title: CTSS_C4_BrU_Rep1

city: San Diego

first: David

middle: M

last: Gilbert

state: California

address: 3525 John Hopkins Ct Ste 200

institute: San Diego Biomedical Research Institute

description: Library name: CTSS_C4_BrU_Rep1

data_processing:
Sequence reads were trimmed using Trim_Galore/cutadapt and aligned to a custom N-masked mm10 reference genome where N replaces 129 or Castaneus SNPs relative to the standard mm10 reference genome.
Aligned reads were haplotype phased using SNP-split and split into 129- or Cas-specific files
Phased reads were counted in 1kb genomic bins using bedtools intersect
Assembly: mm10
Supplementary files format and content: 1 bedgraph file for each parental genome dataset (2 processed files per raw file), where columns 1-3 are the genomic coordinates of each bin and column 4 contains the RPM-normalized read counts.
Library strategy: BRU-Seq

growth_protocol: F121-9 Hybrid mESCs were grown in 2i + LIF

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep kit (Zymo)
Sequencing libraries were prepared according to Paulsen et al 2014 Methods (PMID: 23973811). Briefly, RNA was was fragmented by heating and then BrU-labeled RNA purified using anti-BrdU antibodies and Protein A-conjugated beads.Nascent RNA was then fragmented at 85C for 10 min and converted to cDNA using NEBNext Ultra II RNA First Strand Synthesis Module (NEB) and NEBNext Ultra II Directional Second Strand Synthesis Kit (NEB) according to manufacturer's instructions. cDNA fragments were then constructed into libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).  was then amplified using NEBNext Multiplex Oligos for Illumina (NEB). Libraries were pooled and sequenced on a Novaseq6000 machine.

treatment_protocol: Cells were engineered with various CRISPR-mediated deletions. Cells were labeled with BrU for 30 minutes and then lysed in Trizol for RNA extraction.

value: Embryonic stem cell

value: CRISPR-mediated deletion(s)


title: CTSS_C4_BrU_Rep2

status: Public on Jun 17 2025

type: SRA

country: USA

description: Library name: CTSS_C4_BrU_Rep2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype


title: Myt1l P56-wildtype 2

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage and the pups are weaned on P18~P28.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: strain

value: wild-type

tag: tissue

value: whole brain

tag: age

tag: Sex

value: male


title: BR33 MUT#1 NPC, Wnt3a-treated, replicate 1

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: CB107

data_processing:
Fastq files were assessed for quality using fastqc. Reads were pseudo-aligned using Kallisto and imported into Sleuth for differential expression analysis. Counts were normalized, filtered for low abundance transcripts, and batch effects were regressed using ComBat in the sva package. Principal component analysis (PCA) was performed on the batch-corrected, log-transformed expression matrix using the R function prcomp. Differential expression was assessed using the Sleuth package in R. Pathway enrichment was calculated (queried against the Reactome pathway database) using the R package clusterProfiler and enrichment dot-plots were created using the R package enrichplot. Heatmaps were produced for using the R package pheatmap with color palettes from the R package Seurat.
Assembly: Human hg38
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, batch-corrected for line ID)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM, batch-corrected for line ID and POU3F2 genotype)
Supplementary files format and content: Comma-separated expression matrix (normalized TPM)

organism: Homo sapiens

growth_protocol: In brief, iPSCs were grown in StemFlex media until confluent. Cells were dissociated with collagenase IV and transferred to non-adherent 6-well plates. For the following six days (D2-D7), cells were maintained as embryoid bodies in suspension and fed once every two days with DMEM-F12/N2/B27-RA media containing dual-SMAD inhibitors, 100 nM LDN193189 (Stemgent, #04-0074) and 10 uM SB431542 (STEMCELL Technologies, #72234). On D7, embryonic bodies were resuspended in dual-SMAD inhibition media with the addition of 1 ug/mL laminin (Life Technologies, #23017-015) and transferred to poly-ornithine (Sigma, #P3655-50mg) / laminin (POL) coated 6-well plates. For the following seven days (D8-D14), cells were washed and fed once every two days with dual-SMAD inhibition media with the addition of laminin. On D14, neural rosettes were selected with STEMdiffTM neural rosette selection reagent (STEMCELL Technologies, #05832), which allows for the isolation of NPC-dominant neural rosettes while leaving behind non-NPC cell types that may arise during embryoid body formation (i.e., fibroblasts). Rosettes were resuspended in NPC media (DMEM-F12/N2/B27-RA with the addition of 1 ug/mL laminin and 20 ng/mL FGF2 (Peprotech, #100-18B)) and transferred to POL-coated 6-well plates. For the following seven days (D15-D21), cells were washed and fed once every two days with NPC media. After D21, NPCs were expanded on growth-factor reduced (GFR) Matrigel (Corning, #354230) at high density and fed with NPC media every two days for up to 3 passages.

extract_protocol:
RNA was harvested using the PureLink RNA Mini Kit (ThermoFisher, #12183018A). Quality and integrity of RNA extractions was assessed using a Tapestation RNA Screen Tape (Agilent Technologies, #5067-5576).
Samples were sent to Genewiz (Azenta) for library preparation and sequencing.

treatment_protocol: Mouse fibroblasts that were untransfected (Control; ATCC, #CRL-2648) or stably transfected with a Wnt3a overexpression vector (Wnt3a; ATCC, #CRL-2647) were used to harvest control or Wnt3a conditioned media, respectively. Briefly, fibroblasts were maintained in DMEM (ATCC, #30-2002) containing 10% fetal bovine serum (ThermoFisher, #10131035). Media was harvested according to recommendations from ATCC. Control and Wnt3a media were filtered, aliquoted, and stored at -80C. For treatment, a full media change with either L or Wnt3a conditioned media was performed and the cells were incubated for 24 hours before harvesting.

value: NPC

value: MUT

tag: treatment

value: Wnt3a conditioned media


title: Molm-13, 100nm VTP, 2500nM PF-9363, 6hrs, rep 1

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Nextseq
Reads were aligned to human genome (hg38)
Adapters were trimmed from raw reads using Trim Galore v0.4.3.
Trimmed reads were aligned to the human genome (GRCh38.78) using HiSAT2 v2.2.1
Reads assigned to genes using htseq-count
Assembly: Hg38
Supplementary files format and content: counts matrix in tsv format
Supplementary files format and content: molm_counts_raw_upload.txt

molecule: polyA RNA

growth_protocol: Molm-13 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 100 IU/ml Penicillin, 100 μg/ml streptomycin and 2 mM Glutamax, and

extract_protocol:
Qiagen RNAeasy Kit
Libraries were prepared using the QuantSeq 3’ mRNA-seq Library Prep kit (Lexogen)

treatment_protocol: Molm-13 cell were treated with either 2500nM PF-9363, 100nm VTP, 2500nM PF-9363 and 100nm VTP, or vehicle for 6 and 24 hours.

value: acute myeloid leukemia


title: Molm-13, 100nm VTP, 6hrs, rep 3

value: 100nm VTP, 6hrs


title: CTSS_C12_BrU_Rep1

description: Library name: CTSS_C12_BrU_Rep1


title: CTSS_C12_BrU_Rep2

description: Library name: CTSS_C12_BrU_Rep2


title: Myt1l P56-wildtype 1


title: BR24 MUT#2 NPC, Wnt3a-treated, replicate 1

description: Library name: CB119

value: female


title: Molm-13, 100nm VTP, 6hrs, rep 2


title: BR33 WT NPC, Wnt3a-treated, replicate 3

description: Library name: CB106

value: WT


title: COSN12_D3_BrU__Rep2

description: Library name: COSN12_D3_BrU__Rep2


title: Myt1l P56-hetero 5

value: Myt1l heterozygote


title: BR33 WT NPC, Wnt3a-treated, replicate 2

description: Library name: CB105


title: Molm-13, 100nm VTP, 6hrs, rep 1


title: COSN12_D3_BrU__Rep1

description: Library name: COSN12_D3_BrU__Rep1


title: BR33 MUT#1 NPC, Wnt3a-treated, replicate 3

description: Library name: CB109


title: BR33 WT NPC, Wnt3a-treated, replicate 1

description: Library name: CB104


title: Molm-13, Vehicle, 6hrs, rep 3

value: Vehicle, 6hrs


title: Myt1l P56-hetero 3


title: COSN12_B6_BrU_Rep2

description: Library name: COSN12_B6_BrU_Rep2


title: BR24 MUT#2 NPC, L-treated, replicate 3

description: Library name: CB103

value: L conditioned media


title: Molm-13, Vehicle, 6hrs, rep 2


title: COSN12_B6_BrU_Rep1

description: Library name: COSN12_B6_BrU_Rep1


title: Molm-13, Vehicle, 6hrs, rep 1


title: BTSS-CTSS_cloneH11_BrU

description: Library name: BTSS-CTSS_cloneH11_BrU


title: Myt1l P56-hetero 2


title: Myt1l P56-hetero 1


title: BTSS-CTSS_cloneG3_BrU

description: Library name: BTSS-CTSS_cloneG3_BrU


title: BR24 MUT#2 NPC, L-treated, replicate 1

description: Library name: CB101


title: Molm-13, 2500nM PF-9363, 6hrs, rep 2


title: BTSS-CTSS_cloneC11_BrU

description: Library name: BTSS-CTSS_cloneC11_BrU


title: Myt1l P21-wildtype 5


title: BR24 WT NPC, L-treated, replicate 3

description: Library name: CB100


title: Molm-13, 2500nM PF-9363, 6hrs, rep 3


title: BR24 WT NPC, L-treated, replicate 2

description: Library name: CB99


title: Molm-13, 2500nM PF-9363, 6hrs, rep 1


title: Myt1l P21-wildtype 4


title: Myt1l P21-wildtype 3


title: BR24 WT NPC, L-treated, replicate 1

description: Library name: CB98


title: BTSS_A10_Bru

description: Library name: BTSS_A10_Bru


title: Myt1l P56-hetero 4


title: Molm-13, 100nm VTP, 2500nM PF-9363, 24hrs, rep 3


title: Myt1l P21-wildtype 2


title: BR33 MUT#1 NPC, L-treated, replicate 3

description: Library name: CB91


title: Molm-13, 100nm VTP, 2500nM PF-9363, 24hrs, rep 2


title: BR33 MUT#1 NPC, L-treated, replicate 2

description: Library name: CB90


title: Myt1l P21-wildtype 1


title: ATSS-BTSS-CTSS_cloneC4_Bru

description: Library name: ATSS-BTSS-CTSS_cloneC4_Bru


title: Myt1l P21-hetero 5


title: Molm-13, 100nm VTP, 2500nM PF-9363, 24hrs, rep 1


title: BR33 MUT#1 NPC, L-treated, replicate 1

description: Library name: CB89


title: ATSS-BTSS-CTSS_cloneA8_Bru

description: Library name: ATSS-BTSS-CTSS_cloneA8_Bru


title: Myt1l P21-hetero 4


title: ATSS-BTSS-CTSS_cloneA1_Bru

description: Library name: ATSS-BTSS-CTSS_cloneA1_Bru


title: BR33 WT NPC, L-treated, replicate 3

description: Library name: CB88


title: AOSN-C2OSN-129_ESC_cloneG2_BrU

description: Library name: AOSN-C2OSN-129_ESC_cloneG2_BrU


title: BR24 MUT#2 NPC, L-treated, replicate 2

description: Library name: CB102


title: Myt1l P21-hetero 3


title: BR33 WT NPC, L-treated, replicate 2

description: Library name: CB87


title: AOSN-BOSN12-COSN123_D6_Bru

description: Library name: AOSN-BOSN12-COSN123_D6_Bru


title: Myt1l P21-hetero 2


title: Molm-13, Vehicle, 24hrs, rep 3

value: Vehicle, 24hrs


title: BR33 WT NPC, L-treated, replicate 1

description: Library name: CB86


title: AOSN-C2OSN-129_ESC_cloneF3_BrU

description: Library name: AOSN-C2OSN-129_ESC_cloneF3_BrU


title: A-C2OSN-129_ESC_cloneD6_BrU

description: Library name: A-C2OSN-129_ESC_cloneD6_BrU


title: Molm-13, 100nm VTP, 24hrs, rep 3

value: 100nm VTP, 24hrs


title: Myt1l P21-hetero 1


title: DU145 cells

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: Library name: DU145_cells

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Txt file includes raw counts for each Sample
Supplementary files format and content: Txt file includes FPKM values for each Sample

