title: E0771 Tumor, Trametinib, CP-4294

description:
Library name: E0771_CP-4294
Column name in processed files: E0771_CP-4294


title: Bd21-3, Mutant, M0463, juvenile leaf tissue

status: Public on Mar 09 2026

type: SRA

city: Aarhus

first: Guillaume

last: Ramstein

address: Moellers Alle

country: Denmark

institute: Aarhus University

description:
Library name: 222A1
Row name in SIEVE_M6_TPM.csv: M0463

library_source: transcriptomic

data_processing:
Sequencing reads were aligned using hisat2, with default options and converted into bam files using samtools.
The number of reads were counted using the featureCounts function of subread configured to count fragments instead of reads (-p), using the Bd21-3 genome annotations (-a BdistachyonBd21_3_537_v1.2.gene.gff3).
Assembly: BdistachyonBd21_3_537_v1.2
Supplementary files format and content: Tab-delimited file contained transcripts per million (TPM) for each sample

molecule: total RNA

organism: Brachypodium distachyon

source_name: leaf

growth_protocol: Seeds from Brachypodium distachyon accession Bd21-3 were treated with 0 mM (controls) or 7 mM (mutants) of the mutagen sodium azide at the M1 generation (first generation after seed mutagenesis). Then, plants were grown in the greenhouse (20h/4h light/dark, 21°C/18°C target temperature, at Aarhus University Flakkebjerg) and allowed to self-fertilize naturally across 6 generations, from M1 to M6.

extract_protocol:
Tissue sampling was performed in three independent biological replicates per line. The three replicates from each line were subsequently pooled for total RNA extraction. RNA extraction was conducted by Azenta GeneWiz (Leipzig, Germany).
Library preparation was performed using Poly(A) selection and paired-end sequencing (2 × 150 bp) was conducted on an Illumina NovaSeq platform at Azenta GeneWiz (Leipzig, Germany).

treatment_protocol: M6 seeds were pre-incubated for one week at 37°C and 20% relative humidity to enhance and synchronize germination. Germination and seedling growth were carried out in climate-controlled chambers at Aarhus University Flakkebjerg under a 16h/8h light/dark photoperiod, 23°C/21°C day/night temperatures, and 60% relative humidity. At the three-leaf stage (approximately 16 days post-germination), the blades of all three fully expanded leaves (excluding the cotyledons) were harvested and immediately frozen in liquid nitrogen, then stored at –80 °C until further processing.

tag: tissue

value: leaf

tag: cell line

tag: cell type

value: juvenile leaf tissue

tag: genotype

tag: treatment

value: Mutant

tag: batch


title: Bd21-3, Mutant, M0852, juvenile leaf tissue

description:
Library name: 207A1
Row name in SIEVE_M6_TPM.csv: M0852


title: C3-TAG Tumor, Erlotinib, CP-4966

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

country: USA

institute: University of North Carolina at Chapel Hill

description:
Library name: C3-TAG_CP-4966
Column name in processed files: C3-TAG_CP-4966

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts.
The raw counts were upper quartile-normalized.
Assembly: mm10
Supplementary files format and content: Salmon-quantified, upper quartile-normalized read-counts. First column is the gene name, subsequent columns are individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: mammary tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to isolate the RNA according to the manufacturer's protocol.
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit.

value: mammary tumor

tag: tumor model

value: Erlotinib


title: Bd21-3, Mutant, M0791, juvenile leaf tissue

description:
Library name: 210A1
Row name in SIEVE_M6_TPM.csv: M0791


title: Bd21-3, Mutant, M0756, juvenile leaf tissue

description:
Library name: 204A1
Row name in SIEVE_M6_TPM.csv: M0756


title: Bd21-3, Mutant, M0567, juvenile leaf tissue

description:
Library name: 206A1
Row name in SIEVE_M6_TPM.csv: M0567


title: Bd21-3, Mutant, M0672, juvenile leaf tissue

description:
Library name: 208A1
Row name in SIEVE_M6_TPM.csv: M0672


title: C3-TAG Tumor, Erlotinib, CP-4967

description:
Library name: C3-TAG_CP-4967
Column name in processed files: C3-TAG_CP-4967


title: pool-12, well-3, GEX

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

description:
Library name: XHLT2-POOL-DB12-SCG3_GEX
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2 (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Gencode v32-primary assembly) and the raw fastqs of surface protein expression to a TotalSeq-C antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of individual participants from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3) was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-800 and >6,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <400-2,000 and >40,000), mitochondrial content (>15%), and ribosomal content (<8-15% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
For processing of follow-up timepoint, the baseline samples were reanalyzed along with the the follow-up timepoint (separated by ~19 months). After generating single-cell count data from sequencing reads and performing quality control, the identification of cell subsets in the follow-up data was performed using Azimuth. The Seurat object from original baseline data was converted to Azimuth reference, and the follow-up dataset was mapped onto it using Azimuth, which provided predicted cell subset labels for single cells.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format for the high-quality single-cells
Supplementary files format and content: cell_metadata_baseline.rds and cell_metadata_followup.rds are R object files containing metadata for single-cells in baseline and follow-up datasets, respectively. The metadata include sample id (donor id + timepoint id), library id, cell annotations, and timepoint.
Library strategy: CITE-seq

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Blood was collected in EDTA tubes within a 90 min window for all participants of the study. Peripheral blood mononuclear cells (PBMC) were obtained by density gradient centrifugation of whole blood at 800g for 30 min at room temperature without brake, using Ficoll-Paque (Cytiva). Isolated cells were cryopreserved in a solution containing fetal Bovine Serum and 10% DMSO (Sigma). Thawed PBMC suspensions from 14-16 individuals were pooled together with equivalent numbers to a total of 1 million live cells. Pools were resuspended in Cell Staining Buffer (Biolegend) and incubated with Fc Receptor Blocking Solution (Biolegend) at 20mg/mL for 10 minutes on ice. Cells were then stained with a cocktail of 140 TotalSeq-C oligo-tagged antibodies (Biolegend) for 30 minutes at 4°C. Stained cells were washed in PBS containing 1% BSA, filtered through a 70uM filter, and re-suspended in a final solution of PBS containing 0.04% BSA.
Stained cells (n=60,000) were loaded on the Chromium Controller (10X Genomics) for GEM generation. The cDNA libraries were generated using the Chromium Next GEM Single Cell 5’ v1.1 Library Kit for gene expression (GEX) and the Chromium Single Cell 5’ Feature Barcode Library kit for antibody derived tag (ADT) according to manufacturer’s instructions (10X Genomics). Each batch of 14-16 samples was sampled four times to prepare four independent cDNA libraries per batch to obtain a sufficient number of cells per sample. The libraries were subsequently sequenced on a NovaSeq 6000 S4 platform (Illumina).

value: PBMC

tag: library type

value: mRNA


title: pool-12, well-2, GEX

description:
Library name: XHLT2-POOL-DB12-SCG2_GEX
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1


title: Bd21-3, Mutant, M0537, juvenile leaf tissue

description:
Library name: 205A1
Row name in SIEVE_M6_TPM.csv: M0537


title: Bd21-3, Mutant, M0710, juvenile leaf tissue

description:
Library name: 203A1
Row name in SIEVE_M6_TPM.csv: M0710


title: pool-12, well-1, ADT

description:
Library name: XHLT2-POOL-DB12-SCG1_ADT
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1

library_source: other

molecule: protein

value: ADT


title: C3-TAG Tumor, Erlotinib, CP-4936

description:
Library name: C3-TAG_CP-4936
Column name in processed files: C3-TAG_CP-4936


title: Bd21-3, Mutant, M0589, juvenile leaf tissue

description:
Library name: 201A1
Row name in SIEVE_M6_TPM.csv: M0589


title: pool-12, well-2, ADT

description:
Library name: XHLT2-POOL-DB12-SCG2_ADT
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1


title: Bd21-3, Mutant, M0585, juvenile leaf tissue

description:
Library name: 202A1
Row name in SIEVE_M6_TPM.csv: M0585


title: Bd21-3, Mutant, M0196, juvenile leaf tissue

description:
Library name: 200A1
Row name in SIEVE_M6_TPM.csv: M0196


title: pool-12, well-1, GEX

description:
Library name: XHLT2-POOL-DB12-SCG1_GEX
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1


title: Bd21-3, Mutant, M0441, juvenile leaf tissue

description:
Library name: 1A1
Row name in SIEVE_M6_TPM.csv: M0441


title: Bd21-3, Mutant, M0247, juvenile leaf tissue

description:
Library name: 19A1
Row name in SIEVE_M6_TPM.csv: M0247


title: C3-TAG Tumor, Trametinib, CP-4968

description:
Library name: C3-TAG_CP-4968
Column name in processed files: C3-TAG_CP-4968

value: Trametinib


title: Bd21-3, Mutant, M0141, juvenile leaf tissue

description:
Library name: 199A1
Row name in SIEVE_M6_TPM.csv: M0141


title: C3-TAG Tumor, Trametinib, CP-4935

description:
Library name: C3-TAG_CP-4935
Column name in processed files: C3-TAG_CP-4935


title: Bd21-3, Mutant, M0150, juvenile leaf tissue

description:
Library name: 196A1
Row name in SIEVE_M6_TPM.csv: M0150


title: pool-11, well-4, GEX

description:
Library name: XHLT2-POOL-DB11-SCG4_GEX
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: Bd21-3, Mutant, M0100, juvenile leaf tissue

description:
Library name: 198A1
Row name in SIEVE_M6_TPM.csv: M0100


title: Bd21-3, Mutant, M0345, juvenile leaf tissue

description:
Library name: 194A1
Row name in SIEVE_M6_TPM.csv: M0345


title: Bd21-3, Mutant, M0297, juvenile leaf tissue

description:
Library name: 193A1
Row name in SIEVE_M6_TPM.csv: M0297


title: Bd21-3, Mutant, M0426, juvenile leaf tissue

description:
Library name: 197A1
Row name in SIEVE_M6_TPM.csv: M0426


title: 4T1 Tumor, Erlotinib, CP-4066

description:
Library name: 4T1_CP-4066
Column name in processed files: 4T1_CP-4066


title: pool-11, well-3, ADT

description:
Library name: XHLT2-POOL-DB11-SCG3_ADT
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: 4T1 Tumor, Erlotinib, CP-4065

description:
Library name: 4T1_CP-4065
Column name in processed files: 4T1_CP-4065


title: pool-11, well-3, GEX

description:
Library name: XHLT2-POOL-DB11-SCG3_GEX
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: 4T1 Tumor, Erlotinib, CP-4064

description:
Library name: 4T1_CP-4064
Column name in processed files: 4T1_CP-4064


title: Bd21-3, Mutant, M0166, juvenile leaf tissue

description:
Library name: 192A1
Row name in SIEVE_M6_TPM.csv: M0166


title: C3-TAG Tumor, Trametinib, CP-4934

description:
Library name: C3-TAG_CP-4934
Column name in processed files: C3-TAG_CP-4934


title: Bd21-3, Mutant, M0347, juvenile leaf tissue

description:
Library name: 191A1
Row name in SIEVE_M6_TPM.csv: M0347


title: 4T1 Tumor, Trametinib, CP-4069

description:
Library name: 4T1_CP-4069
Column name in processed files: 4T1_CP-4069


title: pool-11, well-2, ADT

description:
Library name: XHLT2-POOL-DB11-SCG2_ADT
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: Bd21-3, Mutant, M0344, juvenile leaf tissue

