor_volume_mm3=1001.76384; sample_status=RNAlater

value: Isotype


title: J10

description:
Library name: J10
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: M1-ChIP-seq_dTAG-MED26_HS_dTAG_rep1 (ChIP)

description: Library name: Sample 56, ChIP

value: HS


title: The good group,age 49,female,temporal muscle,G2

description: Library name: G2

value: temporal muscle

value: age 49


title: J1

description:
Library name: J1
DAP-seq

value: genotype


title: RNASeq_144 01_09_S_d23

description:
Library name: 01_09_S_d23
study day=23; RIN=6.0; tumor_volume_mm3=1001.76384; sample_status=RNAlater

value: Spleen

value: BALB/c


title: M1-ChIP-seq_dTAG-MED26_HS_DMSO_rep2 (ChIP)

description: Library name: Sample 55, ChIP

value: WT


title: RNASeq_144 01_08_TDLN_d23

description:
Library name: 01_08_TDLN_d23
study day=23; RIN=7.4; tumor_volume_mm3=1623.4306; sample_status=RNAlater

value: Tumor draining lymph node


title: I9

description:
Library name: I9
DAP-seq

value: ChIP antibody


title: M1-ChIP-seq_dTAG-MED26_HS_DMSO_rep1 (ChIP)

description: Library name: Sample 54, ChIP

value: colon cancer cells


title: The good group,age 45,female,temporal muscle,G4

description: Library name: G4

value: age 45

value: female


title: RNASeq_144 01_08_S_d23

description:
Library name: 01_08_S_d23
study day=23; RIN=7.1; tumor_volume_mm3=1623.4306; sample_status=RNAlater


title: M1-ChIP-seq_dTAG-MED26_NT_DMSO_rep2 (ChIP)

description: Library name: Sample 53, ChIP

value: NT

value: MED1 (Abcam, #Ab64965)


title: The good group,age 39,female,temporal muscle,G5

description: Library name: G5

value: age 39

value: angiogenesis-competent cohort


title: RNASeq_144 01_09_T_d23

description:
Library name: 01_09_T_d23
study day=23; RIN=7.8; tumor_volume_mm3=1001.76384; sample_status=RNAlater

value: Tumor

value: Isotype


title: I7

description:
Library name: I7
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: RNASeq_144 01_06_TDLN_d16

description:
Library name: 01_06_TDLN_d16
study day=16; RIN=7.9; tumor_volume_mm3=522.541244; sample_status=RNAlater


title: I6

description:
Library name: I6
DAP-seq

value: genotype


title: Inp_ChIP-seq_dTAG-MED26_HS_dTAG (Input)

description: Library name: Sample 51, INPUT

value: KD

value: HS


title: The good group,age 32,female,temporal muscle,G7

description: Library name: G7

value: temporal muscle

value: age 32


title: RNASeq_144 01_04_TDLN_d16

description:
Library name: 01_04_TDLN_d16
study day=16; RIN=8.3; tumor_volume_mm3=161.326968; sample_status=RNAlater

value: Tumor draining lymph node

value: BALB/c


title: I5

description:
Library name: I5
DAP-seq

value: WT

value: ChIP antibody


title: The good group,age 51,female,temporal muscle,G8

description: Library name: G8

value: age 51

value: female


title: I4

description:
Library name: I4
DAP-seq


title: RNASeq_144 01_01_T_d23

description:
Library name: 01_01_T_d23
study day=23; RIN=5.5; tumor_volume_mm3=1319.835106; sample_status=Fresh-frozen


title: Inp_ChIP-seq_dTAG-MED26_NT_DMSO (Input)

description: Library name: Sample 49, INPUT

value: colon cancer cells

value: NT


title: The good group,age 4,female,temporal muscle,S1

description: Library name: S1

value: age 4

value: angiogenesis-competent cohort


title: I3

description:
Library name: I3
DAP-seq

value: Klebsiella pneumoniae


title: M26-ChIP-seq_dTAG-MED15_HS_dTAG_rep2 (ChIP)

description: Library name: Sample 48, ChIP

value: MED26 (Cell Signaling Technology, #14950S)


title: LysMcre;Nlrp3A350V;Il181r-/- 4

city: La Jolla

first: Rongbo

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San DIego

description:
Library name: SAMPLE 17
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx

