title: 2153 Tumor, Carboplatin + Paclitaxel, CP-4677

description:
Library name: 2153_CP-4677
Column name in raw_counts_All_Samples.txt: 2153_CP-4677


title: XHLT2-HS51-BLE1

status: Public on Mar 09 2026

type: SRA

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

country: USA

institute: University of California San Francisco

description:
Library name: XHLT2-HS51-BLE1
Baseline PBMC: donor HS51

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the human reference genome and Ensembl annotation (GRCh38 genome build, version 95) using STAR (v2.7.5c) with the following parameters: --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 -outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 -alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000. Duplicate reads were removed using Picard Tools (v2.23.3).
The raw read counts per gene from *ReadsPerGene.out.tab output of STAR are provided here.
Nucleotide variants were identified from the resulting bam files using the Genome Analysis Tool Kit (v4.0.11.0) following the best practices for RNA-seq variant calling. This included splitting spliced reads, calling variants with HaplotypeCaller (added parameters: --dont-use-soft-clipped-bases -standcall-conf 20.0), and filtering variants with VariantFiltration (added parameters: -window 35 cluster 3 --filter-name FS -filter FS >30.0 --filter-name QD -filter QD <2.0). Variants were further filtered to include a list of high quality SNP for identification of the subject of origin of individual cells by removing all novel variants, maintaining only biallelic variants with MAF greater than 5%, a max missing of one individual with a missing variant call at a specific site and requiring a minimum depth of two (parameters: --max-missing 1.0 --min-alleles 2 --max-alleles 2 --removeindels --snps snp.list.txt --min-meanDP 2 --maf 0.05 --recode --recode-INFO-all –out). The filtered VCF files are provided here.
Assembly: hg38
Supplementary files format and content: .vcf files are variant call format files derived from bulk RNA-seq of PBMC
Supplementary files format and content: .ReadsPerGene.out.tab files are output of STAR, containing four columns: (1) gene ID, (2) counts for unstranded RNA-seq, (3) counts for the 1st read strand aligned with RNA (htseq-count option -s yes), (4) counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

molecule: total RNA

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). Cell counts and viability of thawed PBMCs were determined using CellacaMX and 0.5 million cells were used for each sample. RNA was extracted using the Quick-RNA MagBead kit (Zymo Research) on the KingFisher automated extraction and purification system (ThermoFisher) according to manufacturer’s instructions. Quality and quantification of extracted RNA was assessed on the 5300 Fragment Analyzer System (Agilent).
The cDNA libraries were generated using the Universal Plus mRNA-Seq with NuQuant kit according to manufacturer’s instructions (Tecan). The libraries were subsequently sequenced on a HiSeq 4000 platform (Illumina).

tag: tissue

value: PBMC


title: XHLT2-HS4-BLE1

description:
Library name: XHLT2-HS4-BLE1
Baseline PBMC: donor HS4


title: MDA5_HT29_METTL3KD1_MT_NT_rep1

city: Oxford

first: Yucheng

last: Wang

state: Oxfordshire

address: Roosevelt Drive, Headington

country: United Kingdom

institute: University of Oxford

description: Library name: MDA5_HT29_METTL3KD1_MT_NT_rep1

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 (v2.7.9a). MDA5-protected regions were identified as sequencing signal peaks from RNaseA-treated samples against total cytoplasmic RNA samples. For each sample, total BAM files were split into forward strand aligned and reverse strand aligned bam files, and then peaks were called from strand-specific BAM files using MACS2 (v2.2.6) with the following parameters: -q 0.01 –keep-dup all –nomodel. Peaks identified from the forward and reverse strands were combined for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Colorectal cancer

growth_protocol: HT29 and HCT116 human colorectal cancer cell lines were cultured in McCoy’s 5A medium supplemented with penicillin-streptomycin (1%), and Fetal-Bovine-serum (10%).

extract_protocol:
We used the RNase A protection assay followed by RNA sequencing as previously described [9]. In brief, the RNA from cytosolic fraction was isolated using a QIAGEN RNeasy mini kit from colorectal cancer cell lines. Isolated cytosolic RNA was pre-incubated with MDA5-Δ2CARD protein (150 nM)room temperature for 10 min in 20 mM HEPES pH 7.5, 50 mM NaCl, 2 mM MgCl2 and 2 mM DTT, followed by addition of RNase A (final concentration 2 n/ul) and incubation for another 5 min at room temperature. The RNase A digestion was inactivated by adding TRIzol reagent and the RNA was purified with a Directzol RNA miniprep kit, using the manufacturer’s protocol. To remove small fragments resulting from RNase A digestion (less than 100 bp), the extracted RNA was further cleaned up using the QIAGEN RNeasy mini kit. The final RNA was used for the cDNA library preparation.
One hundred nanograms of RNA was used by WIMM single cell Genomics for the cDNA library construction using KAPA RNA Hyper-Prep with RiboErase Library Preparation Kit (Roche) according to the manufacturer's instruction, with the following modifications. For the fragmentation step, total CytoRNA was heated at 94 °C for 8 min. MDA5-protected RNA was heated at 65 °C for 1 min. 1.5µM KAPA Unique Dual-Indexed Adapters were used for adapter ligation. Libraries were incubated in C1000 Touch Thermal Cycler (Bio-rad) for 45s at 98°C and 11 PCR cycles were used  (for total CytoRNA) and 16 PCR cycles were used (for MDA5-protected samples), for 15s at 98°C, 30s at 60°C, and 30s at 72°C. The libraries were then incubated at 72°C for 1min for final extension. Following a 1x Kapa Pure Bead clean-up, post-PCR enriched libraries were eluted in 20uL of 10mM Tris-HCl (pH8.0) and validated using Agilent D5000 ScreenTape and Reagents on the 2200 TapeStation System  The cDNA libraries for total CytoRNA and MDA5-protected were pooled and 6 pM of cDNA libraries were sequenced using paired-ended 150-bp reads on  NovaSeq X Plus by Novogene.

value: Colorectal cancer

tag: cell line

tag: cell type

value: human colorectal cancer cell line

tag: genotype

value: METTL3 knock-down

tag: treatment

value: Mock treated


title: 2153 Tumor, anti-PD1 + anti-CTLA4, CP-4675

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

institute: University of North Carolina at Chapel Hill

description:
Library name: 2153_CP-4675
Column name in raw_counts_All_Samples.txt: 2153_CP-4675

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: anti-PD1 + anti-CTLA4


title: pool-6, well-4, GEX

description:
Library name: XHLT2-POOL-DB6-SCG4_GEX
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-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

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).