source_name: prostate

growth_protocol: LNCAP/PC3/DU145 cells were maintained at standard culture conditions (37°C, 5% CO2) in 1640/EMEM/F12K medium with 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

value: prostate cancer cells


title: Molm-13, Vehicle, 24hrs, rep 2


title: A-C2OSN-129_ESC_cloneA3_BrU

description: Library name: A-C2OSN-129_ESC_cloneA3_BrU

value: Embryonic stem cell

value: CRISPR-mediated deletion(s)


title: Molm-13, 100nm VTP, 24hrs, rep 1


title: PC3 cells

description: Library name: PC3_cells


title: Molm-13, Vehicle, 24hrs, rep 1


title: Myt1l P3-wildtype 7

value: wild-type

value: whole brain

value: male


title: A-BOSN12-COSN123-BTSS_C4_Bru

description: Library name: A-BOSN12-COSN123-BTSS_C4_Bru


title: LNCAP cells

description: Library name: LNCAP_cells

value: LNCAP


title: Molm-13, 2500nM PF-9363, 24hrs, rep 3

value: acute myeloid leukemia


title: Myt1l P3-wildtype 6


title: RIP

city: Hefei

first: Xu

last: Junchao

state: Anhui

address: No. 443, Mount Huangshan Road, Daoxiangcun Street

institute: University of Science and Technology of China

description: Library name: Sample 2

data_processing:
Use Solexa pipeline version 1.8 (Off Line Base Caller software, version 1.8) for image processing and base recognition. FastQC software is used to evaluate the sequencing quality of reads, and then cutadapt is used to remove the 3 'and 5' adapters. Align to the reference genome using Hisat2 software. Use StringTie software to estimate transcription abundance by referencing official database annotation information. Use R software Ballgown - to perform FPKM calculations at the gene and transcript levels, and calculate the expression differences at both the gene and transcript levels to screen for differentially expressed genes between samples or groups. The prediction of new genes/transcripts was assembled and merged separately for each sample using StringTie, and compared with official annotation information. The results were obtained through Ballgown calculations, and the coding ability of the new transcripts was predicted using CPAT. Use rMATS for alternative splicing event detection, differential calculation, and mapping. PCA analysis and correlation analysis based on gene expression levels, clustering of differentially expressed genes, GO functional significance enrichment analysis, pathway significance enrichment analysis, and other further data mining analyses were completed through our company's custom program (Python/R/shell, etc.).
Assembly: hg38, GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: MCF-7 cells were cultured in RPMI-1640 (31800022, Gibco, Carlsbad, USA) supplemented with 10% FBS (ExCell Bio, Shanghai, China) at 37℃ and 5% CO2. All medium contained 1% Pen-Strep solution (C0222, Beyotime, Shanghai, China).

extract_protocol:
RIP assay was performed by using anti-HNRNPAB antibody (ab199724, Abcam, Cambridge, UK) and according to the manufacturer’s protocol of the EZ-Magna RIP™ Kit (17-701, Millipore, Darmstadt, Germany). Finally, RNA was purified after proteinase K digestion and extracted using TRIzol reagent (GK20008, GlpBio, California, USA). Then we sent the RIP experiment's input group and the anti-HNRNPAB antibody enrichment group to Aksomics (KangChen Bio-tech, Shanghai, China) for RIP-seq.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following manufacturer's protocols.

value: Human breast cancer cells


title: Molm-13, 100nm VTP, 24hrs, rep 2


title: A-BOSN12-COSN123_A6_Bru

description: Library name: A-BOSN12-COSN123_A6_Bru


title: Molm-13, 2500nM PF-9363, 24hrs, rep 2


title: A-BOSN12-COSN123_C11_Bru

description: Library name: A-BOSN12-COSN123_C11_Bru


title: Myt1l P3-wildtype 5


title: Molm-13, 2500nM PF-9363, 24hrs, rep 1


title: Input

description: Library name: Sample 1


title: Myt1l P3-wildtype 3


title: JNJ_3

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 mouse assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM34 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

growth_protocol: HuCCT-1 cells were maintained in DMEM-F12 supplemented with 10% FBS and antibiotics

extract_protocol:
Total RNA from cells was extracted using the automated Maxwell system from Promega. 100 ng of total RNA was used for the construction of sequencing libraries.
Library preparation was be performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer's protocol.

treatment_protocol: HuCCT-1 cells were treated with 6 nM JNJ-64619178 for 4 days (JNJ), and as a control cells were treated with the same volume of DMSO (Control).

value: JNJ 6nM


title: biallelic Etoposide replicate 4

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

description: Library name: bi_GFPpos_ETO_4

data_processing:
Quality control, mapping and differential gene expression analysis were performed using the SUSHI bioinformatics pipeline. Gene set enrichement analysis was performed using the GSEA software developed jointly by UC San Diego and the Broad Institute.
Assembly: NCBI
Supplementary files format and content: excel, normalized counts

source_name: hematopoietic progenitor line

extract_protocol:
RNA was harvested using the Rneasy Plus mini kit (Qiagen)
Library construction was done with the Illumina TruSeq mRNA kit

value: hematopoietic progenitor line

value: hematopoietic progenitor cells

value: Biallelic Trp53 mutation

value: Etoposide

value: female


title: wild-type (biallelic background) Etoposide replicate 4

description: Library name: bi_GFPneg_ETO_4

value: Trp53 wild-type


title: biallelic DMSO replicate 4

description: Library name: bi_GFPpos_DMSO_4

value: DMSO


title: JNJ_2


title: Myt1l P3-wildtype 2


title: Myt1l P3-wildtype 8


title: T47D cells, hypoxia and  DMSO co-treatment, total RNA, biol rep 3

city: Solna

first: Kathleen

middle: Diane

last: Watt

address: Tomtebodevägen 23

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: Library name: T47D_DMSO_H_rep3

data_processing:
NanoCAGE sequencing reads with each of the six barcodes were extracted using TagDust (version 2.33), and Nextera XT N-Series 3’ adapters were trimmed using Cutadapt (v1.18) (settings: -e 0.15 -01 -n 4 -m 25). PCR duplicates were defined as reads with identical UMI and sequence in the first 25 bp, and were filtered to keep only one unique read. Ribosomal RNA was removed using bbduk.sh from the BBTools software suite, with default settings. A summary of the nanoCAGE preprocessing can be seen in Fig S1A. Next, reads were aligned to the human genome hg38 using Bowtie (v1.2.2) (settings: -a -m 1 --best --strata -n 2 -l 28), and reads that uniquely aligned or failed to align were collected for a second alignment step to a custom index of 5’UTR sequences. This custom index was created by extending RefSeq 5’UTR sequences82 by 78 bases upstream using genomic sequence, and 78 bases downstream using mRNA sequences. These extensions were selected based on the criteria that the nanoCAGE read architecture allows for a maximal length of 78 after adapter trimming. Alignment to the custom index was also performed using Bowtie (settings: -a --best –strata -n 3 -l 25). Reads were trimmed by 1-2 based at the 5’ end in the event of alignment mismatches at the first or second positions, and strand invasion artefacts were removed using the perl script provided by Tang et al. (Nucleic Acids Res, 2015) (settings: -e 2).
Assembly: GRCh38/hg38 for genomic alignment, and RefSeq rel_109.20201120 for transcript annotations.
Librairies were prepared with mutliple barcodes for each sample and pooled. The pool was sequenced on 2 lanes. Reads from individual barcodes were extracted using TagDust (Lassmann, BMC Bioinformatics, 2015) and each raw file provided here contains reads from one barcode and index after demulitplexing, with reads from both lanes merged.
Supplementary files format and content: DPN files (ZZZ tab separated) in the format: RefSeq ID, counts per TSS position, TSS positions relative to the translation start site (AUG). This file format was created to easily summarize and load bam files into R, and reduce computation times.
Supplementary files format and content: Raw counts table with expression of transcription start site clusters. ClusterIDs are provided in the format: RefSeqID_startPosition_endPosition, where positions are given relative to the translation start site for a given transcript (AUG start codon).
Library strategy: nanoCAGE

growth_protocol: T47D cells (ATCC, Manassas, Virginia, USA) were grown in RPMI-1640 Medium (Gibco, Cat#11875093) with 10% fetal bovine serum (FBS) (Corning).  Cells were maintained at 37 °C with 5% CO2 in a humidified environment.

extract_protocol:
Total RNA was extracted from hypoxia and normoxia-treated T47D and H9 cells using TRIZOL.
The quantity and quality of total RNA from hypoxia-treated T47D and H9 cells was assessed by Qubit (Life Technologies) and Bioanalyzer (Agilent Technologies), and 75 ng of RNA was used as input material to prepare nanoCAGE libraries as described previously (Lorent et al., EMBO, 2019) (T47D n = 3, H9 n = 4). Note that the Template Switching Oligonucleotides (TSO) include 8 nt random unique molecular identifiers (UMIs) that allow for the identification of duplicate transcripts arising from PCR amplification, and one of six barcodes for increased multiplexing (ACAGAT, GTATGA, ATCGTG, GAGTGA, TATAGC, GCTGCA). Sequencing was performed at the SciLifeLab NGI (Sweden) facility using the HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 100-base pair single-end setup using HiSeq Rapid SBS Kit vs chemistry.