description:
Library name: 18A1
Row name in SIEVE_M6_TPM.csv: M0344


title: KPB1-A Tumor, Erlotinib, CP-4285

description:
Library name: KPB1-A_CP-4285
Column name in processed files: KPB1-A_CP-4285


title: 4T1 Tumor, Trametinib, CP-4068

description:
Library name: 4T1_CP-4068
Column name in processed files: 4T1_CP-4068


title: Bd21-3, Mutant, M0374, juvenile leaf tissue

description:
Library name: 189A1
Row name in SIEVE_M6_TPM.csv: M0374


title: pool-11, well-2, GEX

description:
Library name: XHLT2-POOL-DB11-SCG2_GEX
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: Bd21-3, Mutant, M0305, juvenile leaf tissue

description:
Library name: 188A1
Row name in SIEVE_M6_TPM.csv: M0305


title: Bd21-3, Mutant, M0091, juvenile leaf tissue

description:
Library name: 190A1
Row name in SIEVE_M6_TPM.csv: M0091


title: pool-11, well-4, ADT

description:
Library name: XHLT2-POOL-DB11-SCG4_ADT
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: 4T1 Tumor, Trametinib, CP-4067

description:
Library name: 4T1_CP-4067
Column name in processed files: 4T1_CP-4067


title: Bd21-3, Mutant, M0286, juvenile leaf tissue

description:
Library name: 187A1
Row name in SIEVE_M6_TPM.csv: M0286


title: Bd21-3, Control, C20, juvenile leaf tissue

description:
Library name: 185A1
Row name in SIEVE_M6_TPM.csv: C20

value: Control


title: Bd21-3, Mutant, M0217, juvenile leaf tissue

description:
Library name: 181A1
Row name in SIEVE_M6_TPM.csv: M0217


title: pool-10, well-4, GEX

description:
Library name: XHLT2-POOL-DB10-SCG4_GEX
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: Bd21-3, Mutant, M0214, juvenile leaf tissue

description:
Library name: 182A1
Row name in SIEVE_M6_TPM.csv: M0214


title: Bd21-3, Mutant, M0234, juvenile leaf tissue

description:
Library name: 183A1
Row name in SIEVE_M6_TPM.csv: M0234


title: pool-11, well-1, GEX

description:
Library name: XHLT2-POOL-DB11-SCG1_GEX
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: pool-10, well-4, ADT

description:
Library name: XHLT2-POOL-DB10-SCG4_ADT
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: Bd21-3, Mutant, M0383, juvenile leaf tissue

description:
Library name: 180A1
Row name in SIEVE_M6_TPM.csv: M0383


title: 2336 Tumor, Erlotinib, CP-3529

description:
Library name: 2336_CP-3529
Column name in processed files: 2336_CP-3529


title: Bd21-3, Mutant, M0378, juvenile leaf tissue

description:
Library name: 179A1
Row name in SIEVE_M6_TPM.csv: M0378


title: pool-10, well-3, ADT

description:
Library name: XHLT2-POOL-DB10-SCG3_ADT
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: 2336 Tumor, Trametinib, CP-3536

description:
Library name: 2336_CP-3536
Column name in processed files: 2336_CP-3536


title: Bd21-3, Mutant, M0320, juvenile leaf tissue

description:
Library name: 178A1
Row name in SIEVE_M6_TPM.csv: M0320


title: pool-10, well-3, GEX

description:
Library name: XHLT2-POOL-DB10-SCG3_GEX
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: 2336 Tumor, Trametinib, CP-3535

description:
Library name: 2336_CP-3535
Column name in processed files: 2336_CP-3535


title: Bd21-3, Mutant, M0228, juvenile leaf tissue

description:
Library name: 186A1
Row name in SIEVE_M6_TPM.csv: M0228


title: Bd21-3, Mutant, M0301, juvenile leaf tissue

description:
Library name: 17A1
Row name in SIEVE_M6_TPM.csv: M0301


title: pool-10, well-2, ADT

description:
Library name: XHLT2-POOL-DB10-SCG2_ADT
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: Bd21-3, Mutant, M0223, juvenile leaf tissue

description:
Library name: 175A1
Row name in SIEVE_M6_TPM.csv: M0223


title: Bd21-3, Mutant, M0371, juvenile leaf tissue

description:
Library name: 174A1
Row name in SIEVE_M6_TPM.csv: M0371


title: pool-11, well-1, ADT

description:
Library name: XHLT2-POOL-DB11-SCG1_ADT
Pool of XHLT2-HS22-AAE6, XHLT2-HS28-BLE1, XHLT2-HS46-AAE6, XHLT2-HS68-AAE6, XHLT2-HS75-BLE1, XHLT2-HS88-AAE6


title: 9263 Tumor, Erlotinib, CP-3560

description:
Library name: 9263_CP-3560
Column name in processed files: 9263_CP-3560


title: Bd21-3, Mutant, M0030, juvenile leaf tissue

description:
Library name: 173A1
Row name in SIEVE_M6_TPM.csv: M0030


title: Bd21-3, Mutant, M0439, juvenile leaf tissue

description:
Library name: 176A1
Row name in SIEVE_M6_TPM.csv: M0439


title: pool-10, well-1, ADT

description:
Library name: XHLT2-POOL-DB10-SCG1_ADT
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: Bd21-3, Mutant, M0256, juvenile leaf tissue

description:
Library name: 172A1
Row name in SIEVE_M6_TPM.csv: M0256


title: Bd21-3, Mutant, M0227, juvenile leaf tissue

description:
Library name: 170A1
Row name in SIEVE_M6_TPM.csv: M0227


title: Bd21-3, Mutant, M0037, juvenile leaf tissue

description:
Library name: 171A1
Row name in SIEVE_M6_TPM.csv: M0037


title: pool-10, well-2, GEX

description:
Library name: XHLT2-POOL-DB10-SCG2_GEX
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: 9263 Tumor, Erlotinib, CP-3558

description:
Library name: 9263_CP-3558
Column name in processed files: 9263_CP-3558


title: 9263 Tumor, Erlotinib, CP-3559

description:
Library name: 9263_CP-3559
Column name in processed files: 9263_CP-3559


title: pool-10, well-1, GEX

description:
Library name: XHLT2-POOL-DB10-SCG1_GEX
Pool of XHLT2-HS24-BLE1, XHLT2-HS47-AAE6, XHLT2-HS68-BLE1, XHLT2-HS93-AAE6


title: Bd21-3, Mutant, M0033, juvenile leaf tissue

description:
Library name: 16A1
Row name in SIEVE_M6_TPM.csv: M0033


title: Bd21-3, Mutant, M0390, juvenile leaf tissue

description:
Library name: 177A1
Row name in SIEVE_M6_TPM.csv: M0390


title: POP92_TGFP_rep2

city: Oxford

first: Yucheng

last: Wang

state: Oxfordshire

address: Roosevelt Drive, Headington

country: United Kingdom

institute: University of Oxford

description: Library name: POP92_TGFP_rep2

data_processing:
All sequencing FASTQ files were trimmed using the Trim_Galore program. The trimmed FASTQ files were then aligned to the human genome (hg38) using the STAR aligner program unless otherwise specified. Duplicates were marked and removed using the Picard program. A Gene Transfer Format (GTF) file containing annotations for human reference genes was downloaded from the UCSC Genome Browser as gencode.v21.annotation_GRCh38.gtf. This GTF file for gene annotation was used with the featureCounts command of the subread tools.
Assembly: hg38
Supplementary files format and content: CPM, bigwig

source_name: Colorectal cancer

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit. Purified RNA was quantified by a NanoDrop 2000 spectrophotometer, and purity was considered acceptable if A260/A280 values were ≥ 1.8.
Library preparation for total RNA-sequencing was done by GENEWIZ. Briefly, 500 ng of total RNA from the indicated sample was used for strand-specific RNA-seq library preparation with rRNA depletion, followed by Illumina paired-end sequencing (2 × 150 bp) to generate approximately 50 million reads per sample.

value: Colorectal cancer

value: Patient-derived xenograft CRC model

value: wild type


title: Bd21-3, Mutant, M0101, juvenile leaf tissue

description:
Library name: 168A1
Row name in SIEVE_M6_TPM.csv: M0101


title: 9263 Tumor, Trametinib, CP-3566

description:
Library name: 9263_CP-3566
Column name in processed files: 9263_CP-3566


title: Bd21-3, Mutant, M0405, juvenile leaf tissue

description:
Library name: 167A1
Row name in SIEVE_M6_TPM.csv: M0405


title: Bd21-3, Mutant, M0368, juvenile leaf tissue

description:
Library name: 165A1
Row name in SIEVE_M6_TPM.csv: M0368


title: Bd21-3, Mutant, M0231, juvenile leaf tissue

description:
Library name: 169A1
Row name in SIEVE_M6_TPM.csv: M0231


title: Bd21-3, Mutant, M0326, juvenile leaf tissue

description:
Library name: 166A1
Row name in SIEVE_M6_TPM.csv: M0326


title: 2336 Tumor, Trametinib, CP-3534

description:
Library name: 2336_CP-3534
Column name in processed files: 2336_CP-3534


title: 2336 Tumor, Erlotinib, CP-3530

description:
Library name: 2336_CP-3530
Column name in processed files: 2336_CP-3530


title: NCIH716_TGFP_rep2

description: Library name: NCIH716_TGFP_rep2

value: human colorectal cancer cell line


title: 2250 Tumor, Erlotinib, CP-3545

description:
Library name: 2250_CP-3545
Column name in processed files: 2250_CP-3545


title: Bd21-3, Mutant, M0108, juvenile leaf tissue

description:
Library name: 160A1
Row name in SIEVE_M6_TPM.csv: M0108


title: Bd21-3, Mutant, M0001, juvenile leaf tissue

description:
Library name: 15A1
Row name in SIEVE_M6_TPM.csv: M0001


title: POP92_TGFP_rep1

description: Library name: POP92_TGFP_rep1


title: 2250 Tumor, Erlotinib, CP-3544

description:
Library name: 2250_CP-3544
Column name in processed files: 2250_CP-3544


title: 9263 Tumor, Trametinib, CP-3564

description:
Library name: 9263_CP-3564
Column name in processed files: 9263_CP-3564


title: Bd21-3, Mutant, M0417, juvenile leaf tissue

description:
Library name: 159A1
Row name in SIEVE_M6_TPM.csv: M0417


title: Bd21-3, Mutant, M0293, juvenile leaf tissue

description:
Library name: 164A1
Row name in SIEVE_M6_TPM.csv: M0293


title: NCIH716_METTL3KD4_rep1

description: Library name: NCIH716_METTL3KD4_rep1

value: METTL3 knock-down 4


title: 9263 Tumor, Trametinib, CP-3565

description:
Library name: 9263_CP-3565
Column name in processed files: 9263_CP-3565


title: Bd21-3, Mutant, M0078, juvenile leaf tissue

description:
Library name: 162A1
Row name in SIEVE_M6_TPM.csv: M0078


title: 2250 Tumor, Erlotinib, CP-3543

description:
Library name: 2250_CP-3543
Column name in processed files: 2250_CP-3543


title: NCIH716_TGFP_rep1

description: Library name: NCIH716_TGFP_rep1


title: P. aeruginosa PAO1W ΔsadB exponential phase bio rep 3

city: Nottingham

first: Maria

last: Papangeli

address: University Park

institute: University of Nottingham

description:
Library name: DS_exp_3
DS_exp

data_processing:
The data analysis was conducted by Novogene (UK) Co., Ltd. (Cambridge, UK). Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by trimming reads containing adapter and removing poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from the genome website directly. Both building index of the reference genome and aligning clean reads to the reference genome were conducted using Bowtie2. v2.3.4.3
FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: genome_gene.fa.zip
Supplementary files format and content: xlsx file that includes the normalised counts (FPKM) for each group sample

organism: Pseudomonas aeruginosa

growth_protocol: Planktonic cultures were prepared in 5 ml LB medium in 50 ml falcon tubes from single colonies incubated at 37°C, 200 rpm shaking. The overnight cultures were used to set up overday cultures until OD600 of 0.6 to 0.8. The same cultures were used as inoculum for overnight (19 h) cultures. 0.5 ml of exponential phase or overnight cultures were incubated with 1 ml of RNAprotect to preserve the RNA integrity.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN, UK). After the extraction of the RNA the remaining genomic DNA (gDNA) was digested using the Turbo DNA-free kit (Invitrogen, US). PCR verified the absence of gDNA contamination. The RNA quality and quantity were measured using the Agilent 2100 Bioalanyser and the Agilent RNA 6000 Nano Kit. The RNA integrity number (RIN) was always> 9.2.
RNA sequencing was conducted by Novogene (UK) Co., Ltd. (Cambridge, UK). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and the library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and pairedend reads were generated.