tag: batch

tag: library type

value: mRNA


title: MDA5_HT29_METTL3KD1_MT_RNaseA_rep1

description: Library name: MDA5_HT29_METTL3KD1_MT_RNaseA_rep1


title: MDA5_HT29_METTL3KD1_MT_RNaseA_rep2

description: Library name: MDA5_HT29_METTL3KD1_MT_RNaseA_rep2


title: XHLT2-HS48-BLE1

description:
Library name: XHLT2-HS48-BLE1
Baseline PBMC: donor HS48


title: XHLT2-HS49-BLE1

description:
Library name: XHLT2-HS49-BLE1
Baseline PBMC: donor HS49


title: 2153 Tumor, anti-PD1 + anti-CTLA4, CP-4673

description:
Library name: 2153_CP-4673
Column name in raw_counts_All_Samples.txt: 2153_CP-4673


title: p53RB-626 Tumor, Untreated, CP-4549

description:
Library name: p53RB-626_CP-4549
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4549

value: Untreated


title: pool-7, well-1, ADT

description:
Library name: XHLT2-POOL-DB7-SCG1_ADT
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1

library_source: other

molecule: protein

value: ADT


title: pool-7, well-2, GEX

description:
Library name: XHLT2-POOL-DB7-SCG2_GEX
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1


title: MDA5_HT29_TGFP_MT_NT_rep1

description: Library name: MDA5_HT29_TGFP_MT_NT_rep1

value: wild type


title: MDA5_HT29_TGFP_MT_NT_rep2

description: Library name: MDA5_HT29_TGFP_MT_NT_rep2


title: XHLT2-HS50-BLE1

description:
Library name: XHLT2-HS50-BLE1
Baseline PBMC: donor HS50


title: XHLT2-HS46-BLE1

description:
Library name: XHLT2-HS46-BLE1
Baseline PBMC: donor HS46


title: pool-6, well-3, GEX

description:
Library name: XHLT2-POOL-DB6-SCG3_GEX
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: XHLT2-HS47-BLE1

description:
Library name: XHLT2-HS47-BLE1
Baseline PBMC: donor HS47


title: 2153 Tumor, anti-PD1 + anti-CTLA4, CP-4674

description:
Library name: 2153_CP-4674
Column name in raw_counts_All_Samples.txt: 2153_CP-4674


title: MDA5_HT29_TGFP_MT_RNaseA_rep1

description: Library name: MDA5_HT29_TGFP_MT_RNaseA_rep1


title: pool-7, well-1, GEX

description:
Library name: XHLT2-POOL-DB7-SCG1_GEX
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1


title: pool-6, well-4, ADT

description:
Library name: XHLT2-POOL-DB6-SCG4_ADT
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: MDA5_HT29_METTL3KD1_MT_NT_rep2

description: Library name: MDA5_HT29_METTL3KD1_MT_NT_rep2


title: pool-6, well-3, ADT

description:
Library name: XHLT2-POOL-DB6-SCG3_ADT
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: p53RB-626 Tumor, Untreated, CP-4548

description:
Library name: p53RB-626_CP-4548
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4548


title: XHLT2-HS45-BLE1

description:
Library name: XHLT2-HS45-BLE1
Baseline PBMC: donor HS45


title: p53RB-626 Tumor, Untreated, CP-4547

description:
Library name: p53RB-626_CP-4547
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4547


title: 2153 Tumor, Untreated, CP-4543

description:
Library name: 2153_CP-4543
Column name in raw_counts_All_Samples.txt: 2153_CP-4543


title: pool-6, well-2, ADT

description:
Library name: XHLT2-POOL-DB6-SCG2_ADT
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: pool-6, well-2, GEX

description:
Library name: XHLT2-POOL-DB6-SCG2_GEX
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: 2208 Tumor, Untreated, CP-4536

description:
Library name: 2208_CP-4536
Column name in raw_counts_All_Samples.txt: 2208_CP-4536


title: pool-6, well-1, GEX

description:
Library name: XHLT2-POOL-DB6-SCG1_GEX
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: Red9 Wildtype, rep2

city: Auckland

first: Yongyan

last: Peng

state: Auckland

address: 120 Mt Albert Road

department: Kiwifruit New Cultivars

country: New Zealand

institute: Plant and Food Research

description:
Library name: Sample 11
Red9WTS2

data_processing:
Data quality check (QC) was performed with FastQC 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with Trim Galore! 0.6.6 (Krueger, 2015). Processed reads were mapped to the A. chinensis var. chinensis Red5_PS1_1.69.0 genome (Pilkington et al., 2018) using STAR v2.6.1d (Dobin et al., 2013). The alignment quality was checked and visualized with Qualimap v2.2.2 (Garcia-Alcalde et al., 2012; Okonechnikov et al., 2016). PCR artifacts were checked with dupRadar v1.18.0  (Sayols et al., 2016), gene expression quantification for each sample (including read counts, FPKM and TPM) was generated using Salmon v1.3.0 (Patro et al., 2017), and ultimately presented as fragments per kilobase of transcript per million reads (FPKM) ± SE of three biological replicates. Differentially expressed genes (DEGs) were identified using DESeq2 v1.28.0 (Anders & Huber, 2010) based on the raw read counts from each sample. DEGs were selected based on the cut-off of log2fold-change ≥ 1 or ≤ -1 and adjusted p-value ≤0.05.
Assembly: A. chinensis var. chinensis Red5_PS1_1.69.0 genome (Pilkington et al., 2018)
Supplementary files format and content: FPKM counts for all samples

organism: Actinidia chinensis

source_name: Shoot apices

growth_protocol: The overexpression construct pHEX2:AcCEN4-6xHA and the empty vector control were transformed into kiwifruit Actinidia chinensis Red 9. Accen/cen4 mutants were generated in kiwifruit Red 9 female background as previously reported (Varkonyi-Gasic et al., 2019). The Accen/cen4 lines that flowered at approximately 15 nodes were deemed fast flowering and introduced back into tissue culture after sterilisation. The stems were cut into smaller pieces containing two nodes with leaves trimmed, rinsed with hand soap and water for five times before stirring the stems in 70% ethanol for 30 seconds in the laminar flow hood. The stems were then incubated in dissolved antibacterial tablet solution (Milton, Australia) with 0.1% Tween-20 for 15 minutes before rinsing clean with autoclaved water for five times. The sterilised stems were dried and placed onto maintenance media containing MS, 0.2mg/L indolebutyric acid, 0.2 mg/L zeatin, 2% sucrose, 0.65% agar, pH:5.8. These fast flowering Accen/cen4 mutant female lines were maintained in tissue culture, along with non-edited kiwifruit Red 9 female plants. Approximately 45 - 50 lines for each construct and the respective controls were maintained in tissue culture for shoot apex sampling. The growth condition for tissue culture plants were maintained at 23°C with a photoperiod of 16 h light and 8 h dark with cool white fluorescent light (35–45 µmol m-2 s-1).

extract_protocol:
total RNA was extracted using Spectrum Plant Total RNA kit (Sigma-Aldrich, USA) following manufacturer's protocol.
The quantity and quality of RNA samples were checked using a Bioanalyzer 2100 (Agilent Technologies, USA) with the RIN score above 7. RNA was sent to Novogene (Hong Kong) for directional strand-specific mRNA library preparation and NovaSeq 6000 PE150 sequencing.

treatment_protocol: Shoot apices of tissue culture grown kiwifruit overexpressing 35S:AcCEN4-6xHA, and empty vector, and the shoot apices of the gene-edited Accen/cen4 and the non-edited lines were sampled for the RNA-sequencing experiment. One biological replicate consisted of approximately 15 shoot apices and three biological replicates were collected for each group.