treatment_protocol: For all experiments, cells were plated 24 h prior to the treatment (1.2 x 106 in 60 mm dishes or 5.8 x105 in 6-well plates). For compound 48 (C48) (Axon Medchem, #2809/batch1) treatments, media was replaced with fresh RPMI 10% FBS containing 10 µM C48 or the equivalent volume of DMSO as vehicle control. Cells were treated with DMSO for 48h, or 24h DMSO followed by 24h 10µM C48 additional 24h. For OICR9429 (S7833,  Selleckchem) and hypoxia co-treatments cells were treated with 25 µM OICR9429 or an equivalent volume of DMSO as vehicle control. After 48 h media was replaced with fresh media containing 25 µM OICR9429 or DMSO and cells were placed under hypoxia for an additional 48 h before harvesting cells for RNA extraction.

value: Human breast cancer

value: Hypoxia (0.5% O2) and DMSO co-treatment


title: JNJ_1


title: wild-type (biallelic background) DMSO replicate 4

description: Library name: bi_GFPneg_DMSO_4


title: Myt1l P3-wildtype 1


title: T47D cells, hypoxia and  DMSO co-treatment, total RNA, biol rep 2

description: Library name: T47D_DMSO_H_rep2


title: C_3


title: monoallelic Etoposide replicate 4

description: Library name: mono_GFPpos_ETO_4

value: Monoallelic Trp53 mutation


title: Myt1l P3-hetero 8

value: Myt1l heterozygote


title: C_2


title: wild-type (monoallelic background) Etoposide replicate 4

description: Library name: mono_GFPneg_ETO_4


title: Myt1l P3-hetero 7

value: whole brain


title: T47D cells, hypoxia and  OICR9429 co-treatment, total RNA, biol rep 3

description: Library name: T47D_OICR_H_rep3

value: Hypoxia (0.5% O2) and OICR9429 (25 uM) co-treatment


title: Myt1l P3-wildtype 4

value: wild-type

value: male


title: C_1


title: H9 cells, normoxia, polysomal RNA, biol rep 2

description: Library name: H9_N_P_2

library_source: other

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
RNA sequencing read quality was assessed using FastQC v.0.11.8 and MultiQC.
Sequencing adapters and reads mapping to ribosomal RNA were removed using BBDuk from the BBTools suite (http://jgi.doe.gov/data-and-tools/bb-tools/) prior to alignment to hg38 using HISAT2 with default settings.
Reads were summarized using the featureCounts function of the Rsubread R package with default settings and RefSeq gene definitions.
Assembly: GRCh38
Supplementary files format and content: Matrix of raw gene expression counts based on RefSeq gene definitions.

molecule: other

growth_protocol: T47D cells (ATCC, Manassas, Virginia, USA) were grown in RPMI-1640 Medium (Gibco, Cat#11875093) with 10% fetal bovine serum (FBS) (Corning).  Cells were maintained at 37 °C with 5% CO2. H9 hESCs were obtained from WiCell and the use of hESCs was approved by the Stem Cell Oversight Committee of Canada. hESCs were cultured on plates prepared with Corning® Matrigel® hESC-Qualified Matrix (#07181, Stemcell Technologies) and fed daily using pre-warmed mTeSR™1 feeder-free medium supplemented with mTeSR™1 5X Supplement (#85850, Stemcell Technologies). Colony quality, confluence, and spontaneous differentiation was visually monitored daily and differentiated colonies were manually scraped off the plate. hESCs were passaged using StemPro™ EZPassage™ Disposable Stem Cell Passaging Tool (23181010, Thermo Fisher). All cells were maintained at 37°C and 5% CO2 in a humidified environment.

extract_protocol:
Cells (8 x 106 cells per condition) were seeded in 15cm plates 24h prior to the experiment. Media was changed before cells were exposed to normoxia or hypoxia (0.5% O2) for 24h or 48h. Cells were pre-treated with 100 μg/ml cycloheximide for 5 min and scraped in ice-cold, cycloheximide supplemented (100 μg/ml) PBS, using rubber scrapers. Cells were then pelleted in 15 ml conical tubes at 240 × g for 5 min at 4°C, and lysed on ice in 500 μl of hypotonic lysis buffer (5 mM Tris–HCl, pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg/ml cycloheximide, 1 mM DTT, 0.5% Triton, 0.5% sodium deoxycholate) for 15 min. Subsequently, lysates were cleared through a 15 min, 20 817 × g centrifugation at 4°C. Cleared lysates were diluted with hypotonic lysis buffer to set their optical density (OD) at 260 nm to 10–20. Sucrose gradients (5–50%) were generated in polypropylene tubes (Beckman Coulter, 331372, 14 × 89 mm) using a gradient maker (Biocomp Gradient Master 108), according to the manufacturer's instructions. A volume of 500 μl was removed from the top of the sucrose gradient to allow for sample loading. Lysates were then layered over the top of linear sucrose gradients and centrifuged at 4°C for 2 h at 222 228 × g (36 000 rpm) using an ultracentrifuge (Beckman Coulter, Optima XPN-80, rotor SW41Ti), while 10% of the sample was kept for total cytosolic mRNA extraction. Ultracentrifuged samples were fractionated into 2 ml tubes using a density gradient fractionation system (Brandel, BR-188-177), resulting in 12 fractions of 800 μl each. Input samples, as well as sucrose gradient fractions, were mixed with 1000 μl of TRIzol LS reagent (Invitrogen) and kept at −80°C for subsequent RNA isolation.
RNAseq libraries for total and polysome-associated mRNA fractions from T47D, H9, cells cultured under hypoxia (1% O2) and normoxia  (20% O2) were prepared using the Smart-seq2 protocol as previously described83. RNA quantity and quality was assessed by Qubit (Life Technologies) and Bioanalyzer (Agilent Technologies), and 10 ng of RNA was used as input material. After pre-amplification PCR 70 pg of cDNA underwent tagmentation in a total volume of 20 uL using the Nextera XT Kit (Illumina). Sequencing was then performed at the SciLifeLab National Genomics Infrastructure (NGI, Sweden) facility using the NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 50-base paired-end setup using the ‘NovaSeqStandard’ workflow and S1 flow cell.

treatment_protocol: For hypoxia experiments media was changed to fresh full-serum media and cells were incubated in normoxia (regular incubator) or hypoxia (Biospherix OxyCycler model C42 or ProOx model C21 chambers housed in a regular incubator) at 1% O2 for either 24 (H9 cells) or 48 hrs (T47D).

value: Human embryonic stem cell

value: normoxia (20% oxygen, 24 hrs)


title: wild-type (monoallelic background) DMSO replicate 4

description: Library name: mono_GFPneg_DMSO_4

value: hematopoietic progenitor line


title: 04_PE_RNA

city: Heidelberg

first: Dominik

last: Lindenhofer

address: Meyerhofstraße 1

country: Germany

institute: EMBL Heidelberg

description: SDR-seq

data_processing:
Barcode identification, count matrices consisting of either cell-reads (gDNA and RNA) or cell-UMIs (RNA) were generated using SDRranger (https://github.com/hawkjo/SDRranger).
Assembly: Targeted references were constructed for the PCR amplicons for gDNA and RNA libraries. Sequences for this study were extracted from the human GRCh38 assembly
Supplementary files format and content: Tab-separated values and matrix files.  The gDNA processed files contain read matrices for cell vs gDNA site with reads.
Library strategy: scDNA-scRNA-seq (SDR-seq)

extract_protocol:
Human iPSCs were fixed in either PFA or glyoxal, in-situ reverse transcription was performed and cells were subjected to the Tapestri machine from MissionBio (v2). Multiplexed PCR amplified both gDNA and RNA simultenously in the same cell together with cell barcoding.
For POP a common library for both gDNA and RNA was prepared. For all other runs separate sequencing libraries were performed for both gDNA and RNA.

value: human iPSCs


title: Myt1l P3-hetero 6


title: Myt1l P3-hetero 5


title: biallelic Etoposide replicate 3

description: Library name: bi_GFPpos_ETO_3

value: hematopoietic progenitor cells

value: Biallelic Trp53 mutation


title: Myt1l P3-hetero 4


title: wild-type (biallelic background) Etoposide replicate 3

description: Library name: bi_GFPneg_ETO_3

value: Etoposide

value: female


title: 04_PE_gDNA

description: SDR-seq

library_source: genomic

molecule: genomic DNA


title: H9 cells, normoxia, total RNA, biol rep 2

description: Library name: H9_N_T_2


title: 03_CRISPRi_RNA

description: SDR-seq


title: Myt1l P3-hetero 3


title: biallelic DMSO replicate 3

description: Library name: bi_GFPpos_DMSO_3

value: DMSO


title: T47D cells, DMSO, total RNA, biol rep 3

description: Library name: T47D_DMSO_rep3

value: Human breast cancer

value: DMSO (48 hrs)


title: T47D cells, hypoxia and  DMSO co-treatment, total RNA, biol rep 1

description: Library name: T47D_DMSO_H_rep1

value: Hypoxia (0.5% O2) and DMSO co-treatment


title: 03_CRISPRi_gDNA

description: SDR-seq


title: T47D cells, DMSO, total RNA, biol rep 4

description: Library name: T47D_DMSO_rep4


title: T47D cells, DMSO, total RNA, biol rep 2

description: Library name: T47D_DMSO_rep2


title: T47D cells, hypoxia and  OICR9429 co-treatment, total RNA, biol rep 1

description: Library name: T47D_OICR_H_rep1


title: Myt1l P3-hetero 2

value: Myt1l heterozygote


title: Myt1l P3-hetero 1

value: whole brain


title: T47D cells, hypoxia and  OICR9429 co-treatment, total RNA, biol rep 2

description: Library name: T47D_OICR_H_rep2

value: Hypoxia (0.5% O2) and OICR9429 (25 uM) co-treatment


title: monoallelic Etoposide replicate 3

description: Library name: mono_GFPpos_ETO_3

value: Monoallelic Trp53 mutation


title: T47D cells, C48, total RNA, biol rep 4

description: Library name: T47D_C48_rep4

value: C48 (DMSO for 24 hrs, followed by 10µM C48 for, 24 hrs)


title: OCS_treated_Dox_04h

city: New Haven

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description:
Library name: OCS_DOX_04H
DOX, On-chip stimulated
dox_veh_ocs_timecourse.rds

