title: CRISPR_TF_SERPINB5_JustLowBulk_low

description:
Library name: CRISPR_TF_SERPINB5_low
FACS Antibody Serpin B5 (C-8): sc-271694 LOW

data_processing:
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For SLAM-seq, single end 100 base pair sequencing reads were mapped to hg38 3’UTR exons, filtered, TC snps identified, and reads counted using the slamdunk package with default settings (Herzog et al. 2017). Counted TC converted transcript reads were compiled for each gene in each sample by summing reads mapping to different 3’UTR exons for a given gene.
For RNA-seq, fastq files were pseudo-aligned using Kallisto (single-end mode) in bootstrap mode (100) pseudo-alignment was performed using the NCBI_hg38_p12 transcriptome resulting TPM per transcripts were collapsed into gene level TPM values
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
Assembly: hg38
Supplementary files format and content: Text files containing transcriptome wide expression levels combined by cell line for RNA-seq and SLAM-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.
Library strategy: CRISPR Screen


title: CRISPR_GW_SERPINB5_low

status: Public on Oct 08 2025

type: SRA

city: Cold Spring Harbor

first: Patrick

middle: Joseph

last: Cunniff

state: NY

address: 1 Bungtown Road

department: Cancer Center

country: USA

institute: Cold Spring Harbor Laboratory

description:
Library name: CRISPR_GW_SERPINB5_low
FACS Antibody Serpin B5 (C-8): sc-271694 LOW

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation. SLAM-seq experiments were performed using the SLAM-seq Explorer Kit Anabolic Kinetic Module (Lexogen) following manufacturer instructions.
RNA-seq and ChIP-seq ibraries were constructed using Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

tag: cell line

tag: cell type

value: human pancreatic cancer cell line

tag: genotype

tag: treatment


title: AsPC1_sgRosa_for_sgCHD4_rep2

description: Library name: AsPC1_sgRosa_for_sgCHD4_rep2

library_source: transcriptomic

data_processing:
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For SLAM-seq, single end 100 base pair sequencing reads were mapped to hg38 3’UTR exons, filtered, TC snps identified, and reads counted using the slamdunk package with default settings (Herzog et al. 2017). Counted TC converted transcript reads were compiled for each gene in each sample by summing reads mapping to different 3’UTR exons for a given gene.
For RNA-seq, fastq files were pseudo-aligned using Kallisto (single-end mode) in bootstrap mode (100) pseudo-alignment was performed using the NCBI_hg38_p12 transcriptome resulting TPM per transcripts were collapsed into gene level TPM values
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
Assembly: hg38
Supplementary files format and content: Text files containing transcriptome wide expression levels combined by cell line for RNA-seq and SLAM-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

molecule: polyA RNA

value: sgRosa

tag: batch


title: CRISPR_GW_SERPINB5_bulk

description:
Library name: CRISPR_GW_SERPINB5_bulk
FACS Antibody Serpin B5 (C-8): sc-271694 BULK


title: CRISPR_GW_SERPINB5_high

description:
Library name: CRISPR_GW_SERPINB5_high
FACS Antibody Serpin B5 (C-8): sc-271694 HIGH


title: AsPC1_EV_CB6644_rep3

description: Library name: AsPC1_EV_CB6644_rep3

value: Lv-Empty


title: AsPC1_sgCHD4_rep3

description: Library name: AsPC1_sgCHD4_rep3


title: AsPC1_sgCHD4_rep4

description: Library name: AsPC1_sgCHD4_rep4


title: T3M4_NVP2_4h_rep2.2

description:
Library name: T3M4_NVP2_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module

value: 4h NVP2


title: AsPC1_sgRosa_for_sgCHD4_rep4

description: Library name: AsPC1_sgRosa_for_sgCHD4_rep4


title: T3M4_NVP2_4h_rep2.1

description:
Library name: T3M4_NVP2_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_NEG_4h_rep2.1

description:
Library name: T3M4_NEG_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module

value: 4h dTAG-NEG


title: T3M4_NEG_4h_rep2.2

description:
Library name: T3M4_NEG_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: T3M4_dTAG_4h_rep2.2

description:
Library name: T3M4_dTAG_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module

value: 4h dTAGv1


title: AsPC1_sgRosa_for_sgCHD4_rep3

description: Library name: AsPC1_sgRosa_for_sgCHD4_rep3


title: T3M4_dTAG_4h_rep2.1

description:
Library name: T3M4_dTAG_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_DMSO_4h_rep2.2

description:
Library name: T3M4_DMSO_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module

value: 4h DMSO


title: T3M4_DMSO_4h_rep2.1

description:
Library name: T3M4_DMSO_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_CB6644_4h_rep2.2

description:
Library name: T3M4_CB6644_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: T3M4_NVP2_4h_rep1.1

description:
Library name: T3M4_NVP2_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_NEG_4h_rep1.2

description:
Library name: T3M4_NEG_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: T3M4_dTAG_4h_rep1.1

description:
Library name: T3M4_dTAG_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_NEG_4h_rep1.1

description:
Library name: T3M4_NEG_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_DMSO_4h_rep1.1

description:
Library name: T3M4_DMSO_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_dTAG_4h_rep1.2

description:
Library name: T3M4_dTAG_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: T3M4_DMSO_4h_rep1.2

description:
Library name: T3M4_DMSO_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NVP2_4h_rep2.1

description:
Library name: AsPC1_NVP2_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NEG_4h_rep3.4

description:
Library name: AsPC1_NEG_4h_rep3.4
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NVP2_4h_rep2.2

description:
Library name: AsPC1_NVP2_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NEG_4h_rep3.2

description:
Library name: AsPC1_NEG_4h_rep3.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NEG_4h_rep3.3

description:
Library name: AsPC1_NEG_4h_rep3.3
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NVP2_4h_rep1.1

description:
Library name: AsPC1_NVP2_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_CB6644_4h_rep1.1

description:
Library name: T3M4_CB6644_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep3.4

description:
Library name: AsPC1_dTAG_4h_rep3.4
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep3.3

description:
Library name: AsPC1_dTAG_4h_rep3.3
SLAM-seq - Lexogen Anabolic Module


title: T3M4_CB6644_4h_rep2.1

description:
Library name: T3M4_CB6644_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_NVP2_4h_rep1.2

description:
Library name: T3M4_NVP2_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep3.2

description:
Library name: AsPC1_dTAG_4h_rep3.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep3.1

description:
Library name: AsPC1_dTAG_4h_rep3.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_DMSO_12h_rep4

description:
Library name: AsPC1_DMSO_12h_rep4
SLAM-seq - Lexogen Anabolic Module

value: 12h DMSO


title: AsPC1_NEG_4h_rep3.1

description:
Library name: AsPC1_NEG_4h_rep3.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_DMSO_12h_rep1

description:
Library name: AsPC1_DMSO_12h_rep1
SLAM-seq - Lexogen Anabolic Module


title: T3M4_CB6644_4h_rep1.2

description:
Library name: T3M4_CB6644_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_12h_rep4

description:
Library name: AsPC1_CB6644_12h_rep4
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_12h_rep3

description:
Library name: AsPC1_CB6644_12h_rep3
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_DMSO_12h_rep3

description:
Library name: AsPC1_DMSO_12h_rep3
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_12h_rep2

description:
Library name: AsPC1_CB6644_12h_rep2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_12h_rep1

description:
Library name: AsPC1_CB6644_12h_rep1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_EV_CB6644_rep1

description: Library name: AsPC1_EV_CB6644_rep1


title: AsPC1_NEG_4h_rep2.1

description:
Library name: AsPC1_NEG_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_sgRosa_for_sgCHD4_rep1

description: Library name: AsPC1_sgRosa_for_sgCHD4_rep1


title: AsPC1_NVP2_4h_rep1.2

description:
Library name: AsPC1_NVP2_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep2.2

description:
Library name: AsPC1_dTAG_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep2.1

description:
Library name: AsPC1_dTAG_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NEG_4h_rep2.2

description:
Library name: AsPC1_NEG_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_A62T_CB6644_rep3

description: Library name: AsPC1_A62T_CB6644_rep3


title: AsPC1_DMSO_4h_rep2.2

description:
Library name: AsPC1_DMSO_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Tel1-SAE2_4h

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description: Library name: FLAG-Tel1-SAE2_4h

data_processing:
Sequencing quality control was determined using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC. Reads with Phred quality score less than 30 were filtered out. For Tel1 and Spo11 ChIP-seq in the sae2Δ mutant, paired-end reads were mapped to Cer3H4L2 saccharomyces cerevisiae genome (PMID: 31649282) using Bowtie2 (v2.3.4.3)(68) with default parameters. Only mapped reads were filtered in using samtools view (--exclude-flags 4)67. Duplicate tags were removed using Picard Tools MarkDuplicates and mapped tags were processed for further analysis. For all subsequent analyses, mitochondrial genome, plasmid genome, and ribosomal DNA (rDNA) loci were blacklisted and removed. For visualization purpose, mapped tags were converted into BigWig and normalized by their library size (FPKM) using bamCoverage.
Assembly: Cer3H4L2
Supplementary files format and content: bedGraph

organism: Saccharomyces cerevisiae

growth_protocol: Pre-culture of 8 – 10 colonies were performed in YPD + AU (Yeast Extract 1%, Peptone 2%, Glucose 2%, Adenine and Uracil 0.0137%) for 30h at 30°C, 210rpm agitation. 0.2 OD/ml of cells were incubated in 200ml pre-sporulation medium (SPS: Yeast Extract 0.5%, Peptone 1%, Yeast Nitrogen Base 0.17%, Potassium Acetate 1%, Ammonium Sulphate 0.5%, Potassium Hydrogen Phtalate 0.05M, Antifoam 0.001%) for 14h at 30°C with 250rpm agitation. Cells were collected and washed with water, before incubation at 30°C with 250rpm agitation in pre-warmed sporulation medium (SPM: 1% Potassium Acetate, Antifoam 0.001%). Sample were collected at different time point and treated accordingly to the following experiments.

extract_protocol:
For each meiotic time point, 2 x 108 cells were fixed in paraformaldehyde (1% final). FLAG-Tel1 cells were fixed for 30min, while FLAG-Spo11 strain were fixed for 15min, quenched by glycine for 5min (125mM final) and washed in TBS 1X two times. Cells were lysed using mechanical lysis (Fastprep, 4 cycles at 6.5M/sec 30sec) together with a Lysis buffer (50mM HEPES-KOH, 140mM NaCl, 1mM EDTA pH8, 1% Triton X100, 0.1% Sodium Deoxycholate) complemented with protease inhibitor cocktail tablet (Roche, Ref 05 892 791 001), PMSF (1mM final), pepstatin (0.1mM final) and leupeptin (1mM final). After cell lysis, chromatin was sheared by sonication into 500 – 1000pb fragment (30sec ON/30sec OFF, 6 cycles, 4°C, Diagenode Bioruptor Pico). 10µl was kept aside as the input, and samples were divided in two halves, for minus and plus antibody treatment. FLAG-Tel1 immunoprecipitation was performed with 2µl of anti-FLAG antibody (M2 monoclonal, Sigma, Ref F1804) and incubation at 4°C for 2 hours. Pan-IgG mouse magnetic beads were incorporated for 2 more hours at 4°C. IP samples were washed by a 500mM NaCl containing lysis buffer and LiCl buffer (10mM Tris-HCl pH8, 0.25LiCl, 1mM EDTA pH8, 0.5% Triton X-100, 0.5% Sodium Deoxycholate). Chromatin was eluted from magnetic beads in elution buffer (TE 1X, 0.5% SDS) at 65°C for 10min. DNA-protein interaction was disrupted by incubation at 65°C overnight for IP and input samples. RNA was digested by RNAse A treatment (20µg total, 15min at 37°C) and proteins by proteinase K treatment (100µg total, 1hour at 42°C). DNA was purified on column (Qiagen DNA purification kit).
Tel1 and Spo11 ChIP-seq were performed following the ChIP-qPCR protocol with some modifications. For both FLAG-Tel1 and FLAG-Spo11 strain, cells were fixed in paraformaldehyde for 30min. Protein G magnetic beads were washed (0.1M NaHPO4 pH7.5, 0.01%Tween20, pH8.2) and saturated with BSA (0.1M NaP, 0.01% Tween20, 5mg/ml BSA) for 3hours at 4°C. Anti-FLAG antibody (M2 Monoclonal, Sigma) was pre-incubated with saturated-magnetic beads for 4hours at 4°C. Cell lysis was performed as for the ChIP-qPCR protocol. Chromatin shearing was performed in Diagenode tube 15ml with beads (900 – 1000mg) by 7 cycles of sonication (30sec ON/30sec OFF, 4°C). Chromatin was immunoprecipitated with antibody-protein G mix by overnight incubation at 4°C. Samples were washed as for the ChIP-seq protocol, and DNA was eluted with IPure v2 Diagenode kit. DNA quantity was measured by QuBit and fragmentation quality was controlled by Agilent chip (Bio-analyser). DNA was sequenced with a NovaSeq sequencer (Illumina) using a 100nt paired-end protocol (TruSeq) at the Institut Curie sequencing facility (Paris, France).