value: Shoot apices

value: Red 9

value: wildtype


title: 2153 Tumor, Untreated, CP-4542

description:
Library name: 2153_CP-4542
Column name in raw_counts_All_Samples.txt: 2153_CP-4542


title: 2208 Tumor, Untreated, CP-4537

description:
Library name: 2208_CP-4537
Column name in raw_counts_All_Samples.txt: 2208_CP-4537


title: XHLT2-HS43-BLE1

description:
Library name: XHLT2-HS43-BLE1
Baseline PBMC: donor HS43


title: Red9 Fast Flowering, rep2

description:
Library name: Sample 8
Red9FFS2

value: Accen/cen4 gene edited


title: pool-6, well-1, ADT

description:
Library name: XHLT2-POOL-DB6-SCG1_ADT
Pool of XHLT2-HS100-BLE1, XHLT2-HS103-BLE1, XHLT2-HS11-BLE1, XHLT2-HS17-BLE1, XHLT2-HS23-BLE1, XHLT2-HS24-BLE1, XHLT2-HS25-BLE1, XHLT2-HS32-BLE1, XHLT2-HS37-BLE1, XHLT2-HS39-BLE1, XHLT2-HS60-BLE1, XHLT2-HS68-BLE1, XHLT2-HS69-BLE1, XHLT2-HS75-BLE1, XHLT2-HS83-BLE1, XHLT2-HS91-BLE1


title: 2153 Tumor, Untreated, CP-4541

description:
Library name: 2153_CP-4541
Column name in raw_counts_All_Samples.txt: 2153_CP-4541


title: Red9 Wildtype, rep3

description:
Library name: Sample 12
Red9WTS3


title: Red9 Fast Flowering, rep3

description:
Library name: Sample 9
Red9FFS3


title: pool-5, well-4, ADT

description:
Library name: XHLT2-POOL-DB5-SCG4_ADT
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: XHLT2-HS42-BLE1

description:
Library name: XHLT2-HS42-BLE1
Baseline PBMC: donor HS42


title: p53RB-624 Tumor, Carboplatin + Paclitaxel, CP-4534

description:
Library name: p53RB-624_CP-4534
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4534

value: Carboplatin + Paclitaxel


title: pool-5, well-4, GEX

description:
Library name: XHLT2-POOL-DB5-SCG4_GEX
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: Red9 Wildtype, rep1

description:
Library name: Sample 10
Red9WTS1


title: XHLT2-HS41-BLE1

description:
Library name: XHLT2-HS41-BLE1
Baseline PBMC: donor HS41


title: XHLT2-HS40-BLE1

description:
Library name: XHLT2-HS40-BLE1
Baseline PBMC: donor HS40


title: p53RB-624 Tumor, Carboplatin + Paclitaxel, CP-4533

description:
Library name: p53RB-624_CP-4533
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4533


title: pool-5, well-3, GEX

description:
Library name: XHLT2-POOL-DB5-SCG3_GEX
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: pHEX2 empty vector, rep3

description:
Library name: Sample 6
pHEX2_S3

value: pHEX2 empty vector


title: 2208 Tumor, Untreated, CP-4535

description:
Library name: 2208_CP-4535
Column name in raw_counts_All_Samples.txt: 2208_CP-4535


title: XHLT2-HS44-BLE1

description:
Library name: XHLT2-HS44-BLE1
Baseline PBMC: donor HS44

value: PBMC


title: MDA5_HT29_TGFP_MT_RNaseA_rep2

description: Library name: MDA5_HT29_TGFP_MT_RNaseA_rep2

value: Colorectal cancer


title: pool-5, well-3, ADT

description:
Library name: XHLT2-POOL-DB5-SCG3_ADT
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: XHLT2-HS39-BLE1

description:
Library name: XHLT2-HS39-BLE1
Baseline PBMC: donor HS39


title: Red9 Fast Flowering, rep1

description:
Library name: Sample 7
Red9FFS1


title: XHLT2-HS3-BLE1

description:
Library name: XHLT2-HS3-BLE1
Baseline PBMC: donor HS3


title: XHLT2-HS38-BLE1

description:
Library name: XHLT2-HS38-BLE1
Baseline PBMC: donor HS38


title: pool-5, well-2, ADT

description:
Library name: XHLT2-POOL-DB5-SCG2_ADT
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: p53RB-624 Tumor, Carboplatin + Paclitaxel, CP-4532

description:
Library name: p53RB-624_CP-4532
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4532


title: pHEX2 empty vector, rep2

description:
Library name: Sample 5
pHEX2_S2


title: p53RB-624 Tumor, Untreated, CP-4525

description:
Library name: p53RB-624_CP-4525
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4525


title: XHLT2-HS37-BLE1

description:
Library name: XHLT2-HS37-BLE1
Baseline PBMC: donor HS37


title: pool-5, well-2, GEX

description:
Library name: XHLT2-POOL-DB5-SCG2_GEX
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: pool-5, well-1, ADT

description:
Library name: XHLT2-POOL-DB5-SCG1_ADT
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: pHEX2 empty vector, rep1

description:
Library name: Sample 4
pHEX2_S1


title: CEN4, rep3

description:
Library name: Sample 3
CEN4_S3


title: XHLT2-HS36-BLE1

description:
Library name: XHLT2-HS36-BLE1
Baseline PBMC: donor HS36


title: pool-5, well-1, GEX

description:
Library name: XHLT2-POOL-DB5-SCG1_GEX
Pool of XHLT2-HS109-BLE1, XHLT2-HS13-BLE1, XHLT2-HS19-BLE1, XHLT2-HS28-BLE1, XHLT2-HS29-BLE1, XHLT2-HS34-BLE1, XHLT2-HS36-BLE1, XHLT2-HS43-BLE1, XHLT2-HS44-BLE1, XHLT2-HS48-BLE1, XHLT2-HS50-BLE1, XHLT2-HS63-BLE1, XHLT2-HS74-BLE1, XHLT2-HS79-BLE1, XHLT2-HS85-BLE1, XHLT2-HS87-BLE1


title: CEN4, rep2

description:
Library name: Sample 2
CEN4_S2


title: p53RB-624 Tumor, Untreated, CP-4524

description:
Library name: p53RB-624_CP-4524
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4524


title: pool-4, well-4, ADT

description:
Library name: XHLT2-POOL-DB4-SCG4_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS33-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: KPB1-B Tumor, Carboplatin + Paclitaxel, CP-4521

description:
Library name: KPB1-B_CP-4521
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4521


title: pool-4, well-4, GEX

description:
Library name: XHLT2-POOL-DB4-SCG4_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS33-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: CEN4, rep1

description:
Library name: Sample 1
CEN4_S1


title: KPB1-B Tumor, Carboplatin + Paclitaxel, CP-4522

description:
Library name: KPB1-B_CP-4522
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4522


title: XHLT2-HS35-BLE1

description:
Library name: XHLT2-HS35-BLE1
Baseline PBMC: donor HS35


title: XHLT2-HS32-BLE1

description:
Library name: XHLT2-HS32-BLE1
Baseline PBMC: donor HS32


title: XHLT2-HS34-BLE1

description:
Library name: XHLT2-HS34-BLE1
Baseline PBMC: donor HS34


title: XHLT2-HS33-BLE1

description:
Library name: XHLT2-HS33-BLE1
Baseline PBMC: donor HS33


title: KPB1-B Tumor, Carboplatin + Paclitaxel, CP-4520

description:
Library name: KPB1-B_CP-4520
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4520


title: Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_2

city: Tarrytown

first: Varenka

last: Rodriguez DiBlasi

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc

description: Library name: 1735446_Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_2

library_source: genomic

data_processing:
The tools used in the ATAC-seq workflow include Bowtie2 for mapping reads to the human reference genome (hg38), Trimmomatic for adapter sequence trimming, Picard Tools for PCR duplicate removal, Rsamtools and GenomicRanges for correcting BAM files for Tn5 offset, Samtools for BAM to BED file conversion and read counting, Bedtools for generating bedGraph files and intersecting reads with regions, UCSCtools (bedGraphToBigWig) for generating normalized BigWig files, Preseq for library complexity analysis, Macs2 for peak calling, HOMER for peak annotation and motif analysis, ChIPseeker for peak annotation, DiffBind for differential analysis using DBA objects, DESeq2 for statistical analysis of differential peaks, DeepTools2 for correlation scores, heatmap plotting, and signal profiling, and IGV Browser for visualization of aligned fragments and peaks.
Assembly: hg38
Supplementary files format and content: Peaks for each treatment and replicate in narrowPeak (BED) format.
Supplementary files format and content: Normalized coverage tracks (CPM) for each in bigwig format.