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the transcriptome (GRCh38 Gencode v26) supplemented with ERCC spike in sequences utilizing STAR v2.5.0 with the following non-default parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
Cells were pre-filtered for total detected features (>4k) and fraction of reads aligned to control features (ERCC + mitochondrial) (<0.7). Batch correction and normalization performed with RUVseq RUVs19, with number of unwanted variance factors k=10 as estimated by PCA analysis.
Assembly: hg38
Supplementary files format and content: RDS file of pre-process counts in single cell experiment format
Supplementary files format and content: dox_veh_ocs_timecourse.rds

growth_protocol: HCT-116 cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
The C1 integrated fluidics circuits (IFCs) for mRNA seq (small-cell, 5–10 μm) was primed according to the standard Fluidigm mRNA-seq protocol using C1 harvest reagent, C1 preloading reagent, C1 blocking reagent, and Fluidigm cell wash buffer. Priming was performed immediately prior to sample preparation. HCT-116 cells were trypsinised and resuspended in serum-free media at a concentration of 333,000 cells/mL. The standard suspension ratio of 3:2 was used (60 µL of cell suspension was added to 40 µL of Fluidigm suspension reagent) to achieve the final cell mix for IFC loading. After mixing several time the cell preparation, 6 µL of the cell mix was loaded. Following cell loading, light microscopy using EVOS microscope, was used in order to assess each of the 96 capture sites individually and the outcome of loading was recorded in terms of the number of cells present in each capture site and whether debris were present. This information was used as a quality control step to ensure that only confirmed single cell samples were taken forward. Finally, the IFC was placed into the C1 the script “mRNA Seq: Cell Load (1771x/1772x/1773x)” was run. Following the loading, buffer mixes for lysis, reverse transcription and PCR were pipetted into the IFC. The IFC was then placed into the C1 system and the script “mRNA Seq: RT & Amp (1771x/1772x/1773x)” was run overnight. Samples were harvested from the IFC by transferring 3.5 µL of product to a 96 well plate and diluted with 10 µL C1 DNA dilution reagent. The samples corresponding to the confirmed single cell captures were highlighted according to the arrangement on the harvest plate described by Fluidigm. Samples were stored at 4ºC short term and -20ºC long term prior to subsequent quantification and library preparation.
Library preparation was performed using the modified Illumina Nextera XT DNA library preparation protocol provided by Fluidigm. The cDNA concentration was quantified using the PicoGreen Assay (Quant-IT PicoGreen dsDNA Assay Kit, Thermo Fisher Scientific, P11496) using 2 µL per 96 samples processed into 2 replicates in a 384-well plate giving a final well volume of 60 µL for reading in a fluorometer. The data was then processed using the Microsoft Excel worksheet, Single-Cell mRNA Seq PicoGreen Template (Fluidigm, PN 100-6260), to quantify the library. Samples were transferred to a new 96-well plate in order to obtain a sample within the range 0.1-0.3 ng/µL by diluting with C1 Harvest Reagent. Only samples with at least 0.1 ng/µL were taken forward for library preparation. Sequencing libraries were prepared using Nextera XT DNA Library (Illumina) with a modified protocol provided by Fluidigm.

treatment_protocol: Cells were treated with dox at a concentration of 0.2 μg/ml or equivalent volume of vehicle (ddh20) for the indicated time.

value: Doxorubicin 0.2 µg/ml 4 hours  - On chip stimulated


title: OCS_treated_Veh_04h

description:
Library name: OCS_VEH_04H
VEH, On-chip stimulated
dox_veh_ocs_timecourse.rds

value: Vehicle - On chip stimulated


title: wild-type (biallelic background) DMSO replicate 3

description: Library name: bi_GFPneg_DMSO_3

value: hematopoietic progenitor line

value: Trp53 wild-type


title: T47D cells, C48, total RNA, biol rep 3

description: Library name: T47D_C48_rep3


title: 02_Panel_size_RNA_480

description: SDR-seq

value: human iPSCs


title: T47D cells, C48, total RNA, biol rep 2

description: Library name: T47D_C48_rep2


title: 02_Panel_size_RNA_120-2

description: SDR-seq


title: wild-type (monoallelic background) Etoposide replicate 3

description: Library name: mono_GFPneg_ETO_3

value: hematopoietic progenitor cells


title: 02_Panel_size_gDNA_480

description: SDR-seq


title: monoallelic DMSO replicate 3

description: Library name: mono_GFPpos_DMSO_3


title: 02_Panel_size_RNA_120-1

description: SDR-seq


title: 02_Panel_size_gDNA_240

description: SDR-seq


title: T47D cells, C48, total RNA, biol rep 1

description: Library name: T47D_C48_rep1


title: biallelic Etoposide replicate 2

description: Library name: bi_GFPpos_ETO_2

value: Biallelic Trp53 mutation

value: Etoposide


title: Bulk_treated_Dox_04h

description:
Library name: BLK_DOX_04H
DOX, bulk-treated, 04h
dox_veh_ocs_timecourse.rds

value: Doxorubicin 0.2 µg/ml 4 hours


title: Bulk_treated_Dox_24h

description:
Library name: BLK_DOX_24H
DOX, bulk-treated, 24h
dox_veh_ocs_timecourse.rds

value: Doxorubicin 0.2 µg/ml 24 hours


title: 02_Panel_size_RNA_240

description: SDR-seq


title: wild-type (monoallelic background) DMSO replicate 3

description: Library name: mono_GFPneg_DMSO_3

value: DMSO

value: female


title: wild-type (biallelic background) Etoposide replicate 2

description: Library name: bi_GFPneg_ETO_2


title: 02_Panel_size_gDNA_120-2

description: SDR-seq


title: T47D ATAC, DMSO, biol rep1

description: Library name: T47D_DMSO_R1

data_processing:
Raw ATAC-seq fastq files were processed using the nf-core/atacseq pipeline 2.1.2 (available at https://github.com/nf-core/atacseq). Reads were aligned to GRCh38/hg38 in paired-end mode and all other parameters were kept as default. Duplicates, multi-mapping, unpaired, and ENCODE blacklist reads were filtered out of final BAM files.
Assembly: GRCh38/hg38, RefSeq rel_109.20201120
Supplementary files format and content: Nucleoatac signal files are Bedgraph tracks with normalized cross-correlation signal derived using the nucleoATAC algorithm.
Supplementary files format and content: Smooth Nucleoatac signal files are smoothed versions of the nucleoatac_signal bedgraph tracks.
Supplementary files format and content: Nucpos.bed files are nucleosome dyad calls from the nucleoATAC algorithm. Columns are: (1) chrom, (2) dyad position (0-based), (3) dyad position(1-based), (4) z-score, (5) nucleosome occupancy estimate (6) lower bound for nucleosome occupancy estimate, (7) upper bound for nucleosome occupancy estimate (8) log likelihood ratio, (9) normalied nucleoatac signal value, (10) cross-correlation signal value before normalization, (11) number of potentially nucleosome-sized fragments, (12) number of fragments smaller than nucleosome sized, (13) "fuzziness" (measure of how wide signal peak is)

extract_protocol:
ATAC-seq libraries were generated following a modified Omni-ATAC-seq protocol (PMID: 28846090). Following treatment, both control and treated samples were washed, trypsinized and counted in a hemocytometer. To check viability, cells were counted with 0.4% trypan blue. Cell viability >85% is required. After counting, 100,000 cells were pelleted at 500 RCF for 5 min at 4°C and lysed on ice for 3 min with ATAC-Resuspension Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl and 3mM MgCl2) containing 0.1% Tween-20 (Fisher cat no. BP337), 0.1% IGEPAL® CA-630 (Sigma cat no. I3021), 0.01% Digitonin (ThermoFisher Scientific cat no. BN2006). After incubation with lysis buffer, cell lysates were washed with ATAC-Resuspension Buffer containing 0.1% Tween-20. After washing, nuclei were pelleted at 500 RCF for 10 min at 4°C.
Pelleted nuclei was resuspended in transposition mix containing the Illumina Tagment DNA TDE1 Enzyme (Tn5) and Buffer (Illumina cat no. 20034197), 0.1% Tween-20 and 0.01% Digitonin, and incubated in a thermomixer at 1000 RPM for 30 min at 37°C. After tagmentation, fragments were cleaned using MinElute PCR Purification Kit (Qiagen cat no. 28004). Cleaned up fragments were resuspended in ultrapure water. The transposed fragments were then amplified with NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs cat no. M0541S) and indexed with Illumina Nextera XT Index Kit (Illumina cat no. FC-131-1001). Final libraries were cleaned up and size selected with AMPure XP SPRI Reagent (Beckman Coulter cat no. A63880). To assess library quality, 1ul of each sample was submitted to Agilent Bioanalyzer at Queen's University Department of Pathology and Molecular Medicine. Finally, samples were sent to Genome Quebec Innovation Center and sequenced on an Illumina NovaSeq6000 platform using a 100 base-pair paired-end read set-up.

treatment_protocol: For hypoxia experiments media was changed to fresh full-serum media and cells were incubated in normoxia (regular incubator) or hypoxia (Biospherix OxyCycler model C42 or ProOx model C21 chambers housed in a regular incubator) at 1% O2 for 48 hrs T47D. For compound 48 (C48) (Axon Medchem, #2809/batch1) treatments, media was replaced with fresh RPMI 10% FBS containing 10 µM C48 or the equivalent volume of DMSO as vehicle control. Cells were treated with DMSO for 48h, or 24h DMSO followed by 24h 10µM C48 additional 24h.

value: Human breast cancer

value: DMSO (24 hrs)


title: 02_Panel_size_gDNA_120-1

description: SDR-seq


title: Bulk_treated_Veh_04h

description:
Library name: BLK_VEH_04H
VEH, bulk-treated
dox_veh_ocs_timecourse.rds

value: Vehicle


title: biallelic DMSO replicate 2

description: Library name: bi_GFPpos_DMSO_2


title: T47D cells, DMSO, total RNA, biol rep 1

description: Library name: T47D_DMSO_rep1

value: DMSO (48 hrs)


title: T47D ATAC, C48, biol rep2

description: Library name: T47D_C48_R2


title: GBM005-BT935i-iRFP-T27,AC133 bottom 5%-repB

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
Library name: GBM_88
Genome-wide knockout screen, cells grown in neurocult complete media

data_processing:
Reads were trimmed by extracting the flanking 20 bp after each 8bp anchor was found in barcoding primers. A 2 bp mismatch was allowed for the anchor search. After trimming, a quality-control alignment was performed using Bowtie v.0.12.8 (allowing for a maximum of 2 bp mismatches) and sgRNAs were quantified.
Read counts for all samples in the screen were combined into a matrix and normalized by dividing each read count by the sum of all of the read counts in the sample and then multiplying by the expected read number (10 million).
Fold change was calculated to a reference sample (T12 unsorted). Calculated fold changes were then used to generate normalized Z scores using drugZ (v.1.1.0.2).
Assembly: TKOv3 sgRNA library
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPR Screen

source_name: Patient Derived Cell Line

growth_protocol: Cells were cultured in Neurocult Complete media supplemented with EGF, FGF, and heparin plus 1% Penicillin/Streptomycin, and serially passaged for up to 30 days (propagated in biological triplicates).  Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

value: Patient Derived Cell Line

value: Glioblastoma

value: TKOv3 (lentiCRISPRv2)


title: GBM005-BT935i-iRFP-T27,AC133 bottom 5%-repC

description:
Library name: GBM_89
Genome-wide knockout screen, cells grown in neurocult complete media


title: Bulk_treated_Dox_08h

description:
Library name: BLK_DOX_08H
DOX, bulk-treated, 08h
dox_veh_ocs_timecourse.rds

value: Doxorubicin 0.2 µg/ml 8 hours


title: wild-type (biallelic background) DMSO replicate 2

description: Library name: bi_GFPneg_DMSO_2

value: hematopoietic progenitor line

value: Trp53 wild-type


title: T47D ATAC, C48, biol rep1

description: Library name: T47D_C48_R1


title: Lung  (mixed sample)

city: Livermore

first: Dina

last: Weilhammer

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

description:
10x Genomics
CD45+ Uninfected; CD45+ 488+ Infected; CD45+ 488- Infected; Whole Lung Infected

data_processing:
Data processing, including demultiplexing, alignment, barcode assignment, and gene expression quantification, was performed using the Cell Ranger software pipeline version 7.2.0 and the mm10 2020-A reference transcriptome from 10x Genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: The processed data files for each experimental group are the standard 10x Cell Ranger output files, including a gene list (features.tsv), cell barcodes (barcodes.tsv), and gene/barcode matrices (matrix.mtx).