value: Meiotic Time courses


title: AsPC1_DMSO_4h_rep2.1

description:
Library name: AsPC1_DMSO_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_4h_rep2.2

description:
Library name: AsPC1_CB6644_4h_rep2.2
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Tel1-SAE2_3h

description: Library name: FLAG-Tel1-SAE2_3h


title: INPUT_FLAG-Tel1-SAE2_3h

description: Library name: INPUT_FLAG-Tel1-SAE2_3h


title: AsPC1_CB6644_4h_rep2.1

description:
Library name: AsPC1_CB6644_4h_rep2.1
SLAM-seq - Lexogen Anabolic Module


title: no.tag-dsae2-Rep2

description: Library name: no.tag-dsae2-Rep2


title: AsPC1_NEG_4h_rep1.4

description:
Library name: AsPC1_NEG_4h_rep1.4
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_DMSO_12h_rep2

description:
Library name: AsPC1_DMSO_12h_rep2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_NEG_4h_rep1.3

description:
Library name: AsPC1_NEG_4h_rep1.3
SLAM-seq - Lexogen Anabolic Module


title: INPUT_no.tag-dsae2-Rep2

description: Library name: INPUT_no.tag-dsae2-Rep2


title: AsPC1_NEG_4h_rep1.2

description:
Library name: AsPC1_NEG_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Tel1-dsae2-4h-Rep3

description: Library name: FLAG-Tel1-dsae2-4h-Rep3


title: AsPC1_NEG_4h_rep1.1

description:
Library name: AsPC1_NEG_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep1.4

description:
Library name: AsPC1_dTAG_4h_rep1.4
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep1.3

description:
Library name: AsPC1_dTAG_4h_rep1.3
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Tel1-dsae2-0h-Rep3

description: Library name: FLAG-Tel1-dsae2-0h-Rep3


title: no.tag-dsae2-6h

data_processing:
Sequencing quality control was determined using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC. Reads with Phred quality score less than 30 were filtered out. For Tel1 and Spo11 ChIP-seq in the sae2Δ mutant, paired-end reads were mapped to Cer3H4L2 saccharomyces cerevisiae genome (PMID: 31649282) using Bowtie2 (v2.3.4.3)(68) with default parameters. Only mapped reads were filtered in using samtools view (--exclude-flags 4)67. Duplicate tags were removed using Picard Tools MarkDuplicates and mapped tags were processed for further analysis. For all subsequent analyses, mitochondrial genome, plasmid genome, and ribosomal DNA (rDNA) loci were blacklisted and removed. For visualization purpose, mapped tags were converted into BigWig and normalized by their library size (FPKM) using bamCoverage.
Assembly: Cer3H4L2
Supplementary files format and content: BigWig

source_name: yeast

value: yeast


title: AsPC1_dTAG_4h_rep1.2

description:
Library name: AsPC1_dTAG_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_dTAG_4h_rep1.1

description:
Library name: AsPC1_dTAG_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: no.tag-dsae2-0h


title: AsPC1_DMSO_4h_rep1.3

description:
Library name: AsPC1_DMSO_4h_rep1.3
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Spo11-dsae2-0h-Rep1


title: FLAG-Spo11-dsae2-6h-Rep2


title: AsPC1_DMSO_4h_rep1.1

description:
Library name: AsPC1_DMSO_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: AsPC1_CB6644_4h_rep1.3

description:
Library name: AsPC1_CB6644_4h_rep1.3
SLAM-seq - Lexogen Anabolic Module


title: FLAG-Spo11-dsae2-6h-Rep1


title: FLAG-Tel1-dsae2-6h-Rep2


title: AsPC1_CB6644_4h_rep1.1

description:
Library name: AsPC1_CB6644_4h_rep1.1
SLAM-seq - Lexogen Anabolic Module


title: U-CLL1_H3K27me3_CUT&Tag

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

description:
Library name: EPI0000970
2 × 75 bp, 5-10 million paired-reads

data_processing:
Quality control of the fastq files was performed using fastqc-0.11.9
Data from fastq files were trimmed using trimmomatic-0.36 (first stage trimming)
First stage trimmed data were trimmed using kseq_test (second stage trimming)
Final trimmed data were aligned using Bowtie 2-2.2.5
Alignment data were filtered using samtools-1.9
Filtered alignment data were sorted using picard-2.8.0
Duplicates were marked using picard-2.8.0 and removed using samtools-1.9
Filtering out of reads >= 120bp was performed using samtools-1.9
Peak calling was performed using macs2-2.2.6 with q<0.01 and using the corresponding IgG as control
Assembly: hg38
Supplementary files format and content: UCLL.specificregions files: tsv file of a consensus matrix containing the consensus peaks and their signal across all the samples included
Library strategy: CUT&Tag

source_name: Peripheral Blood

growth_protocol: Patient-derived CLL cells were grown in vitro with supportive stromal MM1 cell line for 6 days to perform CUT&Tag.

extract_protocol:
DNA was extracted with phenol chloroform after performing CUT&Tag protocol.
CUT&Tag libraries were generated following the instructions from CUT&Tag-IT Assay Kit (Active Motif).

tag: tissue

value: Peripheral Blood

value: No cell line. Patient-derived cells

value: Cryopreserved cells from patient

value: WT

value: No treatment


title: FLAG-Tel1-dsae2-6h-Rep3

description: Library name: FLAG-Tel1-dsae2-6h-Rep3


title: U-CLL1_H3K4me1_CUT&Tag

description:
Library name: EPI0000971
2 × 75 bp, 5-10 million paired-reads


title: Heart_AAV9-Empty Control, biol rep 3

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

description: Library name: Sample 3_N1069

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina)
FASTQ files were adapter- and quality-trimmed using Trim Galore! (version 0.4.1) with default settings except for the quality cutoff (-q/--quality) which was set to a Phred score of 15. Trim Galore! used Cutadapt (version 1.9.1) as subroutine. Quality control of FASTQ files was performed by FastQC (version 0.11.4) before and after trimming.
After trimming, FASTQ files were mapped against a reference genome with the splice-aware aligner STAR (version 2.5.4a) to generate BAM files. The BAM files were built in a 2-pass mapping (two-pass Mode Basic) and were finally sorted (out SAM type BAM SortedByCoordinate).
The genome index files were created by STAR with default settings using Mus musculus sequence and annotation data taken from GENCODE.org (GRCm38.p6 release M17). Quantification was performed with feature counts from the subread package (version 1.6.1) for paired-end reads (-p) with default settings except for the setting of strandedness (-s 2) and the minimum mapping quality score (-Q 10). Annotation data were again taken from GENCODE.org (GRCm38.p6 release M17).
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table”, which was set to “Yes”
Assembly: GRCm38.p6 release M17
Supplementary files format and content: count matrices for each sample

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Total RNA was isolated using TriFast peqGOLD (Avantor). 500 ng total RNA was used for  library preparation.
500 ng total RNA was subjected to rRNA depletion (NEBNext rRNA Depletion Kit, NEB), followed by stranded cDNA library generation (NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, NEB) as recommended by the manufacturer apart from downscaling reaction volumes to 2/3 of the described volumes. In addition, one extra purification step (1x ‘Agencourt® AMPure® XP Beads, Beckman Coulter) was performed at the end of the standard procedure. Single indexing was utilised (NEBNext Multiplex Oligos for Illumina – Set 1’ (Index Primer 2,4,5,6,7,12), NEB).

treatment_protocol: On the first day of the experiment, mice received intravenous injections of either AAV9-Empty or AAV9-MR at a dose of 2 × 10¹² viral particles per animal in a 100 µL volume. Two weeks later, osmotic minipumps (Alzet® model; ALZET LLC, Campbell, CA, USA) were implanted to deliver either saline (0.9% NaCl) or aldosterone (300 µg/kg/day) in the respective groups. Aldosterone was prepared in 0.9% NaCl solution to maintain consistency with the control treatment. The pumps remained in place for 14 days and were removed at the end of this period, corresponding to four weeks after the beginning of the study. Another 14 days later the end point was reached and tissue samples were collected.

value: Heart

tag: strain

value: Control


title: Heart_AAV9-MR Aldosterone, biol rep 3

description: Library name: Sample 6_N1068

value: Aldosterone


title: Heart_AAV9-MR Aldosterone, biol rep 2

description: Library name: Sample 5_N1067


title: FLAG-Tel1-dsae2-0h-Rep2


title: U-CLL1_H3K27ac_CUT&Tag

description:
Library name: EPI0000973
2 × 75 bp, 5-10 million paired-reads


title: Heart_AAV9-Empty Control, biol rep 2

description: Library name: Sample 2_N1065


title: Heart_AAV9-Empty Control, biol rep 1

description: Library name: Sample 1_N1064


title: M-CLL5_LEF1_rep1

description:
Library name: EPI0000772
2 × 75 bp, 10-25 million paired-reads

data_processing:
Quality control of the fastq files was performed using fastqc-0.11.9
Data from fastq files were trimmed using trimmomatic-0.36 (first stage trimming)
First stage trimmed data were trimmed using kseq_test (second stage trimming)
Final trimmed data were aligned using Bowtie 2-2.2.5
Alignment data were filtered using samtools-1.9
Filtered alignment data were sorted using picard-2.8.0
Duplicates were marked using picard-2.8.0 and removed using samtools-1.9
Filtering out of reads >= 120bp was performed using samtools-1.9
Peak calling was performed using macs2-2.2.6 with q<0.01 and using the corresponding IgG as control
Assembly: hg38
Supplementary files format and content: peaks.narrowPeak_clean files: narrowPeak file resulting from peak calling and containing the coordinates and different information about the signal and the statistics of the called peaks
Supplementary files format and content: counts files: tsv file of a consensus matrix containing the consensus peaks and their signal across all the samples included
Library strategy: CUT&Run

source_name: Peripheral blood

growth_protocol: Patient-derived CLL cells were grown in vitro with supportive stromal MM1 cell line for 6 days to perform CUT&RUN.

