title: KO_SMARTA_rep2_ATACseq

description: ATAC-seq

data_processing:
Low quality reads and adaptor sequences were trimmed by Cutadapt (Version 4.0). Paired-end reads that passed quality control by FastQC (V 0.11.9) were mapped to the mm10 reference genome using Bowtie2 (V 2.5.0) with –x1000
Reads that aligned to the mitochondrial genome and PCR duplicates were removed with picard MarkDuplicates (V 2.18.2)
MACS2 was used with default parameter to identify narrow peaks.
Read counts for open chromatin regions in all samples were obtained using the DiffBind with DESeq2 normalization
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
The sorted cell pellets were lysed in the lysis buffer (ATAC-seq Kit, Activemotif) and purified with DNA Clean and Concentrator-5 Kit (Zymo Research).
Library amplification was performed with NEBNext Ultra II Q5 2X master mix. The ATAC-seq libraries were purified with SPRI Beads (ATAC-seq Kit), quantified with NEBNext Library Quant Kit, and sequenced on the NovaSeq 6000 sequencing system in paired end 150 bp read, with at least 50 million reads per sample.

treatment_protocol: WT or tamoxifen-inducible deletion of TRAF3 (iTraf3−/−)  SMARTA cells were transferred to recipient mice, followed by LCMV armstrong infection. On day 5 post-infection, fifty to one hundred thousand WT or iTraf3−/− SMARTA CXCR5+SLAMlo TFH cells were sorted into the RP10 medium.

value: SMARTA TFH cells

value: ERT2cre+, Traf3fl/fl

value: tamoxifen, LCMV armstrong infection

value: day 5 post-infection


title: IGF_004

status: Public on Feb 15 2025

type: RNA

city: Sacramento

first: Yongheng

last: Wang

state: CA

address: 3101 Clinical Lab Building (Research II), UC Davis Medical Center, 4625 2nd Ave.

country: USA

institute: University of California Davis

description:
raw data file: slide3.tar
CosMx 6000 human gene panel

hyb_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

scan_protocol: Sample processing and imaging followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

data_processing: Data was processed using AtoMx

label: Flurorescent probes (red, green, blue, yellow)

molecule: polyA RNA

organism: Homo sapiens

source_name: Immediate graft function allograft

treatment_protocol: Kidneys were collected from donors and transplanted to the recipients. Human kidney biopsies collected one hour post-transplantation.

tag: subject

value: Patient 4 IGF 004

tag: tissue

value: kidney

tag: condition

value: Immediate graft function allograft

tag: age

value: 59 years

tag: Sex

value: Male


title: ATAC_E15.5Neurod1KO_1

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description: Bulk cell ATAC-seq

library_source: genomic

data_processing:
For CUT&RUN data, overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Peak calling was performed on individual samples using MACS2 (v2.2.6), retaining peaks with a P value less than 10-3. Reproducibility between two biological replicates was assessed using idr (v2.0.4.2). Different irreproducible discovery rate (IDR) thresholds were applied depending on the CUT&RUN targets. For CUT&RUN targeting NGN3 in Ngn3low cells, peaks with an IDR larger than 250 were retained for downstream analysis. For CUT&RUN targeting NGN3 in Ngn3high cells and NEUROD1, the threshold was set to 400. Genome regions overlapping with the ENCODE blacklist were filtered out from the final identified peaks. Tag intensities were calculated as Tags per ten million (TP10M) values and stored in bedGraph files using Homer (v4.7.2).
For bulk-cell ATAC-seq data, Overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Prior to peak calling, reads generated from biological replicates were combined. ATAC-seq peaks were then identified using MACS2 (v2.2.6), retaining peaks with a false discovery rate (FDR) less than 0.01. Genome regions overlapping with the ENCODE blacklist were excluded from further analysis. Tag intensities were calculated as TP10M values and stored in bedGraph files using Homer (v4.7.2).
For snATAC-seq, preprocessing was conducted using cellranger-atac (v1.2.0) with default parameters against the refdata-cellranger-atac-mm10-1.2.0 genome. Cells with detected UMI counts greater than 1,000 and reads in promoter regions (RIPR) between 15% and 45% were retained for downstream analysis. The mm10 genome was segmented into discrete 5 kb intervals, serving as bins for each cell. The tag intensities for each bin were calculated based on the frequency of sequence tags and imported into the R package Signac (v1.3.0) for downstream analysis.
For smart-seq2 snRNA-seq, sequencing reads were aligned to the mm10 mouse genome assembly using TopHat (v2.1.0). Gene-level quantification of mapped reads was performed with HTSeq (v0.6.6) using the parameters “-s no -a 30”. Cells exhibiting fewer than 0.2 million mapped reads or fewer than 4,000 detected genes were excluded from further analysis. Gene expression levels were quantified using TPM (transcripts per million).
For smart-seq3 snRNA-seq, Trimmomatic (v0.39) was utilized to remove primer and adaptor sequences from the reads. Subsequently, the trimmed forward reads (Read 1) were aligned to the mm10 mouse genome using HISAT2 (v2.1.0). The resulting aligned reads were annotated to gene features using featureCounts (v2.0.0), considering both the 5' and internal fragments. Cells were filtered out if they exhibited fewer than 4,000 detected genes. Gene expression levels were quantified using TPM.
For 10x Genomics scRNA-seq, preprocessing was conducted using Cell Ranger (v3.0.1) with default parameters aligned to the refdata-cellranger-mm10-1.2.0 reference genome. The “filtered_feature_bc_matrix” output from Cell Ranger was imported into the Seurat package (version 4.1.1) for downstream analysis in R. WT and CKO or OE cells within the same sample were initially distinguished based on TP10K (transcripts per 10 thousand) values of Uty, Eif2s3y, and Ddx3y for male cells, and the TP10K value of Xist for female cells. These values were log-transformed, with cells exhibiting male-related values greater than 0.2 and female-related values equal to 0 classified as male, while cells with female-related values greater than 1 and male-related values equal to 0 classified as female. The downstream analysis, including dimensional reduction, cell clustering, and differential expression analysis, was conducted using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Sparce matrix, Bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: fetal pancreas

extract_protocol:
For Smart-seq2 scRNA-seq, single cells were manually picked from FACS-purified bulk cells using a mouth pipette. cDNA synthesis and amplification were performed following the protocol by Picelli et al. For Smart-seq3 scRNA-seq, single cells were directly sorted into 384-well plates containing lysis buffer. cDNA synthesis and amplification were carried out according to the Smart-seq3 protocol .For 10x Genomics scRNA-seq, the procedure was performed according to the manufacturer’s instructions using the Single Cell 3′ Reagent Kit v3.1. Sorted EpCAM+ pancreatic cells from wild-type (WT), conditional knockout (CKO), or overexpression (OE) embryos of different genders were pooled and processed as one sample. For NGN3-CKO samples, E14.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of two WT male litters and one CKO female litter, and replicate 2 consisted of three WT male litters and three CKO female litters. For NGN3-OE samples, E14.5 EpCAM+ pancreatic cells were pooled from four WT female litters and four OE male litters, and E17.5 EpCAM+ pancreatic cells were pooled from two WT female litters and three OE male litters. For NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of one WT male litter and one CKO female litter, and replicate 2 consisted of two WT female litters and one CKO male litter. The gender of the embryos was determined by genotyping for Y-chromosome-associated gene Sry.
For Smart-seq2 scRNA-seq, libraries were prepared with 2 ng of cDNA using the TruePrep DNA Library Prep Kit (Vazyme, TD502), and sequenced on the Illumina HiSeq 4000 system, generating 150 bp paired-end reads. For Smart-seq3 scRNA-seq, libraries were constructed using the TruePrep DNA Library Prep Kit V2 for lllumina (Vazyme, TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads. For 10x Genomics scRNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 system.
CUT&RUN was conducted following the published protocol with modifications in DNA purification and library construction steps. We used 30,000 cells per CUR&RUN assay with primary antibodies against FLAG (1:25, CST, 2368S), p300 (1;100, CST, 54062S), and NeuroD1 (1:100, Millpore, ABE991). DNA was purified using a spin column (VISTECH, DC2005) and processed for library construction with KAPA Hyper Prep Kit (KAPA biosystems, KK8502). Briefly, after end repair and adaptor ligation, the reaction was purified using VAHTS DNA Clean Beads (Vazyme, N411-03-AA) and subjected to PCR amplification with 2× KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KM2602) and Illumina universal primers. The PCR program was: 98°C for 45 seconds, followed by 19 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. The final DNA was purified using 1× VAHTS DNA Clean Beads.
CUT&RUN libraries were subjected to 150 bp paired-end sequencing or 51 bp single-end sequencing on the Illumina NovaSeq 6000 or Illumina Hiseq 2500 platform.
Bulk-cell ATAC-seq was conducted following the published protocol  with modifications in cell sorting and nuclei preparation. Specifically, 2,000 cells per ATAC-seq were directly sorted into 50 ul lysis buffer in a 200 ul tube for nuclei preparation. Libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502). PCR amplification was performed for 12 cycles under the following conditions: 72°C for 3 minutes, 98°C for 30 seconds, then 12 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 3 minutes, followed by a final extension at 72°C for 5 minutes.
The final DNA was purified using 1× VAHTS DNA Clean Beads and sequenced as 150 bp paired-end reads on the Illumina NovaSeq 6000 platform.
For snATAC-seq, the procedure was performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics). For the Ngn3-CKO samples, E14.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT male litters and two CKO female litters) were pooled and loaded as one sample. To ensure experimental success and an adequate number of nuclei, extra pancreatic cells from WT embryos were included, with a ratio of to EpCAM+ cells of 1:4. For the NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT female litters and three CKO male litters) were pooled and loaded as one sample.
Libraries were sequenced as 50-bp paired-end reads on an NovaSeq 6000 system.
snATAC-seq

value: fetal pancreas

tag: time

tag: genotype

tag: dataset


title: KO_SMARTA_rep1_ATACseq

city: Iowa City

first: Noah

middle: S

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

description: ATAC-seq

source_name: spleen

value: spleen

tag: cell type

tag: treatment


title: OPMHd4_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.7), Trimmomatic (ver. 0.39) and cutadapt (ver. 3.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.104) using STAR (ver. 2.7.10a).
The read count of gene features was performed with the featureCounts tool (ver. 2.0.1)
Assembly: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the QIAseq Stranded mRNA Lib Kit UDI (QIAGEN, 180440).

treatment_protocol: One-day-old worms were cultured for two days on mNGM plates covered with OP50 (control group) or Lactiplantibacillus sp. MH-1.