source_name: Lung

extract_protocol:
For whole lung sequencing, 3x106 cells were fixed per mouse using 10x Genomics Fixation Buffer and fixed cells stored at -80°C prior to sequencing. When thawed, fixed cells were counted again using a Countess 3 (Thermo Fisher) and 500,000 cells each from 3 mice were pooled per reaction. For sequencing of sorted cells, following generation of single cell suspensions, immune cells were enriched using LS columns (Miltenyi Biotec) for MACS separation using anti-CD45 magnetic microbeads (Miltenyi Biotec, 130-052-301) according to manufacturer’s instructions, followed by resuspension in 10x Genomics Fixation Buffer and fixed overnight at 4°C. Fixed cells were pooled and sorted using a BD FACSAria Fusion and BD FACSMelody Cell Sorter to collect AF488– or AF488+ populations. BD FACSDiva Software Version 8.0.1 and BD FACSChorus Software Version 2.0 Application Data Version 1.1.20.0. was used during acquisition to define the sorted populations. Sorted cell suspensions were resuspended in 10x Genomics Quenching Buffer and glycerol according to manufacturer’s instructions and stored at -80°C prior to sequencing.
Single-cell RNA sequencing was performed using the 10x Genomics Chromium Single Cell Fixed RNA Profiling Kit, following the manufacturer's protocol. Following the generation of single-cell suspensions as described above, 3x106 cells per lung sample were fixed using 10x Genomics fixation buffers supplemented with paraformaldehyde to a final working solution of 4% according to manufacturer’s instructions and then stored at -80°C 10x Genomics long-term storage solution prior to library preparation. Each reaction was inclusive of 3 mice validated for fungal infection by plaque assay and pooled at 500,000 cells per mouse.

treatment_protocol: Mice were intranasally infected with Coccidioides for 24hrs then lungs were harvested

value: Lung

tag: infection

value: Uninfected; NR-166 avirulent Coccidioides posadasii (Δcts2/Δard1/Δcts3)

value: Uninfected, MACS bead sorted for CD45+; Coccidioides infection 24 hrs, MACS bead sorted for CD45+; Coccidioides infection 24 hrs


title: T47D ATAC, normoxia, biol rep3

description: Library name: T47D_N_R3

value: normoxia (20% oxygen, 48 hrs)


title: GBM005-BT935i-iRFP-T27,AC133 bottom 5%-repA

description:
Library name: GBM_87
Genome-wide knockout screen, cells grown in neurocult complete media


title: GM-BMDM + cocci cm bio rep 3

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 using P2 reagents. The raw RNA sequencing data was aligned to the mouse genome (mm10) using STAR, and mapped reads were counted using featureCounts.
Subsequently, data normalization was performed using the Trimmed Mean of M-values
DE genes were identified using edgeR (version 4.2.1) in R (version 4.4.1).
Genes were considered significantly expressed when its FDR adjusted p-value was <0.05 and fold change was 1.5. Pathway and biological process enrichment analyses were conducted using the ToppGene Suite, based on the DE genes identified. Heatmaps were generated using the ‘pheatmap’ package (version 1.0.12) in R.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone Marrow

growth_protocol: BMDM were isolated from WT mice and incubated with DMEM/F12 + 10% FBS

extract_protocol:
RNA was isolated from all conditions using RNeasy RNA mini kits according to manufacturer’s instructions.
Sequencing library preparation was performed using Illumina Stranded mRNA Prep, Ligation according to manufacturer's recommendations. Sequencing was performed on an Illumina NextSeq 2000 using P2 reagents. The raw RNA sequencing data was aligned to the mouse genome (mm10) using STAR, and mapped reads were counted using featureCounts. Subsequently, data normalization was performed using the TMM method. Differentially expressed (DE) genes were identified using edgeR (version 4.2.1) in R (version 4.4.1). Genes were considered significantly expressed when its false discovery rate (FDR) adjusted p-value was <0.05 and fold change was >1.5 or <-1.5. Pathway and biological process enrichment analyses were conducted using the ToppGene Suite, based on the DE genes identified. Heatmaps were generated using the ‘pheatmap’ package (version 1.0.12) in R.

treatment_protocol: For direct contact experiments, 500,000 arthroconidia were added to macrophages in DMEM/F12 + 10% FBS and incubated for 24 hours. Supernatants were collected, filtered through a then centrifuged to remove cellular debris and filtered through a 0.22 µM filter to generate conditioned media. Conditioned media was also collected from mock-infected cells. For conditioned media experiments, GM-BMDM were incubated for 24 hours with conditioned media supplemented with an additional 5% FBS from GM-BMDM infected with Coccidioides or mock-infected cells.

value: Bone Marrow

value: Bone marrow derived macrophages

value: High GM-CSF BMDM + conditioned media from Coccidioides infection 24 hrs


title: monoallelic Etoposide replicate 2

description: Library name: mono_GFPpos_ETO_2

value: hematopoietic progenitor cells

value: Monoallelic Trp53 mutation

value: Etoposide

value: female


title: wild-type (monoallelic background) Etoposide replicate 2

description: Library name: mono_GFPneg_ETO_2


title: T47D ATAC, DMSO, biol rep2

description: Library name: T47D_DMSO_R2

value: Human breast cancer

value: DMSO (24 hrs)


title: GBM005-BT935i-iRFP-T27,AC133 top 5%-repC

description:
Library name: GBM_86
Genome-wide knockout screen, cells grown in neurocult complete media

value: Patient Derived Cell Line

value: Glioblastoma

value: TKOv3 (lentiCRISPRv2)


title: T47D ATAC, normoxia, biol rep2

description: Library name: T47D_N_R2


title: monoallelic DMSO replicate 2

description: Library name: mono_GFPpos_DMSO_2

value: hematopoietic progenitor line

value: DMSO


title: GM-BMDM + cocci cm bio rep 2


title: T47D ATAC, normoxia, biol rep1

description: Library name: T47D_N_R1


title: GBM005-BT935i-iRFP-T27,AC133 top 5%-repB

description:
Library name: GBM_85
Genome-wide knockout screen, cells grown in neurocult complete media


title: GM-BMDM + cocci cm bio rep 1


title: T47D ATAC, hypoxia, biol rep3

description: Library name: T47D_H_R3

value: hypoxia (1% oxygen, 48 hrs)


title: biallelic Etoposide replicate 1

description: Library name: bi_GFPpos_ETO_1

value: Biallelic Trp53 mutation


title: GBM005-BT935i-iRFP-T27,Unsorted-repC

description:
Library name: GBM_83
Genome-wide knockout screen, cells grown in neurocult complete media


title: GM-BMDM + cocci bio rep 4

value: High GM-CSF BMDM + Coccidioides infection  24 hrs


title: GM-BMDM + cocci bio rep 3

value: Bone Marrow


title: T47D ATAC, hypoxia, biol rep2

description: Library name: T47D_H_R2


title: wild-type (monoallelic background) DMSO replicate 2

description: Library name: mono_GFPneg_DMSO_2

value: Trp53 wild-type


title: wild-type (biallelic background) Etoposide replicate 1

description: Library name: bi_GFPneg_ETO_1


title: GM-BMDM + cocci cm bio rep 4

value: Bone marrow derived macrophages

value: High GM-CSF BMDM + conditioned media from Coccidioides infection 24 hrs


title: monoallelic DMSO replicate 4

description: Library name: mono_GFPpos_DMSO_4

value: hematopoietic progenitor cells

value: Monoallelic Trp53 mutation


title: T47D ATAC, hypoxia, biol rep1

description: Library name: T47D_H_R1


title: biallelic DMSO replicate 1

description: Library name: bi_GFPpos_DMSO_1

value: female


title: GM-BMDM + cocci bio rep 2


title: GM-BMDM + cocci bio rep 1


title: GBM005-BT935i-iRFP-T27,Unsorted-repB

description:
Library name: GBM_82
Genome-wide knockout screen, cells grown in neurocult complete media


title: wild-type (biallelic background) DMSO replicate 1

description: Library name: bi_GFPneg_DMSO_1


title: T47D Input, ChIP, DMSO, biol rep4

description: Library name: T47D_DMSO_input_R4

data_processing:
Raw H3K4me3 fastq files were processed using the nf-core/chipseq pipeline v.1.2.0 (available at https://github.com/nf-core/chipseq). Reads were aligned to GRCh38/hg38 in paired-end mode and all other parameters were kept as default.
The filtered aligned reads were extracted from the BAM files and re-aligned to a custom index of 5’UTR sequences using Bowtie (version 1.2.2) (settings: -v 2 -X 1000 -a). This custom index was created from genomic sequence regions corresponding to RefSeq transcripts with 2,000 bp of genomic sequence added upstream of the annotated TSS, and 10,000 bp added downstream of the TSS.
Bedtools genomeCoverageBed (v2.29.1) was then used to compute the genome coverage of H3K4me3 with -dz and -pc options, and -scale to normalize for library size. The cumulative sum of H3K4me3 coverage was calculated for each genomic region corresponding to RefSeq transcripts, and genomic regions were trimmed at the position where 95% of cumulative H3K4me3 signal had already occurred.
In order to reduce file sizes and computation time, the position (relative to the transcription start site), and the H3K4me3 coverage were collected for every 0.1% increase in the cumulative sum of H3K4me3 signal, such that each genomic region corresponding to RefSeq transcripts would have 1,000 data points summarizing the distribution of the histone mark.
Assembly: GRCh38/hg38 for genomic alignment, and RefSeq rel_109.20201120 for transcript annotations.
Supplementary files format and content: CDF files (ZZZ tab separated) in the format: RefSeq ID, cumulative sum of H3K4me3 read coverage, positions relative to the transcription start site where the cumulative sum of read coverage increases by 0.1%, and read coverage at these positions, scaled to total library size. This file format was created§ to easily summarize and load large bam files into R, and reduce computation times.