extract_protocol:
DNA was extracted with phenol chloroform after performing CUT&RUN protocol.
CUT&RUN libraries were prepared with NEBNext Ultra II DNA library preparation kit following Nan Lui's protocol (DOI: dx.doi.org/10.17504/protocols.io.bagaibse)

value: Peripheral blood

value: Cryopreserved CLL cells from patient


title: AsPC1_DMSO_4h_rep1.2

description:
Library name: AsPC1_DMSO_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module

value: human pancreatic cancer cell line


title: FLAG-Tel1-dsae2-6h-Rep1


title: MEC1_I6 ov_LEF1

description:
Library name: EPI0001446
2 × 75 bp, 10-25 million paired-reads

value: CLL cell line

value: Overexpression of LEF1 I6

value: Lentiviral infection with LEF1-FL vector


title: MEC1_FL ov_LEF1

description:
Library name: EPI0001445
2 × 75 bp, 10-25 million paired-reads

value: Overexpression of LEF1 FL


title: shCtrl+shp300/CBP #2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Library name: MR456

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, RPKM/FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt file of RPKM/FPKM values

source_name: Prostate

growth_protocol: LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin

extract_protocol:
RNA was extracted using the nucleospin RNA kit (Takara) according to the manufacturer’s recommended protocol
RNA-seq libraries were prepared from 0.5μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: RNA-seq were performed in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 48 hours

value: Prostate

value: LNCaP

value: Prostate cancer cell


title: shHOXB13 #2

description: Library name: MR457


title: shHOXB13+shp300/CBP #2

description: Library name: MR460


title: AsPC1_CB6644_4h_rep1.2

description:
Library name: AsPC1_CB6644_4h_rep1.2
SLAM-seq - Lexogen Anabolic Module


title: HG3_I5 ov_LEF1

description:
Library name: EPI0001444
2 × 75 bp, 10-25 million paired-reads

value: Overexpression of LEF1 I5


title: HG3_I6 ov_LEF1

description:
Library name: EPI0001443
2 × 75 bp, 10-25 million paired-reads


title: U-CLL1_H3K4me3_CUT&Tag

description:
Library name: EPI0000972
2 × 75 bp, 5-10 million paired-reads

value: Peripheral Blood

value: No cell line. Patient-derived cells

value: Cryopreserved cells from patient


title: shCtrl+shCBP #2

description: Library name: MR455

value: WT

value: shCtrl+shCBP


title: HG3_FL ov_LEF1

description:
Library name: EPI0001442
2 × 75 bp, 10-25 million paired-reads


title: shCtrl #2

description: Library name: MR453

value: shCtrl


title: INPUT_FLAG-Tel1-dsae2-4h-Rep3

description: Library name: INPUT_FLAG-Tel1-dsae2-4h-Rep3

value: Meiotic Time courses


title: Bcell12 I5_LEF1

description:
Library name: EPI0001536
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: No cell line. Primary B cells

value: B cells from PBMCs from healthy donors (buffy coat)

value: Retroviral infection with LEF1-I5 vector


title: Bcell12 I6_LEF1

description:
Library name: EPI0001535
2 × 75 bp, 10-25 million paired-reads

value: Overexpression of LEF1 I6

value: Retroviral infection with LEF1-I6 vector


title: shCtrl+shp300 #2

description: Library name: MR454

value: Prostate


title: shHOXB13+shp300/CBP #1

description: Library name: MR452

value: LNCaP


title: Heart_AAV9-MR Aldosterone, biol rep 1

description: Library name: Sample 4_N1066

value: Heart

value: Aldosterone


title: shHOXB13+shp300 #2

description: Library name: MR458

value: Prostate cancer cell


title: U-CLL1_IgG_CUT&Tag

description:
Library name: EPI0000968
2 × 75 bp, 5-10 million paired-reads

value: Peripheral Blood

value: No cell line. Patient-derived cells

value: No treatment


title: shHOXB13+shCBP #1

description: Library name: MR451

value: WT


title: M-CLL4_LEF1_rep1

description:
Library name: EPI0000715
2 × 75 bp, 10-25 million paired-reads

value: Cryopreserved CLL cells from patient


title: Bcell12 FL_LEF1

description:
Library name: EPI0001534
2 × 75 bp, 10-25 million paired-reads

value: Overexpression of LEF1 FL

value: Retroviral infection with LEF1-FL vector


title: shHOXB13+shp300 #1

description: Library name: MR450


title: M-CLL3_I5 ov_LEF1

description:
Library name: EPI0001544
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: Overexpression of LEF1 I5


title: shHOXB13 #1

description: Library name: MR449


title: MEC1_I5 ov_LEF1

description:
Library name: EPI0001447
2 × 75 bp, 10-25 million paired-reads

value: CLL cell line

value: Lentiviral infection with LEF1-FL vector


title: M-CLL3_I6 ov_LEF1

description:
Library name: EPI0001543
2 × 75 bp, 10-25 million paired-reads

value: Overexpression of LEF1 I6

value: Retroviral infection with LEF1-I6 vector


title: shCtrl+shp300/CBP #1

description: Library name: MR448

value: Prostate

value: LNCaP


title: M-CLL3_FL ov_LEF1

description:
Library name: EPI0001542
2 × 75 bp, 10-25 million paired-reads


title: M-CLL1_CT_IgG

description:
Library name: EPI0001497
2 × 75 bp, 10-25 million paired-reads

value: Retroviral infection with control vector


title: M-CLL1_I5 ov_LEF1

description:
Library name: EPI0001501
2 × 75 bp, 10-25 million paired-reads

value: Retroviral infection with LEF1-I5 vector


title: shCtrl+shp300 #1

description: Library name: MR446

value: Prostate cancer cell


title: shCtrl+shCBP #1

description: Library name: MR447

value: shCtrl+shCBP


title: shCtrl #1

description: Library name: MR445

value: shCtrl


title: shHOXB13 CCS1477 #3

description: Library name: MR444

value: WT

value: shHOXB13 CCS1477


title: M-CLL1_FL ov_ LEF1

description:
Library name: EPI0001499
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells

value: Cryopreserved CLL cells from patient

value: Overexpression of LEF1 FL


title: M-CLL1_I6 ov_LEF1

description:
Library name: EPI0001500
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood


title: Tcell3_IgG

description:
Library name: EPI0000921
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Primary T cells

value: T cells from PBMCs from healthy donors (buffy coat)

value: No treatment


title: shHOXB13 CCS1477 #1

description: Library name: MR442


title: shHOXB13 CCS1477 #2

description: Library name: MR443


title: shHOXB13 DMSO #3

description: Library name: MR441

value: shHOXB13 DMSO


title: Nrsn2 OE 3

city: Jerusalem

first: Gali

last: Umschweif

address: Ein Karem Campus | Jerusalem

department: pharmacology section. school of pharmacy

country: Israel

institute: The Hebrew University of Jeursalem

description:
Library name: sample 7
OE_7_counts

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10. The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39
Supplementary files format and content: processed data Yumna.xlsx

growth_protocol: Mouse neuroblastoma N2a (ATCC, Manassas, VA, USA) cells were cultured in high-glucose DMEM, supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from N2a cells using the NucleoSpin RNA kit (Macherey-Nagel)
Libraries were constructed using Truseq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA).poly A RNA-seq. 300 bp long, single-end fragments were sequenced

treatment_protocol: Transient overexpression of the stress-responsive protein Nrsn2 (GeneCopoeia, Rockville, MD, USA) was achieved using TransIT-X2 Transfection Reagent (Mirus Bio, Madison, WI ). Cells were collected 24 hours post-transfection for RNA-seq

value: Nrsn2 OE


title: Tcell3_LEF1

description:
Library name: EPI0000922
2 × 75 bp, 10-25 million paired-reads


title: Nrsn2 OE 1

description:
Library name: sample 5
OE_5_counts


title: Tcell2_LEF1

description:
Library name: EPI0000918
2 × 75 bp, 10-25 million paired-reads


title: shHOXB13 DMSO #2

description: Library name: MR440

value: Prostate

value: LNCaP


title: shHOXB13 DMSO #1

description: Library name: MR439


title: Tcell2_IgG

description:
Library name: EPI0000917
2 × 75 bp, 10-25 million paired-reads


title: Nrsn2 OE 4

description:
Library name: sample 8
OE_8_counts


title: Nrsn2 OE 2

description:
Library name: sample 6
OE_6_counts


title: control 4

description:
Library name: sample 4
C_4_counts

value: control


title: control 2

description:
Library name: sample 2
C_2_counts


title: control 3

description:
Library name: sample 3
C_3_counts


title: Tcell_LEF1

description:
Library name: EPI0000914
2 × 75 bp, 10-25 million paired-reads


title: control 1

description:
Library name: sample 1
C_1_counts


title: shCtrl CCS1477 #3

description: Library name: MR438

value: Prostate cancer cell

value: shCtrl CCS1477


title: P74

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

country: China

institute: Chinese Academy of Sciences

description: Library name: P74

data_processing:
Low quality sequencing reads and adapters were removed by Cutadapt
HISAT2 tools software was used to map clean reads to GRCm38 genome.
The gene counts were calculated with gene annotation from UCSC database using FeatureCounts
Assembly: GRCm38.90
Supplementary files format and content: txt count

source_name: spinal cord

extract_protocol:
The lumbar spinal cord of each mouse (3 mice per group) was collected and homogenized through a tissue homogenizer. TRIzolTM reagent (Thermo Scientific, 15596026) was subsequently used to extract total RNA from each sample according to the manufacturer’s instructions.
After passing the detection of total RNA samples, purification is carried out based on the characteristics of mRNA from different sources. The end of eukaryotic mRNA3 has a polyA tail structure, and magnetic beads with Oligo (dT) were selected for enrichment and purification; Prokaryotic mRNA does not possess this characteristic, so a reagent kit was used to remove rRNA to obtain more effective information. Add Fragmentation Buffer to the purified mRNA to make its fragments short. Using the fragmented RNA as a template, reverse transcription was performed using random primers to synthesize the first strand of cDNA, and the second strand of cDNA was synthesized by adding the 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix. After end repair, addition of base A, sequencing adapter, magnetic bead screening to recover the target fragment, and PCR amplification, the entire library preparation work was completed.

value: spinal cord


title: P67

description: Library name: P67


title: CRISPR_TF_SERPINB5_JustLowBulk_bulk

description:
Library name: CRISPR_TF_SERPINB5_bulk
FACS Antibody Serpin B5 (C-8): sc-271694 BULK

value: human pancreatic cancer cell line


title: E77

description: Library name: E77


title: shCtrl DMSO #2

description: Library name: MR435

value: WT

value: shCtrl DMSO


title: shCtrl CCS1477 #2

description: Library name: MR437


title: E90

description: Library name: E90


title: shHOXB13+shCBP #2

description: Library name: MR459


title: shCtrl DMSO #3

description: Library name: MR436


title: P66

description: Library name: P66


title: U-CLL4_LEF1

description:
Library name: EPI0001467
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells

value: Cryopreserved CLL cells from patient


title: C79

description: Library name: C79


title: ATAC-seq of mus musclus: E12.5 embryo male lung epithelia cells, CKO, replicate 2

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

description: Library name: ATACseq_CKO_rep2

data_processing:
ATAC-seq data were analyzed using a standardized ENCODE ATAC-seq pipeline (v2.2.2, https://github.com/ENCODE-DCC/atac-seq-pipeline). The mouse reference genome (mm10) was used in the pipeline. Trimming, mapping, and duplicate-removing were performed as ENCODE pipeline suggested using Cutadapt (v2.5), Bowtie2 (v2.3.4.3), and Picard (v2.20.7, https://broadinstitute.github.io/picard/) respectively. MACS2 (v2.2.4) was used for peak calling with parameters: --nomodel --shift 100 --extsize 200 --pval 0.01 --SPMR --call-summits.
Assembly: mm10
Supplementary files format and content: bigwig files and peak files

source_name: lung

extract_protocol:
Epithelia nuclei were isolated and fragmented with Tn5 transposase. DNA was isolated using the DNA Clean and Concentrator Kits (Zymo, D4013) and subjected to library construction using Q5 high-fidelity DNA polymerase (New England Biolabs, M0544S).
Epithelia nuclei were isolated and fragmented with Tn5 transposase. DNA was isolated using the DNA Clean and Concentrator Kits (Zymo, D4013) and subjected to library construction using Q5 high-fidelity DNA polymerase (New England Biolabs, M0544S).

value: lung

value: lung epithelia cells

value: CKO


title: U-CLL4_IgG

description:
Library name: EPI0001466
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: No treatment


title: shCtrl DMSO #1

description: Library name: MR429


title: Tcell1_IgG

description:
Library name: EPI0000913
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Primary T cells

value: T cells from PBMCs from healthy donors (buffy coat)


title: LNCaP, HOXB13 ChIP

description: Library name: M854

data_processing:
Reads were aligned to the hg38 reference human genome using bowtie2
Assembly: hg38
Supplementary files format and content: bigwig generated from bam

growth_protocol: LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin.