value: Whole

tag: cell line

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50 +MH-1


title: ATAC_E13.5Ngn3L_2

description: Bulk cell ATAC-seq


title: KO_SMARTA_rep3_ATACseq

description: ATAC-seq


title: OPMHd4_rep1


title: WT_SMARTA_rep3_ATACseq

description: ATAC-seq

value: ERT2cre+, Traf3+/+


title: Ngn3_E13.5Ngn3L_1

description: CUT&RUN

data_processing:
For CUT&RUN data, overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Peak calling was performed on individual samples using MACS2 (v2.2.6), retaining peaks with a P value less than 10-3. Reproducibility between two biological replicates was assessed using idr (v2.0.4.2). Different irreproducible discovery rate (IDR) thresholds were applied depending on the CUT&RUN targets. For CUT&RUN targeting NGN3 in Ngn3low cells, peaks with an IDR larger than 250 were retained for downstream analysis. For CUT&RUN targeting NGN3 in Ngn3high cells and NEUROD1, the threshold was set to 400. Genome regions overlapping with the ENCODE blacklist were filtered out from the final identified peaks. Tag intensities were calculated as Tags per ten million (TP10M) values and stored in bedGraph files using Homer (v4.7.2).
For bulk-cell ATAC-seq data, Overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Prior to peak calling, reads generated from biological replicates were combined. ATAC-seq peaks were then identified using MACS2 (v2.2.6), retaining peaks with a false discovery rate (FDR) less than 0.01. Genome regions overlapping with the ENCODE blacklist were excluded from further analysis. Tag intensities were calculated as TP10M values and stored in bedGraph files using Homer (v4.7.2).
For snATAC-seq, preprocessing was conducted using cellranger-atac (v1.2.0) with default parameters against the refdata-cellranger-atac-mm10-1.2.0 genome. Cells with detected UMI counts greater than 1,000 and reads in promoter regions (RIPR) between 15% and 45% were retained for downstream analysis. The mm10 genome was segmented into discrete 5 kb intervals, serving as bins for each cell. The tag intensities for each bin were calculated based on the frequency of sequence tags and imported into the R package Signac (v1.3.0) for downstream analysis.
For smart-seq2 snRNA-seq, sequencing reads were aligned to the mm10 mouse genome assembly using TopHat (v2.1.0). Gene-level quantification of mapped reads was performed with HTSeq (v0.6.6) using the parameters “-s no -a 30”. Cells exhibiting fewer than 0.2 million mapped reads or fewer than 4,000 detected genes were excluded from further analysis. Gene expression levels were quantified using TPM (transcripts per million).
For smart-seq3 snRNA-seq, Trimmomatic (v0.39) was utilized to remove primer and adaptor sequences from the reads. Subsequently, the trimmed forward reads (Read 1) were aligned to the mm10 mouse genome using HISAT2 (v2.1.0). The resulting aligned reads were annotated to gene features using featureCounts (v2.0.0), considering both the 5' and internal fragments. Cells were filtered out if they exhibited fewer than 4,000 detected genes. Gene expression levels were quantified using TPM.
For 10x Genomics scRNA-seq, preprocessing was conducted using Cell Ranger (v3.0.1) with default parameters aligned to the refdata-cellranger-mm10-1.2.0 reference genome. The “filtered_feature_bc_matrix” output from Cell Ranger was imported into the Seurat package (version 4.1.1) for downstream analysis in R. WT and CKO or OE cells within the same sample were initially distinguished based on TP10K (transcripts per 10 thousand) values of Uty, Eif2s3y, and Ddx3y for male cells, and the TP10K value of Xist for female cells. These values were log-transformed, with cells exhibiting male-related values greater than 0.2 and female-related values equal to 0 classified as male, while cells with female-related values greater than 1 and male-related values equal to 0 classified as female. The downstream analysis, including dimensional reduction, cell clustering, and differential expression analysis, was conducted using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Sparce matrix, Bedgraph
Library strategy: CUT&RUN


title: IGF_002

description:
raw data file: slide2.tar
CosMx 6000 human gene panel

label_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: Patient 2 IGF 002

value: 31 years


title: IGF_001

description:
raw data file: slide1.tar
CosMx 6000 human gene panel

extract_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: Patient 1 IGF 001

value: 42 years


title: ATAC_E13.5Ngn3L_1

description: Bulk cell ATAC-seq


title: ATAC_E13.5Ngn3H_2

description: Bulk cell ATAC-seq


title: IGF_003

value: Patient 3 IGF 003

value: 47 years

value: Female


title: WT_SMARTA_rep2_ATACseq

description: ATAC-seq

value: SMARTA TFH cells

value: tamoxifen, LCMV armstrong infection

value: day 5 post-infection


title: OPd4_rep2

value: feeding OP50


title: OPd4_rep1

value: Whole


title: WT_SMARTA_rep1_ATACseq

description: ATAC-seq

value: spleen


title: Human heart slice DSP cardiomyopathy

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description: Library name: DSP.heart

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using BWA MEM (version 0.7.10) with default parameters. In the reference transcriptome , all exons of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 were used for demultiplexing, reads 1 contain the cel-specific barcodes and the UMI-sequence and a polyT-stretch (see: CEL-seq.2.demultiplexing.barcodes.pdf). After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (Grun 2014,PMID: 24747814 and Muraro 2016,PMID: 27693023). For details, see the online methods and supplementary of the manuscript.
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: Read-, UMI(Barcode)-, Transcript-, count tables for mapped reads per cell as tab separated values (.tsv) for all sections. The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Every other column contains the read/UMI/transcript counts per sections.
Library strategy: Spatial Transcriptomics

source_name: heart

growth_protocol: Isolated primary tissue

extract_protocol:
mRNA extraction, barcoding, reverse transcription and in vitro transcription were performed as described (Junker et al., 2014, PMID: 25417113) using the Message Amp II kit (Ambion). See online methods and supplementary of the manuscript. After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113), but with CEL-Seq v2 reverse transcription primers; See online methods and supplementary of the manuscript.
Illumina TRU-seq libraries were constructed CEL-Seq v1 (but with CEL-Seq sample barcodes), as in (Junker et al 2014); See online methods and supplementary of the manuscript.

value: heart


title: H9 DGCR8 heterozygote HET2 clone replicate 2 (RNA-seq)

status: Public on Feb 14 2025

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

country: Spain

institute: Universitat Jaume I

data_processing:
RNA paired-end reads were aligned to GRCh38.p13 human genome assembly with STAR v2.7.6a.
Transcript counts were quantified with featureCounts v2.0.1 using NCBI Annotation Release 109 and counting only primary alignments.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes featureCounts output with counts.

growth_protocol: All cell lines were grown at 37℃ and 5% CO2 and were maintained on Matrigel (Corning) coated culture plates in mTeSR1 (STEMCELL Technology).

extract_protocol:
Total RNA from three biological replicates from H9 (WT, HET(1) and HET(2)) was extracted using miRNeasy Mini Kit (Qiagen) followed by on-column DNAse digestion.
After extraction, ≥ 200 ng of total RNA was used for rRNA removal stranded library sequencing with DNBseq PE100 by BGI Genomics

value: embryonic stem cells

value: DGCR8 heterozygote


title: H9 DGCR8 heterozygote HET1 clone replicate 2 (RNA-seq)


title: H9 DGCR8 heterozygote HET2 clone replicate 3 (RNA-seq)


title: H9 DGCR8 heterozygote HET2 clone replicate 1 (RNA-seq)


title: H9 wildtype replicate 3 (RNA-seq)

value: wildtype


title: H9 DGCR8 heterozygote HET1 clone replicate 1 (RNA-seq)


title: H9 DGCR8 heterozygote HET1 clone replicate 3 (RNA-seq)


title: H9 wildtype replicate 1 (RNA-seq)


title: H9 wildtype replicate 2 (RNA-seq)


title: Total RNA PA-1 DGCR8 heterozygote replicate 4

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Paired-end reads of 100 nts were aligned to the human genome (GRCh38.p13) using HISAT2 (version 2.1.0) with options: --no-discordant --no-mixed --no-unal.
Transcript counts for each sample were created with featureCounts (Rsubread version 2.2.6), using reverse counts and excluding reads that aligned to the genome multiple times.
Normalisation and statistical analysis was carried out with DESeq2 (version 1.32.0), using apeglm for fold change shrinkage .
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: csv file of gene feature count data (raw)

source_name: PA-1 cells

growth_protocol: PA-1 cell lines were cultured in DMEM + Glutamax supplemented with 20% FBS, 1x non-essential amino acids and 1x penicillin/streptomycin.

extract_protocol:
RNA from either wildtype or DGCR8 heterozygous PA-1 cells was extracted from a 60% confluent T75 cell flask (Gibco) with the miRNeasy Mini Kit (Qiagen), following the protocol for Purification of Total RNA, Including Small RNAs, from Animal Cells was followed, including the additional on-column DNAse digestion.
After extraction, ≥ 200 ng of total RNA was used for rRNA removal stranded library sequencing with DNBseq PE100 by BGI Genomics.

value: Cultured cell line


title: Total RNA PA-1 DGCR8 heterozygote replicate 1


title: Total RNA PA-1 DGCR8 heterozygote replicate 2


title: Total RNA PA-1 DGCR8 heterozygote replicate 3


title: Total RNA PA-1 wildtype replicate 1


title: Total RNA PA-1 wildtype replicate 3


title: Total RNA PA-1 wildtype replicate 2


title: PA-1 DGCR8 heterozygote replicate 4

data_processing:
For each sample, identical small RNA-seq reads were collapsed and only reads that were present more than once were included in further analysis. Mature miRNAs were identified and counted using miRDeep2, using the quantification function with human hairpin and mature miRNA sequences files from miRbase (version 22.1) and allowing no mismatches. Raw miRNA counts were normalized per sample by the total tRNAs detected with blastn (version 2.6.0+) using the commands -num_threads 20 -max_target_seqs 1 -max_hsps 1 1 -outfmt '6 std qseq sseq' -task blastn -word_size 6 -dust no, relative to WT sample 1.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: delimted text files: raw counts data, sample ID as column headers (mirdeep2.txt); normalised counts data, short names as column headers (PA1_tRNA_WT1_normalised_counts.csv)

extract_protocol:
RNA from either wildtype, DGCR8 heterozygous or DGCR8 knockout PA-1 cells was extracted from a 60% confluent T75 cell flask (Gibco) with the miRNeasy Mini Kit (Qiagen), following the protocol for Purification of Total RNA, Including Small RNAs, from Animal Cells was followed, including the additional on-column DNAse digestion.
After extraction, ≥ 200 ng of total RNA was used for library sequencing with DNBseq SE50 by BGI Genomics.