extract_protocol:
Control and treated cells were washed 2x in PBS and collected (500 rcf for 5 minutes at 4°C) and flash frozen. Prior to each ChIP, antibodies were conjugated overnight at 4°C in ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF, 50 ug/mL BSA) with 50/50 mix of Dynabeads™ Protein A (Thermo Fisher, 10001D) and Dynabeads™ Protein G (Thermo Fisher, 10003D) at a ratio of 6 ug of antibody to 25 uL of beads per sample. Prior to IP, beads were washed 2x with ChIP Buffer 1 and resuspended in 25 uL of ChIP Buffer 1. Frozen cells were washed twice in Buffer N (15 mM Tris Base, 15 mM NaCl, 60 mM KCl, 8.5% sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 1x protease inhibitor, 50 ug/mL BSA), then resuspended in 2x cell pellet volume of Buffer N and lysed for 10 minutes on ice in equivalent volume of 2x Lysis Buffer (1x Buffer N, 0.6% NP-40). Nuclei was pelleted (500 rcf for 5 minutes at 4°C) and resuspended in 6x cell pellet volume of Buffer N, then spun through Sucrose Cushion (15 mM Tris Base, 15 mM NaCl, 60mM KCl, 30% sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 1x protease inhibitor, 50 ug/mL BSA) at 500 rcf for 12 minutes at 4°C. Nuclei pellet was resuspended in 2x cell pellet volume of Buffer N. 2 uL of nuclei suspension was diluted with 18 uL of 2 M NaCl in triplicate, vortexed, and sonicated with a water bath sonicator (30x cycle of 30 seconds on, 30 seconds off) prior to measuring the chromatin concentration with NanoDrop Spectrophotometer (Thermo Fisher). Concentration of nuclei suspension was then adjusted to 1 ug/uL and separated into 100ug chromatin aliquots. Nuclei suspensions were prewarmed for 2 minutes at 37°C, then 1.52 uL of MNase (Worthington Biochemical Corporation, LS004797) was added for 12 minutes at 37 °C on a ThermoMixer (Eppendorf) set to 900 rpm. Digestion was stopped by adding 1/10 volume of MNase Stop Buffer (100 mM EDTA and 10 mM EGTA) and placing nuclei on ice. 5M NaCl was slowly added to the suspension to a concentration of 0.6 M on the slowest vortex setting to release the chromatin, insoluble nuclei was then pelleted (18,000 rcf, 1 minute, 4 °C), and supernatant was run through hydroxyapatite (HAP) chromatography. 15 uL of soluble chromatin was saved for visualization and the rest of the soluble chromatin was added to 0.07 g of HAP resin (Bio-Rad, #157-0021) rehydrated in HAP Buffer 1 (5 mM NaPO4 pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF) and rotated for 10 minutes at 4 °C. HAP mixture was run through Ultrafree-MC Centrifugal Filter (Millipore, UFC30HV25) at 600 rcf for 30 seconds at 4 °C and 15 uL of flow-through was saved for visualization. Then the column was washed 4x with 200uL HAP Buffer 1, 4x with 200 uL HAP Buffer 2 (5 mM NaPO4 pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF), and eluted 3x with 100 uL of HAP Elution Buffer (500 mM NaPO4 pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF). Flowthrough after each step was saved for visualization. Chromatin concentration was measured again in triplicate with the combined HAP elutions using NanoDrop. Final chromatin concentration was adjusted to 20 ng/uL using ChIP Buffer 1 prior to IP. 15 uL of chromatin was set aside for input control and chromatin was added to beads conjugated with H3K4me3 antibody (Epigentek, A4033). Chromatin and bead mixture was rotated for 10 minutes at 4 °C, washed 2x with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF, 50 ug/mL BSA), washed 1x ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% NP-40, 200 uM PMSF, 50 ug/mL BSA), and washed 1x with TE buffer, transferring beads to a new tube after each wash step. DNA was finally eluted in 50 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% SDS) at 600 rpm for 10 minutes at 55 °C on a ThermoMixer. 35 uL of ChIP Elution Buffer was also added to the input control to bring the final volume to 50 uL. To both input and eluted ChIP DNA, 2 uL of 5 M NaCl, 1uL of 500 mM EDTA, and 1 uL of 20 mg/mL Proteinase K was added and incubated for 2 hours at 55 °C and DNA was purified using MinElute PCR Purification Kit (Qiagen, 28004). DNA as eluted in ultrapure H2O and concentration was measured before and after purification using Qubit dsDNA Quantitation, High Sensitivity (Thermo Fisher, Q32851). Finally, HAP input and elutions were visualized using 2% agarose gel in 1x TBE ran at 140 V for 40 minutes to confirm fragment sizes.
ChIP DNA was sent to the Institute for Immunology and Cancer (IRIC, Montreal), where it was further validated via Bioanalyzer, followed by shotgun library preparation, and library sequencing via Illumina NovaSeq6000. Samples were sequenced to a depth between ~50-80 and ~75-250 million reads per sample for H3K4me3 and inputs, respectively.

treatment_protocol: For compound 48 (C48) (Axon Medchem, #2809/batch1) treatments, media was replaced with fresh RPMI 10% FBS containing 10 µM C48 or the equivalent volume of DMSO as vehicle control. Cells were treated with DMSO for 48h, or 24h DMSO followed by 24h 10µM C48 additional 24h.

value: Human breast cancer

tag: chip antibody


title: GBM005-BT935i-iRFP-T0

description:
Library name: GBM_80
Genome-wide knockout screen, cells grown in neurocult complete media


title: T47D Input, ChIP, DMSO, biol rep3

description: Library name: T47D_DMSO_input_R3

value: DMSO (24 hrs)


title: monoallelic Etoposide replicate 1

description: Library name: mono_GFPpos_ETO_1

value: Etoposide


title: T47D Input, ChIP, DMSO, biol rep2

description: Library name: T47D_DMSO_input_R2


title: GM-BMDM + cm bio rep 3

value: High GM-CSF BMDM + conditioned media from High GM-CSF cells


title: wild-type (monoallelic background) Etoposide replicate 1

description: Library name: mono_GFPneg_ETO_1


title: GBM005-BT935i-iRFP-T27,AC133 top 5%-repA

description:
Library name: GBM_84
Genome-wide knockout screen, cells grown in neurocult complete media

value: Patient Derived Cell Line

value: Glioblastoma

value: TKOv3 (lentiCRISPRv2)


title: T47D Input, ChIP, DMSO, biol rep1

description: Library name: T47D_DMSO_input_R1


title: monoallelic DMSO replicate 1

description: Library name: mono_GFPpos_DMSO_1

value: hematopoietic progenitor line

value: DMSO


title: GM-BMDM + cm bio rep 2


title: GM-BMDM + cm bio rep 1


title: T47D H3K4me3, ChIP, DMSO, biol rep4

description: Library name: T47D_DMSO_H3K4me3_R4

value: H3K4me3 (Epigentek, A4033)


title: T47D H3K4me3, ChIP, DMSO, biol rep3

description: Library name: T47D_DMSO_H3K4me3_R3


title: NRF2-RNAi-1

city: Nantong,Jiangsu,China

first: Lili

last: Ji

state: 江苏省

address: No. 19 Qixiu Road, Nantong University, Chongchuan District, Nantong City, Jiangsu Province

institute: Nantong University

description:
Library name: Sample 4
Column name in all.genes.expression.annot.xls: NRF2-RNAi-1

data_processing:
The resulting cDNA library was sequenced on an Illumina Novaseq6000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).
To obtain high-quality clean reads, the reads were further filtered using fastp (version 0.18.0).
Differential expression analysis of RNAs was conducted between two different groups using DESeq2 software.
Pathway enrichment analysis was carried out using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg).
Gene set enrichment analysis (GSEA) was conducted using GSEA software and MSigDB software to determine whether two groups exhibited significant differences in regard to a set of genes in specific KEGG pathways.
Assembly: Ensembl release 106
Supplementary files format and content: all.genes.expression.annot.xls file includes raw counts for each Sample
Supplementary files format and content: all.genes.expression.annot.xls include FPKM values for each Sample

source_name: lung

growth_protocol: The NSCLC cisplatin-resistant cell line A549/DDP (CL-0519) were purchased from Procell Life Science & Technology Co, Ltd. Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 5 mg/mL penicillin-streptomycin, and 1–2 µg/ml DDP specific for A549/DDP cells at 37˚C under 5% CO2.

extract_protocol:
Total RNA was isolated using the Trizol reagent kit (15596026, Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s protocol. The quality of the RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified by RNase free agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).

value: lung

value: tumor-cell line from a human lung carcinoma

value: Nrf2 knockdown


title: Con-RNAi-3

description:
Library name: Sample 3
Column name in all.genes.expression.annot.xls: Con-RNAi-3

value: WT


title: wild-type (monoallelic background) DMSO replicate 1

description: Library name: mono_GFPneg_DMSO_1

value: hematopoietic progenitor cells

value: Trp53 wild-type


title: GM-BMDM bio rep 6

value: Bone Marrow

value: Bone marrow derived macrophages

value: High GM-CSF BMDM


title: GBM005-BT935i-iRFP-T27,Unsorted-repA

description:
Library name: GBM_81
Genome-wide knockout screen, cells grown in neurocult complete media


title: Con-RNAi-2

description:
Library name: Sample 2
Column name in all.genes.expression.annot.xls: Con-RNAi-2


title: GM-BMDM + cm bio rep 4


title: HCD-4

city: Nanjing

first: Jialu

last: Shi

address: No.87 DingJiaQiao

institute: southeast university

description:
Library name: Sample 9
C19_fpkm

data_processing:
1 Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. 2 Reads mapping to the reference genome The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome. 3 Novel transcripts Prediction The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results 4 Gene functional annotation Gene function was annotated based on the following databases: Nr (NCBI non-redundant protein sequences);Pfam (Protein family); KOG/COG (Clusters of Orthologous Groups of proteins); Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database); GO (Gene Ontology). 5 Quantification of gene expression levels Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}} 6 Differential expression analysis For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 & Fold Change≥2 found by DESeq2 were assigned as differentially expressed. For the samples without biological replicates: Differential expression analysis of two samples was performed using the edgeR.The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression. 7 GO enrichment analysis Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the clusterProfiler packages based Wallenius non-central hyper-geometric distribution（Young et al, 2010）,which can adjust for gene length bias in DEGs. 8 KEGG pathway enrichment analysis KEGG (Kanehisa et al., 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (Mao et al., 2005)database and clusterProfiler software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Mus_musculus.GRCm38_release95.genome.fa
Supplementary files format and content: Processed data.xlsx

source_name: Intestine

extract_protocol:
Total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer. The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Intestine

value: no

value: Small intestinal epithelial cells

value: cell type

value: OVA treatment


title: Con-RNAi-1

description:
Library name: Sample 1
Column name in all.genes.expression.annot.xls: Con-RNAi-1


title: T47D H3K4me3, ChIP, DMSO, biol rep2

description: Library name: T47D_DMSO_H3K4me3_R2

value: Human breast cancer

value: DMSO (24 hrs)