molecule: genomic DNA

source_name: cell line

growth_protocol: HPAF-II (ATCC® CRL1977TM)were maintained in Eagle’s Minimum Essential Medium supplemented with 10% FBS, 2mM L-Glutamine, and 1x penicillin-streptomycin. KATO III (ATCC® HTB-103TM) were maintained in Iscove’s Modified Dulbeco’s Medium supplemented with 20% FBS, 2mM L-Glutamine, and 1x penicillin-streptomycin.

extract_protocol:
In brief, 50,000 cells were lysed with 100 µL ice- cold ATAC Lysis Buffer and centrifuged at 500xg for 10 min at 4°C. Tagmentation reaction was done by adding 50 µL tagmentation mix followed by incubation for 30 minutes at 37 °C in a thermomixer at 800rpm. Tagmentation product was cleaned up according to the manufacturer’s suggestion.
33.5 µL of transposed product was used for library prep indexing PCR and post PCR cleanup was performed by 1.2x SPRI Select Reagent and final libraries were eluted in 20.5 µL DNA Elution Buffer.

treatment_protocol: DMSO or 1uM LGK-974 (StemRD L974-002) for 24 or 48 hours

value: cell line

value: HPAF-II


title: pool-4, well-3, GEX

description:
Library name: XHLT2-POOL-DB4-SCG3_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: pool-4, well-3, ADT

description:
Library name: XHLT2-POOL-DB4-SCG3_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_3

description: Library name: 1735447_Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_3


title: XHLT2-HS31-BLE1

description:
Library name: XHLT2-HS31-BLE1
Baseline PBMC: donor HS31


title: p53RB-624 Tumor, Untreated, CP-4523

description:
Library name: p53RB-624_CP-4523
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-4523


title: KPB1-B Tumor, Untreated, CP-4513

description:
Library name: KPB1-B_CP-4513
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4513


title: XHLT2-HS30-BLE1

description:
Library name: XHLT2-HS30-BLE1
Baseline PBMC: donor HS30


title: pool-4, well-2, ADT

description:
Library name: XHLT2-POOL-DB4-SCG2_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: KPB1-B Tumor, Untreated, CP-4512

description:
Library name: KPB1-B_CP-4512
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4512


title: Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_1

description: Library name: 1735445_Lgk974_48hr_HPAFII_ATAC_SEQ_SAMPLE_1


title: DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_4

description: Library name: 1735441_DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_4

value: DMSO


title: pool-4, well-2, GEX

description:
Library name: XHLT2-POOL-DB4-SCG2_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: KPB1-B Tumor, Untreated, CP-4511

description:
Library name: KPB1-B_CP-4511
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-4511

value: mammary tumor


title: pool-4, well-1, ADT

description:
Library name: XHLT2-POOL-DB4-SCG1_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS33-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: XHLT2-HS2-BLE1

description:
Library name: XHLT2-HS2-BLE1
Baseline PBMC: donor HS2


title: XHLT2-HS29-BLE1

description:
Library name: XHLT2-HS29-BLE1
Baseline PBMC: donor HS29


title: XHLT2-HS28-BLE1

description:
Library name: XHLT2-HS28-BLE1
Baseline PBMC: donor HS28


title: DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_2

description: Library name: 1735439_DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_2


title: DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_3

description: Library name: 1735440_DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_3


title: pool-4, well-1, GEX

description:
Library name: XHLT2-POOL-DB4-SCG1_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS101-BLE1, XHLT2-HS104-BLE1, XHLT2-HS105-BLE1, XHLT2-HS15-BLE1, XHLT2-HS16-BLE1, XHLT2-HS18-BLE1, XHLT2-HS22-BLE1, XHLT2-HS33-BLE1, XHLT2-HS4-BLE1, XHLT2-HS59-BLE1, XHLT2-HS66-BLE1, XHLT2-HS70-BLE1, XHLT2-HS71-BLE1, XHLT2-HS72-BLE1, XHLT2-HS97-BLE1


title: pool-3, well-4, ADT

description:
Library name: XHLT2-POOL-DB3-SCG4_ADT
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: T12 Tumor, Carboplatin + Paclitaxel, CP-4364

description:
Library name: T12_CP-4364
Column name in raw_counts_All_Samples.txt: T12_CP-4364


title: pool-3, well-4, GEX

description:
Library name: XHLT2-POOL-DB3-SCG4_GEX
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_4

description: Library name: 1735423_Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_4


title: T12 Tumor, Carboplatin + Paclitaxel, CP-4363

description:
Library name: T12_CP-4363
Column name in raw_counts_All_Samples.txt: T12_CP-4363


title: XHLT2-HS27-BLE1

description:
Library name: XHLT2-HS27-BLE1
Baseline PBMC: donor HS27


title: T12 Tumor, Untreated, CP-4355

description:
Library name: T12_CP-4355
Column name in raw_counts_All_Samples.txt: T12_CP-4355


title: XHLT2-HS23-BLE1

description:
Library name: XHLT2-HS23-BLE1
Baseline PBMC: donor HS23


title: T12 Tumor, Carboplatin + Paclitaxel, CP-4362

description:
Library name: T12_CP-4362
Column name in raw_counts_All_Samples.txt: T12_CP-4362


title: pool-3, well-3, ADT

description:
Library name: XHLT2-POOL-DB3-SCG3_ADT
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: KPB1-A Tumor, Carboplatin + Paclitaxel, CP-4510

description:
Library name: KPB1-A_CP-4510
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4510


title: Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_2

description: Library name: 1735421_Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_2


title: pool-3, well-3, GEX

description:
Library name: XHLT2-POOL-DB3-SCG3_GEX
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_1

description: Library name: 1735438_DMSO_48hr_HPAFII_ATAC_SEQ_SAMPLE_1


title: DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_4

description: Library name: 1735417_DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_4


title: XHLT2-HS21-BLE1

description:
Library name: XHLT2-HS21-BLE1
Baseline PBMC: donor HS21


title: T12 Tumor, Untreated, CP-4354

description:
Library name: T12_CP-4354
Column name in raw_counts_All_Samples.txt: T12_CP-4354


title: pool-3, well-2, GEX

description:
Library name: XHLT2-POOL-DB3-SCG2_GEX
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: pool-3, well-2, ADT

description:
Library name: XHLT2-POOL-DB3-SCG2_ADT
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: XHLT2-HS25-BLE1

description:
Library name: XHLT2-HS25-BLE1
Baseline PBMC: donor HS25


title: XHLT2-HS26-BLE1

description:
Library name: XHLT2-HS26-BLE1
Baseline PBMC: donor HS26


title: T12 Tumor, Untreated, CP-4353

description:
Library name: T12_CP-4353
Column name in raw_counts_All_Samples.txt: T12_CP-4353