title: Total RNA PA-1 wildtype replicate 4


title: PA-1 DGCR8 heterozygote replicate 1


title: PA-1 DGCR8 heterozygote replicate 2


title: PA-1 DGCR8 heterozygote replicate 3


title: PA-1 wildtype replicate 4


title: PA-1 wildtype replicate 3


title: PA-1 wildtype replicate 2


title: PA-1 wildtype replicate 1


title: PA-1 DGCR8 heterozygote chromatin_associated replicate3

data_processing:
Paired-end sequencing data from chromatin-associated RNA samples were aligned to the human genome (GRCh38.p13) using HISAT2 (version 2.1.0) with the options --no-discordant --no-mixed --no-unal.  Human pre-miRNA locations were determined by aligning human precursor sequences, obtained using the mature miRNA and hairpin sequences from miRbase (version 22.1) against the same genome using Bowtie2 with options --very-sensitive --no-unal. The genomic locations of the pre-miRNAs plus 100 nts on each side were determined using bedtools getfasta -s. The read depth for each nucleotide in the alignment of chromatin-associated reads on the appropriate strand for each pre-miRNA was extracted using R.
A 10 nt gap between each pre-miRNA and its flanking regions was created by excluding 5 nts from the flanking regions and both sides of the pre-miRNA, creating leeway for potential alternative DROSHA cleaving. For each region, the average read depth of all included nucleotides was used for MPI calculation.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: comma-delimited text, mean values of upstream and downstream flank counts data; sample short_names are used as column header identifiers

extract_protocol:
The chromatin-associated RNA was subsequently DNAse treated using RQ1 DNAse (Promega) according to manufacturer’s instructions at a total volume of 100 µl. After 15 minutes of DNAse incubation at 37 °C, the solution was mixed with equal volume of Acid-Phenol:Chloroform (ThermoFisher) and vortexed until the solution turned white. After centrifuging at maximum speed in a cooled centrifuge, 100 µl of the top aqueous solution was mixed with 250 µl Ethanol and 10 µl 3M sodium acetate pH 5.2 (ThermoFisher). The mixture was then spun down at maximum speed in a cooled centrifuge prior to removing the supernatant. The RNA pellet was then washed with 70% Ethanol, spin centrifuged for 5 minutes in a cool centrifuge at maximum speed. The RNA pellet was then air dried and resuspended in H2O.
After extraction, ≥ 200 ng of total RNA was used for rRNA removal stranded library sequencing with DNBseq PE100 by BGI Genomics.

treatment_protocol: For RNA-seq of steady state chromatin-associated RNA levels of wildtype, DGCR8 heterozygous or DGCR8 knockout PA-1 cells, 8x106 cells grown under regular culturing conditions were trypsinised, resuspended and washed with PBS. Subsequently, cells were lysed for 5 minutes on ice in mild lysis buffer (500 µL: 10 mM Tris pH 7.4; 150 mM NaCl; 0.075% NP-40) prior to layering over sucrose buffer (1 mL: 10 mM Tris pH 7.4; 150 mM NaCl; 24% sucrose). The mixture was then centrifuged for 5 minutes at 3,500 g and the supernatant removed. After washing with PBS, the pellet containing the nuclei was resuspended in glycerol buffer (250 µl : 20 mM Tris pH 7.4; 75 mM NaCl; 0.5 mM EDTA; 50% Glycerol) mixed with nuclear lysis buffer (250 µl: 10 mM Tris pH 7.4, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M Urea, 1% NP-40) and vortexed for 4 seconds. The mixture was then incubated on ice for 2 minutes and spun down for 2 minutes at maximum speed in a cooled centrifuge. The supernatant was removed, and the pellet was washed and resuspended in PBS and sonicated (Bioruptor: 5 times 20 sec on/off intervals) prior to shear the chromatin and release bound RNA and proteins. Subsequrnly, 750 µl Tri-LS Reagent (Sigma) was added to 250 µl of cell suspension and RNA was extracted according to the manufacturer’s protocol and resuspended in 10 µl H2O.


title: PA-1 DGCR8 heterozygote chromatin_associated replicate2


title: PA-1 DGCR8 knockout chromatin_associated replicate3

value: DGCR8 knockout


title: PA-1 DGCR8 heterozygote chromatin_associated replicate4


title: PA-1 DGCR8 knockout chromatin_associated replicate4


title: PA-1 DGCR8 knockout chromatin_associated replicate1


title: PA-1 DGCR8 knockout chromatin_associated replicate2


title: PA-1 wildtype chromatin_associated replicate4


title: PA-1 wildtype chromatin_associated replicate3


title: PA-1 wildtype chromatin_associated replicate1


title: PA-1 DGCR8 heterozygote chromatin_associated replicate1


title: PA-1 wildtype chromatin_associated replicate2


title: NSTR5

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw-intensity data were obtained after image analysis of the fluorescent spot intensity reads. All preprocessing and normalization steps were performed in the R programming environment [www.r-project.org]. Inter-array normalization was conducted using quantile normalization in the vsn package.

label: biotin

source_name: normal stroma

label_protocol: Standard labeling protocol of Genomic Core Facility of the German Cancer Research Center (DKFZ, Heidelberg, Germany)

growth_protocol: Cells were grown as adherent culture in DMEM + 10% FCS  CO2-controlled tissue culture incubator (Nunc, Langenselbold, Germany) as previously described.

extract_protocol: Total RNA was extracted from tissue using the AllPrep Kit (Qiagen) according to manufacturer's instructions. RNA integrity was assessed by the Agilent 2100 Bioanalyzer.

tag: passage

value: dissected normal stroma

tag: abbreviation

value: NSTR


title: GF5/OB

source_name: cell culture

value: normal fibroblasts

value: NF


title: NSTR6


title: HNO281b

source_name: cancer tissue

value: dissected stroma

value: TSTR


title: HNO543


title: NSTR2


title: GF243


title: NSTR3


title: GF39/OB


title: HNO269b


title: GF2/OB


title: HNO722_CAF

value: tumor-associated fibroblasts

value: CAF


title: GF28/OB


title: HNO736_CAF


title: HNO413_CAF


title: HNO467_CAF


title: NSTR1


title: HNO443_CAF


title: GF214


title: GF224


title: HNO432_CAF


title: HNO407_CAF


title: GF3/OB


title: GF24/OB


title: HNO485y


title: NSTR4


title: GF247


title: HNO399_CAF


title: HNO210_CAF


title: HNO736_TUC

value: tumor cells

value: TUC


title: HNO741_CAF


title: meDNA_PS_rep2

city: Noda

first: So

last: Maezawa

state: Chiba

department: Applied Biological Science

institute: Tokyo University of Science

data_processing:
Data analysis was performed in the BioWardrobe Experiment Management System  (PMID: 26248465 ).  Briefly, reads were aligned to mouse genome mm10 with Bowtie (version 1.2.0, PMID: 19261174), assigned to NCBI RefSeq genes or isoforms, and coverage was displayed on a local mirror of the UCSC genome browser. MethylCap-seq peaks were identified using MACS2 (version 2.1.1.20160309, PMID: 18798982) with default parameter setting for narrow peak detection in BioWardrobe.  Pearson correlations for the genome-wide enrichment of the peaks among MethylCap-seq library replicates were analyzed using SeqMonk (Babraham Institute).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: MethylCap-seq

source_name: testis

extract_protocol:
Genome DNA was purified from germ cells using an Genomic DNA Clean & Concentrator Kit (ZynoResearch) according to the manual provided.
Genomic DNA was fragmentated by sonication and methylated DNA fragments were captured by MethylAffinity Methylated DNA Enrichment Kit (GeneCopoeia). DNA libraries were created by ChIPmentation method (PMID: 26280331).

value: testis

value: pachytene spermatocytes


title: HNO210_TUC


title: HNO388_TUC


title: HNO407_TUC


title: HNO387_CAF


title: HNO388_CAF


title: HNO404_CAF


title: HNO443_TUC


title: HNO258_TUC


title: HNO741_TUC


title: HNO432_TUC


title: HNO722_TUC


title: HNO258_CAF


title: HNO404_TUC


title: HNO413_TUC


title: HNO387_TUC


title: HNO212_CAF


title: meDNA_RS_rep2

value: round spermatids


title: meDNA_RS_rep1


title: meDNA_PS_rep1


title: meDNA_KIT-Gonia_rep2

value: KIT-positive spermatogonia


title: meDNA_KIT-Gonia_rep1


title: meDNA_THY1-Gonia_rep2

value: THY1-positive spermatogonia


title: meDNA_THY1-Gonia_rep1


title: bTMM_nega_1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: T cell receptor beta V(D)J segments

data_processing:
*library strategy: bulk TCR sequencing
Sequencing was performed on MiSeq platform in a 301+301 base paired-end mode.
Illumina RTA 1.18.54 software was used for base calling.
We merged Read1 and Read2 of each paired read using PEAR software.
Generated reads were input into the software platform for immune profiling MiXCR v3.0.11 (MiLaboratories Inc.) for T cell receptor repertoire profiling.
Assembly: MiXCR v3.0.11 human TCR refenrece sequences (Built-in V/D/J/C library: repseqio.v1.5)
Supplementary files format and content: mixcr.fullVDJ.tsv: tab-delimited text file including TCR clonotype information (for example, count and fraction)

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using SMARTer Human a/b Profiling Kit (Takara Bio Inc.).

value: T cell


title: bTMM_posi_1

description: T cell receptor beta V(D)J segments


title: HNO467_TUC


title: HNO212_TUC


title: a_mu_TMM_nega

description: T cell receptor alpha V(D)J segments

data_processing:
Sequencing was performed on MiSeq platform in a 301+301 base paired-end mode.
Illumina RTA 1.18.54 software was used for base calling.
We merged Read1 and Read2 of each paired read using PEAR software.
Generated reads were input into the software platform for immune profiling MiXCR v3.0.11 (MiLaboratories Inc.) for T cell receptor repertoire profiling.
Assembly: MiXCR v3.0.11 human TCR refenrece sequences (Built-in V/D/J/C library: repseqio.v1.5)
Supplementary files format and content: mixcr.fullVDJ.tsv: tab-delimited text file including TCR clonotype information (for example, count and fraction)
Library strategy: TCR-Seq


title: bNC_nega_1

description: T cell receptor beta V(D)J segments


title: bNC_posi_1

description: T cell receptor beta V(D)J segments


title: a_mu_NC_nega

description: T cell receptor alpha V(D)J segments


title: Brain, mutant, Tsc2KCplus 4

city: Boston

first: Kellen

last: Winden

state: MA

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

description:
Library name: Tsc2KCplus_4
tsc2_gene_count.txt

data_processing:
Reads passing quality filters were mapped using Hisat2 onto the mouse genome (both PTEN and Tsc2 samples).
For differential expression, EdgeR was used and functional annotation was performed using DAVID.
For WGCNA, the CRAN package was used and gene counts from both genes were normalized using log2 counts per million separately.
Co-expression networks were created from genes with a coefficient of variation > 0.005 using b=6, and clusters were isolated using the cutreeDynamic package.
Module overlap was determined by calculating the Pearson correlation of the kME between two modules. Expression signature was generated from Connectivity Map. Gene set enrichment analysis was performed using the GSEA platform.
Assembly: GRCm39
Supplementary files format and content: gene counts

source_name: Brain

extract_protocol:
RNA extraction was performed using TRIzol (Invitrogen) for PTEN samples and Qiagen RNAeasy kit for Tsc2 samples.
library preparation using the NEBNext Ultra II RNA Library Prep Kit by Illumina, as per manufacturer’s protocols, for PTEN samples. For Tsc2 samples, libraries were constructed with the Kapa Hyperprep library kit using polyA selection (Roche).