treatment_protocol: No treatment

value: sadB knockout

value: exponential phase (OD 0.6-0.8)


title: Bd21-3, Mutant, M0153, juvenile leaf tissue

description:
Library name: 158A1
Row name in SIEVE_M6_TPM.csv: M0153

value: leaf


title: HT29_TGFP_rep2

description: Library name: HT29_TGFP_rep2


title: 2250 Tumor, Trametinib, CP-3551

description:
Library name: 2250_CP-3551
Column name in processed files: 2250_CP-3551


title: P. aeruginosa PAO1W ΔsadB exponential phase bio rep 2

description:
Library name: DS_exp_2
DS_exp


title: NCIH716_METTL3KD4_rep2

description: Library name: NCIH716_METTL3KD4_rep2


title: Bd21-3, Mutant, M0433, juvenile leaf tissue

description:
Library name: 163A1
Row name in SIEVE_M6_TPM.csv: M0433

value: juvenile leaf tissue


title: Bd21-3, Mutant, M0431, juvenile leaf tissue

description:
Library name: 157A1
Row name in SIEVE_M6_TPM.csv: M0431

value: Mutant


title: 2250 Tumor, Trametinib, CP-3550

description:
Library name: 2250_CP-3550
Column name in processed files: 2250_CP-3550

value: mammary tumor


title: HT29_TGFP_rep1

description: Library name: HT29_TGFP_rep1


title: P. aeruginosa PAO1W ΔsadB overnight culture bio rep 3

description:
Library name: DS_on_3
DS_on

value: stationary phase (19 h)


title: 2250 Tumor, Trametinib, CP-3549

description:
Library name: 2250_CP-3549
Column name in processed files: 2250_CP-3549


title: P. aeruginosa PAO1W ΔsadB exponential phase bio rep 1

description:
Library name: DS_exp_1
DS_exp


title: HCT116_TGFP_rep1

description: Library name: HCT116_TGFP_rep1


title: 2336 Tumor, Erlotinib, CP-3528

description:
Library name: 2336_CP-3528
Column name in processed files: 2336_CP-3528

value: Erlotinib


title: Bd21-3, Mutant, M0045, juvenile leaf tissue

description:
Library name: 155A1
Row name in SIEVE_M6_TPM.csv: M0045


title: Bd21-3, Control, C01, juvenile leaf tissue

description:
Library name: 154A1
Row name in SIEVE_M6_TPM.csv: C01


title: 2225 Tumor, Trametinib, CP-3581

description:
Library name: 2225_CP-3581
Column name in processed files: 2225_CP-3581


title: P. aeruginosa PAO1W pMEsadB exponential phase bio rep 1

description:
Library name: OSW_ex_1
OSW_ex

value: WT pMEsadB


title: 2225 Tumor, Trametinib, CP-3580

description:
Library name: 2225_CP-3580
Column name in processed files: 2225_CP-3580


title: CSC73_METTL3KD4_rep1

description: Library name: CSC73_METTL3KD4_rep1


title: Bd21-3, Mutant, M0272, juvenile leaf tissue

description:
Library name: 150A1
Row name in SIEVE_M6_TPM.csv: M0272


title: Bd21-3, Mutant, M0112, juvenile leaf tissue

description:
Library name: 149A1
Row name in SIEVE_M6_TPM.csv: M0112


title: P. aeruginosa PAO1W ΔsadB overnight culture bio rep 2

description:
Library name: DS_on_2
DS_on


title: COLO201_TGFP_rep2

description: Library name: COLO201_TGFP_rep2


title: P. aeruginosa PAO1W exponential phase bio rep 2

description:
Library name: WTW_ex_2
WTW_ex

value: WT


title: COLO201_TGFP_rep1

description: Library name: COLO201_TGFP_rep1


title: Bd21-3, Mutant, M0022, juvenile leaf tissue

description:
Library name: 147A1
Row name in SIEVE_M6_TPM.csv: M0022


title: 2225 Tumor, Trametinib, CP-3579

description:
Library name: 2225_CP-3579
Column name in processed files: 2225_CP-3579

value: Trametinib


title: 2224 Tumor, Erlotinib, CP-3767

description:
Library name: 2224_CP-3767
Column name in processed files: 2224_CP-3767


title: Bd21-3, Mutant, M0107, juvenile leaf tissue

description:
Library name: 148A1
Row name in SIEVE_M6_TPM.csv: M0107


title: COLO201_METTL3KD1_rep2

description: Library name: COLO201_METTL3KD1_rep2

value: METTL3 knock-down 1


title: P. aeruginosa PAO1W exponential phase bio rep 3

description:
Library name: WTW_ex_3
WTW_ex


title: P. aeruginosa PAO1W exponential phase bio rep 1

description:
Library name: WTW_ex_1
WTW_ex


title: P. aeruginosa PAO1W pMEsadB overnight culture bio rep 3

description:
Library name: OSW_on_3
OSW_on


title: CSC73_TGFP_rep2

description: Library name: CSC73_TGFP_rep2

value: Colorectal cancer


title: Bd21-3, Mutant, M0032, juvenile leaf tissue

description:
Library name: 153A1
Row name in SIEVE_M6_TPM.csv: M0032


title: 2224 Tumor, Erlotinib, CP-3768

description:
Library name: 2224_CP-3768
Column name in processed files: 2224_CP-3768


title: 2225 Tumor, Erlotinib, CP-3575

description:
Library name: 2225_CP-3575
Column name in processed files: 2225_CP-3575


title: 2224 Tumor, Erlotinib, CP-3766

description:
Library name: 2224_CP-3766
Column name in processed files: 2224_CP-3766


title: P. aeruginosa PAO1W ΔsadB overnight culture bio rep 1

description:
Library name: DS_on_1
DS_on


title: CSC73_METTL3KD4_rep2

description: Library name: CSC73_METTL3KD4_rep2

value: Patient-derived xenograft CRC model


title: Bd21-3, Mutant, M0262, juvenile leaf tissue

description:
Library name: 152A1
Row name in SIEVE_M6_TPM.csv: M0262


title: Bd21-3, Mutant, M0394, juvenile leaf tissue

description:
Library name: 151A1
Row name in SIEVE_M6_TPM.csv: M0394


title: CSC73_TGFP_rep1

description: Library name: CSC73_TGFP_rep1

value: wild type


title: Bd21-3, Mutant, M0348, juvenile leaf tissue

description:
Library name: 146A1
Row name in SIEVE_M6_TPM.csv: M0348


title: 2225 Tumor, Erlotinib, CP-3573

description:
Library name: 2225_CP-3573
Column name in processed files: 2225_CP-3573


title: 2225 Tumor, Erlotinib, CP-3574

description:
Library name: 2225_CP-3574
Column name in processed files: 2225_CP-3574


title: COLO201_METTL3KD1_rep1

description: Library name: COLO201_METTL3KD1_rep1

value: human colorectal cancer cell line


title: P. aeruginosa PAO1W pMEsadB exponential phase bio rep 3

description:
Library name: OSW_ex_3
OSW_ex


title: P. aeruginosa PAO1W pMEsadB overnight culture bio rep 2

description:
Library name: OSW_on_2
OSW_on


title: Isotype Cut-and-Run

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: Library name: BLaER1_M_DMSO_Isotype_Standard

library_source: genomic

data_processing:
ChIP-Seq: nf-core/chipseq v1.1.0 was run with default parameters to quality check and align the data, create coverage tracks (bigWig) and call peaks.
Cut-and-Run: nf-core/cutandrun: 3.2.2 was run  with default parameters to quality check and align the data, create coverage tracks (bigWig) and call peaks.
Assembly: GRCh38
Supplementary files format and content: .bigWig: genome-wide read coverage track
Library strategy: CUT&Run

molecule: genomic DNA

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640 supplemented with L-glutamine, sodium pyruvate, 100U/ml penicillin-streptomycin (Thermo Fisher) and 10% (v/v) FCS (Omega Scientific).

extract_protocol:
BLaER1 cells were washed with PBS and fixed with 1% formaldehyde for 10 min at RT before quenching the reaction with 0.6 M glycine. Fixed cells were washed with cold PBS and lysed in 50mM TRIS pH 8, 10mM EDTA and 1% SDS. Lysates were sonicated using the Bioruptor (Diagenode) with cycles of 30s ON / 30s OFF in the high-power mode until a fragment length of 200-500bp was achieved. Lysates were mixed with dilution buffer to a final concentration of 20 mM TRIS pH 8, 150 mM NaCl, 2 mM EDTA ,1% Triton-X100 and 0.1% SDS. 2.5% drosophila melanogaster S2 cell derived chromatin (prepared similarly) was spiked into the samples. Lysates were pre-incubated at 4°C for 2 h with ProteinA-coated magnetic beads (G&E) previously blocked in TE with 1% BSA. After removal of the beads, target and spike-in antibodies were added to the lysates and incubated at 4°C overnight. Fresh blocked beads were added and incubated with the lysates for 2h at 4°C. Beads were washed with RIPA buffer (150 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 0.5% Na-deoxycholate, 1% Igepal), high salt buffer (500 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 1% Igepal), LiCl buffer (250 mM LiCl, 50 mM TRIS pH 8, 0.5% Na-deoxycholate, 1% Igepal) and TE wash buffer (10 mM TRIS-HCl, 1 mM EDTA, 50 mM NaCl) and protein DNA complexes were eluted with 100mM NaHCO3 + 1% SDS. ChIP and input samples were incubated overnight at 55°C with 200mM NaCl, 10mM EDTA, 20mM Tris-HCl pH 6.5 and 300 µg/ml Proteinase K (Thermo Fisher). DNA was isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research).
NEBNext Ultra II liabrary prep was performed accoring to manufacturer's instructions