title: E0771 Tumor, Carboplatin + Paclitaxel, CP-4301

description:
Library name: E0771_CP-4301
Column name in raw_counts_All_Samples.txt: E0771_CP-4301


title: DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_3

description: Library name: 1735416_DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_3


title: pool-3, well-1, ADT

description:
Library name: XHLT2-POOL-DB3-SCG1_ADT
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_1

description: Library name: 1735420_Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_1


title: Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_3

description: Library name: 1735422_Lgk974_24hr_HPAFII_ATAC_SEQ_SAMPLE_3


title: XHLT2-HS24-BLE1

description:
Library name: XHLT2-HS24-BLE1
Baseline PBMC: donor HS24


title: XHLT2-HS20-BLE1

description:
Library name: XHLT2-HS20-BLE1
Baseline PBMC: donor HS20


title: DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_2

description: Library name: 1735415_DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_2


title: E0771 Tumor, Carboplatin + Paclitaxel, CP-4300

description:
Library name: E0771_CP-4300
Column name in raw_counts_All_Samples.txt: E0771_CP-4300


title: pool-3, well-1, GEX

description:
Library name: XHLT2-POOL-DB3-SCG1_GEX
Pool of XHLT2-HS14-BLE1, XHLT2-HS3-BLE1, XHLT2-HS30-BLE1, XHLT2-HS31-BLE1, XHLT2-HS47-BLE1, XHLT2-HS49-BLE1, XHLT2-HS51-BLE1, XHLT2-HS54-BLE1, XHLT2-HS6-BLE1, XHLT2-HS62-BLE1, XHLT2-HS80-BLE1, XHLT2-HS84-BLE1, XHLT2-HS88-BLE1, XHLT2-HS9-BLE1, XHLT2-HS94-BLE1, XHLT2-HS99-BLE1


title: XHLT2-HS1-BLE1

description:
Library name: XHLT2-HS1-BLE1
Baseline PBMC: donor HS1


title: pool-2, well-3, ADT

description:
Library name: XHLT2-POOL-DB2-SCG3_ADT
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: KPB1-A Tumor, Carboplatin + Paclitaxel, CP-4288

description:
Library name: KPB1-A_CP-4288
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4288


title: KPB1-A Tumor, Carboplatin + Paclitaxel, CP-4290

description:
Library name: KPB1-A_CP-4290
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4290


title: DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_1

description: Library name: 1735414_DMSO_24hr_HPAFII_ATAC_SEQ_SAMPLE_1


title: pool-2, well-3, GEX

description:
Library name: XHLT2-POOL-DB2-SCG3_GEX
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: U-87MG_Wild-Type-Control_rep2

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description: Library name: U87_WT_B

data_processing:
Basecalls were performed using bcl2fastq v2.20
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v4.1, using minimum-length 18, error-rate 0.2, overlap 5.
Reads were deduplicated on the basis of their unique molecular identifiers (UMIs), using UMI-tools v1.1.2.
Trimmed and depulicated reads were mapped against the hg38 human reference genome, using the STAR spliced alignment algorithm (version 2.7.7a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
Assembly: hg38
Supplementary files format and content: tab delimited raw STAR gene counts file for each sample
Supplementary files format and content: tab delimited raw genecounts for each sample combined

source_name: Human Brain

growth_protocol: U-87MG ATCC (U87) GBM cell lines were cultured in Minimum Essential Medium (MEM) medium (Thermo Fisher Scientific, 11095080) supplemented with 10% heat-inactivated foetal bovine serum (FBS, GE Healthcare, SH30084.03), 1% GlutaMAX (Thermo Fisher Scientific, 35050061), 1% sodium pyruvate (Thermo Fisher Scientific, 11360070), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140050), and 1% penicillin/streptomycin (Thermo Fisher Scientific, 15140122).

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s protocol. RNA integrity was established with Bioanalyzer 2100 (Agilent) trace. 1 μg of total RNA was then subjected to NEB polyA selection with oligo dT beads (New England Biolabs, E7490).
Enriched polyA RNA was utilized for library preparation using the KAPA RNA Hyperprep kit (Roche, 08098107702) following manufacturer’s guidelines.

treatment_protocol: CD47 WT and CRISPR knockout (KO) cell lines for U87 were generated using pLenti-U6-CD47sgRNA-SFFV-Cas9-2A-puromycin (Applied Biological Materials) vector, comprising non-targeting control guide RNAor CD47 guide RNA sequence 5′-CAGCAACAGCGCCGCTACCA-3′, respectively. Lentiviral particles were generated by transfecting HEK293T cells with pLenti plasmid and packing plasmids pLP1 (gag/pol), pLP2 (rev) and pVSVG (envelope) using Lipofectamine 2000 (Thermo Fisher Scientific, 11668027) according to the manufacturer’s protocol. After 48 hr, the supernatant containing lentiviral particles was collected and used to transduce U87 and G5C pBLIV-CMV-RFP-T2A-Fluc cells, which were treated with 4 μg/mL polybrene (Sigma-Aldrich, H9268). Transduced cells were then selected using 2 μg/mL puromycin (Sigma-Aldrich, 540222) for 7 days and subsequently stained with CD47-Alexa-Fluor-647 antibody (BD Biosciences, 561249) at 1:500 dilution in cold 1× PBS containing 2% FBS and 1 mM EDTA (Thermo Fisher Scientific, 17892) for 15 min on ice in the dark. CD47-negative cells were then isolated via two rounds of pooled sorting (for G5C cells) or single-cell sorting (for U87 cells) using MoFlo Astrios Cell Sorter (Beckman Coulter Life Sciences, B52102), with one cell seeded per well into 96-well plates. Clones were grown for 21 to 28 days and then analysed by flow cytometry and compared to WT cells to validate CD47 KO.

value: Human Brain

value: Malignant gliomas

value: WT


title: XHLT2-HS18-BLE1

description:
Library name: XHLT2-HS18-BLE1
Baseline PBMC: donor HS18


title: U-87MG_CD47-CRISPR-Knockout_rep3

description: Library name: U87_CD47_KO_C

value: KO

value: CRISPR Knockout


title: U-87MG_Wild-Type-Control_rep3

description: Library name: U87_WT_C


title: XHLT2-HS14-BLE1

description:
Library name: XHLT2-HS14-BLE1
Baseline PBMC: donor HS14


title: pool-2, well-2, GEX

description:
Library name: XHLT2-POOL-DB2-SCG2_GEX
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1

value: mRNA


title: XHLT2-HS19-BLE1

description:
Library name: XHLT2-HS19-BLE1
Baseline PBMC: donor HS19


title: pool-2, well-2, ADT

description:
Library name: XHLT2-POOL-DB2-SCG2_ADT
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1

value: ADT


title: pool-2, well-4, ADT

description:
Library name: XHLT2-POOL-DB2-SCG4_ADT
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: KPB1-A Tumor, Untreated, CP-4279

description:
Library name: KPB1-A_CP-4279
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4279

value: Untreated


title: pool-2, well-4, GEX

description:
Library name: XHLT2-POOL-DB2-SCG4_GEX
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: E0771 Tumor, Carboplatin + Paclitaxel, CP-4289

description:
Library name: E0771_CP-4289
Column name in raw_counts_All_Samples.txt: E0771_CP-4289


title: E0771 Tumor, Untreated, CP-4293

description:
Library name: E0771_CP-4293
Column name in raw_counts_All_Samples.txt: E0771_CP-4293