value: Brain


title: a_mu_NC_posi

description: T cell receptor alpha V(D)J segments


title: a_mu_TMM_posi

description: T cell receptor alpha V(D)J segments


title: Brain, control, Tsc2CCminus 3

description:
Library name: Tsc2CCminus_3
tsc2_gene_count.txt


title: HNO399_TUC


title: Brain, control, Tsc2CCminus 2

description:
Library name: Tsc2CCminus_2
tsc2_gene_count.txt


title: Brain, control, Tsc2CCminus 1

description:
Library name: Tsc2CCminus_1
tsc2_gene_count.txt


title: Brain, mutant, Tsc2KCplus 2

description:
Library name: Tsc2KCplus_2
tsc2_gene_count.txt


title: Brain, mutant, Tsc2KCplus 1

description:
Library name: Tsc2KCplus_1
tsc2_gene_count.txt


title: Brain, PTEN, HOM 6

description:
Library name: PTEN_HOM_6
pten_gene_count.txt

value: Hom


title: VU_ILD_144_less_fibrotic

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

description: Library name: 8981_2

library_source: transcriptomic single cell

data_processing:
Cellranger multiple versions. 4859_2: v3.1; 6281: 6.0.1; 7539: 6.1.2; 8981: 7.0.1; 9367: 7.0.1; 9564: 7.0.1
Assembly: 4859_2: GRCh38-3.0.0; all others GRCh38-2020-A
Supplementary files format and content: CellRanger filtered_feature_bc_matrix.h5 files

source_name: lung

extract_protocol:
Single cell suspensions were generated using collagenase/dispase digest (1 mg/ml each) using a Gentlemacs Auto-dissociator. After serial filtering, column-based sorting of CD45+ cells (Miltenyi Microbeads) was performed, and CD45+ and CD45- fractions were mixed 1:2 for scRNA-seq library preparation.
10X Genomics 5' v1

value: lung


title: VU_ILD_149

description: Library name: 9367


title: VU_ILD_109_less_fibrotic

description: Library name: 6281_2


title: VU_ILD_144_more_fibrotic

description: Library name: 8981_1


title: VU_ILD_127

description: Library name: 7359


title: VU_ILD_152

description: Library name: 9564


title: VU_ILD_89

description: Library name: 4859_2


title: Brain, PTEN, HOM 5

description:
Library name: PTEN_HOM_5
pten_gene_count.txt


title: Brain, PTEN, HOM 4

description:
Library name: PTEN_HOM_4
pten_gene_count.txt


title: Brain, control, Tsc2CCminus 4

description:
Library name: Tsc2CCminus_4
tsc2_gene_count.txt


title: VU_ILD_109_more_fibrotic

description: Library name: 6281_1


title: Brain, PTEN, HOM 2

description:
Library name: PTEN_HOM_2
pten_gene_count.txt


title: Brain, PTEN, HOM 3

description:
Library name: PTEN_HOM_3
pten_gene_count.txt


title: TE-8

city: Fukushima City

first: Shotaro

last: Nakajima

state: Fukushima

address: 1 Hikariga-oka

department: School of Medicine

institute: Fukushima Medical University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Inc.).
The read counts allocated for each gene and transcript (RefSeq Database 2018.02.25) were quantified using a Transcripts Per Million (TPM) method.
The differentially expressed genes (DEGs) were estimated to be significant if FC (Fold Change) > 1.5 or 2.
Assembly: hg38
Supplementary files format and content: An excel file includes TPM values for all samples.

source_name: cell line_TE-8

growth_protocol: EC cell lines were cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS and penicillin/streptomycin, in a 5% CO₂ atmosphere at 37°C.

extract_protocol:
Total RNA obtained from each sample was subjected to a sequencing library construction using TruSeq Stranded mRNA Library Prep Kit(Illumina, Inc.) according to the manufacturer’s protocols.
The equally pooled libraries of the samples were sequenced using NovaSeq 6000 (Illumina, Inc.) in 101-base-pair (bp) paired-end reads.

treatment_protocol: The third generation of Fn was washed three times with PBS, resuspended in RPMI without FBS and penicillin/streptomycin, added to the EC cell lines at an MOI of 1:100, and incubated in RPMI without FBS and penicillin/streptomycin for 6 hours in a 5% CO₂ atmosphere at 37°C.

value: cell line_TE-8

value: EC cells

value: WT

value: Negative control_6 hours


title: TE-1-Fn

source_name: cell line_TE-1

value: cell line_TE-1

value: Co-culturing with Fn_6 hours


title: TE-8-Fn


title: Brain, PTEN, HOM 1

description:
Library name: PTEN_HOM_1
pten_gene_count.txt


title: Brain, PTEN, HET 6

description:
Library name: PTEN_HET_6
pten_gene_count.txt

value: Het


title: TE-1


title: Brain, PTEN, HET 4

description:
Library name: PTEN_HET_4
pten_gene_count.txt


title: Brain, PTEN, HET 3

description:
Library name: PTEN_HET_3
pten_gene_count.txt


title: KYSE70-Fn

source_name: cell line_KYSE70

value: cell line_KYSE70


title: TE-4

source_name: cell line_TE-4

value: cell line_TE-4


title: TE-6-Fn

source_name: cell line_TE-6

value: cell line_TE-6


title: Brain, PTEN, WT 1

description:
Library name: PTEN_WT_1
pten_gene_count.txt


title: Brain, mutant, Tsc2KCplus 3

description:
Library name: Tsc2KCplus_3
tsc2_gene_count.txt


title: Brain, PTEN, HET 2

description:
Library name: PTEN_HET_2
pten_gene_count.txt


title: KYSE70


title: TE-4-Fn


title: Brain, PTEN, HET 1

description:
Library name: PTEN_HET_1
pten_gene_count.txt


title: resistant H526_8

city: Baltimore

first: John

middle: Christopher

last: Schmitz

state: MD

address: 655 W. Baltimore Street

institute: University of Maryland Baltimore

data_processing:
RSEM 1.3.1 Trimmomatic 0.38 DEseq2 1.30.0
adapter sequences and low-quality sequences are removed using Trimmomatic default library
processed reads were mapped to GRCh38 primary assembly using RSEM star aligner.
output counts were normalized by DEseq2  subsequencely.
Assembly: GRCh38 primary assembly
Supplementary files format and content: comma-separated values file includes deseq2 normalized counts for  each sample

growth_protocol: H526 cells were maintained in RPMI-1640 with 5% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested from resistant and parental H526 cells three separate times using Rneasy Plus Mini kit. RNA was submitted to Novogene for sequencing.
1 ug RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: H526 cells were incubated with 10 nM onvansertib in growth media. Once normal cell proliferation occurred, onvansertib concentration was increased. After one year, H526 cells were grown in 75 nM onvansertib.

value: small cell lung cancer

value: onvansertib-resistant


title: Colonic crypts, GSK503, rep1

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

data_processing:
Transcript reads were aligned to the GRCm39 mouse genome assembly using STAR (RRID:SCR_004463, v2.7.9a) [36]. Counts were calculated from the resulting bam files using rsem (RRID:SCR_000262, v1.3.1)
Assembly: GRCm39
Supplementary files format and content: tissue_count.csv: The raw RNA-seq count per million data. Column names represent the library names, and row names correspond to gene symbols.

source_name: Colonic crypts

extract_protocol:
Total RNA was extracted directly from the crypts of mice using the Direct-zol RNA MicroPrep kit (Zymo Research, Irvine, CA, Cat# R2062).
The libraries from all samples were made and sequenced at The University of Texas MD Anderson Cancer Center (UTMDACC) Advanced Technology Genomics Core (ATGC) on the Illumina Hi-seq4000 instrument generating paired-end 76 base pair (bp) reads. Illumina Stranded Total RNA Prep.

treatment_protocol: Mice were randomized to two arms: EZH2 inhibitor (GSK503) treatment and Control (Vehicle). Tail vein injections were performed twice a weekly using a restraining apparatus and tails were properly sterilized with ethanol prior to injection. GSK-503 (Selleckchem, Houston, TX), an EZH2 inhibitor, was administered at 200μg/kg body weight (50μl injection volume) prepared in sterile PBS. Control animals were administered sterile 20% captisol (Selleckchem, Houston, TX) in PBS.

value: Colonic crypts


title: Colonic crypts, Control, rep2

institute: The University of Texas MD Anderson Cancer Center

value: Control


title: parental H526_2

value: parental


title: Colonic crypts, Control, rep1


title: Brain, PTEN, HET 5

description:
Library name: PTEN_HET_5
pten_gene_count.txt

value: Brain


title: parental H526_3


title: Brain, PTEN, WT 2

description:
Library name: PTEN_WT_2
pten_gene_count.txt


title: VCMsh2THu organoid lines (normal), GSK, rep2

data_processing:
Transcript reads were aligned to the GRCm39 mouse genome assembly using STAR (RRID:SCR_004463, v2.7.9a) [36]. Counts were calculated from the resulting bam files using rsem (RRID:SCR_000262, v1.3.1)
Assembly: GRCm39
Supplementary files format and content: organoid_count.csv: The RNA-seq count per million data. Column names represent the library names, and row names correspond to gene symbols.