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde (Thermo fisher, Cat#28908)) for 10min at room temperature with gentle rotation and then quenched for 5min with 0.125M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris). Drosophila S2 cells were used as a spike-in control to normalize ChIP signals, following the protocol provided by Active Motif.
ChIP–seq libraries were prepared from 3–5ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions.

treatment_protocol: H3K27ac ChIP-seq were performed in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 24 hours.

value: Prostate

value: LNCaP

tag: antibody

value: HOXB13, Abcam, Cat#227879

value: no treatment


title: E75

description: Library name: E75

value: spinal cord


title: U-CLL11_POLR2A

description:
Library name: EPI0000933
2 × 75 bp, 10-25 million paired-reads


title: C85

description: Library name: C85


title: ATAC-seq of mus musclus: E12.5 embryo male lung epithelia cells, CTRL, replicate 2

description: Library name: ATACseq_CTRL_rep2

value: CTRL


title: shCtrl CCS1477 #1

description: Library name: MR430

value: Prostate cancer cell

value: WT

value: shCtrl CCS1477


title: C84

description: Library name: C84


title: U-CLL11_LEF1

description:
Library name: EPI0000930
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells

value: Cryopreserved CLL cells from patient


title: H4

description: Library name: H4


title: U-CLL1_LEF1_rep 2

description:
Library name: EPI0000760
2 × 75 bp, 10-25 million paired-reads


title: H1

description: Library name: H1


title: LNCaP, HDAC3 ChIP

description: Library name: M682

value: HDAC3, Abcam, Cat#7030


title: U-CLL1_IgG

description:
Library name: EPI0000759
2 × 75 bp, 10-25 million paired-reads


title: RNA-seq of mus musclus: E12.5 embryo male lung epithelia cells, CKO, replicate 2

description: Library name: RNAseq_CKO_rep2

data_processing:
We performed RNA-seq analysis as described previously. Briefly, after removing adapters using Cutadapt (v2.5), paired-end reads were aligned to the mm10 mouse genome using Hisat2 (v2.2.1) in paired-end mode with default parameters. Expression level of genes were calculated using StringTie (v2.2.1). Subsequently, raw read counts for genes were calculated using the python script prepDE.py3. Differential expressed genes were identified using the R package DESeq2 (v1.38.3)
Assembly: mm10
Supplementary files format and content: differentially expressed genes list

extract_protocol:
Total RNA from isolated epithelial cells was extracted by using RNeasy Plus Mini Kits (QIAGEN, #74134).
The freshly RNA was purified into mRNA using VAHTS mRNA Capture Beads (Vazyme, #N401). Then, the captured mRNA underwent library generation using Equalbit RNA HS Assay Kits (Vazyme, NR605) following the manufacturer’s instructions.

value: lung

value: lung epithelia cells

value: CKO


title: sgd-2

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

data_processing:
Illumina Casava software used for basecalling.
Clean reads were prepared using Cutadapt version 1.15, and were mapped to Arabidopsis genome using Tophat2 (v2.1.1).
The expression level of each gene was quantified as FPKM using RSEM.
Differentially expressed genes between WT and sgd were identified using DESeq2.
Genome_build: Arabidopsis thaliana genome TAIR10
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: sgd mutant ovules

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
Total RNA were prepared using an RNeasy Plant Mini Kit (Qiagen, Germany).
Libraries for sequencing were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, USA) according to the manufacturer’s instructions

value: Ovules

value: sgd mutant

tag: developmental stage

value: FG1-FG3 stage

tag: background ecotype

value: qrt1 background


title: H2

description: Library name: H2


title: U-CLL1_LEF1_rep 1

description:
Library name: EPI0001004
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: No treatment


title: ATAC-seq of mus musclus: E12.5 embryo male lung epithelia cells, CKO, replicate 1

description: Library name: ATACseq_CKO_rep1


title: sgd-3


title: WT-3

source_name: Wild type ovules

value: wild type


title: ATAC-seq of mus musclus: E12.5 embryo male lung epithelia cells, CTRL, replicate 1

description: Library name: ATACseq_CTRL_rep1

value: CTRL


title: RNA-seq of mus musclus: E12.5 embryo male lung epithelia cells, CTRL, replicate 1

description: Library name: RNAseq_CTRL_rep1


title: RNA-seq of mus musclus: E12.5 embryo male lung epithelia cells, CTRL, replicate 2

description: Library name: RNAseq_CTRL_rep2


title: U-CLL11_IgG

description:
Library name: EPI0000929
2 × 75 bp, 10-25 million paired-reads


title: U-CLL2_LEF1

description:
Library name: EPI0000927
2 × 75 bp, 10-25 million paired-reads


title: CUT&Tag_IgG of mus muscles: E12.5 embryo male lung mesenchymal cells

description: Library name: CUTTag_IgG_Mes

data_processing:
For analyzing CUT&Tag data, we used the ENCODE ChIP-seq pipeline (v2.2.1, https://github.com/ENCODE-DCC/chip-seq-pipeline2). The raw sequencing data were processed to remove adapters and low-quality sequences using Cutadapt (v2.5) with the parameters: -m 5 -e 0.1. Then, clean reads were aligned against the mouse mm10 genome using bwa (v0.7.17). Then, sam files were converted to bam files using samtools (v1.9). PCR duplicates were removed using Picard (v2.20.7, https://broadinstitute.github.io/picard/). Peaks were called using MACS2 (v2.2.4). The conservative narrow peaks were used for downstream analysis. For visualization, bam files were converted to bigWig files using deepTools (v3.3.1), and bigWig files were used to calculate tag density under 50 bp resolution.
Assembly: mm10
Supplementary files format and content: bigwig files and peak files
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag libraries were generated using CUT&Tag Assay Kits (ABclonal, # RK20265) following the manufacturer's guidelines. In brief, cells were captured by Concanavalin A Magnetic Beads, then incubated with primary antibodies at 4°C and then bound to pAGTn5. The Fragmented DNA was purified and finally amplified through PCR to form the libraries. Prepared libraries were sequenced on the Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths. Each sample includes two independent biological replicates, and each replicate library produced at least 40 M reads for comprehensive bioinformatics analysis.
CUT&Tag libraries were generated using CUT&Tag Assay Kits (ABclonal, # RK20265) following the manufacturer's guidelines. In brief, cells were captured by Concanavalin A Magnetic Beads, then incubated with primary antibodies at 4°C and then bound to pAGTn5. The Fragmented DNA was purified and finally amplified through PCR to form the libraries. Prepared libraries were sequenced on the Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths. Each sample includes two independent biological replicates, and each replicate library produced at least 40 M reads for comprehensive bioinformatics analysis.

value: lung mesenchymal cells


title: WT-2


title: U-CLL2_IgG

description:
Library name: EPI0000926
2 × 75 bp, 10-25 million paired-reads

value: WT


title: CUT&Tag_H3K4me3 of mus muscles: E12.5 embryo male lung mesenchymal cells replicate2

description: Library name: CUTTag_H3K4me3_Mes_rep2


title: U-CLL12_pPOLR2A

description:
Library name: EPI0001476
2 × 75 bp, 10-25 million paired-reads


title: treated5-dpi35

type: RNA

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Overnight hybridization according to standard NanoString protocol

scan_protocol: Scanned and quantified via nCounter SPRINT profiler according to standard protocol

data_processing: Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix. Downstream normalization and differential expression analyses were performed via limma.

label: not provided

organism: Chlorocebus sabaeus

source_name: African green monkey, whole blood, 3 days postinfection

label_protocol: standard protocol

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit

tag: nhp

tag: dpi

value: 4' FIU

tag: group

value: Recovered


title: U-CLL12_MYC

description:
Library name: EPI0001474
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells

value: Cryopreserved CLL cells from patient


title: CUT&Tag_CTCF of mus muscles: E12.5 embryo male lung mesenchymal cells replicate2

description: Library name: CUTTag_CTCF_Mes_rep2

value: lung


title: CUT&Tag_H3K4me3 of mus muscles: E12.5 embryo male lung epithelia cells replicate2

description: Library name: CUTTag_H3K4me3_Epi_rep2

value: lung epithelia cells


title: CUT&Tag_H3K4me3 of mus muscles: E12.5 embryo male lung mesenchymal cells replicate1

description: Library name: CUTTag_H3K4me3_Mes_rep1


title: treated3-dpi35


title: U-CLL12_LEF1_rep 2

description:
Library name: EPI0001473
2 × 75 bp, 10-25 million paired-reads


title: CUT&Tag_H3K4me3 of mus muscles: E12.5 embryo male lung epithelia cells replicate1

description: Library name: CUTTag_H3K4me3_Epi_rep1


title: U-CLL12_LEF1_rep 1

description:
Library name: EPI0000764
2 × 75 bp, 10-25 million paired-reads


title: RNA-seq of mus musclus: E12.5 embryo male lung epithelia cells, CKO, replicate 1

description: Library name: RNAseq_CKO_rep1

value: CKO


title: treated4-dpi35


title: CUT&Tag_CTCF of mus muscles: E12.5 embryo male lung epithelia cells replicate2

description: Library name: CUTTag_CTCF_Epi_rep2


title: U-CLL12_IgG_rep2

description:
Library name: EPI0001472
2 × 75 bp, 10-25 million paired-reads


title: U-CLL12_IgG_rep 1

description:
Library name: EPI0000762
2 × 75 bp, 10-25 million paired-reads


title: HBM, day 21, batch 19

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Adapters were trimmed, and light quality trimming was performed, using cutadapt v3.4 with additional parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 --minimum-length 25
Reads were aligned to the GENCODE vM18 assembly (i.e., mm10) with STAR v2.7.8a with the following additional parameters as recommended by the ENCODE consortium: --outFilterType=BySJout --outFilterMultimapNmax=20 --alignSJoverhangMin=8 --alignSJDBoverhangMin=1 --outFilterMismatchNmax=999 --outFilterMismatchNoverReadLmax=0.04   --alignIntronMin=20 --alignIntronMax=1000000 --alignMatesGapMax=1000000 --outSAMunmapped=None.
Aligned reads were counted in genes with featureCounts (subread package, v2.0.1) using the GENCODE vM18 GTF annotations and additional parameter -s2.
Assembly: GENCODE M18 (mm10)
Supplementary files format and content: TSV of raw counts

source_name: pooled newborn calvarial osteoblast cultures

growth_protocol: RNA was collected at days 0, 10, 15, and 21 days of osteoblast differentiation from cultures derived from pooled newborn calvaria (n= 3 independent pooled cultures).