title: XHLT2-HS17-BLE1

description:
Library name: XHLT2-HS17-BLE1
Baseline PBMC: donor HS17


title: XHLT2-HS15-BLE1

description:
Library name: XHLT2-HS15-BLE1
Baseline PBMC: donor HS15


title: KPB1-A Tumor, Untreated, CP-4281

description:
Library name: KPB1-A_CP-4281
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4281


title: U-87MG_CD47-CRISPR-Knockout_rep1

description: Library name: U87_CD47_KO_A


title: KPB1-A Tumor, Untreated, CP-4280

description:
Library name: KPB1-A_CP-4280
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-4280


title: XHLT2-HS13-BLE1

description:
Library name: XHLT2-HS13-BLE1
Baseline PBMC: donor HS13


title: U-87MG_Wild-Type-Control_rep1

description: Library name: U87_WT_A


title: XHLT2-HS16-BLE1

description:
Library name: XHLT2-HS16-BLE1
Baseline PBMC: donor HS16


title: U-87MG_CD47-CRISPR-Knockout_rep2

description: Library name: U87_CD47_KO_B


title: XHLT2-HS12-BLE1

description:
Library name: XHLT2-HS12-BLE1
Baseline PBMC: donor HS12


title: p53RB-426 Tumor, Carboplatin + Paclitaxel, CP-4266

description:
Library name: p53RB-426_CP-4266
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4266


title: p53RB-426 Tumor, Carboplatin + Paclitaxel, CP-4265

description:
Library name: p53RB-426_CP-4265
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4265


title: XHLT2-HS111-BLE1

description:
Library name: XHLT2-HS111-BLE1
Baseline PBMC: donor HS111


title: pool-1, well-3, GEX

description:
Library name: XHLT2-POOL-DB1-SCG3_GEX
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: KPB1-B Tumor, Untreated, CP-3060

description:
Library name: KPB1-B_CP-3060
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-3060


title: p53RB-426 Tumor, Untreated, CP-4204

description:
Library name: p53RB-426_CP-4204
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4204


title: pool-2, well-1, GEX

description:
Library name: XHLT2-POOL-DB2-SCG1_GEX
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: p53RB-426 Tumor, Carboplatin + Paclitaxel, CP-4264

description:
Library name: p53RB-426_CP-4264
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4264


title: pool-1, well-2, GEX

description:
Library name: XHLT2-POOL-DB1-SCG2_GEX
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: pool-1, well-3, ADT

description:
Library name: XHLT2-POOL-DB1-SCG3_ADT
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: XHLT2-HS109-BLE1

description:
Library name: XHLT2-HS109-BLE1
Baseline PBMC: donor HS109


title: XHLT2-HS11-BLE1

description:
Library name: XHLT2-HS11-BLE1
Baseline PBMC: donor HS11


title: p53RB-426 Tumor, Untreated, CP-4202

description:
Library name: p53RB-426_CP-4202
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4202


title: pool-1, well-2, ADT

description:
Library name: XHLT2-POOL-DB1-SCG2_ADT
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: XHLT2-HS110-BLE1

description:
Library name: XHLT2-HS110-BLE1
Baseline PBMC: donor HS110


title: pool-2, well-1, ADT

description:
Library name: XHLT2-POOL-DB2-SCG1_ADT
Pool of XHLT2-HS106-BLE1, XHLT2-HS12-BLE1, XHLT2-HS2-BLE1, XHLT2-HS26-BLE1, XHLT2-HS27-BLE1, XHLT2-HS38-BLE1, XHLT2-HS40-BLE1, XHLT2-HS57-BLE1, XHLT2-HS64-BLE1, XHLT2-HS65-BLE1, XHLT2-HS67-BLE1, XHLT2-HS73-BLE1, XHLT2-HS77-BLE1, XHLT2-HS82-BLE1, XHLT2-HS89-BLE1, XHLT2-HS98-BLE1


title: pool-1, well-4, ADT

description:
Library name: XHLT2-POOL-DB1-SCG4_ADT
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: XHLT2-HS10-BLE1

description:
Library name: XHLT2-HS10-BLE1
Baseline PBMC: donor HS10


title: p53RB-426 Tumor, Untreated, CP-4203

description:
Library name: p53RB-426_CP-4203
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-4203


title: XHLT2-HS108-BLE1

description:
Library name: XHLT2-HS108-BLE1
Baseline PBMC: donor HS108


title: K14-TRT Tumor, Untreated, CP-4186

description:
Library name: K14-TRT_CP-4186
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4186


title: pool-1, well-4, GEX

description:
Library name: XHLT2-POOL-DB1-SCG4_GEX
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: DEK-knockout Hela S3 cells, rep1

type: RNA

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

description: Gene expression data from 1E7

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip Human Transcriptome Array 2.0 arrays according to the manufacturer’s standard procedures.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner according to standard Affymetrix protocols.

data_processing:
Raw CEL files were processed using Affymetrix Transcriptome Analysis Console (TAC).
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

source_name: DEK-knockout Hela S3 cells

label_protocol: cDNA synthesis, amplification, and labeling were performed according to the Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA 2.0) standard protocol

growth_protocol: HeLa S3 wild-type (WT) cells and full-length DEK-deficient HeLa S3 derivative clone 1E7 were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1× Penicillin-Streptomycin (Hyclone).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: The 1E7 cell line represents a TALEN-mediated full-length DEK-deficient HeLa S3 clone expressing a truncated DEK fragment

value: Cervix

value: DEK-knockout


title: DEK-knockout Hela S3 cells, rep3

description: Gene expression data from 1E7


title: HelaS3 cells, rep2

description: Gene expression data from Hela S3 cells

source_name: HelaS3 cells


title: DEK-knockout Hela S3 cells, rep2

description: Gene expression data from 1E7


title: HelaS3 cells, rep1

description: Gene expression data from Hela S3 cells


title: HelaS3 cells, rep3

description: Gene expression data from Hela S3 cells


title: KPB1-B Tumor, Untreated, CP-2825

description:
Library name: KPB1-B_CP-2825
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-2825


title: KPB1-B Tumor, Untreated, CP-2824

description:
Library name: KPB1-B_CP-2824
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-2824


title: K14-TRT Tumor, Untreated, CP-4185

description:
Library name: K14-TRT_CP-4185
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4185


title: XHLT2-HS105-BLE1

description:
Library name: XHLT2-HS105-BLE1
Baseline PBMC: donor HS105


title: T11 Tumor, Untreated, CP-2205

description:
Library name: T11_CP-2205
Column name in raw_counts_All_Samples.txt: T11_CP-2205


title: C3-TAG Tumor, Untreated, CP-2387

description:
Library name: C3-TAG_CP-2387
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-2387


title: pool-1, well-1, GEX

description:
Library name: XHLT2-POOL-DB1-SCG1_GEX
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: p53RB-626 Tumor, Untreated, CP-4090

description:
Library name: p53RB-626_CP-4090
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4090


title: p53RB-626 Tumor, Carboplatin + Paclitaxel, CP-4104

description:
Library name: p53RB-626_CP-4104
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4104

value: Carboplatin + Paclitaxel


title: XHLT2-HS106-BLE1

description:
Library name: XHLT2-HS106-BLE1
Baseline PBMC: donor HS106

value: PBMC


title: hMHO_6

city: Stanford

first: Sabina

last: Kanton

address: 318 Campus Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

description:
Library name: hMHO_6
10x Genomics 3' v3

library_source: transcriptomic single cell

data_processing:
Mapping to reference genome, quality control and UMI counting of Ensembl genes was performed using CellRanger (v.5.0.0) on 10x Cloud services.
Assembly: Human: GRCh38 (10x Genomics human reference GRCh38-2020-A)
Supplementary files format and content: Count matrices, barcodes, and features

source_name: hiPS cell-derived midbrain-hindbrain organoid (hMHO)

growth_protocol: Human midbrain hindbrain organoids were generated using a guided neural organoid protocol to pattern for midbrain hindbrain regions via the modulation of Sonic hedgehog and Wnt signaling pathways.