source_name: normal

growth_protocol: Freshly isolated colons from VCMsh2THu mice were used for organoid preparation. The colon was flushed with PBS to wash feces and undigested food and incised longitudinally. Tissue samples were cut into 2-5 cm pieces, washed with PBS three times to remove remaining contaminants, such as hair and feces, followed by incubation in 2 mM PBS/EDTA on ice for 5 min. Tissue pieces were subsequently incubated in 2 mM PBS/EDTA on a rotating platform at 4⁰C for one hour. Vigorous shaking yielded free crypts and this process was repeated with 5 mM PBS/EDTA for 30 min. Isolated crypts were pelleted at 600x g for 5 min and resuspended in Matrigel (Corning, Corning, NY, Cat# 356234) and dispensed as 50 µL domes into 4 cm petri dishes. After Matrigel polymerization, the embedded cells were overlaid with 4 mL of CMGF++ media per petri dish, as described: Advanced DMEM/F12 supplemented with penicillin/streptomycin (Thermo Fisher Scientific, Cat# 15140122), 10 mM HEPES, 2 mM GlutaMAX, 1 × B27 (Invitrogen), 1 × N2 Supplement (Invitrogen, Cat# 17502048), 100 μg/mL Primocin (Invivogen, Cat# ant-pm-05), 10 mM Prostaglandin E2 (PGE2) (Selleckchem, Houston, TX), 10 mM Nicotinamide (Sigma, St. Louis, MO), 10 nM gastrin I (Sigma), and 1 mM N-acetylcysteine (Wako, San Francisco, CA), 50 ng/ml mouse recombinant EGF (Life Technologies, Carlsbad, CA), 100 ng/ml mouse recombinant Noggin (Peprotech, Cranbury, NJ, Cat# 120-10C), 0.1% 250 μg/mL Amphotericin B (Gibco, Carlsbad, CA, Cat# 15290018), Noggin/R-Spondin/Wnt-3A conditioned medium (in-house cell line), 500 nM A83-01 (Tocris, Minneapolis, MN, Cat# 2939), and 10 μM SB202190 (Sigma, Cat#S7067). A 10 μM Rock inhibitor, Y-27632 (Sigma, Cat# Y0503), was added to the culture medium upon initial passage and freezing. Organoids were cultured with fresh media every 2-3 days in an incubator at 37°C in 5% CO2 and passaged every 7-10 days.

extract_protocol:
Total RNA was extracted directly from the pelleted organoids using the Direct-zol RNA MicroPrep kit (Zymo Research, Irvine, CA, Cat# R2062).
The libraries from all samples were made and sequenced at The University of Texas MD Anderson Cancer Center (UTMDACC) Advanced Technology Genomics Core (ATGC) on the Illumina Hi-seq4000 instrument generating paired-end 76 base pair (bp) reads

treatment_protocol: Organoid lines were treated with 5 μM GSK503. Untreated organoids with DMSO served as controls. Media was changed after 48 hours to replenish GSK503.

value: normal

value: VCMsh2THu organoid lines


title: Colonic crypts, GSK503, rep3


title: TE-6

value: EC cells


title: TE-5

source_name: cell line_TE-5

value: cell line_TE-5

value: WT


title: VCMsh2THu organoid lines (normal), GSK, rep1


title: TE-5-Fn


title: resistant H526_9


title: mouse_MEF_W3_R1

city: ChangChun

first: Mingming

last: Liang

address: xi an Road 5333

institute: Jilin university

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered reads were mapped to hg19 genome using STAR 2.7.0 with  parameters  --bamRemoveDuplicatesType UniqueIdentical
The reads on exon of each genes were counted using Htseq-count 0.12.4 with parameters -s no -t exon -i gene_id -m union
Normalization and differential analysis of gene counts were performed by the DESeq2 package in R
Assembly: GRCm38（mm10）
Supplementary files format and content: XLS files include DESeq2-normalied counts for every gene and every sample
Supplementary files format and content: CPM-normalized bigWig files for each sample were generated using bamCoverage functions in deeptools 3.5.0

source_name: Tail

extract_protocol:
Total RNA was isolated using QIAzol reagent (Qiagen) and quantitated using a Bioan-alyzer 2100 (Agilent).  1 ug of total RNA was used to prepare seqencing library
VAHTS mRNA-seq V3 Library Prep Kit for Illumina  (Vazyme) was used to prepare the seqencing libraries.

value: Tail

value: primary MEF cell line


title: VCMsh2THu organoid lines (normal), Control, rep3


title: VCMsh2THu organoid lines (normal), Control, rep1


title: Colonic crypts, GSK503, rep2


title: Colonic crypts, Control, rep3


title: 12_629

city: Bethesda

first: Stefan

last: Ambs

address: Building 37, Room 3050B

department: CCR

institute: NCI

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR. The average mapping rate of all samples is 94%. Unique alignment is above 74%.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count data for each Sample

source_name: frozen breast tissue

extract_protocol:
RNA isolation was done using TRIzol method . Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina NovaSeq 6000 machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: frozen breast tissue

tag: disease

value: tumor

tag: accession


title: resistant H526_7


title: parental H526_1


title: VCMsh2THu organoid lines (normal), GSK, rep3


title: 16_635


title: 8_625


title: VCMsh2THu organoid lines (normal), Control, rep2


title: VCMsh2THu organoid lines (polyp), GSK, rep2

source_name: polyp

value: polyp


title: mouse_MEF_B3_R1


title: 4_621


title: VCMsh2THu organoid lines (polyp), GSK, rep1


title: mouse_MEF_W2_R1


title: VCMsh2THu organoid lines (polyp), Control, rep2


title: VCMsh2THu organoid lines (polyp), GSK, rep3


title: VCMsh2THu organoid lines (polyp), Control, rep1


title: E. coli, 48 hr, Octanoic acid, Rep 3

city: Gaithersburg

first: Molly

last: Wintenberg

address: 100 Bureau Dr

department: Biosystems and Biomaterials Division

institute: National Institute of Standards and Technology

description: Library name: Ec-45-OA-48-3

data_processing:
Data processing was performed on an AWS EC2 instance and locally with Rstudio
TrimGalore (v0.6.7) with Cutadapt (v3.5) and fastQC (v0.11.9) was used to remove adapter sequences and low-quality reads from each raw read file.
HISAT2 (v2.2.1) was used to align paired-end reads to E. coli MG1655 reference genome (GenBank accession GCA_000005845.2)
Samtools (v1.13) was used for file conversion of SAM files to sorted BAM files before transcript assembly with Stringtie (v2.2.1)
In RStudio running R version 4.2.2, tximport (v1.26.1) prepared count tables from Stringtie transcript-level estimates. DESeq2 (v1.38.3) was used to perform differential gene expression analysis.
Assembly: GCA_000005845.2
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: E. coli MG1655 was cultivated in 50 mL of M9 minimal medium supplemented with glucose at 37 °C and shaking at 250 rpm for 48 hours in biological triplicate. Treated samples contained a final concentration of 100 µMol/L PFOA, PFDoDA, dodecanoic acid, or octanoic acid added into the growth medium prior to inoculation. Untreated control samples contained an equimolar final volume fraction of DMSO (0.1%) as treated samples. Cell pellets were collected for RNA extraction and sequencing at 6 hr, 24 hr, and 48 hr.

extract_protocol:
Total RNA was harvested using Qiagen RNeasy mini kit following the manufacturer’s  instructions. An on column DNase I (Qiagen) digestion was performed using the manufacturer’s instructions.
cDNA libraries were prepared by Azenta life sciences using Illumina TruSeq Stranded mRNA kit

treatment_protocol: E. coli cultures were maintained for 48 hours with one of the following added into the growth medium at 100 uM: PFOA, PFDoDA, dodecanoic acid, or octanoic acid. Control samples contained an equimolar final volume fraction of DMSO (0.1%), but no additional chemical addition.

tag: strain

value: WT K12

value: Octanoic acid


title: E. coli, 48 hr, Octanoic acid, Rep 2

description: Library name: Ec-44-OA-48-2


title: Ethanol 4h replicate 2

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

data_processing:
Reads were aligned to all Ensembl yeast transcripts using Bowtie 2.2.5 with default parameters and counts defined as alignments with an edit distance smaller than 5.
Assembly: Ensembl gene transcripts for Scer3 (retrieved February 2016).
Supplementary files format and content: Tab-separated vector with raw read counts per gene

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Cells were grown in synthetic complete (SC) medium with 2.0 g/L amino acid mix (Sunrise Science) supplemented with 6.7 g/L yeast nitrogen base (Sigma-Aldrich) and 2% w/v glucose.

extract_protocol:
Cells were disrupted using glass beads, and their aqueous content was extracted using phenol/chloroform. Nucleic acids were then precipitated using ethanol and genomic DNA was removed using DNase treatment (Qiagen).
RNA was quantified using Qubit (Thermo Scientific) and assessed for quality with a 2100 Bioanalyzer (Agilent Technologies). Poly-A selected transcriptome libraries were generated using the Kapa RNA HyperPrep (Roche).

treatment_protocol: Cells were induced for 1 h with either 5 nM of beta-estradiol (in ethanol solvent) or with ethanol as a negative control.

value: yeast cell

value: Ethanol


title: 11_628


title: mouse_liver_W3.raw_1

source_name: Liver

value: Liver


title: E. coli, 24 hr, Octanoic acid, Rep 3

description: Library name: Ec-42-OA-24-3


title: mouse_MEF_B1_R1


title: E. coli, 48 hr, Octanoic acid, Rep 1

description: Library name: Ec-43-OA-48-1


title: 9_626


title: 10_627


title: E. coli, 24 hr, Octanoic acid, Rep 2

description: Library name: Ec-41-OA-24-2


title: 3_620


title: 7_624


title: mouse_liver_W2.raw_1


title: E. coli, 6 hr, Octanoic acid, Rep 3

description: Library name: Ec-39-OA-6-3


title: mouse_MEF_W1_R1


title: E. coli, 6 hr, Octanoic acid, Rep 2

description: Library name: Ec-38-OA-6-2


title: E. coli, 24 hr, Octanoic acid, Rep 1

description: Library name: Ec-40-OA-24-1


title: mouse_MEF_B2_R1


title: Ex.27, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA61485

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 or X platform in a 28+90, 28+91 or 151+151 base paired-end mode.
Illumina RTA3 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0, -7.0.0 or -7.1.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2020-A and vdj_GRCh38_alts_ensembl-4.0.0 or -7.0.0
Supplementary files format and content: CellRanger output file: filtered_feature_bc_matrix.h5 (mRNA and HTO)
Supplementary files format and content: CellRanger output file: filtered_contig_annotations.csv (TCR)
Library strategy: scRNA/TCR sequencing

molecule: protein

source_name: PBMC

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

treatment_protocol: stim protocol: PBMCs were labeled with CellTrace Violet (CTV) and cultured in the presence of Mtb crude lipid or synthetic GMM or heat-killed Mtb H37Rv for 10 days. Recombinant human IL-2, human IL-7 and human IL-15 were added at day 2, day 5 and day 8. After staining with anti-human CD3 antibody and TotalSeq-C antibodies (see HTO_ information.xlsx), CTVlow and CD3+ cells were sorted by Cell Sorter and used for single-cell TCR-RNA-seq analyses. TMM-stim protocol: PBMCs were labeled with CellTrace Violet (CTV) and cultured in the presence of purified TMM for 10 days. After staining with anti-human CD3 antibody and TotalSeq-C antibodies (see HTO_ information.xlsx), CTVlow and CD3+ cells were sorted by Cell Sorter and used for single-cell TCR-RNA-seq analyses. unstim tetramer-staining protocol: The fresh or thawed PBMCs were stained with human CD1b-TMM-tetramer and incubated for 15 min at room temperature in the dark. Without washing, anti-human CD3 antibody and TotalSeq-C Hashtags (see HTO_ information.xlsx) were added and incubated on ice for 20 min. After washing and filtrating, PI was added. TMM-tetramer+ cells within CD3+ gated population were sorted by Cell Sorter and used for single-cell TCR-RNA-seq analyses.