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-estradiol (Sigma-Aldrich)

value: monocytes

value: IFNAR1-/- IFNAR2-/- MORC3.AID.V5 + sgAAVS2

tag: chip antibody

value: anti-rabbit-IgG antibody; DA1E, cell signaling technology


title: 2224 Tumor, Trametinib, CP-3762

description:
Library name: 2224_CP-3762
Column name in processed files: 2224_CP-3762


title: Bd21-3, Mutant, M0158, juvenile leaf tissue

description:
Library name: 144A1
Row name in SIEVE_M6_TPM.csv: M0158

value: leaf


title: Bd21-3, Mutant, M0040, juvenile leaf tissue

description:
Library name: 145A1
Row name in SIEVE_M6_TPM.csv: M0040

value: juvenile leaf tissue


title: P. aeruginosa PAO1W pMEsadB overnight culture bio rep 1

description:
Library name: OSW_on_1
OSW_on


title: Bd21-3, Mutant, M0327, juvenile leaf tissue

description:
Library name: 143A1
Row name in SIEVE_M6_TPM.csv: M0327

value: Mutant


title: 2224 Tumor, Trametinib, CP-3760

description:
Library name: 2224_CP-3760
Column name in processed files: 2224_CP-3760

value: mammary tumor


title: H3K4me3 Cut-and-Run

description: Library name: BLaER1_M_DMSO_H3K4me3_Standard_R1

value: IFNAR1-/- IFNAR2-/- MORC3.AID.V5 + sgAAVS1

value: anti-H3K4me3 antibody, C42D8, cell signaling technology


title: Bd21-3, Mutant, M0055, juvenile leaf tissue

description:
Library name: 142A1
Row name in SIEVE_M6_TPM.csv: M0055


title: P. aeruginosa PAO1W overnight culture bio rep 2

description:
Library name: WTW_on_2
WTW_on

value: stationary phase (19 h)


title: PDX12, PDX, shAMBRA1, in vivo, biol rep1

city: Paris

first: Jacob

last: Torrejon Diaz

address: 26 Rue d'Ulm

country: France

institute: Curie Institute

description:
Library name: Sample 2
Scipio

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cytonaut softaware version 1.8 (https://scipio.bio/ressources/cytonaut-user-guide-v1-8-current)
Assembly: hg38 (PDX KD AMBRA1)
Supplementary files format and content: Tab-separated values files (bardcodes and features) and matrix files

source_name: PDX12 (PDX)

growth_protocol: Tumor cells for PDXs were isolated from PDX tumor chunks with a Percoll gradient. PDX cells were cultured and infected in adherent conditions (poly-D-lysine + matrigel precoated dishes). Growth medium for PDX cells consisted of Neurobasal™ Medium (GIBCO) supplemented with 0.45% D+-Glucose (Sigma), 4 mM L-Glutamine (GIBCO), 100 U/mL penicillin/streptomycin (GIBCO), 1X Serum-free supplement B27 (GIBCO).

extract_protocol:
Asteria™ Single-cell RNA-seq Benchtop Kit (Cat#001-1000, Scipio bioscience, France)
barcode sequence at the P5 side, and 3’ end of the captured mRNA at the P7 side. single cell 3’ end cDNA. NEBNext Ultra II FS DNA Library Prep kit for Illumina (NEB #E7805S) with NEBNext Multiplex Oligos for Illumina (Set 1, NEB #E7335),

treatment_protocol: Lentiviral infection with shRNAs. Cells were harvested 3 days after infection, and injected orthotopically into nu/nu mice. Tumors were isolated and dissociated prior to scRNAseq analysis.

value: PDX12 (PDX)

value: Medulloblastoma


title: P. aeruginosa PAO1W overnight culture bio rep 3

description:
Library name: WTW_on_3
WTW_on

value: WT


title: 2208 Tumor, Trametinib, CP-4060

description:
Library name: 2208_CP-4060
Column name in processed files: 2208_CP-4060

value: Trametinib


title: Bd21-3, Mutant, M0134, juvenile leaf tissue

description:
Library name: 140A1
Row name in SIEVE_M6_TPM.csv: M0134


title: Bd21-3, Mutant, M0275, juvenile leaf tissue

description:
Library name: 13A1
Row name in SIEVE_M6_TPM.csv: M0275


title: P. aeruginosa PAO1W overnight culture bio rep 1

description:
Library name: WTW_on_1
WTW_on


title: 2208 Tumor, Erlotinib, CP-4056

description:
Library name: 2208_CP-4056
Column name in processed files: 2208_CP-4056

value: Erlotinib


title: 2208 Tumor, Erlotinib, CP-4055

description:
Library name: 2208_CP-4055
Column name in processed files: 2208_CP-4055


title: aPS-MyeloidCapture2

city: Tampa

first: Christopher

middle: Bernardo

last: Medina

state: FL

address: 3011 W Holly Dirve

department: Immunology

institute: Moffitt Cancer Center

description:
Library name: Sample4
10x Genomics

data_processing:
Samples were aligned, filtered, and counted for barcodes and unique molecular identifiers using Cellranger v3.1
Data was further analyzed using R and Seurat package v5.0.1. Cells with less than a 500 RNA count or greater than 3500 were excluded. Additionally, cells with percentage of mitochondrial genes above 4%, heat shock proteins above 1%, ribosomal genes below 10% were excluded. Any T cells, NK cells or B cells that were not efficiently sorted were excluded from downstream analysis by excluding cells with high CD3, CD19, or NK gene counts.
Assembly: Mouse mm10
Supplementary files format and content: Barcode, Matrix and features in tsv or mtx files.

source_name: Spleen

extract_protocol:
Spleen were digested in 2mg/ml Collagenase D for 30 min at 37C. Samples were passed throught a 70um strainer, cells were then washed and stained for CD11b+, CD3, NK1.1, CD19. CD11b+ CD3- NK1.1- CD19- myeloid cells were sorted for scRNAseq.
Single cell RNAseq libraries were made using the Chromium single cell 5’ Library and Gel Bead kit (10x Genomics). Sorted cells were captured into Gel Beads-in-emulsion (GEM). Samples were reverse transcribed, and cDNA was isolated and pooled. Barcoded cDNA was fragmented, end repaired, and A-tails were followed by PCR.

value: Spleen

value: CD11b+ Myeloid

value: C57Bl/6 WT

value: mch1N11 PS-targeting Ab


title: 2208 Tumor, Trametinib, CP-4059

description:
Library name: 2208_CP-4059
Column name in processed files: 2208_CP-4059


title: IgG-MyeloidCapture2

description:
Library name: Sample2
10x Genomics

value: IgG Control


title: HCT116_TGFP_rep2

description: Library name: HCT116_TGFP_rep2

value: Colorectal cancer

value: human colorectal cancer cell line

value: wild type


title: aPS-MyeloidCapture1

description:
Library name: Sample3
10x Genomics


title: IgG-MyeloidCapture1

description:
Library name: Sample1
10x Genomics


title: RpoC-his10 (input) CasPRIB1 biol rep1

city: Seattle

first: Alexander

last: Meeske

state: WA

address: 750 Republican St

institute: University of Washington

description: Library name: RpoC-his10 (input) CasPRIB1 biol rep1

data_processing:
Reads were mapped to the L. seeligeri genome using Bowtie2 with settings -I 10 and -X 700.
Coverage across the genome was calculated from the resulting BAM files using bamCoverage with a bin size of 1 nucleotide, and coverage was normalized to 10M reads per sample. Coverage at each nucleotide position in the resulting wig files was normalized twice: first the values for each IP sample were divided by the values in their corresponding total DNA sample, then the normalized coverage values in samples expressing CasPRs (or RpoC-his10) were divided by an empty vector control.
Assembly: NC_013891.1
Supplementary files format and content: wig

organism: Listeria seeligeri

source_name: bacterial culture

growth_protocol: BHI + kanamycin 50µg/mL 30°C to OD 0.3-0.8

extract_protocol:
10 min 1% formaldehyde, glycine quench. Cultures were pelleted via centrifugation at 4C and washed 3 times by resuspension in 10 mL ice cold 1X PBS. After washes, pellets were resuspended in 1.5 mL  lysis buffer (50 mM HEPES pH 7.0, 150 mM NaCl, 5 mM MgCl2, 10 mM imidazole, 1 mg/mL lysozyme, 1 mM PMSF, 5% glycerol), and incubated at 37C for 15 min. Samples were sonicated (Qsonica Q500) on ice using 15% amplitude in 10 s intervals with a 50% duty cycle for 10 minutes of processing time, which resulted in DNA fragments averaging 500 bp.  Processed lysates were centrifuged for 10 minutes at 4C. Here, 50 μL of clarified lysates were reserved as “total DNA” matched pairs for each sample. Remaining supernatants were applied to 100 μL of equilibrated Ni-NTA agarose resin (ThermoFisher) and incubated at 4C with rotation for two hours. Then, mixtures were centrifuged at 4C and 2000 rpm for 1 min to pellet beads. Beads were washed with 1 mL of cold wash buffer (20 mM HEPES pH 7.0, 150 mM NaCl, 5 mM MgCl2, 10 mM imidazole, 5% glycerol) and further incubated at 4C for 5 min. This was repeated twice for three total washes. After the final wash, 50μL elution buffer (20 mM HEPES pH 7.0, 150 mM NaCl, 5 mM MgCl2, 250 mM imidazole, 5% glycerol) was added to each bead pellet. Samples were incubated at RT for 5 minutes and centrifuged at 4C and 2000 rpm for 1 min before carefully harvesting the IP supernatant. Total DNA and IP samples were incubated at 60C overnight to reverse crosslinks. After overnight incubation, 450 μL of wash buffer was added to each sample and samples were treated with RNase A (0.2 mg/mL) at 37C for 1 h and subsequently with Proteinase K (0.2 mg/mL) at 37C for 30 min. Next, an equal volume of phenol/chloroform (1:1) was added to each sample and vortexed before centrifuging samples at RT for 10min at 13,000 rpm. The aqueous phase of each sample was then harvested and combined with 50 μL sodium acetate. DNA was precipitated with two volumes of cold ethanol and pelleted by centrifugation (15,000 rpm) at 4C for 15min. Pellets were washed two times with 70% ethanol before resuspending IP samples in 10 μL water and total DNA samples in 50 μL water.
DNA fragments for each sample were barcoded and prepared for sequencing using the Illumina TruSeq DNA Library Preparation kit according to the manufacturer’s instructions. Purification steps were performed using Ampure beads and samples were pooled equally by weight to form final libraries. CasPR ChIP-seq libraries were sequenced by Azenta on the Illumina NextSeq platform (2x150 bp reads). RpoC-his10 libraries were sequenced on the Illumina MiSeq i100 platform (2x50 bp reads).

value: rpoC-his10 and pBH228 (inducible type I-B CRISPR system)

value: bacterial culture

value: aTc 500ng/mL (to induce CRISPR)


title: Bd21-3, Mutant, M0285, juvenile leaf tissue

description:
Library name: 139A1
Row name in SIEVE_M6_TPM.csv: M0285

value: leaf

value: juvenile leaf tissue

value: Mutant


title: RpoC-his10 (input)  CasPRIB1 biol rep2

description: Library name: RpoC-his10 (input)  CasPRIB1 biol rep2


description: Library name: RpoC-his10 (input) empty vector biol rep2


title: Bd21-3, Mutant, M0360, juvenile leaf tissue

description:
Library name: 141A1
Row name in SIEVE_M6_TPM.csv: M0360


title: 2208 Tumor, Erlotinib, CP-4057

description:
Library name: 2208_CP-4057
Column name in processed files: 2208_CP-4057

value: mammary tumor


title: Wollemia leaf mRNA replicate3

city: Cold Spring Harbor

first: W. Richard

last: McCombie

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Library name: Leaf3

data_processing:
Trimmed sequence reads were mapped to the W. nobilis assembly using STAR aligner
Read count extraction and normalization were performed using featureCounts against the W. nobilis gene annotations
Assembly: Wnobilis v1.6
Supplementary files format and content: tab-delimited text files include feature counts for each sample

organism: Wollemia nobilis

source_name: Leaf

extract_protocol:
RNA was harvested using PureLink Plant RNA Reagent (Invitrogen). 100ng total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Kapa mRNA Hyper prep kit following manufacturer's protocols.