extract_protocol:
Organoid tissue was dissociated using a Papain-based based protocol using a previously published protocol. Briefly, hMHO were cut into smaller pieces, transferred to a six-well plate and incubated for 45 mins at 37°C in 3 ml enzymatic dissociation solution (containing of 30 U ml−1 papain (Worthington Biochemical, LS003127), 1× Earle’s balanced salt solution (Sigma-Aldrich, E7510), 0.46% d+-glucose, 0.5 mM ethylenediaminetetraacetic acid (EDTA), 26 mM NaHCO3, 125 U ml−1 Deoxyribonuclease I (Worthington Biochemical, LS002007) and 6.1 mM l-cysteine (Sigma-Aldrich, C7880)). The tissue in the solution was gently swirled after 20-25 mins of initial incubation. After enzyme incubation was completed, samples were transferred to a 15 ml conical tube and centrifuged at 200xg for 1 min at RT. The supernatant was removed and the samples were washed with 1 ml of inhibitor solution (2% trypsin inhibitor, Worthington Biochemical, LS00308). The samples were then triturated in a total of 1 ml of inhibitor solution in multiple steps using 200 µl of solution and a p1000 and p200 until the tissue was fully dissociated. Once dissociation was completed, 1 ml of 4% trypsin inhibitor solution was slowly added underneath the cell suspension to generate a gradient. The solution was then centrifuged at 200xg for 5 mins, the supernatant was gently removed and the resulting cell pellet was resuspended in PBS with 0.2% BSA. The cell suspension was filtered through a 40 µm Flowmi cell strainer filter (SP Bel-Art, H13680-0040) and counted with Trypan Blue using Countess Automated Cell counter.
Single cell suspension was encapsulated into GEMs using Chromium 10x platform and the 3’ Single Cell Gene Expression kit v3.1 (10x Genomics, 1000123) targeting 7000 or 8000 cells per lane in a 10x microfluidic chip. Single-cell libraries were prepared using 10x single index barcodes (10x Genomics, 1000213) using the 10x library construction kit (10x Genomics, 1000190).

value: Multiple cell types

value: Ctrl

tag: time point

value: day 69

value: batch 3


title: K14-TRT Tumor, Untreated, CP-4184

description:
Library name: K14-TRT_CP-4184
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4184

value: mammary tumor


title: XHLT2-HS107-BLE1

description:
Library name: XHLT2-HS107-BLE1
Baseline PBMC: donor HS107


title: hMHO_8

description:
Library name: hMHO_8
10x Genomics 3' v3

value: hiPS cell-derived midbrain-hindbrain organoid (hMHO)

value: batch 4


title: pool-1, well-1, ADT

description:
Library name: XHLT2-POOL-DB1-SCG1_ADT
Pool of XHLT2-HS1-BLE1, XHLT2-HS107-BLE1, XHLT2-HS110-BLE1, XHLT2-HS111-BLE1, XHLT2-HS21-BLE1, XHLT2-HS42-BLE1, XHLT2-HS46-BLE1, XHLT2-HS52-BLE1, XHLT2-HS55-BLE1, XHLT2-HS56-BLE1, XHLT2-HS7-BLE1, XHLT2-HS76-BLE1, XHLT2-HS78-BLE1, XHLT2-HS8-BLE1, XHLT2-HS93-BLE1, XHLT2-HS95-BLE1


title: p53RB-626 Tumor, Carboplatin + Paclitaxel, CP-4103

description:
Library name: p53RB-626_CP-4103
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4103


title: KPB25L-APOBEC Tumor, Untreated, CP-2838

description:
Library name: KPB25L-APOBEC_CP-2838
Column name in raw_counts_All_Samples.txt: KPB25L-APOBEC_CP-2838


title: E15_2019: E15-RANKL, rep1

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Bone and bone marrow

extract_protocol:
Bones were isolated from limbs and minced with scissors or tweezers. The fragmented bones were incubated in DMEM containing Collagenase P, Liberase TH and DNase I at 37ºC with gentle shaking for 1h. Dissociated cells were collected every 20 min and strained with a 100 μm nylon mesh. Cells were collected by centrifuge and resuspended in FACS buffer (2% FBS/2 mM EDTA/PBS). For experiments on bone marrow cells prepared from 3-week-old mice, red blood cells were removed by 0.165 M ammonium chloride treatment. The isolated cells were stained with antibodies against CD45, Ter119 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification. Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: Bone and bone marrow

value: tdTomato+

value: Tnfsf11-tTA; LC1; R26-tdTom

tag: developmental stage


title: XHLT2-HS104-BLE1

description:
Library name: XHLT2-HS104-BLE1
Baseline PBMC: donor HS104


title: p53RB-626 Tumor, Carboplatin + Paclitaxel, CP-4105

description:
Library name: p53RB-626_CP-4105
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4105


title: hMHO_7

description:
Library name: hMHO_7
10x Genomics 3' v3


title: XHLT2-HS102-BLE1

description:
Library name: XHLT2-HS102-BLE1
Baseline PBMC: donor HS102


title: 9w: adult_WholeBone

value: 9 weeks


title: XHLT2-HS103-BLE1

description:
Library name: XHLT2-HS103-BLE1
Baseline PBMC: donor HS103


title: hMHO_5

description:
Library name: hMHO_5
10x Genomics 3' v3


title: p53RB-626 Tumor, Untreated, CP-4089

description:
Library name: p53RB-626_CP-4089
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4089


title: XHLT2-HS101-BLE1

description:
Library name: XHLT2-HS101-BLE1
Baseline PBMC: donor HS101


title: hMHO_4

description:
Library name: hMHO_4
10x Genomics 3' v3


title: CD90posCD55pos, biol rep2

data_processing:
Quality control was performed using fastp package (v.0.12.4).
Sequence reads in FASTQ format were mapped to mouse reference genome (GRCm39) from Ensembl (release 104) using HISAT2 (v.2.1.0).
Count matrix for genes was generated using featureCounts (v.2.0.1).
Assembly: mm39
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each sample.

source_name: bone and bone marrow

extract_protocol:
Bones were isolated from limbs and minced with scissors or tweezers. The fragmented bones were incubated in DMEM containing Collagenase P, Liberase TH and DNase I at 37ºC with gentle shaking for 1h. Dissociated cells were collected every 20 min and strained with a 100 μm nylon mesh. Cells were collected by centrifuge and resuspended in FACS buffer (2% FBS/2 mM EDTA/PBS). The isolated cells were stained with antibodies against CD45, Ter119 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Cells were sorted directly into SMART-Seq reaction buffer for library construction.
RNA libraries for RNA-seq were prepared using SMART-Seq HT Plus Kit (Takara Bio) following manufacturer's protocols.