value: PBMC

value: T cell

value: Mixed sample (HD-1, HD-2, HD-3, HD-4, HD-5, HD-6, HD-7)


title: E. coli, 6 hr, Octanoic acid, Rep 1

description: Library name: Ec-37-OA-6-1


title: Ex.27, TCR-derived cDNA

description:
TCR V(D)J segments
GA61484


title: mouse_liver_B3.raw_1


title: E. coli, 48 hr, Dodecanoic acid, Rep 2

description: Library name: Ec-35-DD-48-2

value: Dodecanoic acid


title: E. coli, 48 hr, Dodecanoic acid, Rep 3

description: Library name: Ec-36-DD-48-3


title: E. coli, 48 hr, Dodecanoic acid, Rep 1

description: Library name: Ec-34-DD-48-1


title: E. coli, 24 hr, Dodecanoic acid, Rep 2

description: Library name: Ec-32-DD-24-2


title: Ex.27, mRNA-derived cDNA

description:
poly A RNA
GA61483


title: E. coli, 24 hr, Dodecanoic acid, Rep 3

description: Library name: Ec-33-DD-24-3


title: Ex.22_PBMC, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA58555

value: Mixed sample (Active-1, Active-2, Active-3, Worker-1, Worker-2, Worker-3)


title: mouse_liver_B1.raw_1


title: E. coli, 24 hr, Dodecanoic acid, Rep 1

description: Library name: Ec-31-DD-24-1


title: E. coli, 6 hr, Dodecanoic acid, Rep 3

description: Library name: Ec-30-DD-6-3


title: mouse_brain_W3_L1_1

value: Brain


title: E. coli, 6 hr, Dodecanoic acid, Rep 2

description: Library name: Ec-29-DD-6-2


title: mouse_brain_W2_L1_1


title: E. coli, 6 hr, Dodecanoic acid, Rep 1

description: Library name: Ec-28-DD-6-1


title: E. coli, 48 hr, PFDoDA, Rep 3

description: Library name: Ec-27-PD-48-3

value: PFDoDA


title: Ex.22_PBMC, mRNA-derived cDNA

description:
poly A RNA
GA58551


title: mouse_liver_W1.raw_1


title: E. coli, 48 hr, PFDoDA, Rep 2

description: Library name: Ec-26-PD-48-2


title: Ex.22_PBMC, TCR-derived cDNA

description:
TCR V(D)J segments
GA58553


title: E. coli, 48 hr, PFDoDA, Rep 1

description: Library name: Ec-25-PD-48-1


title: Ex.22_day0, TCR-derived cDNA

description:
TCR V(D)J segments
GA58552


title: mouse_brain_B2_L1_1


title: Ex.22_day0, mRNA-derived cDNA

description:
poly A RNA
GA58550


title: E. coli, 24 hr, PFDoDA, Rep 1

description: Library name: Ec-22-PD-24-1


title: E. coli, 6 hr, PFDoDA, Rep 3

description: Library name: Ec-21-PD-6-3


title: mouse_brain_W1_L1_1


title: Ex.22_day0, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA58554


title: mouse_brain_B1_L1_1


title: E. coli, 24 hr, PFDoDA, Rep 2

description: Library name: Ec-23-PD-24-2


title: Ex.18_day1, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA53604

value: Mixed sample (HD-1, HD-2, HD-3)


title: E. coli, 6 hr, PFDoDA, Rep 2

description: Library name: Ec-20-PD-6-2


title: BMDM cells, MetSA, WT3

city: St Louis

first: Maxim

middle: N.

last: Artyomov

state: Missouri

address: 660 S Euclid Ave

department: Pathology & Immunology

institute: Washington University in St Louis

data_processing:
Paired-end sequencing (PE150) using the Illumina NovaSeq X Plus to generate high-quality sequencing data was conducted
Reads were aligned to the mouse mm10 genome using STAR (PMID: 23104886)
Aligned reads were quantified using featureCounts program (PMID:  24227677)
Assembly: mm10 (10x 2020-A, GENCODE vM23, Ensembl98)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow-derived macrophages

growth_protocol: BMDMs were seeded in 12-well plates 1E6 cells/well in 1 ml. Cells were cultured fro 2 h in 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated using RNAeasy PLUS mini kit (QIAGEN) according to the manufacturer’s instructions.
Total RNA was submitted to Haplox international for library construction and RNA sequencing. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA molecules were fragmented into small pieces using a fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. cDNA fragments were amplified with adapters from the previous step. PCR products were purified with AMPure XP Beads (AGENCOURT) and dissolved in EB solution. The library was validated on the Agilent Agilent 4200 Tapestation.

treatment_protocol: Metabolites were added AS 50 mM stock in RPMI to final concentration 5 mM.

value: Bone marrow-derived macrophages

value: WT

value: MetSA


title: E. coli, 48 hr, PFOA, Rep 2

description: Library name: Ec-17-PFOA-48-2

value: PFOA


title: Ex.18_day1, TCR-derived cDNA

description:
TCR V(D)J segments
GA53602


title: E. coli, 48 hr, PFOA, Rep 3

description: Library name: Ec-18-PFOA-48-3

value: WT K12


title: BMDM cells, MA, WT3

value: MA


title: Ex.18_day1, mRNA-derived cDNA

description:
poly A RNA
GA53601


title: BMDM cells, IA, WT3

value: IA


title: E. coli, 48 hr, Untreated control, Rep 3

description: Library name: Ec-15-Con-48-3

value: Untreated control


title: E. coli, 48 hr, Untreated control, Rep 2

description: Library name: Ec-14-Con-48-2


title: E. coli, 48 hr, Untreated control, Rep 1

description: Library name: Ec-13-Con-48-1


title: E. coli, 24 hr, PFDoDA, Rep 3

description: Library name: Ec-24-PD-24-3


title: BMDM cells, M, WT3

value: M


title: mouse_brain_B3_L1_1

source_name: Brain


title: Ex.17, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA52454

value: PBMC

value: Mixed sample (day10_HD1_NC, day10_HD1_TMM, day10_HD2_NC, day10_HD2_TMM, day10_Latent_NC, day10_Latent_TMM, day8_HD2_NC, day8_HD2_TMM, day8_HD3_NC, day8_HD3_TMM, day8_HD4_NC, day8_HD4_TMM)


title: E. coli, 24 hr, PFOA, Rep 3

description: Library name: Ec-12-PFOA-24-3


title: Ex.17, TCR-derived cDNA

description:
TCR V(D)J segments
GA52452

value: T cell


title: BMDM cells, MetSA, WT2


title: E. coli, 24 hr, PFOA, Rep 1

description: Library name: Ec-10-PFOA-24-1


title: Ex.17, mRNA-derived cDNA

description:
poly A RNA
GA52451


title: E. coli, 24 hr, PFOA, Rep 2

description: Library name: Ec-11-PFOA-24-2


title: E. coli, 24 hr, Untreated control, Rep 3

description: Library name: Ec-9-Con-24-3


title: BMDM cells, MA, WT2


title: E. coli, 24 hr, Untreated control, Rep 2

description: Library name: Ec-8-Con-24-2


title: E. coli, 24 hr, Untreated control, Rep 1

description: Library name: Ec-7-Con-24-1


title: E. coli, 6 hr, PFDoDA, Rep 1

description: Library name: Ec-19-PD-6-1


title: E. coli, 6 hr, PFOA, Rep 3

description: Library name: Ec-6-PFOA-6-3


title: BMDM cells, IA, WT2


title: Ex.14_2, TCR-derived cDNA

description:
TCR V(D)J segments
GA46624

value: Mixed sample (CD14neg_NC, CD14neg_crude, CD3pos_NC, CD3pos_crude, CD3pos_crude_CTVhi, CD3pos_crude_CTVlow)


title: E. coli, 48 hr, PFOA, Rep 1

description: Library name: Ec-16-PFOA-48-1


title: E. coli, 6 hr, PFOA, Rep 1

description: Library name: Ec-4-PFOA-6-1


title: BMDM cells, MetSA, WT1


title: E. coli, 6 hr, Untreated control, Rep 2

description: Library name: Ec-2-Con-6-2


title: E. coli, 6 hr, Untreated control, Rep 3

description: Library name: Ec-3-Con-6-3


title: Ex.14_1, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA46627


title: E. coli, 6 hr, Untreated control, Rep 1

description: Library name: Ec-1-Con-6-1


title: BMDM cells, MA, WT1


title: Ex.14_1, TCR-derived cDNA

description:
TCR V(D)J segments
GA46623


title: BMDM cells, IA, WT1


title: Ethanol 1h replicate 2

value: yeast cell

value: Ethanol


title: Estradiol 4h replicate 2

value: Estradiol


title: Ex.14_1, mRNA-derived cDNA

description:
poly A RNA
GA46621


title: Ex.14_2, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA46628


title: Estradiol 2h replicate 2


title: HD_Ex.8, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA39750

value: Mixed sample (HD_NC, HD_crude, HD_GlcMM, HD_GroMM, HD_Rv)


title: Untreated control replicate 2


title: Estradiol 1h replicate 2


title: MEF

city: Davis

first: Anna

middle: Carolina

last: Denicol

address: 450 BIOLETTI WAY, MEYER HALL

department: Animal Science

institute: University of California Davis

description:
Library name: Sample 5
S4 PE150

data_processing:
Trimmomatic was used to trim adaptors with the following settings: SLIDINGWINDOW:4:15 MINLEAN: 36 LEADING:3 TRAILING:3.
Assembly: Alignment was performed using star/2.7.10a (default settings) and Bos taurus reference genome UCD2.0 NCBI.
Supplementary files format and content: Raw counts table was prepared using FeatureCounts (subread/1.6.2), using -p -O -g gene_id arguments. Raw data was processed removing low counts and normalization with edgeR, TMM function.

source_name: Embryonic fibroblasts

growth_protocol: Bovine ESCs were derived from early (eBL) or full (BL) blastocyst-staged embryos and maintained in NBFR medium on mouse embryonic fibroblast feeders (Samples 1-4) or feeder-free on vitronectin-N (Samples 6-9). MEF (Sample 5) were grown according to manufacturer protocols (Gibco, A34180).