value: Leaf


title: P. aeruginosa PAO1W pMEsadB exponential phase bio rep 2

description:
Library name: OSW_ex_2
OSW_ex

value: WT pMEsadB

value: exponential phase (OD 0.6-0.8)


title: PDX12, PDX, shCTR, in vivo, biol rep1

description:
Library name: Sample 1
Scipio

value: PDX12 (PDX)

value: Medulloblastoma


title: 2208 Tumor, Trametinib, CP-4058

description:
Library name: 2208_CP-4058
Column name in processed files: 2208_CP-4058

value: Trametinib


title: 2153 Tumor, Erlotinib, CP-4084

description:
Library name: 2153_CP-4084
Column name in processed files: 2153_CP-4084

value: Erlotinib


title: Bd21-3, Control, C10, juvenile leaf tissue

description:
Library name: 137A1
Row name in SIEVE_M6_TPM.csv: C10

value: Control


description: Library name: RpoC-his10 (input) empty vector biol rep1


title: RpoC-his10 (ChIP)  CasPRIB1 biol rep2

description:
Library name: RpoC-his10 (ChIP)  CasPRIB1 biol rep2
normalized wig file of reads mapped to LS1 genome


title: 2153 Tumor, Erlotinib, CP-4083

description:
Library name: 2153_CP-4083
Column name in processed files: 2153_CP-4083


title: Wollemia leaf mRNA replicate2

description: Library name: Leaf2


title: Bd21-3, Mutant, M0095, juvenile leaf tissue

description:
Library name: 136A1
Row name in SIEVE_M6_TPM.csv: M0095


title: Wollemia leaf mRNA replicate1

description: Library name: Leaf1


title: Bd21-3, Mutant, M0188, juvenile leaf tissue

description:
Library name: 135A1
Row name in SIEVE_M6_TPM.csv: M0188


title: 2153 Tumor, Erlotinib, CP-4082

description:
Library name: 2153_CP-4082
Column name in processed files: 2153_CP-4082


title: GCM1 knockout organoids chromatin accessibility

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: GCM1_ATAC
Chromatin accessibility profile of GCM1 knockout organoids using 10x Genomics Multiome

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger ARC (10x Genomics) to generate filtered feature-barcode matrices for both gene expression and chromatin accessibility with GRCh38-2020-A-2.0.0 reference genome.
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: H5 format filtered feature-barcode matrices (filtered_feature_bc_matrix.h5) containing gene expression counts for quality-controlled nuclei.
Supplementary files format and content: Gzip-compressed tab-separated fragments files (atac_fragments.tsv.gz) containing ATAC-seq fragment coordinates per cell barcode and BED format peak coordinate files (atac_peaks.bed) for chromatin accessibility analysis.

source_name: organoid-derived nuclei

growth_protocol: GCM1 knockout and AAVS1 control hTSCs were generated by CRISPR-Cas9 editing targeting exon 3 of GCM1 or the AAVS1 safe harbor locus, respectively. These hTSCs were seeded onto AggreWell 400 plates in ECSY medium and transferred to rotational culture using a ClinoStar bioreactor with FGF2 and BMP4 supplementation.Organoids were generated by rotational culture under simulated microgravity conditions using a ClinoStar bioreactor at 37°C with 5% CO₂ and continuous rotation, with medium supplemented with 50 ng/ml FGF2 and 20 ng/ml BMP4.

extract_protocol:
Single nuclei were isolated from organoids using the Chromium Nuclei Isolation Kit (10x Genomics) following manufacturer's protocol. Organoids were dissociated and nuclei were purified for multiome analysis. Approximately 10,000 nuclei per sample were processed for library preparation.
Single-nucleus multiome libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to manufacturer specifications. Approximately 10,000 nuclei were loaded onto a 10x Genomics Chromium Controller, enabling simultaneous profiling of chromatin accessibility and gene expression from individual nuclei. Libraries were sequenced on MGI DNBSEQ G400 with approximately 400M reads per lane across 2 lanes.

value: organoid-derived nuclei

value: GCM1 knockout

value: epithelial cell


title: Bd21-3, Mutant, M0304, juvenile leaf tissue

description:
Library name: 138A1
Row name in SIEVE_M6_TPM.csv: M0304


title: 2153 Tumor, Trametinib, CP-4087

description:
Library name: 2153_CP-4087
Column name in processed files: 2153_CP-4087


description:
Library name: RpoC-his10 (ChIP) empty vector biol rep1
normalized wig file of reads mapped to LS1 genome

value: rpoC-his10 and pBH228 (inducible type I-B CRISPR system)

value: bacterial culture


title: RpoC-his10 (ChIP) CasPRIB1 biol rep1

description:
Library name: RpoC-his10 (ChIP) CasPRIB1 biol rep1
normalized wig file of reads mapped to LS1 genome

value: aTc 500ng/mL (to induce CRISPR)


title: Bd21-3, Mutant, M0057, juvenile leaf tissue

description:
Library name: 134A1
Row name in SIEVE_M6_TPM.csv: M0057

value: leaf

value: juvenile leaf tissue


title: GCM1 knockout organoids gene expression

description:
Library name: GCM1_RNA
Gene expression profile of GCM1 knockout organoids using 10x Genomics Multiome


title: 2153 Tumor, Trametinib, CP-4086

description:
Library name: 2153_CP-4086
Column name in processed files: 2153_CP-4086

value: mammary tumor


description:
Library name: RpoC-his10 (ChIP) empty vector biol rep2
normalized wig file of reads mapped to LS1 genome


title: AAVS1 organoids chromatin accessibility

description:
Library name: AAVS1_ATAC
Chromatin accessibility profile of AAVS1 organoids using 10x Genomics Multiome

value: AAVS1 knockout


title: Bd21-3, Mutant, M0284, juvenile leaf tissue

description:
Library name: 133A1
Row name in SIEVE_M6_TPM.csv: M0284

value: Mutant


title: empty vector (Total) biol rep2

description: Library name: empty vector (Total) biol rep2

value: wild-type


title: 2153 Tumor, Trametinib, CP-4085

description:
Library name: 2153_CP-4085
Column name in processed files: 2153_CP-4085


title: AAVS1 organoids gene expression

description:
Library name: AAVS1_RNA
Gene expression profile of AAVS1 organoids using 10x Genomics Multiome


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 10

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

description: Library name: 4-010

data_processing:
Reads were aligned to the human genome (hg38) using HISAT2 (v2.2.0)
Counts were generated using featureCounts in R (v3.6.3) providing the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

source_name: Neutrophil

growth_protocol: Neutrophils (purity >97%) were isolated from peripheral blood by separation of leukocytes from erythrocytes using HetaSep, then centrifugation through density-gradient reagent (Ficoll Paque). Remaining erythrocytes were removed by hypotonic lysis using ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
100bp Paired-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

tag: group

value: Rheumatoid arthritis

value: 0h no treatment


title: Bd21-3, Mutant, M0024, juvenile leaf tissue

description:
Library name: 131A1
Row name in SIEVE_M6_TPM.csv: M0024


title: empty vector (Total) biol rep1

description: Library name: empty vector (Total) biol rep1


title: Tom+ and Tom– sorted CD19+ B cells loaded on cartridge 2

city: Lund

first: Joan

last: Yuan

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: Library name: Rhapsody_Cartridge_2

data_processing:
FASTQ files were processed with the Seven Bridges cloud-based platform, following the BD Rhapsody Sequence Analysis Pipeline.
Data was filtered for high quality cell and doublets were removed.
Data from the two separate BD Rhapsody cartridges  were merged.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Peritoneal cavity, spleen and Peyer's patches

extract_protocol:
FACS sorted B cells were labelled with BD Mouse immune Single-cell Multiplexing kit. Next a total of 60000 and 50000 viable cells were loaded on 2 separate BD Rhapsody cartridges and loaded on the BD Rhapsody Express Instrument, resulting in gravity diriven distribution of single cells into microwells. Single cell bead capture, lysis and barcoding and cDNA synthesis were performed according to manufacturer's instructions.
Targeted PCR amplification was performed according to manufacturer's instructions. The BD Rhapsody Immune Response Panel Mm was supplemented with custom primers adding up to 463 detectable transcripts. cDNA libraries were purifed with AMPure XP Reagent and quantified with Qubit Fluorometer (dsDNA HS Assay Kit). Final cDNA library  quality was assessed with Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: Mice were time-stamped with tamoxifen (50 mg/kg).

value: Tom+ and Tom- CD19+ B cells

value: Day 19 time-stamped


title: Day 10 time-stamped WT control mouse 98, FACS sorted Tom– B cells

description:
Library name: Sample_98_TN
Column name in count_matrix.txt: Sample_98_WT_TN

data_processing:
FASTQ files were processed with nf-core/rnaseq v 3.14 bioinformatics pipeline.
Sequence reads were trimmed and STAR alignment was performed with mm10 reference genome.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for all samples.

source_name: Peripheral blood

extract_protocol:
FACS sorted B cells were lysed in RNAzol (Sigma-Aldrich) and total RNA was extracted with Direct-zol RNA MiniPrep Kit (Zymo Research) according to manufacturer's instructions.
cDNA libraries were constructed wit SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and amplified with Nextera XT DNA library prep kit (Illumina). Final cDNA libraries were purified with AMPure XP Reagent, quantified with Qubit Fluorometer (dsDNA HS Assay Kit) and quality was assessed with Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

value: Peripheral blood

value: CD19+ Tom- B cells

value: WT

value: Day 10 time-stamped


title: Tom+ and Tom– sorted CD19+ B cells loaded on cartridge 1

description: Library name: Rhapsody_Cartridge_1

value: Peritoneal cavity, spleen and Peyer's patches


title: Bd21-3, Mutant, M0324, juvenile leaf tissue

description:
Library name: 130A1
Row name in SIEVE_M6_TPM.csv: M0324


title: Bd21-3, Mutant, M0230, juvenile leaf tissue

description:
Library name: 132A1
Row name in SIEVE_M6_TPM.csv: M0230


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 9

description: Library name: 4-009


title: empty vector (Mock IP) biol rep1

description: Library name: empty vector (Mock IP) biol rep1

value: bacterial culture

value: aTc 500ng/mL (to induce CRISPR)


title: Bd21-3, Mutant, M0109, juvenile leaf tissue

description:
Library name: 12A1
Row name in SIEVE_M6_TPM.csv: M0109

value: leaf

value: juvenile leaf tissue


title: Bd21-3, Mutant, M0148, juvenile leaf tissue

description:
Library name: 129A1
Row name in SIEVE_M6_TPM.csv: M0148


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 6

description: Library name: 4-006


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom– B cells

description:
Library name: Sample_97_TN
Column name in count_matrix.txt: Sample_97_TCL_TN


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 8

description: Library name: 4-008


title: CasPRhom1-his6 (input) biol rep2

description: Library name: CasPRhom1-his6 (input) biol rep2

value: pBH228 (inducible type I-B CRISPR system)


title: Day 10 time-stamped WT control mouse 98, FACS sorted Tom+ B cells

description:
Library name: Sample_98_TP
Column name in count_matrix.txt: Sample_98_WT_TP

value: CD19+ Tom+ B cells


title: empty vector (Mock IP) biol rep2

description: Library name: empty vector (Mock IP) biol rep2

value: wild-type


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 5

description: Library name: 4-005

value: Neutrophil


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 7

description: Library name: 4-007

value: Rheumatoid arthritis


title: CasPRhom1-his6 (input) biol rep1

description: Library name: CasPRhom1-his6 (input) biol rep1


title: Bd21-3, Mutant, M0316, juvenile leaf tissue

description:
Library name: 128A1
Row name in SIEVE_M6_TPM.csv: M0316

value: Mutant


title: CasPRhom7-his6 (input) biol rep2

description: Library name: CasPRhom7-his6 (input) biol rep2


title: Bd21-3, Mutant, M0042, juvenile leaf tissue

description:
Library name: 124A1
Row name in SIEVE_M6_TPM.csv: M0042


title: CasPRhom7-his6 (input) biol rep1

description: Library name: CasPRhom7-his6 (input) biol rep1


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom+ B cells

description:
Library name: Sample_97_TP
Column name in count_matrix.txt: Sample_97_TCL_TP