extract_protocol:
Osteoblast RNA was prepared using the Qiagen RNeasy kit (74106, Qiagen, Germantown, MD) with on-column DNase digestion.
polyA selected

tag: day

value: HBM


title: Mm-Hx-K999N-1

city: Pittsburgh

first: Shu-Ting

last: Cho

state: PA

address: 450 Technology Drive

department: Computational and Systems Biology

institute: University of Pittsburgh

data_processing:
Sequence reads were trimmed for adaptor and low-quality sequences using Trim Galore! (v0.6.7) with default settings.
Trimmed sequence reads were pseudo-aligned and quantified using Sailfish (v0.10.1.1) with default settings against the GRCm39/mm39 reference genome.
Quantification and normalization was performed directly using Sailfish, providing transcript-level expression estimates.
To quantify the RNA editing level, mouse RNA-seq raw reads were mapped against the mouse genome build mm39 using STAR aligner
Processed with JACUSA2 with the same parameters as in human and (G/G+A) percent was calculated in the same way.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes TPM values and raw counts for each sample

source_name: Lung

growth_protocol: Lungs were isolated from wild-type or Adar1 K999N mice

extract_protocol:
QiAzol extraction of total RNA was performed according to the manufacturer's instructions.
Unstranded, paired-end sequencing was then performed on Illumina HiSeq 2000 at 50 cycles/bp to generate 50 bp paired-end reads.
The libraries were quantified using KAPA library quantification kit.

treatment_protocol: Mice were explosed with  hypoxia (10% oxygen, Hx) or normoxia (21% oxygen, Nx) for 3 weeks.

value: Lung

value: Adar1 K999N

value: Hypoxia


title: CUT&Tag_CTCF of mus muscles: E12.5 embryo male lung epithelia cells replicate1

description: Library name: CUTTag_CTCF_Epi_rep1


title: treated2-dpi35


title: HBM, day 21, batch 21

value: pooled newborn calvarial osteoblast cultures


title: CUT&Tag_CTCF of mus muscles: E12.5 embryo male lung mesenchymal cells replicate1

description: Library name: CUTTag_CTCF_Mes_rep1


title: Mm-Hx-K999N-3

description: 50 cycles/bp to generate 50 bp paired-end reads


title: Mm-Hx-K999N-2


title: treated1-dpi35


title: U-CLL12_POLR2A

description:
Library name: EPI0000767
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: No treatment


title: Mm-Hx2

description: read 75 cycles, 40-50M reads/sample

value: wildtype


title: HBM, day 21, batch 18


title: treated5-dpi28


title: Mm-Hx1

description: read 75 cycles, 40-50M reads/sample


title: HBM, day 15, batch 18


title: HBM, day 15, batch 21


title: treated2-dpi28


title: treated3-dpi28


title: Mm-Nx3

description: read 75 cycles, 40-50M reads/sample

value: Normoxia


title: M-CLL13_LEF1

description:
Library name: EPI0001531
2 × 75 bp, 10-25 million paired-reads

value: WT


title: HBM, day 15, batch 19


title: M-CLL25_LEF1

description:
Library name: EPI0001532
2 × 75 bp, 10-25 million paired-reads


title: HBM, day 10, batch 21


title: M-CLL27_LEF1

description:
Library name: EPI0001533
2 × 75 bp, 10-25 million paired-reads


title: CUT&Tag_IgG of mus muscles: E12.5 embryo male lung epithelia cells

description: Library name: CUTTag_IgG_Epi


title: Mm-Hx3

description: read 75 cycles, 40-50M reads/sample


title: HBM, day 10, batch 19


title: treated4-dpi28

value: 4' FIU


title: M-CLL30_MYC

description:
Library name: EPI0001479
2 × 75 bp, 10-25 million paired-reads


title: treated1-dpi28

value: Recovered


title: Mm-Nx2

description: read 75 cycles, 40-50M reads/sample


title: HBM, day 10, batch 18


title: treated5-dpi21


title: treated4-dpi21


title: M-CLL30_LEF1

description:
Library name: EPI0001478
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells


title: treated3-dpi21


title: HBM, day 0, batch 21


title: M-CLL24_LEF1

description:
Library name: EPI0001530
2 × 75 bp, 10-25 million paired-reads

value: Cryopreserved CLL cells from patient


title: LNCaP, shHOXB13+shCBP, H3K27ac ChIP

description: Library name: M1717

value: Prostate

value: LNCaP

value: Prostate cancer cell

value: H3K27ac, Cst, Cat#8173S


title: M-CLL3_LEF1_rep 2

description:
Library name: EPI0001008
2 × 75 bp, 10-25 million paired-reads


title: treated2-dpi21


title: HBM, day 0, batch 19

value: HBM


title: LNCaP, shHOXB13+shp300/CBP, H3K27ac ChIP

description: Library name: M1718


title: Mm-Nx1

description: read 75 cycles, 40-50M reads/sample

value: Lung


title: WT, day 21, batch 21


title: LNCaP, shHOXB13+shp300, H3K27ac ChIP

description: Library name: M1716


title: HBM, day 0, batch 18


title: M-CLL3_IgG_rep 1

description:
Library name: EPI0000757
2 × 75 bp, 10-25 million paired-reads


title: treated1-dpi21


title: LNCaP, shHOXB13, H3K27ac ChIP

description: Library name: M1715


title: M-CLL3_IgG_rep 2

description:
Library name: EPI0001180
2 × 75 bp, 10-25 million paired-reads


title: treated5-dpi15


title: treated4-dpi15


title: LNCaP, shp300, H3K27ac ChIP

description: Library name: M1712


title: M-CLL3_LEF1_rep 1

description:
Library name: EPI0000758
2 × 75 bp, 10-25 million paired-reads


title: M-CLL5_POLR2A

description:
Library name: EPI0001021
2 × 75 bp, 10-25 million paired-reads


title: LNCaP, shp300/CBP, H3K27ac ChIP

description: Library name: M1714


title: treated2-dpi15


title: M-CLL4_POLR2A

description:
Library name: EPI0001016
2 × 75 bp, 10-25 million paired-reads


title: LNCaP, shctr, H3K27ac ChIP

description: Library name: M1711

value: shctrl


title: WT, day 15, batch 21

value: pooled newborn calvarial osteoblast cultures


title: WT, day 21, batch 19


title: WT, day 21, batch 18


title: M-CLL5_IgG

description:
Library name: EPI0000770
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood


title: M-CLL5_LEF1_rep2

description:
Library name: EPI0001017
2 × 75 bp, 10-25 million paired-reads

value: No treatment


title: treated5-dpi12

value: Transitional


title: M-CLL4_LEF1_rep2

description:
Library name: EPI0001012
2 × 75 bp, 10-25 million paired-reads


title: treated4-dpi12


title: WT, day 15, batch 18


title: LNCaP, shHOXB13, DMSO, H3K27ac ChIP

description: Library name: M1639

value: shHOXB13, DMSO


title: LNCaP, shCBP, H3K27ac ChIP

description: Library name: M1713

value: WT

value: shCBP


title: M-CLL4_IgG

description:
Library name: EPI0000714
2 × 75 bp, 10-25 million paired-reads


title: WT, day 10, batch 21


title: treated1-dpi15

value: 4' FIU

value: Recovered


title: M-CLL9_LEF1

description:
Library name: EPI0000720
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells

value: Cryopreserved CLL cells from patient


title: treated3-dpi15


title: LNCaP, shctr, CCS1477, H3K27ac ChIP

description: Library name: M1638

value: Prostate

value: LNCaP

value: shctr, CCS1477


title: M-CLL9_IgG

description:
Library name: EPI0000719
2 × 75 bp, 10-25 million paired-reads


title: LNCaP, shctr, DMSO, H3K27ac ChIP

description: Library name: M1637

value: Prostate cancer cell

value: H3K27ac, Cst, Cat#8173S

value: shctr, DMSO


title: WT, day 10, batch 19

value: pooled newborn calvarial osteoblast cultures


title: treated3-dpi12


title: WT, day 10, batch 18


title: U-CLL2_LEF1_Day 0

description:
Library name: EPI0001463
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood


title: treated2-dpi12


title: LNCaP, p300ChIP

description: Library name: M1499

value: no treatment


title: treated1-dpi12

value: Transitional


title: U-CLL12_LEF1_Day 0

description:
Library name: EPI0001465
2 × 75 bp, 10-25 million paired-reads

value: No treatment


title: WT, day 0, batch 21

value: WT


title: WT, day 15, batch 19


title: U118, LRRC15-

city: Los Angeles

first: Michael

last: Cheng

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description:
Library name: U118_NEG
10X Genomics Chromium

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using CellRanger software v 6.0 (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: tab-separated and matrix format

source_name: cell line

extract_protocol:
For each cell line, cells were FACS sorted for the top 1% LRRC15+ cells by AlexaFluor647-DUNP19 staining with a target cell population of 10,000 viable cells. Cells were resuspended in 1x PBS+0.04% BSA solution and counted for viability before performing the 10X Genomics single cell protocols for library preparation.
Single cells were captured within gel bead emulsions (GEM) according to 10X Genomics’ Chromium Single Cell platform protocols. Within individual GEM droplets, cells are lysed and barcoded before reverse transcription and cDNA pooling. Post-GEM cleanup was performed with Dynabeads and cDNA amplified, cleaned, and quantified. A 3’GEX library was constructed and quality control performed with Agilent ScreenTape Analysis. Libraries were sequenced with Novaseq S4 (2000-2500 M reads per lane), with a read depth of 20,000.

value: cell line

value: U118-MG (glioblastoma)

value: brain cancer cell


title: U-CLL1_LEF1_Day 0

description:
Library name: EPI0001179
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells


title: WT, day 0, batch 19


title: control6-dpi11

value: Control

value: Late


title: LNCaP, shHOXB13, CCS1477, H3K27ac ChIP

description: Library name: M1640

value: Prostate

value: LNCaP

value: shHOXB13, CCS1477


title: WT, day 0, batch 18


title: U118, LRRC15+

description:
Library name: U118_POS
10X Genomics Chromium


title: treated5-dpi09

value: 4' FIU


title: U-CLL17_LEF1_Day 0

description:
Library name: EPI0001508
2 × 75 bp, 10-25 million paired-reads

value: Cryopreserved CLL cells from patient


title: treated4-dpi09


title: U-CLL19_LEF1_Day 0

description:
Library name: EPI0001507
2 × 75 bp, 10-25 million paired-reads


title: Dock8 KO T cell_ migrating_ rep 002

city: Montreal

first: Judith

last: Mandl

state: QC

address: 3649 Promenade Sir William Osler

country: Canada

institute: McGill University

data_processing:
pre-alignment QC: FastQC, MultiQC
alignment: HISAT2 (-k 1 --rna-strandness RF) ; mapping to GRCm38/mm10
post-alignment processing: QC: Samtools Flagstat, FastQC, Picard Tools, MultiQC.
post-alignment QC: Flagstat, FastQC, Picard Tools, MultiQC.
read summarization: featureCounts (-t exon -g gene_name -s 0 -p --donotsort)
Assembly: GRCm38/mm10
Supplementary files format and content: comma delimited CSV file including summarized counts per gene (row, gene symbol) for each sample (column)