title: HCD-5

description:
Library name: Sample 10
C20_fpkm


title: NRF2-RNAi-3

description:
Library name: Sample 6
Column name in all.genes.expression.annot.xls: NRF2-RNAi-3


title: GM-BMDM bio rep 4


title: HCD-3

description:
Library name: Sample 8
C13_fpkm


title: GM-BMDM bio rep 5


title: GM-BMDM bio rep 3


title: T47D H3K4me3, ChIP, DMSO, biol rep1

description: Library name: T47D_DMSO_H3K4me3_R1

value: H3K4me3 (Epigentek, A4033)


title: NRF2-RNAi-2

description:
Library name: Sample 5
Column name in all.genes.expression.annot.xls: NRF2-RNAi-2

value: lung


title: HCD-2

description:
Library name: Sample 7
C12_fpkm


title: GM-BMDM bio rep 2


title: T47D Input, ChIP, C48, biol rep3

description: Library name: T47D_C48_input_R3


title: HCD-1

description:
Library name: Sample 6
C11_fpkm


title: T47D cells, normoxia, total RNA, biol rep 1

data_processing:
NanoCAGE sequencing reads with each of the six barcodes were extracted using TagDust (version 2.33), and Nextera XT N-Series 3’ adapters were trimmed using Cutadapt (v1.18) (settings: -e 0.15 -01 -n 4 -m 25). PCR duplicates were defined as reads with identical UMI and sequence in the first 25 bp, and were filtered to keep only one unique read. Ribosomal RNA was removed using bbduk.sh from the BBTools software suite, with default settings. A summary of the nanoCAGE preprocessing can be seen in Fig S1A. Next, reads were aligned to the human genome hg38 using Bowtie (v1.2.2) (settings: -a -m 1 --best --strata -n 2 -l 28), and reads that uniquely aligned or failed to align were collected for a second alignment step to a custom index of 5’UTR sequences. This custom index was created by extending RefSeq 5’UTR sequences82 by 78 bases upstream using genomic sequence, and 78 bases downstream using mRNA sequences. These extensions were selected based on the criteria that the nanoCAGE read architecture allows for a maximal length of 78 after adapter trimming. Alignment to the custom index was also performed using Bowtie (settings: -a --best –strata -n 3 -l 25). Reads were trimmed by 1-2 based at the 5’ end in the event of alignment mismatches at the first or second positions, and strand invasion artefacts were removed using the perl script provided by Tang et al. (Nucleic Acids Res, 2015) (settings: -e 2).
Librairies were prepared with mutliple barcodes for each sample and pooled. The pool was sequenced on 2 lanes. Reads from individual barcodes were extracted using TagDust (Lassmann, BMC Bioinformatics, 2015) and each raw file provided here contains reads from one barcode and index after demulitplexing, with reads from both lanes merged.
Supplementary files format and content: BAM files aligned to modified RefSeq reference described above.
Supplementary files format and content: DPN files (ZZZ tab separated) in the format: RefSeq ID, counts per TSS position, TSS positions relative to the translation start site (AUG). This file format was created to easily summarize and load bam files into R, and reduce computation times.
Supplementary files format and content: Raw counts table with expression of transcription start site clusters. ClusterIDs are provided in the format: RefSeqID_startPosition_endPosition, where positions are given relative to the translation start site for a given transcript (AUG start codon).
Library strategy: nanoCAGE

treatment_protocol: For all experiments, cells were plated 24 h prior to the treatment (1.2 x 106 in 60 mm dishes or 5.8 x105 in 6-well plates). For hypoxia experiments, media was changed to fresh RPMI 10% FBS and cells were incubated in normoxia (regular incubator) or hypoxia (Biospherix OxyCycler model C42 or ProOx model C21 chambers housed in a regular incubator) at 0.5% O2 for the indicated time (24 hours for H9 cells, and 48 hours for T47Ds). For compound 48 (C48) treatments with T47D cells, media was replaced with fresh RPMI 10% FBS containing 10µM C48 or the equivalent volume of DMSO as vehicle control.

value: normoxia (20% oxygen, 48 hrs)


title: T47D Input, ChIP, C48, biol rep4

description: Library name: T47D_C48_input_R4


title: T47D Input, ChIP, C48, biol rep2

description: Library name: T47D_C48_input_R2


title: GM-BMDM bio rep 1


title: T47D cells, hypoxia, total RNA, biol rep 3

value: hypoxia (1% oxygen, 48 hrs)


title: NCD-5

description:
Library name: Sample 5
C10_fpkm

value: untreated


title: T47D cells, hypoxia, total RNA, biol rep 2


title: T47D Input, ChIP, C48, biol rep1

description: Library name: T47D_C8_input_R1


title: NCD-4

description:
Library name: Sample 4
C9_fpkm


title: T47D cells, hypoxia, total RNA, biol rep 1


title: TAZAKT_V_3

source_name: Liver

growth_protocol: To induce CCA, 5 weeks-old C57BL/6J mice by hydrodynamic tail vein injection (HTVI) of plasmids coding for mutant TAZ (TAZS89A, 10 µg/mouse), myr-AKT (10 µg/mouse) and the sleeping beauty transposase (SB, 0.8 µg/mouse).

extract_protocol:
Total RNA from fresh frozen tissues was extracted using the automated Maxwell system from Promega. 100 ng of total RNA was used for the construction of sequencing libraries.
Library preparation was be performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer's protocol.

treatment_protocol: As reported for other HTVI oncogene-induced CCA models treatments started two days after HTVI. JNJ-64619178 was administered at 10 mg/Kg p-o. daily (TAZAKT_JNJ), and vehicle group received the same volume of vehicle (TAZAKT_V). C57BL/6J mice without HTVI injection nor treatment were used as healthy controls (C).

value: Liver

value: Vehicle


title: H9 cells, normoxia, total RNA, biol rep 4

value: Human embryonic stem cell

value: normoxia (20% oxygen, 24 hrs)


title: T47D cells, normoxia, total RNA, biol rep 3


title: T47D H3K4me3, ChIP, C48, biol rep4

description: Library name: T47D_C48_H3K4me3_R4


title: TAZAKT_V_2


title: NCD-3

description:
Library name: Sample 3
C3_fpkm


title: T47D H3K4me3, ChIP, C48, biol rep3

description: Library name: T47D_C48_H3K4me3_R3


title: NCD-2

description:
Library name: Sample 2
C2_fpkm


title: TAZAKT_V_1


title: T47D H3K4me3, ChIP, C48, biol rep2

description: Library name: T47D_C48_H3K4me3_R2


title: H9 cells, normoxia, total RNA, biol rep 2


title: TAZAKT_JNJ_2


title: H9 cells, normoxia, total RNA, biol rep 3


title: TAZAKT_JNJ_3


title: H9 cells, normoxia, total RNA, biol rep 1


title: TAZAKT_JNJ_1


title: WT BMDC 2

first: Matthew

middle: Allan

last: Heard

address: 2534 Pheasant Drive

department: Surgery

institute: UC San Diego

description:
Library name: Sample 3 WT
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were all performed using Cell Ranger pipelines Cell Ranger Count v6.0.2 and Cell Ranger Aggr v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For running Cell Ranger Count, the following setting were used: chemistry = auto, include_introns = false, no_bam = false, and no_secondary_analysis = false. For running Cell Ranger Aggr, the following settings were used: no_secondary_analysis = false, normalization_mode = mapped. Each sample/library mentioned above was run through Cell Ranger Count individually.
Assembly: mm10
Supplementary files format and content: Each H5 file contains the scRNA-seq raw feature count matrix outputted from running Cell Ranger Count (v6.0.2) on the respective sample of single cells. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

source_name: Bone marrow

growth_protocol: M-CSF for 7 days

extract_protocol:
Collected from petri dish, counted, centrifuged, and resuspended for loading
Library was constructed following the manufacturer's instructions for use of the Next GEM Single Cell 3' Gene Expression kit by 10x Genomics.

value: Bone marrow

value: BMDC

value: Wildtype


title: H9 cells, hypoxia, total RNA, biol rep 4

value: hypoxia (1% oxygen, 24 hrs)


title: NCD-1

description:
Library name: Sample 1
C1_fpkm

value: Intestine

value: no

value: Small intestinal epithelial cells

value: cell type


title: C_3

value: healthy control


title: WT BMDC 1

description:
Library name: Sample 1 WT
10x Genomics


title: H_KO_Th9_1

city: Los Angeles

first: Sai

last: Xiao

address: 1500 E. Duarte Road

institute: City of Hope

data_processing:
The raw reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to the reference genome with orientation mode using STAR (version 2.7.4).
Peak calling results with IP and input libraries were generated by exomePeak2.
The m6A binding motif was analyzed by HOMER (version 4.11).
Called peaks were annotated by intersection with gene and transcript architecture using bedtools (version 2.30.0) . The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files. The DEGs were detected with R package edgeR (version v. 3.28.1)
Assembly: mm10
Supplementary files format and content: comma-delimited text files contain raw counts values
Supplementary files format and content: comma-delimited text files contain includes callpeak sites

source_name: Th9 cells

growth_protocol: WT and Ythdf2-KO Th9 cells were grown in RPMI1640 (Gibco) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Gibco).

extract_protocol:
For m6A-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen). Fragmented mRNA (5 μg mRNA) was used for m6A immunoprecipitation (m6A-IP) using an m6A antibody (Synaptic, 202003) following the standard protocol of the Magna MeRIP m6A Kit (Merck Millipore). For Ythdf2 RIP-seq, fifty million Th9 cells were harvested and washed twice with cold PBS, and the cell pellet was lysed with two volumes of lysis buffer [10 mM HEPES pH 7.6, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 Protease Inhibitor cocktail (Thermo Fisher Scientific), and 400 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)]. The lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. One-tenth volume of cell lysate was saved as input. The rest of the cell lysate was incubated with 5 μg anti-YTHDF2 (MBL, Cat No. RN123PW) that was pre-coupled with Protein A magnetic beads (Invitrogen, Cat: 10001D) at 4℃ for 2h with gentle rotation. Afterward, the beads were washed five times with 1 ml ice-cold washing buffer (50 mM HEPES pH 7.6, 200 mM NaCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, and 200 U/mL RNase inhibitor). Immunoprecipitated samples were subjected to Proteinase K digestion in wash buffer supplemented with 1% SDS and 2 mg/mL Proteinase K (Thermo Fisher Scientific) incubated with shaking at 1200 rpm at 55℃ for 1 h. Total RNA was extracted from both input and immunoprecipitated RNA by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo Research).  For bulk RNA-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen).
RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina NovaSeq 6000  machine with 100-bp paired-end reads (PE100).
m6a-seq, RIP-seq, poly-RNA-seq