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

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

value: Lung


title: The good group,age 5,male,temporal muscle,S2

description: Library name: S2

value: age 5

value: male


title: I20

description:
Library name: I20
DAP-seq

value: strain

value: genotype


title: M26-ChIP-seq_dTAG-MED15_HS_dTAG_rep1 (ChIP)

description: Library name: Sample 47, ChIP

value: KD

value: HS


title: LysMcre;Nlrp3A350V;Il181r-/- 2

description:
Library name: SAMPLE 15
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: I2

description:
Library name: I2
DAP-seq

value: WT


title: The good group,age 35,female,temporal muscle,S4

description: Library name: S4

value: temporal muscle

value: age 35


title: I19

description:
Library name: I19
DAP-seq

value: ChIP antibody


title: LysMcre;Nlrp3A350V;Il181r-/- 1

description:
Library name: SAMPLE 14
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: FL35 additional cells

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

address: 75 Ames St

institute: Broad Institute

description: Library name: Pool103-2_3

data_processing:
Raw fastq files for all 10x runs were aligned and quantified using Cellranger version 5.0.0 and reference package GRCh38 3.0.0 for the gene expression libraries. TCR sequencing data for all runs was processed using cellranger vdj (v5.0.0) and the GRCh38_vdj_v5.0.0 reference package.
For all cell multiplexed samples, we ran souporcell v2020.7 to identify genotype clusters using the 1000 genomes common SNP sites. To match genotype clusters across the eight different channels, we performed hierarchical clustering of all inferred genotypes using a Hamming distance and single linkage calculated at all sites with covered loci. Genotype clusters with fewer than 100 cells or fewer than 1000 variants in a given pool were filtered due to lack of confidence. Clustering of genotypes into 10 clusters was observed by dendrogram as expected and used to group cells from the same individual across different 10x channels. Finally, the identity of each individual was labeled based on the average expression of the hash antibodies across all cells in a given individual.
Assembly: GRCh38, cellranger reference package version 3.0.0
Supplementary files format and content: cellranger sparse gene x cell matrix

source_name: Lymph Node

extract_protocol:
Frozen aliquots of cells were thawed into RPMI with 10% FBS. Samples were washed with media and a dead cell depletion (Miltenyi Biotec 130-090-101) was performed prior to staining with cell hashtag antibodies (TotalSeq-C, Biolegend). After washing, samples were pooled and stained with cell surface antibodies (TotalSeq-C, Biolegend) according to manufacturer’s protocol prior to single-cell RNA-sequencing (10X genomics, 5’ kit with TCR and BCR). A total of 40,000 cells were loaded onto eight 10x channels. About 20,000 cells per sample were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s instructions.
The scRNAseq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2, and the TCR/BCR libraries were done using Chromium single cell human TCR/BCR amplification kits, and the hashing libraries were processed using Chromium 5’ feature barcode kit (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). All the sequencing libraries were normalized to 4nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters used were: Read 1 of 26bp, Read 2 of 90bp, Index 1 of 10bp and Index 2 of 10bp. Given lower initial relative cell numbers from FL35, this sample was reprocessed individually using similar methods and sequenced on a single lane without cell hashing to improve representation of cells from this sample. Samples were pooled and sequenced on a NovaSeqS4 (Illumina) as described.

value: Lymph Node


title: M26-ChIP-seq_dTAG-MED15_HS_DMSO_rep1 (ChIP)

description: Library name: Sample 45, ChIP

value: colon cancer cells


title: I18

description:
Library name: I18
DAP-seq

source_name: Klebsiella pneumoniae


title: LysMcre;Nlrp3A350V;Il181r+/- 3

description:
Library name: SAMPLE 13
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: Pool of 10 FL/tFL samples, pool 8

description: Library name: Pool93_47


title: LysMcre;Nlrp3A350V;Il181r+/- 2

description:
Library name: SAMPLE 12
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: I17

description:
Library name: I17
DAP-seq


title: M26-ChIP-seq_dTAG-MED15_NT_DMSO_rep1 (ChIP)

description: Library name: Sample 43, ChIP

value: NT


title: Pool of 10 FL/tFL samples, pool 7

description: Library name: Pool93_46


title: M1-ChIP-seq_dTAG-MED15_HS_dTAG_rep2 (ChIP)

description: Library name: Sample 42, ChIP

value: MED1 (Abcam, #Ab64965)


title: Pool of 10 FL/tFL samples, pool 6

description: Library name: Pool93_45


title: I15

description:
Library name: I15
DAP-seq

value: Klebsiella pneumoniae


title: Il18r1 control 4

description:
Library name: SAMPLE 10
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx

value: Il18r1 control


title: M1-ChIP-seq_dTAG-MED15_HS_dTAG_rep1 (ChIP)

description: Library name: Sample 41, ChIP


title: Pool of 10 FL/tFL samples, pool 5

description: Library name: Pool93_44


title: Il18r1 control 3

description:
Library name: SAMPLE 9
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx

value: Lung


title: M1-ChIP-seq_dTAG-MED15_HS_DMSO_rep2 (ChIP)

description: Library name: Sample 40, ChIP


title: I13

description:
Library name: I13
DAP-seq


title: Pool of 10 FL/tFL samples, pool 4

description: Library name: Pool93_43


title: Il18r1 control 2

description:
Library name: SAMPLE 8
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: Pool of 10 FL/tFL samples, pool 3

description: Library name: Pool93_42


title: I12

description:
Library name: I12
DAP-seq


title: Il18r1 control 1

description:
Library name: SAMPLE 7
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx


title: Pool of 10 FL/tFL samples, pool 2

description: Library name: Pool93_41


title: M1-ChIP-seq_dTAG-MED15_NT_DMSO_rep2 (ChIP)

description: Library name: Sample 38, ChIP


title: I11

description:
Library name: I11
DAP-seq


title: M1-ChIP-seq_dTAG-MED15_NT_DMSO_rep1 (ChIP)

description: Library name: Sample 37, ChIP


title: LysMcre;Nlrp3A350V 2

description:
Library name: SAMPLE 5
LysMcre_Nlrp3A350V_summary.xlsx


title: Pool of 10 FL/tFL samples, pool 1

description: Library name: Pool93_40


title: I10

description:
Library name: I10
DAP-seq


title: Inp_ChIP-seq_dTAG-MED15_HS_dTAG (Input)

description: Library name: Sample 36, INPUT


title: Rh30, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep2

description:
Library name: Library 42
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh30_CKMScreen_HighPopulation_Rep2

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

source_name: cell line

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

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

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

value: cell line

value: Rhabdomyosarcoma

value: Fusion-Positive

tag: screen

value: CKM Flow-Based Screen


title: I1

description:
Library name: I1
DAP-seq

value: strain

value: genotype


title: Rh30, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep1

description:
Library name: Library 41
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh30_CKMScreen_HighPopulation_Rep1


title: H9

description:
Library name: H9
DAP-seq

value: WT


title: Control 3

description:
Library name: SAMPLE 3
LysMcre_Nlrp3A350V_summary.xlsx

value: control


title: Inp_ChIP-seq_dTAG-MED15_NT_DMSO (Input)

description: Library name: Sample 34, INPUT


title: Rh30, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep2

description:
Library name: Library 40
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh30_CKMScreen_LowPopulation_Rep2


title: Control 2

description:
Library name: SAMPLE 2
LysMcre_Nlrp3A350V_summary.xlsx


title: M26-ChIP-seq_HSF1-SA_HS_rep2 (ChIP)

description: Library name: Sample 33, ChIP

value: SA

value: HS

value: MED26 (Cell Signaling Technology, #14950S)


title: Rh30, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep1

description:
Library name: Library 39
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh30_CKMScreen_LowPopulation_Rep1


title: H7

description:
Library name: H7
DAP-seq

value: ChIP antibody


title: Control 1

description:
Library name: SAMPLE 1
LysMcre_Nlrp3A350V_summary.xlsx


title: M26-ChIP-seq_HSF1-SA_HS_rep1 (ChIP)

description: Library name: Sample 32, ChIP

value: colon cancer cells


title: LysMcre;Nlrp3A350V 1

description:
Library name: SAMPLE 4
LysMcre_Nlrp3A350V_summary.xlsx


title: Inp_ChIP-seq_dTAG-MED15_HS_DMSO (Input)

description: Library name: Sample 35, INPUT


title: Rh28, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep2

description:
Library name: Library 38
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh28_CKMScreen_HighPopulation_Rep2


title: H6

description:
Library name: H6
DAP-seq


title: M26-ChIP-seq_HSF1-SA_NT_rep2 (ChIP)

description: Library name: Sample 31, ChIP

value: NT


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo+US-treated, U4

city: Hangzhou

first: Bihan

last: Wu

state: other

address: 88 Jiefang Road

institute: Zhejiang University

description:
Library name: U4
Column name in raw_counts.tsv: U4

data_processing:
Raw sequencing data were demultiplexed according to sample-specific index sequences to generate per-sample FASTQ files.
Raw reads of fastq were firstly processed using fastp and the low-quality/adapter reads were trimmed to obtain the clean reads.
Trimmed clean reads were mapped to the reference genome using HISAT2 with default parameters.
Reads count were obtained by featureCounts.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file include raw counts for each sample