source_name: lymph node and spleen

extract_protocol:
RNA extraction was performed using the PureLink RNA Mini Kit (Invitrogen). 150 ng of material was used to generate the sequencing libraries.
RNA libraries prepared using RiboCop rRNA Depletion Kit HMR (Lexogen, kit #037.96), KAPA RNA HyperPrep Kit (Roche, kit #8098107702), and TruSeq DNA UDI 96 Indexes (Illumina, kit #20022370)

value: lymph node and spleen

value: primary cells

value: activated CD8+ T cell

value: Dock8 KO

value: migrating in Nutragen 2 mg/mL


title: SAOS2, LRRC15-

description:
Library name: SAOS2_NEG
10X Genomics Chromium

value: SAOS2 (osteosarcoma)

value: bone cancer cell


title: SAOS2, LRRC15+

description:
Library name: SAOS2_POS
10X Genomics Chromium

value: cell line


title: M-CLL10_LEF1_Day 0

description:
Library name: EPI0001462
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: WT

value: No treatment


title: RPMI7951, LRRC15-

description:
Library name: RPMI7951_NEG
10X Genomics Chromium

value: RPMI7951 (melanoma)

value: melanoma cell


title: M-CLL3_LEF1_Day 0

description:
Library name: EPI0001178
2 × 75 bp, 10-25 million paired-reads

value: No cell line. Patient-derived cells


title: Dock8 KO T cell_ migrating_ rep 001


title: RPMI7951, LRRC15+

description:
Library name: RPMI7951_POS
10X Genomics Chromium


title: treated3-dpi09

value: Transitional


title: M-CLL30_LEF1_Day 0

description:
Library name: EPI0001464
2 × 75 bp, 10-25 million paired-reads


title: Dock8 KO T cell_ migrating_ rep 003


title: HUO9, LRRC15-

description:
Library name: HUO9_NEG
10X Genomics Chromium

value: HUO9 (osteosarcoma)


title: WT T cell_ migrating_ rep 001


title: M-CLL19_LEF1_Day 0

description:
Library name: EPI0001506
2 × 75 bp, 10-25 million paired-reads

value: Cryopreserved CLL cells from patient


title: KASUMI2, LRRC15+

description:
Library name: KASUMI2_POS
10X Genomics Chromium

value: KASUMI-2 (leukemia)

value: leukemia cell


title: control6-dpi09

value: Control

value: Late


title: treated1-dpi09

value: 4' FIU


title: KASUMI2, LRRC15-

description:
Library name: KASUMI2_NEG
10X Genomics Chromium


title: treated2-dpi09


title: WT T cell_ migrating_ rep 003

value: lymph node and spleen

value: primary cells

value: activated CD8+ T cell

value: migrating in Nutragen 2 mg/mL


title: M-CLL4_IgG_Day 0

description:
Library name: EPI0001461
2 × 75 bp, 10-25 million paired-reads

value: Peripheral blood

value: WT


title: WT T cell_ migrating_ rep 002


title: treated5-dpi06

value: Middle


title: treated4-dpi06


title: M-CLL18_LEF1_Day 0

description:
Library name: EPI0001509
2 × 75 bp, 10-25 million paired-reads

value: No treatment


title: treated3-dpi06


title: HUO9, LRRC15+

description:
Library name: HUO9_POS
10X Genomics Chromium

value: cell line

value: bone cancer cell


title: Dock8 KO T cell_ media_ rep 002

value: Dock8 KO

value: media


title: Dock8 KO T cell_ media_ rep 003


title: YCCEL1 cells, sgMAEA, Alpelisib, rep3

city: Boston

first: Yin

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively

growth_protocol: YCCEL1 cells were cultured in EMEM medium (ATCC) with 10% fetal Bovine Serum (FBS)  in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using the RNeasy Mini kit (Qiagen) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: YCCEL1 cells were transduced with lentiviruses expressing control or MAEA sgRNA.  The cells were further treated with DMSO or 0.5uM alpelisib for 30h.

value: Gastric cancer

value: MAEA knockout

value: CRISPR KO


title: CALU1, LRRC15-

description:
Library name: CALU1_NEG
10X Genomics Chromium

value: CALU1 (non-small-cell lung cancer)

value: lung cancer cell


title: YCCEL1 cells, sgMAEA, Alpelisib, rep2


title: YCCEL1 cells, sgMAEA, Alpelisib, rep1


title: control6-dpi06

value: Control


title: WT T cell_ media_ rep 003

value: lymph node and spleen

value: primary cells


title: CALU1, LRRC15+

description:
Library name: CALU1_POS
10X Genomics Chromium


title: treated1-dpi06

value: 4' FIU


title: WT T cell_ media_ rep 001

value: activated CD8+ T cell


title: YCCEL1 cells, sgMAEA, DMSO, rep3


title: WT T cell_ media_ rep 002

value: WT


title: TF1_GC543_1

city: Hong Kong

first: Margaret

middle: H. L.

last: Ng

address: Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, NT

department: Anatomical and Cellular Pathology

institute: The Chinese University of Hong Kong

data_processing:
HTSeq (v0.6.1) was used to count the reads.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: TF1 cells were transduced with GC543 lentivirus

extract_protocol:
RNA was extracted using QIAamp RNA Blood Mini Kit (Qiagen).
The library was prepared using the NEBNext RNA Library preparation kit.

value: Human AML cell line

tag: transduction

value: GC543 lentivirus


title: YCCEL1 cells, sgControl, Alpelisib, rep3

value: Control knockout


title: TF1_GC543_2


title: treated4-dpi00

value: Baseline


title: treated5-dpi00


title: WT, TAC, 4wk, rep3

city: Columbus

first: Thomas

last: Hund

state: OH

address: 473 W 12th Ave

institute: Ohio State University

description:
Library name: Sample 7
W3

data_processing:
BGI Genomics performed quality control on the raw Fastq reads, including  quality control and read trimming using FASTQC.
Processed fastq files were aligned using Hisat2 against the reference genome version GRCm38.p6
Reference gene mapping was performed using Bowtie2.
Assembly: GRCm38.p6
Supplementary files format and content: .xlsx file contains FPKM values and raw counts for each sample

source_name: heart

extract_protocol:
Trizol was used for RNA extraction.
RNA libraries for RNA-seq were prepared by BGI Genomics for DNBSEQ stranded mRNA library generation

value: heart

value: 4 weeks transoartic constriction (TAC)


title: treated3-dpi00


title: YCCEL1 cells, sgMAEA, DMSO, rep1

value: Gastric cancer


title: YCCEL1 cells, sgMAEA, DMSO, rep2

value: MAEA knockout


title: WT, TAC, 4wk, rep2

description:
Library name: Sample 6
W2


title: WT, TAC, 4wk, rep4

description:
Library name: Sample 8
W4


title: treated2-dpi06

value: Middle


title: TF1_GC_2

source_name: TF1 cells were transduced with GC lentivirus

value: GC lentivirus


title: Dock8 KO T cell_ media_ rep 001

value: Dock8 KO

value: media


title: treated2-dpi00


title: TF1_GC_1


title: YCCEL1 cells, sgControl, Alpelisib, rep2

value: CRISPR KO


title: TF1_EV_1

source_name: TF1 cells were transduced with EV lentivirus

value: EV lentivirus


title: WT, TAC, 4wk, rep1

description:
Library name: Sample 5
W1


title: control6-dpi00

value: Control


title: YCCEL1 cells, sgControl, Alpelisib, rep1


title: STAT3 S727A, TAC, 4wk, rep4

description:
Library name: Sample 4
S4

value: STAT3 S727A


title: YCCEL1 cells, sgControl, DMSO, rep3


title: control2-dpi13

value: Late


title: M07E_GC543_1

source_name: M07E cells were transduced with GC543 lentivirus

value: Human AML cell line


title: treated1-dpi00

value: 4' FIU


title: TF1_EV_2


title: STAT3 S727A, TAC, 4wk, rep3

description:
Library name: Sample 3
S3


title: M07E_GC_2

source_name: M07E cells were transduced with GC lentivirus


title: STAT3 S727A, TAC, 4wk, rep2

description:
Library name: Sample 2
S2


title: YCCEL1 cells, sgControl, DMSO, rep1

value: Control knockout


title: YCCEL1 cells, sgPIK3CA, rep2

treatment_protocol: (1) YCCEL1 I cells were treated with DMSO or 5uM alpelisib for 6h. (2) YCCEL1 cells were transduced with lentiviruses expressing control or PIK3CA sgRNA.

value: PIK3CA knockout


title: YCCEL1 cells, sgControl, DMSO, rep2


title: M07E_GC_1


title: M07E_EV_2

source_name: M07E cells were transduced with EV lentivirus


title: STAT3 S727A, TAC, 4wk, rep1

description:
Library name: Sample 1
S1

value: heart


title: YCCEL1 cells, sgPIK3CA, rep1


title: control5-dpi11


title: M07E_EV_1


title: control5-dpi10


title: SG2M_E95_3

city: Charlottesville

first: Jordon

middle: W

last: Aragon

state: VA

department: Cell Biology

institute: University of Virginia

description: Library name: SG2M_E95_3

data_processing:
Data was aligned to mm10 transcriptome using STAR aligner and output as .tab out files. The files were read into DeSEQ2 and pairwise analysis was conducted to detemine enriched / downregulated genes in EG1, LG1, and S/G2/M. Significantly differentialy expressed genes were filtered (p = < 0.5) and then combined into one table. (3 Biological replicates averaged per column)
Assembly: mm10
Supplementary files format and content: .rds file, table containing differential expression data from all timepoints by cell cycle state.

source_name: Embryonic

extract_protocol:
Cells were spun down at 300g at 4°C for 10 minutes, and digestion buffer replaced with 1X HBSS + 10% FBS. Cells were filtered, into a FACS tube and incubated with anti-CD31 BV421 and anti-CD45 per-CP antibodies. CD31+ CD45- endothelial cells in different cell cycle states were sorted using a FACS Melody, collected in lysis buffer and RNA extracted via Qiagen Rneasy Micro kit.
Library was constructed via NovoGene™ low input RNA sequencing pipeline using illumina chemistry.