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom– B cells

description:
Library name: Sample_95_TN
Column name in count_matrix.txt: Sample_95_TCL_TN


title: Bd21-3, Mutant, M0379, juvenile leaf tissue

description:
Library name: 126A1
Row name in SIEVE_M6_TPM.csv: M0379


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 4

description: Library name: 4-004

value: 0h no treatment


title: CasPRhom3-his6 (input) biol rep2

description: Library name: CasPRhom3-his6 (input) biol rep2


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom+ B cells

description:
Library name: Sample_95_TP
Column name in count_matrix.txt: Sample_95_TCL_TP


title: CasPRhom3-his6 (input) biol rep1

description: Library name: CasPRhom3-his6 (input) biol rep1


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom– B cells

description:
Library name: Sample_94_TN
Column name in count_matrix.txt: Sample_94_TCL_TN


title: Bd21-3, Mutant, M0233, juvenile leaf tissue

description:
Library name: 123A1
Row name in SIEVE_M6_TPM.csv: M0233


title: Bd21-3, Mutant, M0351, juvenile leaf tissue

description:
Library name: 122A1
Row name in SIEVE_M6_TPM.csv: M0351


title: CasPRIIA1-his6 (input) biol rep2

description: Library name: CasPRIIA1-his6 (input) biol rep2

value: pAM600 (type II-A CRISPR system)


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 2

description: Library name: 4-002


title: Bd21-3, Mutant, M0424, juvenile leaf tissue

description:
Library name: 121A1
Row name in SIEVE_M6_TPM.csv: M0424


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom+ B cells

description:
Library name: Sample_94_TP
Column name in count_matrix.txt: Sample_94_TCL_TP

value: Peripheral blood


title: CasPRIIA1-his6 (input) biol rep1

description: Library name: CasPRIIA1-his6 (input) biol rep1


title: CasPRIB2-his6 (input) biol rep2

description: Library name: CasPRIB2-his6 (input) biol rep2


title: Bd21-3, Mutant, M0118, juvenile leaf tissue

description:
Library name: 11A1
Row name in SIEVE_M6_TPM.csv: M0118


title: Blood neutrophil, 0h, Healthy young, replicate 9

description: Library name: 3-011

value: Healthy young


title: Blood neutrophil, 0h, Healthy young, replicate 10

description: Library name: 3-012


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom+ B cells

description:
Library name: Sample_86_TP
Column name in count_matrix.txt: Sample_86_TCL_TP


title: Bd21-3, Mutant, M0161, juvenile leaf tissue

description:
Library name: 119A1
Row name in SIEVE_M6_TPM.csv: M0161


title: CasPRIB2-his6 (input) biol rep1

description: Library name: CasPRIB2-his6 (input) biol rep1


title: Bd21-3, Control, C14, juvenile leaf tissue

description:
Library name: 118A1
Row name in SIEVE_M6_TPM.csv: C14

value: Control


title: Blood neutrophil, 0h, Healthy young, replicate 7

description: Library name: 3-009


title: Blood neutrophil, 0h, Healthy young, replicate 8

description: Library name: 3-010


title: Day 10 time-stamped WT control mouse 83, FACS sorted Tom– B cells

description:
Library name: Sample_83_TN
Column name in count_matrix.txt: Sample_83_WT_TN

value: CD19+ Tom- B cells

value: WT

value: Day 10 time-stamped


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 3

description: Library name: 4-003


title: Bd21-3, Mutant, M0113, juvenile leaf tissue

description:
Library name: 114A1
Row name in SIEVE_M6_TPM.csv: M0113


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom+ B cells

description:
Library name: Sample_85_TP
Column name in count_matrix.txt: Sample_85_WT_TP


title: Bd21-3, Mutant, M0029, juvenile leaf tissue

description:
Library name: 117A1
Row name in SIEVE_M6_TPM.csv: M0029


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom– B cells

description:
Library name: Sample_85_TN
Column name in count_matrix.txt: Sample_85_WT_TN


title: Bd21-3, Mutant, M0292, juvenile leaf tissue

description:
Library name: 113A1
Row name in SIEVE_M6_TPM.csv: M0292


title: CasPRhom1-his6 (ChIP) biol rep2

description:
Library name: CasPRhom1-his6 (ChIP) biol rep2
normalized wig file of reads mapped to LS1 genome

value: bacterial culture

value: aTc 500ng/mL (to induce CRISPR)


title: CasPRhom1-his6 (ChIP) biol rep1

description:
Library name: CasPRhom1-his6 (ChIP) biol rep1
normalized wig file of reads mapped to LS1 genome


title: Blood neutrophil, 0h, Healthy young, replicate 5

description: Library name: 3-007


title: Blood neutrophil, 0h, Rheumatoid arthritis, replicate 1

description: Library name: 4-001


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom– B cells

description:
Library name: Sample_86_TN
Column name in count_matrix.txt: Sample_86_TCL_TN


title: CasPRIB1-his6 (input) biol rep1

description: Library name: CasPRIB1-his6 (input) biol rep1


title: Day 10 time-stamped WT control mouse 83, FACS sorted Tom+ B cells

description:
Library name: Sample_83_TP
Column name in count_matrix.txt: Sample_83_WT_TP


title: Blood neutrophil, 0h, Healthy young, replicate 6

description: Library name: 3-008


title: Bd21-3, Mutant, M0338, juvenile leaf tissue

description:
Library name: 112A1
Row name in SIEVE_M6_TPM.csv: M0338

value: leaf

value: juvenile leaf tissue


title: Blood neutrophil, 0h, Healthy young, replicate 4

description: Library name: 3-005


title: CasPRhom7-his6 (ChIP) biol rep2

description:
Library name: CasPRhom7-his6 (ChIP) biol rep2
normalized wig file of reads mapped to LS1 genome

value: pBH228 (inducible type I-B CRISPR system)


title: CasPRhom7-his6 (ChIP) biol rep1

description:
Library name: CasPRhom7-his6 (ChIP) biol rep1
normalized wig file of reads mapped to LS1 genome


title: CasPRIB1-his6 (input) biol rep2

description: Library name: CasPRIB1-his6 (input) biol rep2


title: Bd21-3, Mutant, M0312, juvenile leaf tissue

description:
Library name: 110A1
Row name in SIEVE_M6_TPM.csv: M0312


title: NTg_m5

first: Ari

last: Sudwarts

address: 4001 E Fletcher Ave

institute: USF

description: Library name: NTg_m5

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: csv file contains matrix data of gene counts for each sample

source_name: Brain

extract_protocol:
RNA was isolated using Direct-zol RNA Miniprep Plus kit (Zymo Research)
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

value: Brain

value: Ntg

tag: Sex

value: male


title: Bd21-3, Mutant, M0343, juvenile leaf tissue

description:
Library name: 111A1
Row name in SIEVE_M6_TPM.csv: M0343

value: Mutant


title: PS19_m5

description: Library name: PS19_m5


title: NTg_m4

description: Library name: NTg_m4


title: Blood neutrophil, 0h, Healthy young, replicate 2

description: Library name: 3-002

value: Neutrophil

value: 0h no treatment


title: Blood neutrophil, 0h, Healthy young, replicate 3

description: Library name: 3-004


title: Bd21-3, Mutant, M0389, juvenile leaf tissue

description:
Library name: 10A1
Row name in SIEVE_M6_TPM.csv: M0389


title: PS19_m4

description: Library name: PS19_m4


title: CasPRhom3-his6 (ChIP) biol rep1

description:
Library name: CasPRhom3-his6 (ChIP) biol rep1
normalized wig file of reads mapped to LS1 genome


title: Blood neutrophil, 0h, Healthy young, replicate 1

description: Library name: 3-001


title: NTg_m3

description: Library name: NTg_m3


title: Blood neutrophil, 0h, Healthy old, replicate 8

description: Library name: 2-014

value: Healthy old


title: CasPRhom3-his6 (ChIP) biol rep2

description:
Library name: CasPRhom3-his6 (ChIP) biol rep2
normalized wig file of reads mapped to LS1 genome


title: Bd21-3, Mutant, M0138, juvenile leaf tissue

description:
Library name: 109A1
Row name in SIEVE_M6_TPM.csv: M0138


title: Bd21-3, Mutant, M0422, juvenile leaf tissue

description:
Library name: 108A1
Row name in SIEVE_M6_TPM.csv: M0422


title: NTg_f4

description: Library name: NTg_f4

value: female


title: Blood neutrophil, 0h, Healthy old, replicate 9

description: Library name: 2-015


title: Bd21-3, Mutant, M0096, juvenile leaf tissue

description:
Library name: 107A1
Row name in SIEVE_M6_TPM.csv: M0096


title: PS19_m3

description: Library name: PS19_m3


title: NTg_f5

description: Library name: NTg_f5


title: CasPRIB2-his6 (ChIP) biol rep2

description:
Library name: CasPRIB2-his6 (ChIP) biol rep2
normalized wig file of reads mapped to LS1 genome


title: CasPRIIA1-his6 (ChIP) biol rep2

description:
Library name: CasPRIIA1-his6 (ChIP) biol rep2
wig file of normalized reads mapped to LS1 genome and pAM600 plasmid

value: pAM600 (type II-A CRISPR system)


title: CasPRIIA1-his6 (ChIP) biol rep1

description:
Library name: CasPRIIA1-his6 (ChIP) biol rep1
wig file of normalized reads mapped to LS1 genome and pAM600 plasmid


title: Blood neutrophil, 0h, Healthy old, replicate 5

description: Library name: 2-007


title: CasPRIB2-his6 (ChIP) biol rep1

description:
Library name: CasPRIB2-his6 (ChIP) biol rep1
normalized wig file of reads mapped to LS1 genome


title: Bd21-3, Mutant, M0334, juvenile leaf tissue

description:
Library name: 105A1
Row name in SIEVE_M6_TPM.csv: M0334


title: PS19_f3

description: Library name: PS19_f3


title: Blood neutrophil, 0h, Healthy old, replicate 7

description: Library name: 2-013


title: CasPRIB1-his6 (ChIP) biol rep2

description:
Library name: CasPRIB1-his6 (ChIP) biol rep2
normalized wig file of reads mapped to LS1 genome


title: Bd21-3, Mutant, M0314, juvenile leaf tissue

description:
Library name: 104A1
Row name in SIEVE_M6_TPM.csv: M0314


title: Blood neutrophil, 0h, Healthy old, replicate 6

description: Library name: 2-009


title: PS19_f2

description: Library name: PS19_f2


title: CasPRIB1-his6 (ChIP) biol rep1

description:
Library name: CasPRIB1-his6 (ChIP) biol rep1
normalized wig file of reads mapped to LS1 genome


title: Bd21-3, Mutant, M0051, juvenile leaf tissue

description:
Library name: 106A1
Row name in SIEVE_M6_TPM.csv: M0051


title: Bd21-3, Mutant, M0276, juvenile leaf tissue

description:
Library name: 103A1
Row name in SIEVE_M6_TPM.csv: M0276


title: NTg_f3

description: Library name: NTg_f3


title: Bd21-3, Mutant, M0263, juvenile leaf tissue

description:
Library name: 102A1
Row name in SIEVE_M6_TPM.csv: M0263


title: serum, control, rep4

city: Delhi

first: Neeru

last: Khanna

state: Delhi

address: Mall road

department: Functional Genomics Unit

country: India

institute: CSIR-IGIB

data_processing:
nf-core/smrnaseq v2.1.0 pipeline was used.
qiaseq protocol was used for adapter removal and data preprocessing
mirbase human mature and hairpin database was used as a reference.
Assembly: mirbase 22.1
Supplementary files format and content: csv file includes raw read counts for each sample

source_name: serum

extract_protocol:
RNA was isolated from serum using miRNeasy serum/plasma advanced kit (Qiagen, USA)
library preparation was done using QIAseq miRNA Library Kit (Qiagen, USA) using manufacturer's protocol. 5ul of each concentrated sample was used to prepare miRNA libraries.