value: Th9 cells


title: H9 cells, hypoxia, total RNA, biol rep 3


title: H_KO_Th9_2


title: C_2


title: H_WT_Th9_3


title: H_WT_Th9_2


title: H9 cells, hypoxia, total RNA, biol rep 1


title: H_WT_Th9_1


title: C_1


title: T47D H3K4me3, ChIP, C48, biol rep1

description: Library name: T47D_C48_H3K4me3_R1

value: Human breast cancer

value: H3K4me3 (Epigentek, A4033)


title: KO BMDC 2

description:
Library name: Sample 4 KO
10x Genomics

value: CHRNA7 KO


title: BY4741_EtOH_20hr_bio_rep3

city: Kunigami-gun

first: Yuta

last: Yamazaki

address: Tancha 1919-1

country: Japan

institute: Okinawa Institute of Science and Technology

description:
Library name: Sample39
colomn name in all_counts_BY4741.csv EtOH-20hr_rep3

data_processing:
Raw sequence data in FASTQ format generated by NovaSeq 6000 were used for further analysis. The quality of the reads was analyzed by FastQC software (v0.11.9). We removed the low-quality reads and adaptors using trimmomatic software (v0.39). The quality of the raw reads and cleaned reads were compared using FastQC software. The reads from S. cerevisiae were mapped to the reference genome (R64-1-1) using STAR software (v2.7.8). To map the reads from S. pastorianus, we generated a reference genome from previously published S. pastorianus genome information using Yeast Annotation Pipeline. Then, the reads from S. pastorianus were mapped to the annotated genome information using STAR software. Quantification of reads was performed by featureCounts software (v2.0.1).
Assembly: R64-1-1 for S. cerevisiae. BBYY00000000.1 (GeneBank) for S. pastorianus
Supplementary files format and content: Comma separated values files includes raw counts for each sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741

growth_protocol: We cultured yeasts in YPD media (1% yeast extract, 2% bacto peptone, and 2% glucose) at 25℃.

extract_protocol:
We extracted total RNA using an RNeasy mini kit (QIAGEN, Germany). We added 600 µl of RTL buffer and glass beads to the cell pellets. The cells were disrupted by shaking at 3000 rpm for 2 min with cooling using TOMMY Micro Smash MS-100R. The cell debris was removed by centrifuging at 12,000 rpm for 2 min at 4℃. 350 µl of the supernatant was mixed with an equal volume of 70 % EtOH. We transferred the mixture to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We added 350 µl of RW1 buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. To remove residual DNA, we added an RNase-Free DNase Set (QIAGEN, Germany) to the column. After 15 min digestion at room temperature, we added RW1 buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We added 500 µl of RPE buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We repeated this process twice. We collected RNA by adding 50 µl of RNase-free water to the column and centrifuging it at 10,000xg for 30 seconds at 4℃. We measured the RNA concentration by nanodrop. The quality and integrity of the RNA samples were assessed using an Agilent 2200 TapeStation (Agilent Technologies)
We prepared the library using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). For indexing, we used NEBNext Multiplex Oligos for Illumina (NEB #E6440). We followed the manufacturer's protocol to prepare the libraries.

treatment_protocol: S. cerevisiae and S. pastorianus were cultured in 100 ml YPD media overnight until OD595 reached 0.1–0.2. The cultures were separated into two aliquots and transferred to 150 ml YPD (total 200 ml x2). We incubated them until OD595 reached around 0.1. From one of the aliquots, we took 20 ml of the culture (control). We then added 6 ml of YPD and 14 ml of 99.5 % EtOH (7% EtOH). In another aliquot, we added 200 µl of 10% SDS (0.01% SDS). We collected the culture 0.5, 1, 2, 4, 8, and 20 hr after the addition of SDS or EtOH (Fig. 1B). The cells were washed twice with PBS, flash-frozen by liquid nitrogen, and stored in -80℃ until lysis. Three biological replicates were collected in all conditions.

value: Saccharomyces cerevisiae BY4741

value: Yeast cells

value: WT

value: 7% EtOH


title: CJ B6 6M CR 50W F5

city: Houston

first: EMRE

last: AKSAN

state: TX

address: 6501 Fannin St NB302

department: Ophthalmology

institute: Baylor College of Medicine

description: Library name: DP_74367

data_processing:
Quality control was performed using Rosalind platform with default trimming settings.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files with normalized gene expression counts (e.g., TPM or DESeq2-normalized counts) for all samples.

source_name: conjunctiva

extract_protocol:
Total RNA was extracted from cornea and conjunctiva tissues using RNeasy Mini Kit (Qiagen).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer’s instructions.

value: conjunctiva

value: calorie-restricted feeding


title: H_KO_Th9_3


title: intestine, Butyrate

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

institute: Peking University

description: Library name: Butyrate

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 6000 or less than 500 were removed.
Normalization of the count matrix was performed, and dataset integration was achieved using Harmony.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for UMAP. UAMP were performed by R package Seurat (version 4.0.4)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: intestine

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

value: intestine

value: 1% butyrate diet


title: BY4741_EtOH_20hr_bio_rep2

description:
Library name: Sample38
colomn name in all_counts_BY4741.csv EtOH-20hr_rep2


title: cDC2_OP9_rep2

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: cDC2 cultured in OP9

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) was used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts were obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: hg38
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes normalized counts for each sample

source_name: in vitro classical type 2 DCs (cDC2)

growth_protocol: CD34+ cells are differentiated with recombinant human cytokines as described in the associated manuscript.

extract_protocol:
RNA isolation was performed using Qiagen micro RLT kits and RNA quality was analyzed using Agilent RNA 6000 Nano kit and samples had a RIN value above 9.5.
Illumina Stranded mRNA library was prepared using 100 ng of RNA sequencing procedures are carried out using NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) and performed a 50 bp paired end sequencing with a total of 60 million read coverage using NovaSqq 6000

treatment_protocol: conventional type I (CD141+Clec9A+) and type 2 (CD1c+FCERA+) dendritic cells from the in vitro cultures were enriched by flow cytometry

value: in vitro classical type 2 DCs (cDC2)

value: OP9 feeder


title: intestine, RA

description: Library name: RA

value: standard chow


title: cDC2_OP9_rep1

description: cDC2 cultured in OP9


title: CJ B6 6M CR 50W F4

description: Library name: DP_74366


title: BY4741_EtOH_20hr_bio_rep1

description:
Library name: Sample37
colomn name in all_counts_BY4741.csv EtOH-20hr_rep1


title: KO BMDC 1

city: San Diego

description:
Library name: Sample 2 KO
10x Genomics

value: Bone marrow

value: BMDC


title: 116-H3B-1

city: Wuhan

first: Chen

last: Zeyu

state: Huibei

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: Sample 16
Column name in gene_count.csv:116-H3B-1

data_processing:
Initial quantification was performed using Qubit 2.0, diluting the library to 1.5 ng/ul, followed by detection of the insert size of the library using Agilent 2100, and after the insert size met expectations, qRT-PCR was performed to accurately quantify the effective concentration of the library (effective library concentration above 2 nM) to ensure library quality.
After passing the library inspection, the different libraries were pooled according to the effective concentration and the target amount of data to be sequenced by Illumina
The raw sequencing reads (raw reads) contain low-quality, spliced reads, so we use the default parameters of fastp for quality control to filter the unqualified reads, and the resulting clean reads are used for subsequent analysis.
Clean Reads were quickly and accurately compared with the reference genome using HISAT2 software to obtain information on the positioning of Reads on the reference genome
Assembly: GRCh38
Supplementary files format and content: csv file includes gene counts for each Sample

source_name: colorectal cancer

growth_protocol: MHCC-97H, MDA-MB-231 and HCT-116 cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
RNA is extracted from cells using Trizol
RNA is extracted from cells using standard extraction methods, followed by rigorous quality control of the RNA samples, primarily by means of an Agilent 2100 bioanalyzer: precise detection of RNA integrity

treatment_protocol: DMSO or 20 nM H3B-8800 in the presence of 10% FBS until 24hrs.

value: colorectal cancer

value: colorectal cancer cell lines

tag: time

value: day 1


title: 116-H3B-3

description:
Library name: Sample 18
Column name in gene_count.csv:116-H3B-3


title: 116-H3B-2

description:
Library name: Sample 17
Column name in gene_count.csv:116-H3B-2


title: 116-DMSO-2

description:
Library name: Sample 14
Column name in gene_count.csv:116-DMSO-2

value: DMSO


title: cDC1_OP9_rep3

description: cDC1 cultured in OP9

source_name: in vitro classical type 1 DCs (cDC1)

value: in vitro classical type 1 DCs (cDC1)


title: H9 cells, hypoxia, total RNA, biol rep 2

extract_protocol:
Total RNA was extracted from hypoxia and normoxia-treated T47D and H9 cells using TRIZOL.
The quantity and quality of total RNA from hypoxia-treated T47D and H9 cells was assessed by Qubit (Life Technologies) and Bioanalyzer (Agilent Technologies), and 75 ng of RNA was used as input material to prepare nanoCAGE libraries as described previously (Lorent et al., EMBO, 2019) (T47D n = 3, H9 n = 4). Note that the Template Switching Oligonucleotides (TSO) include 8 nt random unique molecular identifiers (UMIs) that allow for the identification of duplicate transcripts arising from PCR amplification, and one of six barcodes for increased multiplexing (ACAGAT, GTATGA, ATCGTG, GAGTGA, TATAGC, GCTGCA). Sequencing was performed at the SciLifeLab NGI (Sweden) facility using the HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 100-base pair single-end setup using HiSeq Rapid SBS Kit vs chemistry.

value: Human embryonic stem cell

value: hypoxia (1% oxygen, 24 hrs)


title: 116-DMSO-3

description:
Library name: Sample 15
Column name in gene_count.csv:116-DMSO-3

value: WT


title: CJ B6 6M CR 50W F2

description: Library name: DP_74364

value: conjunctiva


title: BY4741_EtOH_8hr_bio_rep3

description:
Library name: Sample36
colomn name in all_counts_BY4741.csv EtOH-8hr_rep3

value: Saccharomyces cerevisiae BY4741

value: Yeast cells

value: 7% EtOH


title: CJ B6 6M CR 50W F3

description: Library name: DP_74365

value: calorie-restricted feeding


title: CJ B6 6M CR 50W F1

description: Library name: DP_74363


title: 116-DMSO-1

description:
Library name: Sample 13
Column name in gene_count.csv:116-DMSO-1


title: 231-H3B-3

description:
Library name: Sample 12
Column name in gene_count.csv:231-H3B-3

source_name: breast cancer

value: breast cancer

value: breast cancer cell lines


title: cDC1_OP9_rep1

description: cDC1 cultured in OP9

value: OP9 feeder


title: BY4741_EtOH_8hr_bio_rep1

description:
Library name: Sample34
colomn name in all_counts_BY4741.csv EtOH-8hr_rep1


title: CJ B6 6M AL-50W F5

description: Library name: DP_74362

value: ad libitum feeding


title: BY4741_EtOH_4hr_bio_rep3

description:
Library name: Sample33
colomn name in all_counts_BY4741.csv EtOH-4hr_rep3