extract_protocol:
RNA was isolated using the Purelink Mini Kit (12183018A, Invitrogen) with DNAse treatment (12185010, Invitrogen).
Library preparation was performed using 1000 ng input with the KAPA mRNA Hyper Prep kit (Batch 1) or NEBNext Ultra II kit (Batch 2).

value: Embryonic fibroblasts

value: MEF

value: CF1, irradiated

tag: batch


title: Ethanol 4h replicate 1


title: HD_Ex.8, TCR-derived cDNA

description:
TCR V(D)J segments
GA39746


title: BMDM cells, M, WT1

value: Bone marrow-derived macrophages

value: WT


title: Ethanol 2h replicate 1


title: BMDM cells, M, WT2


title: 3135-HL-27

city: Ann Arbor

first: Yaozhong

last: Liu

state: MICHIGAN

address: 2800 Plymouth Road

department: Internal Medicine

institute: University of Michigan

description:
Library name: No aneurysm_3
3135-HL-27

data_processing:
The reads were trimmed using Cutadapt v2.3. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin). FastQC (Andrews, 2010) (v0.11.8) was run on .bam files in a post-alignment step, including both aligned and un-aligned reads, to ensure data quality.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: suprarenal abdominal aorta

extract_protocol:
Total RNA was extracted from tissues using RNeasy Micro Kit (74004, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, cDNA libraries were prepared using the Illumina NEBNext Ultra RNA Library Prep Kit and sequencing was performed on the NovaSeq 6000 platform to generate 151-base pair paired-end reads. An average of 43 million paired-reads were generated per sample.

treatment_protocol: 8-week-old male mice were fed on a western diet for 2 weeks, and Ang II was infused subcutaneously via mini-pump for another 2 weeks to induce AAA formation

value: suprarenal abdominal aorta

tag: group

value: No aneurysm

value: Ldlr KO

value: AngII


title: Ethanol 1h replicate 1


title: Ex.14_2, mRNA-derived cDNA

description:
poly A RNA
GA46622

tag: tissue

value: PBMC


title: HD_Ex.8, mRNA-derived cDNA

description:
poly A RNA
GA39744


title: Estradiol 4h replicate 1


title: E. coli, 6 hr, PFOA, Rep 2

description: Library name: Ec-5-PFOA-6-2

value: WT K12

value: PFOA


title: 3135-HL-26

description:
Library name: No aneurysm_2
3135-HL-26

growth_protocol: 8-week-old male mice were fed on a western diet


title: Estradiol 2h replicate 1


title: Estradiol 1h replicate 1


title: Ethanol 2h replicate 2


title: 3135-HL-25

description:
Library name: No aneurysm_1
3135-HL-25


title: Active_Ex.8, TCR-derived cDNA

description:
TCR V(D)J segments
GA39745

value: T cell

value: Mixed sample (Active_NC, Active_crude, Active_GlcMM, Active_GroMM, Active_Rv)


title: Untreated control replicate 1

value: yeast cell


title: 3135-HL-22

description:
Library name: Dissection_3
3135-HL-22

value: Dissection


title: RNA-seq of Mpneumo strain, rep1

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

data_processing:
Bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: 10.5281/zenodo.7198985
Supplementary files format and content: Bigwig files for forward-strand, reverse-strand and unstranded coverage are provided.

extract_protocol:
RNA was extracted using MN Nucleospin RNA kit and following manufacturer instructions.
Directional mRNA library (rRNA removal) was prepared by the Biomics platform of Institut Pasteur, Paris and Paired-end sequencing (PE150) was performed by Novogene.

tag: background

tag: Stage

value: Asy

tag: hash


title: RNA-seq of Mpneumo strain, rep2

value: INOTQD


title: RNA-seq of Mmyco strain, rep3


title: 3135-HL-21

description:
Library name: Dissection_2
3135-HL-21


title: RNA-seq of Mmyco strain, rep2


title: RNA-seq of Mmyco strain, rep1


title: Ex.4_2, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA38054

value: Mixed sample (crude lipid-1, crude lipid-2, NC)


title: Ex.4_2, TCR-derived cDNA

description:
TCR V(D)J segments
GA38048


title: 3135-HL-20

description:
Library name: Dissection_1
3135-HL-20


title: Ex.4_2, mRNA-derived cDNA

description:
poly A RNA
GA38046


title: MNase-seq of Mpneumo strain, rep1

data_processing:
Bowtie2 was used to align paired-end MNase-seq data on the appropriate genome reference. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools and fragments smaller than 130 or longer than 200 bp were manually removed.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: 10.5281/zenodo.7198985
Supplementary files format and content: Bigwig files for Mnase-seq coverage (fragments ranging from 130 to 200bp) are provided.

growth_protocol: Five 1.5ml Tubes were prepared with 1.5 x 10^8 asynchronous yeast cells: cells were centrifuged, pelleted, washed in 1x PBS and frozen at -80C.

extract_protocol:
Cell pellets were thawed on ice and resuspended in 1mL 1xPBS supplemented with 27ul 37% formaldehyde. Cells were fixed for 20min at room temperature on rotation. 200ul of 2.5M Glycine was added for a further 5 min incubation. Cells were centrifuged at 2500g, 4C for 5 min. Pellets were gently washed with cold 1xPBS before resuspension in 500ul of lysis solution (Sorbitol 1M, EDTA 10mM, Zymo100T 250ug) and incubation at 37C with gently shaking for 30min/45min or until complete spheroplasting.
Cells were gently washed with cold 1xPBS and resuspended in 50ul 1X Nuclease Digest buffer plus an increasing amount of Mnase (NEB, M0247S) enzyme starting with 0.2ul. Digestion was performed at 22C in a shaker set at 1250rpm for 15min. 5ul of 0.5M EGTA and 3ul of 20% SDS were added for incubation at 22C in a shaker set at 1250rpm for 5 min. 65ul of TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) was added and samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified using Zymo Research DNA Clean and Concentrator™-5 Kit. Mnase digestion was verified on a Bioanalyzer System using HS DNA kit. DNA was purified using 1.2x volume of AmpureXP beads and librairies prepared with Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.


title: 3135-HL-17

description:
Library name: Dilation_2
3135-HL-17

value: Dilation


title: MNase-seq of Mpneumo strain, rep2


title: MNase-seq of Mmyco strain, rep1

value: ZXAMER


title: Ex.4_1, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA38053


title: 3135-HL-19

description:
Library name: Dilation_3
3135-HL-19


title: Active_Ex.8, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA39749


title: Hi-C of XVIfMmycot2 strain (G1)

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: 10.5281/zenodo.7198985
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.


title: MNase-seq of Mmyco strain, rep2


title: 3135-HL-15

description:
Library name: Dilation_1
3135-HL-15


title: Ex.4_1, TCR-derived cDNA

description:
TCR V(D)J segments
GA38047


title: 3135-HL-14

description:
Library name: Saline_3
3135-HL-14

value: Saline


title: RNA-seq of Mpneumo strain, rep3


title: Hi-C of XVIfMmycot1 strain (G1)


title: Hi-C of XVIfMmycot2 strain (G2/M)


title: Ex.4_1, mRNA-derived cDNA

description:
poly A RNA
GA38045


title: Hi-C of XVIfMmycot1 strain (G2/M)

value: DNJEQF


title: Hi-C of XVIfMmyco strain (G1)

value: XVIfMmyco

value: CTGJED


title: Ex.1,  HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA33907

value: Mixed sample (crude lipid, GMM537, GMM535, Rv, NC)


title: Hi-C of XVIfMmyco strain (G2/M)


title: 3135-HL-12

description:
Library name: Saline_2
3135-HL-12

value: suprarenal abdominal aorta

value: Ldlr KO


title: 3135-HL-11

description:
Library name: Saline_1
3135-HL-11


title: Active_Ex.8, mRNA-derived cDNA

description:
poly A RNA
GA39743

value: PBMC


title: Hi-C of Mpneumo strain (Wpl1 deletion, G2/M)


title: mouse_liver_B2.raw_1

value: Liver


title: Hi-C of Mpneumo strain (G2/M)


title: Ex.1, TCR-derived cDNA

description:
TCR V(D)J segments
GA33906

value: T cell


title: Hi-C of Mmyco strain (G1)


title: Hi-C of Mmyco strain (Wpl1 deletion, G2/M)


title: Ex.1, mRNA-derived cDNA

description:
poly A RNA
GA33905


title: Hi-C of Mpneumo strain (G1)


title: Hi-C of Mmyco strain (G2/M)

value: PRWGZZ


title: FACS-sorted neutrophils from mice brain tumor (SB28), sample 1

city: Tampa

first: Xiaoxian

state: FL

address: 13131 USF Magnolia Drive

institute: Moffitt Cancer Center

description:
Library name: PMN-TUMOR-S1
10X Genomics

data_processing:
The Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v7.1.0 software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Mice were injected with 10,000 SB28. After 18 days, neutrophils were sorted from tumor and blood. Blood was collected by submandibular puncture followed by cardiac puncture (right atrium). After blood collection, mice were perfused with 20 mL of PBS 1X through the left ventricle and the tumor was collected and process as previously described. Neu were then FACS sorted in MACS buffer, as previously described. After sorting, Neu were washed in RPMI containing 10% FBS and 1U/μL of Protector RNase inhibitor (Sigma, PN-3335399001). The media was filtered through 0,22 μm before the use. Cells were then counted and resuspended at a concentration of 1,000 cells/μL. 20,000 cells per lane were loaded for encapsulation.
Cells were then processed with 10X Chromium 3’ scRNA-seq, 40,000 reads/cell using NovaSeq S1-100 and NovaSeq SP-100 sequencing run

value: brain tumor

tag: mouse model

value: sb28 mice


title: FACS-sorted neutrophils from mice brain tumor (SB28), sample 2

description:
Library name: PMN-TUMOR-S2
10X Genomics


title: FACS-sorted neutrophils from blood of mice with brain tumors (SB28), sample 2

description:
Library name: PMN-BLOOD-S2
10X Genomics

source_name: blood

value: blood


title: PolII ChIP-seq of XVIfMmycot2 strain (IP)

data_processing:
For standard ChIP-seq, bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. For calibrated Scc1 ChIP-seq, bowtie2 was used in two rounds of alignments, first on C. glabrata (CBS138) and then on the appropriate S. cerevisiae genome reference, allowing the generation of IP and input (WCE) alignments that exclusively mapped on S. cerevisiae (and vice-versa for C. glabrata).
Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded. PCR duplicates were removed using samtools. When available, the input was similarly processed.
Fragment coverage was normalized by library depth (CPM) and converted into a genomic track (bigwig) using deepTools. Input-normalized fragment coverage was also generated, when possible, using bamCompare from deepTools with “--scaleFactorsMethod readCount”.
For calibrated Scc1 ChIP-seq, CPM-normalized fragment coverages were also multiplied by the ORi factor for calibration (WCEglabrata x IPcerevisiae / WCEcerevisiae x IPglabrata, in which WCEglabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads).
MACS2 2.2.7.1 was used to call peaks using the input alignment files as control.
Assembly: 10.5281/zenodo.7198985
Supplementary files format and content: Bigwig files for ChIP-seq coverage (IP, IP/Input and calibrated) are provided. Peaks are provided as .narrowPeak files.