value: serum

value: Female

tag: disease

value: Control

tag: disease state


title: PS19_m2

description: Library name: PS19_m2


title: Blood neutrophil, 0h, Healthy old, replicate 4

description: Library name: 2-005


title: NTg_f2

description: Library name: NTg_f2


title: Blood neutrophil, 0h, Healthy old, replicate 2

description: Library name: 2-003


title: Bd21-3, Mutant, M0450, juvenile leaf tissue

description:
Library name: 100A1
Row name in SIEVE_M6_TPM.csv: M0450


title: serum, control, rep3


title: Blood neutrophil, 0h, Healthy old, replicate 1

description: Library name: 2-001


title: serum, control, rep2

value: Male


title: PS19_f1

description: Library name: PS19_f1


title: Blood neutrophil, 0h, Frailty, replicate 10

description: Library name: 1-019

value: Frailty


title: Wollemia ovule mRNA replicate3

description: Library name: Ovule3

source_name: Ovule

value: Ovule


title: Blood neutrophil, 0h, Frailty, replicate 9

description: Library name: 1-017


title: Wollemia ovule mRNA replicate2

description: Library name: Ovule2


title: NTg_f1

description: Library name: NTg_f1


title: serum, control, rep1


title: serum, CCS, rep6

value: Coronary Artery Disease

value: Chronic


title: Blood neutrophil, 0h, Frailty, replicate 8

description: Library name: 1-016


title: serum, CCS, rep5


title: Wollemia ovule mRNA replicate1

description: Library name: Ovule1


title: PS19_m1

description: Library name: PS19_m1

value: Brain


title: Blood neutrophil, 0h, Healthy old, replicate 3

description: Library name: 2-004


title: NTg_m2

description: Library name: NTg_m2

value: Ntg


title: Blood neutrophil, 0h, Frailty, replicate 7

description: Library name: 1-013


title: serum, CCS, rep4


title: Wollemia pollen mRNA replicate3

description: Library name: Pollen3

source_name: Pollen

value: Pollen


title: Wollemia pollen mRNA replicate2

description: Library name: Pollen2


title: PS19_Cx3_m5

description: Library name: PS19_Cx3_m5

value: male


title: serum, CCS, rep2


title: Wollemia pollen mRNA replicate1

description: Library name: Pollen1


title: Blood neutrophil, 0h, Frailty, replicate 5

description: Library name: 1-009

value: Neutrophil


title: serum, CCS, rep3


title: aPS-TD-BiolRep2

description:
Library name: Sample12
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-TD-2

data_processing:
Reads were aligned with HISAT2 version 2.0.5 to the mm10 genome (accessed through Ensembl) and featureCounts was used to assign reads to genes using Ensemble genome annotation.
Assembly: Mouse mm10
Supplementary files format and content: csv files include raw counts for each sample

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA micro kit (Qiagen) according to the manufacturer’s protocol.
mRNA library was preparred with the clontech SMART-Seq V4. TakaraBio's SMART-Seq v4 Ultra Low Input RNA Kit.

value: Spleen

tag: strain

value: CD8 T cell

value: WT

value: mch1N11 PS-targeting Ab


title: Blood neutrophil, 0h, Frailty, replicate 6

description: Library name: 1-011

value: 0h no treatment


title: serum, ACS, rep2

value: serum

value: Acute


title: serum, ACS, rep1

value: Male


title: aPS-Trans-BiolRep2

description:
Library name: Sample10
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-Trans-2


title: PS19_Cx3_f4

description: Library name: PS19_Cx3_f4

value: female


title: NTg_m1

description: Library name: NTg_m1


title: Blood neutrophil, 0h, Frailty, replicate 3

description: Library name: 1-006

value: Frailty


title: Blood neutrophil, 0h, Frailty, replicate 2

description: Library name: 1-005


title: PS19_Cx3_f5

description: Library name: PS19_Cx3_f5


title: Blood neutrophil, 0h, Frailty, replicate 4

description: Library name: 1-007


title: Blood neutrophil, 0h, Frailty, replicate 1

description: Library name: 1-001


title: PS19_Cx3_m2

description: Library name: PS19_Cx3_m2


title: aPS-Stem-BiolRep2

description:
Library name: Sample8
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-Stem-2


title: aPS-TD-BiolRep1

description:
Library name: Sample11
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-TD-1


title: PS19_Cx3_m3

description: Library name: PS19_Cx3_m3


title: Tumor breast cancer 64

type: genomic

city: Ciudad de Mexico

first: Martha-Eugenia

last: Ruiz-Tachiquin

state: Ciudad de Mexico

address: Av. Cuauhtemoc No.330, Col. Doctores, Alcaldia Cuauhtemoc

department: Unidad de Investigacion Medica en Enfermedades Oncologicas

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Hybridized to Cytoscan HD Affymetrix

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the GeneChip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (version v3.2.2). Copy number values were extracted and converted from CEL files into CYCHP files using Chromosome Analysis Suite software (v4.4.0.63). Reference file was CytoScan HD Array.na33.r3, ChAS Browser was NefAffx Build hg38 (20200828).

label: Biotin

source_name: Tumor breast cancer 64

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA extraction was done with a QIAamp® micro kit (QIAGEN) according to the manufacturer’s instructions. The extractions were modified to include an initial incubation at 95°C for 15 min followed by 5 min at room temperature as described previously, before being digested with proteinase K for 3 days at 56°C in a water-bath with addition of fresh enzyme at 24 h intervals.

tag: specimen

value: Tissue


title: serum, CCS, rep1

value: Coronary Artery Disease

value: Chronic


title: T47D knock down with siGADD45A2 repeat2

city: Taipei

first: Yi-Ru

last: Tseng

address: No. 201, Sec. 2, Sh ipai Rd.

country: Taiwan

institute: Taipei Veterans General Hospita

description:
Library name: T47D_siGADD45A1-b
T47D knock down with siGADD45A2 repeat2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using CLC Genomics Workbench (v 25.0.3) (parameters- default)
Read count extraction  were performed using CLC Genomics Workbench (v 25.0.3)
Normalization were performed using CLC Genomics Workbench (v 25.0.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MCF-7 and T-47D were treated with DMEM/F12 and RPMI 1640 medium,   supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen™) and 1–bromo–3–chloropropane (BCP) (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries
RNA-seq

treatment_protocol: shRNA knockdown of GADD45A in breast cancer cells

value: breast

value: knock down with siGADD45A2


title: PS19_Cx3_m4

description: Library name: PS19_Cx3_m4

value: Brain

value: male


title: aPS-Trans-BiolRep1

description:
Library name: Sample9
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-Trans-1

value: Spleen


title: aPS-Stem-BiolRep1

description:
Library name: Sample7
Column name in Ctrl_V_PS_RNAseqCounts.csv: PS-Stem-1

value: CD8 T cell


title: PS19_Cx3_f3

description: Library name: PS19_Cx3_f3


title: Leukocytes DNA breast cancer 64

description: Hybridized to Cytoscan HD Affymetrix

source_name: Leukocytes DNA breast cancer 64


title: IgG-TD-BiolRep2

description:
Library name: Sample6
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-TD-2

value: WT

value: IgG Control


title: Tumor breast cancer 30

description: Hybridized to Cytoscan HD Affymetrix

source_name: Tumor breast cancer 30


title: T47D knock down with siGADD45A2 repeat1

description:
Library name: T47D_siGADD45A1-a
T47D knock down with siGADD45A2 repeat1


title: PS19_Cx3_m1

description: Library name: PS19_Cx3_m1


title: PS19_Cx3_f2

description: Library name: PS19_Cx3_f2


title: IgG-TD-BiolRep1

description:
Library name: Sample5
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-TD-1


title: Adjacent tissue breast cancer 30

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue breast cancer 30


title: Leukocytes DNA breast cancer 30

description: Hybridized to Cytoscan HD Affymetrix

source_name: Leukocytes DNA breast cancer 30

value: Blood


title: IgG-Trans-BiolRep2

description:
Library name: Sample4
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-Trans-2


title: MCF7 knock down with siGADD45A2 repeat1

description:
Library name: MCF7_siGADD45A2-a
MCF7 knock down with siGADD45A2 repeat1


title: RNA-seq_Tir1-control, auxin-24h_rep3

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

description:
Library name: RSRS45
RSRS45

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

growth_protocol: E14 mESCs are of XY karyotype and 129P2/Ola genetic background. mESCs were cultured in DMEM+Glutamax (ThermoFisher 10569044) supplemented with 15% Fetal Bovine Serum (ThermoFisher 10437028), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1X non-essential amino-acids (ThermoFisher 11140050), 104U of Leukemia inhibitory factor (Millipore ESG1107), PD0325901 (APExBIO A3013), CHIR-99021 (APExBIO A3011). Cells were maintained at a density of 0.2-1.5x105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48h on 0.1% gelatin-coated dishes at 37°C and 5% CO2. 0.1% gelatin was prepared in 1X PBS using Gelatin powder (Sigma Aldrich G1890). Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection and tested negative.