source_name: lymph nodes

extract_protocol:
Total RNA was extracted using the RNAsimple Total RNA Kit (Tiangen, Beijing, China) following the manufacturer's instructions. Poly(A)⁺ mRNA was enriched from total RNA using Oligo(dT) magnetic beads.
RNA libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: lymph nodes

tag: strain background

value: female

value: bearing B16F10-OVA tumors

value: IPSPlipo+US-treated

tag: time

value: Day 18


title: The good group,age 47,male,temporal muscle,G3

description: Library name: G3

tag: tissue

value: temporal muscle

value: age 47

value: male

value: angiogenesis-competent cohort


title: Rh28, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep1

description:
Library name: Library 37
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh28_CKMScreen_HighPopulation_Rep1

value: cell line

value: Rhabdomyosarcoma

value: Fusion-Positive

value: CKM Flow-Based Screen


title: I8

city: Hongkong

first: Xin

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

institute: City University of Hong Kong

description:
Library name: I8
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: WT


title: M26-ChIP-seq_HSF1-SA_NT_rep1 (ChIP)

description: Library name: Sample 30, ChIP

value: colon cancer cells

value: SA

value: NT

value: MED26 (Cell Signaling Technology, #14950S)


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo+US-treated, U3

description:
Library name: U3
Column name in raw_counts.tsv: U3

value: lymph nodes

value: female

value: bearing B16F10-OVA tumors

value: IPSPlipo+US-treated

value: Day 18


title: H5

description:
Library name: H5
DAP-seq

value: ChIP antibody


title: M1-ChIP-seq_dTAG-MED26_NT_DMSO_rep1 (ChIP)

description: Library name: Sample 52, ChIP

value: MED1 (Abcam, #Ab64965)


title: H8

description:
Library name: H8
DAP-seq


title: RNASeq_144 01_05_TDLN_d16

city: Cambridge

first: Richard

address: 1 Portland St.

institute: Pfizer, Inc.

description:
Library name: 01_05_TDLN_d16
study day=16; RIN=7.9; tumor_volume_mm3=244.1416345; sample_status=RNAlater

source_name: Tumor draining lymph node

value: Tumor draining lymph node

value: BALB/c

value: Isotype


title: The good group,age 24,female,temporal muscle,G6

description: Library name: G6

value: temporal muscle

value: age 24

value: angiogenesis-competent cohort


title: Rh28, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep2

description:
Library name: Library 36
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh28_CKMScreen_LowPopulation_Rep2

value: cell line

value: Rhabdomyosarcoma

value: Fusion-Positive

value: CKM Flow-Based Screen


title: H4

description:
Library name: H4
DAP-seq

value: Klebsiella pneumoniae

value: strain

value: genotype

value: WT


title: Inp_ChIP-seq_dTAG-MED26_HS_DMSO (Input)

description: Library name: Sample 50, INPUT

value: colon cancer cells

value: HS


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo+US-treated, U2

description:
Library name: U2
Column name in raw_counts.tsv: U2

value: lymph nodes

value: female

value: bearing B16F10-OVA tumors

value: IPSPlipo+US-treated

value: Day 18


title: Rh28, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep1

description:
Library name: Library 35
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh28_CKMScreen_LowPopulation_Rep1


title: M26-ChIP-seq_HSF1-WT_HS_rep2 (ChIP)

description: Library name: Sample 29, ChIP

value: MED26 (Cell Signaling Technology, #14950S)


title: H3

description:
Library name: H3
DAP-seq

value: ChIP antibody


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo+US-treated, U1

description:
Library name: U1
Column name in raw_counts.tsv: U1


title: M26-ChIP-seq_HSF1-WT_HS_rep1 (ChIP)

description: Library name: Sample 28, ChIP


title: LysMcre;Nlrp3A350V;Il181r-/- 3

description:
Library name: SAMPLE 16
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx

value: Lung


title: Rh4 Native, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep2

description:
Library name: Library 34
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Native_CKMScreen_HighPopulation_Rep2

value: cell line

value: Rh4 Native

value: Rhabdomyosarcoma


title: H20

description:
Library name: H20
DAP-seq

value: Klebsiella pneumoniae


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo-treated, L4

description:
Library name: L4
Column name in raw_counts.tsv: L4

value: IPSPlipo-treated


title: M26-ChIP-seq_dTAG-MED15_HS_DMSO_rep2 (ChIP)

description: Library name: Sample 46, ChIP


title: M26-ChIP-seq_HSF1-WT_NT_rep2 (ChIP)