growth_protocol: Cells of either S. cerevisiae or Candida glabrata were grown exponentially to OD600 = 0.5. 15 OD600 units of S. cerevisiae cells were mixed with 3 OD600 units of C. glabrata cells to a total volume of 45 mL for Scc1 calibration only.

extract_protocol:
Cells were fixed using 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS. The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transferred in 2mL tubes containing glass beads (ozyme, P000913-LYSK0-A.0) before mechanical cells lysis. The soluble fraction was isolated by centrifugation at 2,000 rpm for 3min then transferred to sonication tubes (Covaris milliTUBE 1ml, 520135) and samples were sonicated to produce sheared chromatin with a size range of 200-1,000bp using a Covaris sonicator. After sonication the samples were centrifuged at 13,200 rpm at 4°C for 20min and the supernatant was transferred into 700µL of ChIP lysis buffer. 80µL (27µl of each sample) of the supernatant was removed (termed ‘whole cell extract [WCE] sample’) and store at -80°C. 5ug of antibody was added to the remaining supernatant which is then incubated overnight at 4°C (wheel cold room). 50µL of protein G Dynabeads or protein A Dynabeads was then added and incubated at 4°C for 2h. Beads were washed 2 times with ChIP lysis buffer, 3 times with high salt ChIP lysis buffer (50mMHEPES-KOH, pH 8.0; 500 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate;1 mM PMSF), 2 times with ChIP wash buffer (10 mM Tris-HCl, pH 8.0; 0.25MLiCl; 0.5% NP-40; 0.5% sodium deoxycholate; 1mM EDTA;1 mMPMSF) and 1 time with TE pH7.5. The immunoprecipitated chromatin was then eluted by incubation in 120µL TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) for 15min at 65°C and the supernatant is collected termed ‘IP sample’. The WCE samples were mixed with 40µL of TES3 buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 3% SDS). ALL (IP and WCE) samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified by a phenol/Chloroform extraction.
The triplicate IP samples were mixed in 1 tube and libraries for IP and WCE samples were prepared using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.

tag: tag

value: PolII

tag: step

value: IP


title: Primary-4

city: New York

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Sequencing adapters were trimmed, and quality metrics were generated using fastp (25). Transcript abundance was quantified by mapping sequencing reads to a reference transcriptome (GENCODE v42, hg38) using Salmon (26).
Assembly: hg38
Supplementary files format and content: Transcript abundance matrices

source_name: RPM Xenograft

extract_protocol:
Total RNA from the primary and metastatic tumors was isolated using Direct-zol RNA Miniprep kit (Zymo Research). Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies). RNA concentrations were measured using the NanoDrop system (Thermo Fisher Scientific). Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine or Northwestern University
Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina), according to the manufacturer’s instructions
The normalized libraries were pooled and sequenced on Illumina Novaseq 6000 sequencer with pair-end 50 cycles.

value: RPM Xenograft

value: RUES2 RPM

tag: cell type

value: Tumor


title: Primary-1


title: PolII ChIP-seq of XVIfMmycot2 strain (input)

value: WCE


title: Calibrated Scc1-PK ChIP-seq of XVIfMmycot2 strain (input)


title: Lung


title: PolII ChIP-seq of XVIfMmycot1 strain (input)


title: Calibrated Scc1-PK ChIP-seq of XVIfMmycot2 strain (IP)


title: Liver-4


title: CD45+ cells of mice brain tumor (SB28), sample 2

description:
Library name: CD45Plus-TUMOR-S2
10X Genomics


title: PolII ChIP-seq of XVIfMmycot1 strain (IP)


title: FACS-sorted neutrophils from blood of mice with brain tumors (SB28), sample 1

description:
Library name: PMN-BLOOD-S1
10X Genomics


title: Liver-1


title: Calibrated Scc1-PK ChIP-seq of XVIfMmycot1 strain (IP)


title: CD45+ cells of mice brain tumor (SB28), sample 1

description:
Library name: CD45Plus-TUMOR-S1
10X Genomics


title: Calibrated Scc1-PK ChIP-seq of XVIfMmyco strain (input)

value: XVIfMmyco

value: PRHTXX


title: 3MBPP1_R3

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

description:
RNA-seq from OV90 cells
rnaseq_ercc_normalized_counts.txt

data_processing:
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: NOT PROVIDED

source_name: CDK7 analog sensitive OV90 cells

growth_protocol: Roughly 7 million early-passage wild-type OV90 cells were grown in MCDB 105 media 1:1 with Medium 199 and supplemented with 15% FBS and 1% Pen-strep per ATCC guidelines.

extract_protocol:
RNA-seq: Cells were then harvested by washing with cold D-PBS, scraped in D-PBS into 15mL conical tubes, and centrifuged at 1000rpm for 5min 4C. RNA was extracted with TRIzol according to the manufacturer’s instructions. DNaseI digestion was then performed with the RNeasy kit (Qiagen) using the on-column protocol (Rimel et al., 2020). RNA was eluted in 50µL RNase-free water and samples analyzed by Qubit and TapeStation. PRO-seq: As previously described in (Levandowski, C. B.; Jones, T.; Gruca, M.; Ramamoorthy, S.; Dowell, R. D.; Taatjes, D. J, 2021), after treatment the cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
RNA-seq: Samples were concentrated, 300-400ng/µL, and of high quality, RIN values >8.6. For deep mRNA sequencing to asses splicing alterations, poly(A) selection was performed with the KAPA mRNA HyperPrep Kit with 1µg of RNA containing 1:100 diluted ERCC RNA spike-in mix (Invitrogen Thermo Fisher). KAPA mRNA HyperPrep Kit, NovaSEQ6000, using a paired-end 150- bp cycle (2x150). PRO-seq: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman).

treatment_protocol: RNA-seq: Cells were then treated in T-75 flasks with one of 3 CDK7 inhibitors or the equivalent DMSO for 30min at 37C, heat-shocked for 30min at 42C, and recovered for 1hr at 37C. RNA-seq experiments with SY5609 also were completed with a no heat-shock condition or were heat-shocked continuously for 2hrs (Xu et al., 2021; Cardiello et al., 2018). PRO-seq: Cells were then treated in T-75 flasks with SY5609 or the equivalent DMSO for 30min at 37C, heat-shocked for 0min, 20min or 45min at 42C with no heat-shock recovery.

value: CDK7 analog sensitive OV90 cells

value: ovarian cancer

tag: treatment

value: 30min pretreatment with 3MBPP1 at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C

tag: time


title: FACS-sorted CD71+ neutrophils from mouse brain tumor tissue, sample1

description: Library name: CD71-PosNeu-TUMOR-1

data_processing:
The raw RNA-seq reads were assessed for quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality trimming was performed using cutadapt to remove reads with adaptor contaminants and low-quality bases. Reads pairs with either end shorter than 25bps were discarded from further analysis. The trimmed and filtered reads were then aligned to the mouse transcriptome (mm10) using STAR
Uniquely aligned reads were counted at gene level using featureCounts and then normalized using DESeq2 package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files include raw count for each sample

extract_protocol:
R1050 Quick-RNA Microprep Kit      Zymo Research
20040525  Illumina Stranded Total RNA Prep with Ribo-Zero Plus

tag: cell line

value: CD71+ neutrophils

tag: cell source

value: SB28 cell line


title: FACS-sorted CD71+ neutrophils from mouse brain tumor tissue, sample2

description: Library name: CD71-PosNeu-TUMOR-2


title: Calibrated Scc1-PK ChIP-seq of Mpneumo strain (input)

value: EHEJFT


title: Calibrated Scc1-PK ChIP-seq of Mpneumo strain (IP)


title: 3MBPP1_R2


title: 3MBPP1_R1


title: PolII ChIP-seq of Mpneumo strain (input)

value: Asy


title: FACS-sorted CD71- neutrophils from mouse brain tumor tissue, sample1

description: Library name: CD71-NegNeu-TUMOR-1

value: brain tumor

value: CD71- neutrophils


title: H3 ChIP-seq of Mpneumo strain (input), rep2

value: PCPOLZ


title: PolII ChIP-seq of Mpneumo strain (IP)

value: PolII

value: IP


title: H3 ChIP-seq of Mpneumo strain (IP), rep2


title: H2A ChIP-seq of Mpneumo strain (IP)


title: H3 ChIP-seq of Mpneumo strain (IP), rep1


title: Calibrated Scc1-PK ChIP-seq of Mmyco strain (input)

value: DTAKMF


title: DMSO_R2_mb

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: FACS-sorted CD71+ neutrophils from in vitro cultures, sample2

description: Library name: CD71-PosNeu-MOUSE-2

source_name: Naive Bone Marrow

value: Naive Bone Marrow

value: In vitro generated neutrophils


title: FACS-sorted CD71+ neutrophils from in vitro cultures, sample1

description: Library name: CD71-PosNeu-MOUSE-1


title: H3 ChIP-seq of Mpneumo strain (input), rep1

value: WCE


title: Calibrated Scc1-PK ChIP-seq of XVIfMmycot1 strain (input)


title: FACS-sorted CD71- neutrophils from in vitro cultures, sample2

description: Library name: CD71-NegNeu-MOUSE-2


title: Calibrated Scc1-PK ChIP-seq of XVIfMmyco strain (IP)

value: XVIfMmyco

value: PRHTXX


title: Calibrated Scc1-PK ChIP-seq of Mmyco strain (IP)


title: SY5102_R3

source_name: wild type OV90 cells

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with SY5102 at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: FACS-sorted CD71- neutrophils from in vitro cultures, sample1

description: Library name: CD71-NegNeu-MOUSE-1


title: FACS-sorted CD71- neutrophils from mouse brain tumor tissue, sample2

description: Library name: CD71-NegNeu-TUMOR-2

value: SB28 cell line


title: DMSO_R3_mb

value: CDK7 analog sensitive OV90 cells


title: H2A ChIP-seq of Mpneumo strain (input)

value: Asy


title: Sir3 ChIP-seq of Mmyco strain (IP)


title: PolII ChIP-seq of Mmyco strain (input), rep2