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
Stranded RNA-seq was performed using 1000ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

treatment_protocol: Degradation of proteins tagged with the Auxin-Inducible Degron (44 amino-acid AID* truncation with residues 71–114) was induced by adding Indole-3-acetic acid sodium (IAA, Sigma Cat #I5148-2G) to a final concentration of 500μM. Degradation of proteins tagged with the FKBP12F36V degron was induced by adding dTAG-13 (abbreviated dTAG - Sigma Cat, SML2601) to a final concentration of 500nM (unless stipulated otherwise).

value: Mouse Embryonic Stem Cells


title: IgG-Trans-BiolRep1

description:
Library name: Sample3
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-Trans-1


title: PS19_Cx3_f1

description: Library name: PS19_Cx3_f1


title: MCF7 knock down with siGADD45A2 repeat2

description:
Library name: MCF7_siGADD45A2-b
MCF7 knock down with siGADD45A2 repeat2


title: Tumor breast cancer 27

description: Hybridized to Cytoscan HD Affymetrix

source_name: Tumor breast cancer 27


title: T47D knock down with scramble repeat2

description:
Library name: T47D_scramble-b
T47D knock down with scramble repeat2

value: knock down with scramble


title: RNA-seq_Tir1-control, auxin-24h_rep2

description:
Library name: RSRS44
RSRS44


title: T47D knock down with scramble repeat1

description:
Library name: T47D_scramble-a
T47D knock down with scramble repeat1


title: MCF7 knock down with scramble repeat2

description:
Library name: MCF7_scramble-b
MCF7 knock down with scramble repeat2


title: IgG-Stem-BiolRep1

description:
Library name: Sample1
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-Stem-1

source_name: Spleen


title: Adjacent tissue breast cancer 27

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue breast cancer 27


title: Leukocytes DNA breast cancer 27

description: Hybridized to Cytoscan HD Affymetrix

source_name: Leukocytes DNA breast cancer 27


title: RNA-seq_Tir1-control, auxin-24h_rep1

description:
Library name: RSRS43
RSRS43


title: IgG-Stem-BiolRep2

description:
Library name: Sample2
Column name in Ctrl_V_PS_RNAseqCounts.csv: Ig-Stem-2


title: MCF7 knock down with scramble repeat1

description:
Library name: MCF7_scramble-a
MCF7 knock down with scramble repeat1


title: hTSC CT27 Matrigel-embedded culture

description:
Library name: CT27_matrigel
Bulk RNA-seq of CT27 hTSC-derived organoids cultured in Matrigel for 11 days

data_processing:
Raw reads were quality-trimmed using TrimGalore (v0.6.7) with 10-bp 5' clipping and adapter removal.
Trimmed reads were aligned to GRCh38/hg38 using STAR (v2.7.11b) with RefSeq annotation and transcript quantification mode.
Transcript abundance was quantified using RSEM (v1.3.3) with strand-specific parameters, generating TPM and raw read counts.
Differential expression analysis was performed using DESeq2. Genes with adjusted P < 0.05 (Benjamini-Hochberg correction) and |log2FC| > 1.0 were considered significantly differentially expressed.
GRCh38/hg38
processed_data_all8.tsv: Tab-delimited text file containing RSEM-derived TPM (Transcripts Per Million) values for all 8 samples. Columns: gene_id (Ensembl gene ID), B31_10cm, B31_rot, B31_matrigel, B31_shake, CT27_10cm, CT27_rot, CT27_matrigel, CT27_shake.
Assembly: GRCh38-2020-A (10x Genomics)
Supplementary files format and content: *processed data files format and content barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene annotation), matrix.mtx.gz (UMI count matrix in Matrix Market format), as generated by Cell Ranger filtered_feature_bc_matrix output. Files are provided separately for CT27 (EVT_CT27_) and CT29 (EVT_CT29_) samples.

source_name: Trophoblast organoids

growth_protocol: hTSCs were dissociated and seeded onto AggreWell 400 24-well plates (Stem Cell Technologies) at 6 × 10⁵ cells/well in ECSY medium (DMEM/F-12, 1% ITS-X, 0.15% BSA, 1% KSR, 200 μM L-ascorbic acid, 1 μg/ml heparin, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, 10 μM Y27632). After 24 hours, spheroids were collected and transferred to four culture conditions: (1) Rotational culture using a ClinoStar bioreactor (CelVivo) at 37°C with 5% CO₂ and continuous rotation (9-20 rpm); (2) Floating culture in non-treated 100 mm dishes without agitation; (3) Shaking culture in non-treated 100 mm dishes with horizontal agitation; (4) Matrigel-embedded culture. All conditions used ECSY medium supplemented with 50 ng/ml FGF2 and 20 ng/ml BMP4, with Y27632 reduced to 2.5 μM. Organoids were cultured for 11 days.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) with genomic DNA removal by ribonuclease-free deoxyribonuclease I.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) with NEBNext Poly(A) mRNA Magnetic Isolation Module for poly(A) selection. Libraries were sequenced on Illumina NovaSeq X Plus (150 bp paired-end reads, 3 Gb per sample).

treatment_protocol: Four culture conditions were compared: rotation (simulated microgravity), floating (static suspension), shaking (horizontal agitation), and Matrigel embedding. Two independent hTSC lines (B31 and CT27) were used as biological replicates.

value: Trophoblast organoids

value: human trophoblast stem cells (hTSCs) CT27

value: trophoblast

value: wild-type

value: Matrigel-embedded culture (11 days)


title: hTSC CT27 Shaking culture

description:
Library name: CT27_shaking
Bulk RNA-seq of CT27 hTSC-derived organoids cultured under horizontal shaking conditions for 11 days

value: Shaking culture (horizontal agitation, 11 days)


title: HSV1 A3G overexpressed HEK293 IP RNaseH

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

description: Library name: HSV1 A3G overexpressed HEK293 IP RNaseH

data_processing:
ChIP-seq and DRIP-seq reads were aligned to the HSV-1 KOS1 reference genome using two parallel strategies. (1) Bowtie2 with default parameters was used to generate the processed bigWig files. (2) BWA-MEM with the parameter -B 0 (all other settings left as default) was used for the analysis of APOBEC-associated mutations.
Alignments were filtered using samtools v1.10 keeping only primary alignments of properly paired reads that had >30 mapping quality score. PCR duplicates were also filtered out.
RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage (.bedgraph and .bigwig) files have been generated with 20 bp resolution using Deeptools bamCoverage v3.5.140.
deepTools were used to the input correction (bigwigCompare)
FreeBayes was used for mutation calling.
Assembly: HSV-1 KOS1 reference sequence
Supplementary files format and content: bigwig files
Supplementary files format and content: vcf files of the mutations

growth_protocol: Jurkat human T lymphoblast cells (ATCC-J.RT3-T3), HEK293-AD pCMVA3A-tGFP and pCMVA3G-tGFP cells, and human retinal pigment epithelium (RPE-1) pdoxA3A-HA cells were clutured according to standard protocols. The KOS1 strain of HSV-1 (ATCC-VR-1493; LOT: 59681562) was cultured in Vero cells.

extract_protocol:
Twenty million HSV-1 infected or mock control cells were grown to near-confluence, followed by crosslinking them with 1% formaldehyde for 10 minutes and quenching with glycine. After washing and lysing, the cells were stored until the chromatin could be prepared. Chromatin was then sheared by sonication to achieve the desired fragment size of 200–500 bp, with 2% of the fragmented material set aside as input DNA. Chromatin Immunoprecipitation (ChIP) was performed using 8 µg of specific polyclonal antibodies: anti-APOBEC3A and anti-APOBEC3G for Jurkat cells, anti-HA for RPE-1 cells, or anti-tGFP for HEK293-AD cells. Concurrently, DNA:RNA Hybrid Immunoprecipitation (DRIP) was conducted on the same samples using the S9.6 monoclonal antibody. For DRIP, 6 µg of genomic DNA was first isolated (omitting RNase A), fragmented by sonication, and then incubated overnight with S9.6 antibody-coated Protein G magnetic beads; a separate sample was treated with RNase H as a control. Following washing steps, the immunoprecipitated material was eluted using proteinase K, and the final DNA was purified using Ampure XP beads and quantified.
Illumina TruSeq ChIP Sample Preparation protocol were used to DRIP-seq. DRIP DNA were end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced (at the EMBL Genomics Core Facility, Heidelberg) using an Illumina HiSeq 2500 instrument in the 2x125 paired-end sequencing mode, and Illumina NovaSeq X Plus PE150 (at Novogene Ltd.).

treatment_protocol: HSV-1 KOS1 virus was employed to infect the above cell lines at a multiplicity of infection (MOI) of 5. HSV-1 infection of RPE-1 pdoxA3A-HA cells was performed 2 hours after the addition of doxycycline (dox) to induce A3A-HA expression, and dox was maintained throughout the experiment (12 hours post-infection). Following incubation of the cells with the virus for 2 hours, excess HSV-1 was removed, and the cells were cultivated for downstream analysis. We fixed cells in 1% formaldehyde (Thermo Fisher Scientific, Pierce™ 16% Formaldehyde (w/v), Methanol-free,) at various time points post-infection.

tag: agent


title: K14-TRT Tumor, Untreated, CP-5314

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: K14-TRT_CP-5314
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-5314

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts.
The raw counts were upper quartile-normalized.
Assembly: mm10
Supplementary files format and content: Salmon-quantified, upper quartile-normalized read-counts. First column is the gene name, subsequent columns are individual samples.

source_name: mammary tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to isolate the RNA according to the manufacturer's protocol.
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit.

value: mammary tumor

value: Untreated


title: HSV1 A3G overexpressed HEK293 input

description: Library name: HSV1 A3G overexpressed HEK293 input


title: Tumor breast cancer 10

description: Hybridized to Cytoscan HD Affymetrix

source_name: Tumor breast cancer 10

value: Tissue


title: K14-TRT Tumor, Untreated, CP-5313

description:
Library name: K14-TRT_CP-5313
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-5313


title: hTSC CT27 Rotational culture

description:
Library name: CT27_rotation
Bulk RNA-seq of CT27 hTSC-derived organoids cultured under rotational conditions for 11 days

value: Rotational culture (simulated microgravity, 11 days)


title: T11 Tumor, Carboplatin + Paclitaxel, CP-5311

description:
Library name: T11_CP-5311
Column name in raw_counts_All_Samples.txt: T11_CP-5311

value: Carboplatin + Paclitaxel


title: Adjacent tissue breast cancer 10

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue breast cancer 10


description: Library name: HSV1 A3G overexpressed HEK293 DRIP-seq IP


title: hTSC CT27 Floating culture

description:
Library name: CT27_floating
Bulk RNA-seq of CT27 hTSC-derived organoids cultured under static floating conditions for 11 days

value: Floating culture (static suspension in 10cm dish, 11 days)


title: Leukocytes DNA breast cancer 10

description: Hybridized to Cytoscan HD Affymetrix

source_name: Leukocytes DNA breast cancer 10


title: T11 Tumor, Carboplatin + Paclitaxel, CP-5310

description:
Library name: T11_CP-5310
Column name in raw_counts_All_Samples.txt: T11_CP-5310


description: Library name: HSV1 A3G overexpressed HEK293 ChIP-seq IP


title: Tumor breast cancer 09

description: Hybridized to Cytoscan HD Affymetrix

source_name: Tumor breast cancer 09


title: Leukocytes DNA breast cancer 09

description: Hybridized to Cytoscan HD Affymetrix

source_name: Leukocytes DNA breast cancer 09


title: T11 Tumor, Carboplatin + Paclitaxel, CP-5309

description:
Library name: T11_CP-5309
Column name in raw_counts_All_Samples.txt: T11_CP-5309


title: KPB25L Tumor, Carboplatin + Paclitaxel, CP-5307

description:
Library name: KPB25L_CP-5307
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5307


title: hTSC B31 Matrigel-embedded culture

description:
Library name: B31_matrigel
Bulk RNA-seq of B31 hTSC-derived organoids cultured in Matrigel for 11 days

value: human trophoblast stem cells (hTSCs) B31


title: HSV1 A3A overexpressed HEK293 IP RNaseH

description: Library name: HSV1 A3A overexpressed HEK293 IP RNaseH


title: Adjacent tissue breast cancer 09

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue breast cancer 09


title: KPB25L Tumor, Carboplatin + Paclitaxel, CP-5308

description:
Library name: KPB25L_CP-5308
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5308


title: hTSC B31 Rotational culture

description:
Library name: B31_rotation
Bulk RNA-seq of B31 hTSC-derived organoids cultured under rotational conditions for 11 days


description: Library name: HSV1 A3A overexpressed HEK293 ChIP-seq IP


title: HSV1 A3A induced RPE-1 input

description: Library name: HSV1 A3A induced RPE-1 input


title: KPB25L Tumor, Carboplatin + Paclitaxel, CP-5306

description:
Library name: KPB25L_CP-5306
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5306