description: Library name: Sample 27, ChIP

value: NT


title: The good group,age 15,female,temporal muscle,S3

description: Library name: S3

value: temporal muscle

value: age 15

value: angiogenesis-competent cohort


title: Rh4 Native, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep1

description:
Library name: Library 33
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Native_CKMScreen_HighPopulation_Rep1

value: Fusion-Positive

value: CKM Flow-Based Screen


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo-treated, L3

description:
Library name: L3
Column name in raw_counts.tsv: L3

value: lymph nodes

value: female

value: bearing B16F10-OVA tumors


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

description:
Library name: Library 32
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Native_CKMScreen_LowPopulation_Rep2


title: H2

description:
Library name: H2
DAP-seq

value: strain

value: genotype

value: WT


title: M26-ChIP-seq_HSF1-WT_NT_rep1 (ChIP)

description: Library name: Sample 26, ChIP

value: colon cancer cells

value: MED26 (Cell Signaling Technology, #14950S)


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo-treated, L2

description:
Library name: L2
Column name in raw_counts.tsv: L2

value: Day 18


title: M26-ChIP-seq_dTAG-MED15_NT_DMSO_rep2 (ChIP)

description: Library name: Sample 44, ChIP


title: Rh4 Native, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep1

description:
Library name: Library 31
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Native_CKMScreen_LowPopulation_Rep1

value: cell line

value: Rh4 Native

value: Rhabdomyosarcoma


title: Inp_ChIP-seq_HSF1-SA_HS (Input)

description: Library name: Sample 25, INPUT

value: SA

value: HS


title: H18

description:
Library name: H18
DAP-seq

value: Klebsiella pneumoniae

value: ChIP antibody


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, IPSP lipo-treated, L1

description:
Library name: L1
Column name in raw_counts.tsv: L1

value: IPSPlipo-treated


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

description:
Library name: Library 30
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Clone_CKMScreen_HighPopulation_Rep2

value: Rh4 Clone

value: Fusion-Positive

value: CKM Flow-Based Screen


title: H17

description:
Library name: H17
DAP-seq

value: strain


title: Inp_ChIP-seq_HSF1-SA_NT (Input)

description: Library name: Sample 24, INPUT

value: NT


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, PBS-treated, P4

description:
Library name: P4
Column name in raw_counts.tsv: P4

value: lymph nodes

value: female

value: bearing B16F10-OVA tumors

value: PBS-treated


title: I16

description:
Library name: I16
DAP-seq

value: genotype

value: WT


title: Inp_ChIP-seq_HSF1-WT_HS (Input)

description: Library name: Sample 23, INPUT

value: colon cancer cells


title: Rh4 Clone, CKM Flow Screen, ARMS sgRNA Library, High Population, Rep1

description:
Library name: Library 29
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Clone_CKMScreen_HighPopulation_Rep1

value: cell line

value: Rhabdomyosarcoma


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, PBS-treated, P3

description:
Library name: P3
Column name in raw_counts.tsv: P3

value: Day 18


title: H16

description:
Library name: H16
DAP-seq

value: Klebsiella pneumoniae

value: ChIP antibody


title: Inp_ChIP-seq_HSF1-WT_NT (Input)

description: Library name: Sample 22, INPUT


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, PBS-treated, P2

description:
Library name: P2
Column name in raw_counts.tsv: P2


title: RNA-seq_dTAG-MED26_HS_dTAG_rep3

description: Library name: Sample 21

value: KD

value: HS


title: H19

description:
Library name: H19
DAP-seq


title: Rh4 Clone, CKM Flow Screen, ARMS sgRNA Library, Low Population, Rep1

description:
Library name: Library 27
Column name in CKM_FlowScreen_sgRNA_ReadCounts.txt: Rh4Clone_CKMScreen_LowPopulation_Rep1

value: Rh4 Clone

value: Fusion-Positive

value: CKM Flow-Based Screen


title: H14

description:
Library name: H14
DAP-seq

value: strain


title: RNA-seq_dTAG-MED26_HS_dTAG_rep2

description: Library name: Sample 20


title: C57BL/6J mouse bearing B16F10-OVA tumors, female, Day 18, PBS-treated, P1

description:
Library name: P1
Column name in raw_counts.tsv: P1

value: lymph nodes

value: female


title: H13

description:
Library name: H13
DAP-seq


title: RNA-seq_dTAG-MED26_HS_dTAG_rep1

description: Library name: Sample 19


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

description:
Library name: Library 25
Column name in P3F1_FlowScreen_sgRNA_ReadCounts.txt: P3F1_FlowScreen_HighPopulation_Rep2

value: P3F1-FLAG Flow-Based Screen


title: H12

description:
Library name: H12
DAP-seq

value: genotype