value: Embryonic

value: Endothelial Cell


title: YCCEL1 cells, sgControl, rep2

value: Gastric cancer


title: control4-dpi10


title: SG2M_E95_2

description: Library name: SG2M_E95_2


title: Mature endosperm jas_3n_rep3

city: Norwich

first: Steven

last: Penfield

address: Norwich Research Park, Colney Ln

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

description: Library name: jas_3n_R3

data_processing:
Raw RNA-seq reads were trimmed using cutadapt-1.9.1
mapped to Arabidopsis thaliana TAIR10 reference genome using STAR-2.5.a
featureCounts (Liao et al., 2014) was used to count the numbers of reads mapped to each gene
Assembly: TAIR10
Supplementary files format and content: TPM values for each gene

source_name: Mature endosperm

growth_protocol: WT Ler and diploid jas-1 were grown in long days (16h light and 8h darkness at 22°C) until bolting, then mother plants were moved to long days at 16°C for the duration of seed set to ensure strong dormancy. Diploid and triploid seeds from diploid jas-1 plants were separated using meshes. Seeds from 2 plants were collected as one biological replicate.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen, 74904).
endosperm-enriched tissues RNA samples were sequenced at BGI (China) using DNBSEQ, 100-bp paired-end sequences with minimum 25 million reads acquired per sample

value: Mature endosperm


title: M07E_GC543_2

value: GC543 lentivirus


title: SG2M_E95_1

description: Library name: SG2M_E95_1


title: control2-dpi10


title: YCCEL1 cells, sgControl, rep1


title: Mature endosperm jas_3n_rep2

description: Library name: jas_3n_R2


title: SG2M_E85_4

description: Library name: SG2M_E85_4


title: YCCEL1 cells, Alpelisib, rep2

value: WT

value: Alpelisib


title: control4-dpi11


title: SG2M_E85_3

description: Library name: SG2M_E85_3


title: Mature endosperm jas_2n_rep3

description: Library name: jas_2n_R3


title: SG2M_E85_2

description: Library name: SG2M_E85_2


title: YCCEL1 cells, DMSO, rep2

value: control


title: Mature endosperm jas_2n_rep2

description: Library name: jas_2n_R2


title: control4-dpi07

value: Middle


title: YCCEL1 cells, DMSO, rep1


title: control3-dpi07

value: Control


title: YCCEL1 cells, Alpelisib, rep1


title: sgd-1

value: Ovules

value: sgd mutant

value: FG1-FG3 stage

value: qrt1 background


title: SG2M_E80_2

description: Library name: SG2M_E80_2


title: SG2M_E80_1

description: Library name: SG2M_E80_1


title: WT-1

value: wild type


title: control3-dpi09

value: Late


title: Mature endosperm Ler_rep2

description: Library name: Ler_R2

value: Ler


title: control5-dpi04

value: Early


title: control1-dpi07


title: Mature endosperm jas_3n_rep1

description: Library name: jas_3n_R1


title: E9.5 Embryonic ECS 2

description: Library name: E9-5EMB2

data_processing:
CellRanger for demulitplexing, barcode aggregation and fastq creation, Seurat V3 for integration and analysis, PhateR for PHATE projection, Moncole3 for pseudotime prediction.
Assembly: mm10
Supplementary files format and content: .rds

extract_protocol:
Cells were spun down at 300g at 4°C for 10 minutes, and digestion buffer replaced with 1X HBSS + 10% FBS. Cells were filtered into a FACS tube and incubated with anti-CD31 BV421 and anti-CD45 per-CP antibodies. CD31+ CD45- endothelial cells were sorted using a FACS Melody, collected, and resuspended in 0.1% BSA solution in 1X PBS for 10X Chromium v3 scRNAseq
10X Genomics Chromium V3 pipeline as per manufacturer instruction

value: Embryonic

value: Endothelial Cells


title: control5-dpi07


title: LG1_E95_2

description: Library name: LG1_E95_2

value: Endothelial Cell


title: control4-dpi04


title: E9.5 Embryonic ECS 1

description: Library name: E9-5EMB1


title: SG2M_E80_5

description: Library name: SG2M_E80_5


title: LNCaP-USP2, replicate 3

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: Library name: LNCaP-USP2_3

data_processing:
Raw data were analyzed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg38) using the STAR spliced alignment algorithm (version 2.5.2b with default parameters).
The reads were assigned to each exon region based on the human genome annotation from GENCODE and assigned reads were summarised as counts using the featureCounts (v.1.6.4) tool.
Differential gene expression analysis was done using DESeq2 (Love, Huber, and Anders 2014) in R.
Assembly: hg38
Supplementary files format and content: Excel file that includes normalised expression (RPKM) for all samples

source_name: LNCaP

growth_protocol: LNCaP cells were modified using lentiviruses to over-express USP2 or a control transgene (mNeonGreen)

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen)
Stranded polyA libraries prepared using Nugen Universal Plus mRNA-seq (Part No. 0508), protocol M01442 v2. Illumina to MGI library conversion was done using am MGIEasy Universal Library Conversion Kit (Part No. MGI1000004155). Libraries were sequenced (single-end) on a MGI DNBSEQ-G400 large Flow cell platform.

treatment_protocol: Cells were grown in baseline conditions (RPMI-1640 supplemented with 10% FBS).

value: LNCaP


title: control2-dpi07


title: LG1_E95_1

description: Library name: LG1_E95_1


title: Mature endosperm Ler_rep3

description: Library name: Ler_R3

value: Mature endosperm


title: control3-dpi04


title: LG1_E85_4

description: Library name: LG1_E85_4


title: Mature endosperm jas_2n_rep1

description: Library name: jas_2n_R1


title: LNCaP-USP2, replicate 1

description: Library name: LNCaP-USP2_1


title: LNCaP-USP2, replicate 2

description: Library name: LNCaP-USP2_2


title: E8.5 Embryonic ECS 2

description: Library name: E8-5EMB2


title: LG1_E85_3

description: Library name: LG1_E85_3


title: E8.0 Embryonic ECS 2

description: Library name: E8-0EMB2


title: control2-dpi04


title: LG1_E95_3

description: Library name: LG1_E95_3


title: E8.5 Embryonic ECS 1

description: Library name: E8-5EMB1


title: LG1_E85_2

description: Library name: LG1_E85_2


title: LNCaP-Control, replicate 3

description: Library name: LNCaP-Control_3


title: Mature endosperm Ler_rep1

description: Library name: Ler_R1


title: control1-dpi04


title: LNCaP-Control, replicate 2

description: Library name: LNCaP-Control_2


title: E8.0 Embryonic ECS 1

description: Library name: E8-0EMB1


title: LG1_E80_5

description: Library name: LG1_E80_5


title: control5-dpi03


title: control4-dpi03


title: Hu_Hx3

description: 50 cycles/bp to generate 50 bp paired-end reads

data_processing:
Sequence reads were trimmed for adaptor and low-quality sequences using Trim Galore! (v0.6.7) with default settings.
Trimmed sequence reads were pseudo-aligned and quantified using Sailfish (v0.10.1.1) with default settings against the GRCh38/hg38 reference genome.
Quantification and normalization was performed directly using Sailfish, providing transcript-level expression estimates.
Differential expression of siADAR1 versus siNC samples was computed using DESEQ.
The JAVA framework for accurate SNV assessment (JACUSA)19 was used for site-specific identification of RNA editing stat score (cutoff score 1.56) from RNA sequencing data.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes TPM values and raw counts for each sample

growth_protocol: primary human pulmonary arterial endothelial cells (hPAECs) were inculated at 37C.

extract_protocol:
QiAzol extraction of total RNA was performed according to the manufacturer's instructions.
TruSeq stranded Total RNA (Ribozero Gold)
The libraries were quantified using KAPA library quantification kit.

treatment_protocol: Human PAECs were explosed with  hypoxia (1% oxygen) for 48 hours. hPAECs were treated with 15nM ADAR1 siRNAs for 48 hours.

value: Lung

value: PAEC

value: Endothelial

value: wildtype

value: Hypoxia


title: LNCaP-Control, replicate 1

description: Library name: LNCaP-Control_1


title: Hu_Hx2


title: LG1_E80_2

description: Library name: LG1_E80_2


title: control3-dpi03

value: Control


title: EG1_E95_3

description: Library name: EG1_E95_3


title: control2-dpi03


title: LG1_E80_1

description: Library name: LG1_E80_1


title: Hu_Hx1


title: 72-hour post-fertilization DAPT-treated 2-arm pluteus larvae; 10X Genomics single-cell RNA-Seq data set

city: Chiba

first: Koki

last: Tsuyuzaki

address: 1-8-1, Inohana, Chuo-ku, Chiba-shi

country: Japan

institute: Chiba University

data_processing:
Data were processed by Cell Ranger（v7.0.0). The index file of the STAR aligner was generated by cellranger mkref and then used in cellranger cont, which counts the Unique Molecular Identifiers (UMIs) in each gene of each droplet. cellranger count automatically removed the low-quality data derived from the empty droplet.
Assembly: The reference genome file (HpulGenome_v1_scaffold.fa) and the annotation file (HpulGenome_v1.gff3) of H. pulcherrimus were retrieved from HpBase (https://cell-innovation.nig.ac.jp/Hpul/).
Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes
Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Genes
Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Matrix

organism: Hemicentrotus pulcherrimus

source_name: 2-arm pluteus larvae

extract_protocol:
Embryos/larvae were collected and washed twice in ice-cold Ca2+-free seawater including 1 mM EGTA. Then, they were dissociated in dissociation buffer (1.0 M glycine, 0.25 mM EDTA) for 10 min at 4 ˚C, with gentle pipetting every 2 min. Spin 500g x 5 min and discard dissociation buffer, and cells are resuspended in Ca2+-free seawater. Cell number and dissociation quality was measured at this time. After filtering by 20 µm mesh, cells are fixed in final 80% ice-cold Methanol for 1 hour at 4 ˚C. Then, the samples were stored at -20 ˚C until use. The samples were rehydrated in 3x SSC containing 0.04% BSA, 1 mM DTT, and 0.2 U/µl RNase inhibitor.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). All cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcribed to cDNA, which contains Unique Molecular Identifier (UMI) and the 10x Barcode.

value: 2-arm pluteus larvae

value: DAPT from 16 hour

tag: time

value: 72 hour


title: Hu_Nx3

value: Normoxia


title: EG1_E95_2

description: Library name: EG1_E95_2


title: Hu_Nx2


title: control5-dpi00

value: Baseline


title: control1-dpi03

value: Early


title: EG1_E95_1

description: Library name: EG1_E95_1

value: Embryonic


title: 36-hour post-fertilization DAPT-treated prism larvae; 10X Genomics single-cell RNA-Seq data set

source_name: prism larvae

value: prism larvae

value: 36 hour


title: 96-hour post-fertilization DAPT-treated 4-arm pluteus larvae; 10X Genomics single-cell RNA-Seq data set

source_name: 4-arm pluteus larvae

value: 4-arm pluteus larvae

value: 96 hour


title: control4-dpi00

source_name: African green monkey, whole blood, 3 days postinfection


title: Hu-siADAR1_3

description: read 75 cycles, 40-50M reads/sample

source_name: Lung

value: Lung

value: ADAR1 siRNA


title: EG1_E85_4

description: Library name: EG1_E85_4

value: Endothelial Cell


title: 96-hour post-fertilization control 4-arm pluteus larvae; 10X Genomics single-cell RNA-Seq data set

value: DMSO from 16 hour


title: Hu_Nx1

value: PAEC

value: Endothelial

value: wildtype


title: 48-hour post-fertilization DAPT-treated early pluteus larvae; 10X Genomics single-cell RNA-Seq data set

source_name: early pluteus larvae

value: early pluteus larvae

value: DAPT from 16 hour

value: 48 hour


title: Hu-siADAR1_2

description: read 75 cycles, 40-50M reads/sample


title: control3-dpi00

value: Control

value: Baseline


title: control2-dpi00


title: 24-hour post-fertilization DAPT-treated gastrula; 10X Genomics single-cell RNA-Seq data set

source_name: gastrula

value: gastrula

value: 24 hour


title: control1-dpi00


title: 72-hour post-fertilization control 2-arm pluteus larvae; 10X Genomics single-cell RNA-Seq data set

value: 2-arm pluteus larvae

value: 72 hour


title: Hu-siADAR1_1

description: read 75 cycles, 40-50M reads/sample


title: EG1_E85_3

description: Library name: EG1_E85_3

value: Embryonic


title: EG1_E85_2

description: Library name: EG1_E85_2


title: 48-hour post-fertilization control early pluteus larvae; 10X Genomics single-cell RNA-Seq data set


title: Mouse HSPC, RNA, Day 5

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description:
Library name: Sample 3
10X Genomics

data_processing:
Raw sequencing data was processed using the CellRanger v8.0.1 pipeline using default parameters.
Cell hashing data was quantified and demultiplexed using the HTODemux function in Seurat R Package.
Assembly: GRCm39
Supplementary files format and content: h5 of gene expression counts
Supplementary files format and content: csv of assigned cell hash assignments

source_name: HSPCs

growth_protocol: Cells cultured at 37C at 5% C02 and in the following media: F12 media supplemented with 1X Insulin-Transferrin-Selenium-Ethanolamine (IST-X), penicillin-streptomycin, 10 mM HEPES, 1 mg/mL 87% polyvinyl alcohol (PVA), 100 ng/mL TPO, and 10 ng/mL SCF.

extract_protocol:
Cells were collected, filtered (40 micron), pelleted and resuspended in staining buffer (PBS + 2% BSA + 0.02% Tween). Cells were then Fc blocked (10 min @ 4C) and then stained with appropriate hashtag antibody (6 in total for each of 6 genotypes, staining for 30 min at 4C). Cells were then washed 4x, resuspended in 'Submission Buffer' (PBS + 0.04% BSA), and pooled equally to a concentration of 3,000 cells/microliter prior to submission.
Single-cell encapsulation and scRNA-seq library prep of was performed on the Chromium instrument (10x Genomics) following the user manual (GEM-X Single Cell 3' Reagent Kits v4). Each sample loaded onto the cartridge contained approximately 30,000 cells (hashed samples) at a final dilution of ~3000 cells/μl. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were doublesize purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina sequencer (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads per cell) at MSK’s Integrated Genomics Operation Core Facility.

value: HSPCs


title: 36-hour post-fertilization control prism larvae; 10X Genomics single-cell RNA-Seq data set

value: prism larvae

value: 36 hour


title: EG1_E80_5

description: Library name: EG1_E80_5

value: Endothelial Cell


title: EG1_E80_2

description: Library name: EG1_E80_2


title: Hu-siNC_3

description: read 75 cycles, 40-50M reads/sample

value: Lung

value: PAEC

value: Negative control siRNA


title: Mouse HSPC, HTO, Day 8

description:
Library name: Sample 2
10X Genomics


title: Hu-siNC_2

description: read 75 cycles, 40-50M reads/sample

value: Endothelial

value: wildtype


title: Hu-siNC_1

description: read 75 cycles, 40-50M reads/sample


title: Mouse HSPC, HTO, Day 5

description:
Library name: Sample 1
10X Genomics


title: EG1_E80_1

description: Library name: EG1_E80_1


title: Primary hepatocytes treated with DMSO and DILI positive and negatives

status: Public on Oct 07 2025

city: Somerville

first: Volker

last: Bergen

state: MA

address: 101 South St

institute: Cellarity

description: Library name: DILImap

data_processing:
Sequencing reads (NextSeq550/NovaSeq6000, 89 bp × 26 bp) were demultiplexed and quality-checked.
Reads were aligned to the human reference genome, gene-level counts were quantified and processed data were stored as count matrices and .h5ad files for downstream analysis.
Assembly: GRCh38 (hg38), GENCODE v43 gene annotation (Ensembl 108) Gene IDs: Ensembl Gene IDs (ENSG); symbols per GENCODE v43.
Supplementary files format and content: Processed data are provided as: AnnData .h5ad: X = raw gene-by-sample count matrix; obs = sample metadata; var = gene metadata

source_name: Liver

growth_protocol: Primary human hepatocytes were cultured in 96-well collagen I-coated plates according to vendor protocols and maintained in a sandwich configuration, consisting of a collagen-coated base and a thin Matrigel (100 μg/mL) overlay. This sandwich configuration preserved liver-specific protein expression over an extended period. Cells were allowed to mature for three days, with daily media changes, before treatment with compounds at multiple concentrations for 24 hours. Following treatment, cells were either analyzed for viability using LDH/ATP assays or lysed for RNA extraction and sequencing.

extract_protocol:
Total RNA was extracted from 96-well cell lysates using a QIAcube HT (Qiagen) with RNeasy 96 QIAcube HT kits following the manufacturer’s protocol.
SMART-Seq DE3 libraries were prepared from total RNA with oligo(dT) priming, cDNA synthesis and amplification, followed by Nextera XT tagmentation. Libraries were indexed with Illumina P5/P7 barcodes, pooled, and sequenced on an Illumina NextSeq550 or NovaSeq6000.

treatment_protocol: Cells were treated with 300 small-molecule compounds (DILI-positive and negative controls) at multiple concentrations, alongside DMSO controls. Treatments were applied for 24 hours before RNA extraction.

value: Liver

value: Primary hepatocyte

value: Multiple drug perturbations


title: 24-hour post-fertilization control gastrula; 10X Genomics single-cell RNA-Seq data set

value: gastrula

value: DMSO from 16 hour


title: mESC CGR8 cells, CHX 5 h, replicate C

city: Lausanne

first: Benjamin

last: Martin

state: Vaud

address: Rte Cantonale

country: Switzerland

institute: EPFL

data_processing:
Sequence reads were trimmed for adaptor sequences bases2fastq v1.8.0.
Trimmed sequence reads were mapped to GRCm39 using STAR with default settings.
Read count extraction and normalization was performed using STAR.
Differential expression analysis was performed in R using DESeq2.
Assembly: GRCm39
Supplementary files format and content: csv file containing raw counts.

growth_protocol: NIH/3T3 cells were routinely cultured in DMEM (Gibco, 41966029), supplemented with 10% fetal bovine serum (Gibco, 10270-106), 1% penicillin/streptomycin (BioConcept, 401F00H) at 37°C, 5% CO2. Cells were passaged by trypsinization (Sigma, T4049-100ML) every 2-3 days and maintained at a confluency < 80%. GCR8 mESCs were cultured in N2B27 + 2i/LIF medium and maintained at 37°C, 5% CO2.

extract_protocol:
RNA was harvested using the Rneasy mini kit (Quiagen).
Illumina stranded mRNA ligation (ISML)

treatment_protocol: Cells were treated with 0.1 µg/mL CHX.

value: embryonic stem cell

value: ROSA26 SLT knock-in

value: 0.1 µg/mL CHX


title: Parental LUN156 tumor,, Replicate 2

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: VEHG12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: TPM, NumReads

source_name: Tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tissue

value: KRAS G12C

value: Parental LUN156 tumor


title: mESC CGR8 cells, CHX 48 h, replicate A


title: Mouse HSPC, RNA, Day 8

description:
Library name: Sample 4
10X Genomics

value: HSPCs


title: RMC-4998-R LUN156, Replicate 1

description: Library name: ON827A

value: RMC-4998 resistant LUN156


title: mESC CGR8 cells, CHX 5 h, replicate B


title: Adagrasib-R LUN156, Replicate 3

description: Library name: OFF451A

value: Adagrasib resistant LUN156


title: Adagrasib-R LUN156, Replicate 1

description: Library name: OFF45A


title: RMC-4998-R LUN156, Replicate 3

description: Library name: ON829B


title: mESC CGR8 cells, CHX 2 h, replicate C


title: Adagrasib-R LUN156, Replicate 2

description: Library name: OFF441B


title: RMC-4998-R LUN156, Replicate 2

description: Library name: ON828B


title: mESC CGR8 cells, CHX 48 h, replicate C


title: mESC CGR8 cells, CHX 5 h, replicate A


title: Parental LUN156 tumor,, Replicate 1

description: Library name: VEHG11


title: mESC CGR8 cells, CHX 2 h, replicate B


title: mESC CGR8 cells, CHX 48 h, replicate B


title: mESC CGR8 cells, CHX 2 h, replicate A


title: mESC CGR8 cells, CHX 1 h, replicate C


title: mESC CGR8 cells, CHX 1 h, replicate B


title: mESC CGR8 cells, CHX 0 h, replicate C


title: mESC CGR8 cells, CHX 1 h, replicate A


title: Parental LUN156 tumor,, Replicate 3

description: Library name: VEHG13


title: NIH/3T3 cells, CHX 48 h, replicate C

value: fibroblast


title: NIH/3T3 cells, CHX 48 h, replicate B


title: NIH/3T3 cells, CHX 48 h, replicate A


title: NIH/3T3 cells, CHX 5 h, replicate A


title: NIH/3T3 cells, CHX 5 h, replicate C


title: NIH/3T3 cells, CHX 5 h, replicate B


title: NIH/3T3 cells, CHX 2 h, replicate C


title: NIH/3T3 cells, CHX 0 h, replicate B


title: NIH/3T3 cells, CHX 2 h, replicate A


title: NIH/3T3 cells, CHX 1 h, replicate C


title: NIH/3T3 cells, CHX 0 h, replicate C


title: NIH/3T3 cells, CHX 0 h, replicate A


title: NIH/3T3 cells, CHX 1 h, replicate A


title: LX-2 cells,con1

city: Wuhan

first: An

last: Zhang

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

description:
Library name: con1
NaBH4-sequencing of LX-2 cells untreated,biological rep1

data_processing:
Use Fastp (version 0.23.2) software for data quality control
Sequence reads were trimmed for adaptor sequence/low-quality sequence using by fastp (version 0.23.1)
Trimmed sequence reads were mapped to hg38 using STAR(version 2.7.6a) with default parameters.
The featureCounts（version 1.5.1）was used for reads distribution statistic.Assembly: accession no. FJ214110
Assembly: hg38
Supplementary files format and content: control.snv.anno.txt
Supplementary files format and content: TGFb.snv.anno.txt
Library strategy: RedaC:T-seq

growth_protocol: LX-2 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and 1% antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent following the manufacturer's recommended protocol.Polyadenylated RNA enrichment was conducted using VAHTS mRNA Capture Beads from the total RNA
RNA libraries for RNA-seq were prepared using components of the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan,China)

treatment_protocol: LX-2 was stimulated by 5ng/ml TGF-β1 (PeproTech, USA) and after 24 hours we extracted the total RNA.

value: hepatic stellate cells

value: WT

value: untreated


title: NIH/3T3 cells, CHX 2 h, replicate B


title: LX-2 cells,TGF-β24h,TGFB1

description:
Library name: TGFB1
NaBH4-sequencing of LX-2 cells treated with human recombinant TGF beta, biological rep1

value: treated with human recombinant TGF-β1


title: LX-2 cells,TGF-β24h,TGFB2

description:
Library name: TGFB2
NaBH4-sequencing of LX-2 cells treated with human recombinant TGF beta, biological rep2


title: LX-2 cells,con2

description:
Library name: con2
NaBH4-sequencing of LX-2 cells untreated,biological rep2


title: NIH/3T3 cells, CHX 1 h, replicate B


title: Male/KO/CL2

city: Nice

first: Jean-Francois

last: Louet

address: C3M 151 route Saint Antoine de Ginestière 151 route Saint Antoine de Ginestière

institute: INSERM

description: Library name: SAMPLES 27/M32

data_processing:
Raw reads were quality controlled, and the raw data were filtered using the filtering software SOAPnuke (v1.5.2). The filtered clean reads were aligned to the reference genome sequence (mouse genome GRCm38 (mm10)) using HISAT2 software (v2.0.4).
Assembly: (mouse genome GRCm38 (mm10))
Supplementary files format and content: FPKM_Samples_group1.xls
Supplementary files format and content: FPKM_Samples_group2.xls

source_name: White adipose tissue

extract_protocol:
Frozen mouse subcutaneous adipose tissue was homogenized in RLT buffer (Qiagen), and RNA extracted using the RNeasy Mini Kit (Qiagen)
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: CL316,243 (0.5 mg/kg body weight) or Nacl during seven days by IP

value: White adipose tissue

value: KO

tag: Sex

value: Male


title: Male/KO/CL3

description: Library name: SAMPLES 28/M33


title: Male/KO/CL4

description: Library name: SAMPLES 29/M34


title: mESC CGR8 cells, CHX 0 h, replicate B

tag: cell line

value: embryonic stem cell


title: Male/KO/Ctrl4

description: Library name: SAMPLES 25/M24

value: Nacl