value: bone and bone marrow

value: Tnfsf11-tTA; LC1; R26-tdTomato


title: hMHO_3

description:
Library name: hMHO_3
10x Genomics 3' v3

value: day 79

value: batch 2


title: p53RB-626 Tumor, Untreated, CP-4088

description:
Library name: p53RB-626_CP-4088
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4088

value: Untreated


title: CD90posCD55neg, biol rep2


title: CD90negCD55pos, biol rep2


title: ID WT mESC ctcf AID Rep1

city: New York

first: Lara

last: Ladney

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

description:
Library name: ID_WT_mESC_ctcf_AID_Rep1
mESCs expressing transgene WT CTCF with degradation of the endogenous CTCF

data_processing:
Base and base modification calling were performed on pod5 files using dorado basecaller using the “--min-qscore 10 sup,5mC_5hmC” option, followed by alignment using dorado aligner against the mm10 and hg38 reference genome for mouse and human samples, respectively. Reads with less than 10 MAPQ score were filtered out using samtools. Methylation in HGC context was called using dorado pileup using the “--combine-strands” option.  GpC overlapping the ENCODE blacklisted regions were excluded as well as sites with more than 100x coverage.
Assembly: mm10 and hg38
Supplementary files format and content: Bigwig files for methylaion percentage at HGC sites (5mC)
Supplementary files format and content: Raw files are the unaligned files generated after dorado's base and base modification calling

source_name: Embryo

growth_protocol: mESCs were cultured under feeder-free conditions in 0.1% gelatin coated dishes  in DMEM  supplemented with 15% fetal bovine serum , 100 U/ml penicillin - 100 μg/ml streptomycin, 1 X GlutaMax supplement, 1 mM sodium pyruvate , 1 X MEM non-essential amino-acids , 50 μM b-mercaptoethanol, 104 U/ml leukemia inhibitory factor , 3 μM CHIR99021 and 1 μM MEK inhibitor PD0325901.  The Hela cells were grown in DMEM supplemented with 10% DBS , 0.2 M glutamine , penicillin/streptomycin and 1X non-essential amino acids.

extract_protocol:
Nuclei were extracted using cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 0.5 mM spermidine, 1.5 mM MgCl2, 0.1 mM EDTA, 0.25% IGEPAL CA-630) for 3-6 minutes.  The nuclei were resuspended in 564 µL 1X GpC MTase reaction buffer and equilibrated to 37°C. This was followed by 6 minutes of enzyme treatment (300 µL 1 M sucrose, 34 µL 10X GpC methyltransferase reaction buffer, 3 µL 32 mM S-Adenosylmethionine (SAM), 100 µL GpC methyltransferase (M.CviPI), followed by another 6 minutes of enzyme treatment (50 µL GpC methyltransferase (M.CviPI), 3 µL 32 mM S-Adenosylmethionine (SAM)). An equal volume of pre-warmed 2X stop buffer (20 mM Tris-HCl pH 7.4, 600 mM NaCl, 10 mM EDTA, 1% SDS) was added and mixed well. Proteinase K (200 µg/mL) was added to the GpC methylation reaction and incubated for 4 hours at 56°C, followed by RNase A (100 µg/mL) for 30 minutes at 37°C, followed by an additional round of proteinase K (200 µg/mL) for 30 minutes at 37°C. HMW DNA was extracted using phenol-chloroform and precipitated by isopropanol. Briefly, an equal volume of phenol-chloroform was added to the samples and mixed vigorously. The samples were centrifuged at 13,000 rpm for 10 minutes at room temperature. The aqueous phase was transferred to a clean tube, and 0.7-1 times the volume of isopropanol was added, mixed well, and incubated at room temperature for 30 minutes. The samples were then centrifuged at 13,000 rpm for 10 minutes at 4°C. The DNA pellet was washed with 1 ml pre-chilled 70% ethanol. After removing all the ethanol, the DNA was dissolved in EB buffer and incubated at 37°C for 30 minutes.
the DNA fragment was sheared to an average size of 20kb with the Covaris G-Tube (#520079) in an Eppendorf 5415D tabletop microcentrifuge following the manufacture’s protocol. Sample size was confirmed on genomic screentape with the Agilent Tapestation system. The sheared DNA (1.5ug) was then input into the SQK-LSK114 library prep from Oxford Nanopore to create the Nanopore library. Components were used from the LSK114 kit along with several buffers and enzymes from New England Biolab (NEB) following the LSK114 protocol from Oxford Nanopore. Following library prep, the sample concentration was verified on the Qubit system using the dsDNA High Sensitivity Kit. The concentration and basepair size were used to calculate Femtomolar concentration for loading. The sample was resuspended with library loading beads and loaded at 150-200 femtomolar concentration onto the Promethion R10.4.1 flow cell according to the LSK protocol. Sample were sequenced on the R10.4.1 Promethion flow cell using the Oxford Nanopore Promethion P24 system with a sequencing run time of 72 hrs. Standard settings were applied during the run setup, special settings were applied and fragments less than 1kb rejected.

treatment_protocol: For degradation, the auxin-inducible degron was induced by adding 500 μM indole-3-acetic acid (IAA, the chemical analog of auxin)  to the media. Expression of transgenes was achieved by the addition of doxycycline (Dox, 1 μg/ml) to the media.

value: Embryo

value: mESCs

value: IAA + doxycycline (48h)

tag: strain


title: XHLT2-HS100-BLE1

description:
Library name: XHLT2-HS100-BLE1
Baseline PBMC: donor HS100

value: PBMC


title: hMHO_2

description:
Library name: hMHO_2
10x Genomics 3' v3

value: Multiple cell types

value: Ctrl

value: day 82

value: batch 1


title: 4T1 Tumor, Carboplatin + Paclitaxel, CP-4072

description:
Library name: 4T1_CP-4072
Column name in raw_counts_All_Samples.txt: 4T1_CP-4072

value: mammary tumor

value: Carboplatin + Paclitaxel


title: 4T1 Tumor, Carboplatin + Paclitaxel, CP-4070

description:
Library name: 4T1_CP-4070
Column name in raw_counts_All_Samples.txt: 4T1_CP-4070


title: hMHO_1

description:
Library name: hMHO_1
10x Genomics 3' v3

value: hiPS cell-derived midbrain-hindbrain organoid (hMHO)


title: WT, colon, single-nucleus RNA-seq

city: Suwon

first: Eun

middle: Jeong

last: Lee

state: Gyeonggi-do

address: 206 World cup-ro, Yeongtong-gu

department: Department of Brain Science

country: South Korea

institute: Ajou University

description:
Library name: Sample 1
10x Genomics Chromium single-cell 3' RNA-seq

data_processing:
FASTQ files were generated and processed with Cell Ranger to align reads to mouse genome and produce gene–barcode UMI count matrices for each library.
Assembly: Mus musculus mm10 (GRCm38), 10x Genomics refdata-gex-mm10-2020-A
Supplementary files format and content: Processed data consist of 10x-style sparse count matrices (*_matrix.mtx.gz) with accompanying barcode (*_barcodes.tsv.gz) and feature (*_features.tsv.gz) files for WT and Pink1KO libraries.

source_name: Colon

growth_protocol: 15 weeks old male Pink1 knockout and wild-type C57BL/6 mice were maintained on a 12-h light/12-h dark cycle under specific pathogen free conditions with ad libitum food and water.

extract_protocol:
Mice were sacrificed by cervical dislocation and the colon was removed followed by flushing with ice-cold PBS, opened longitudinally, and minced. Tissue fragments were transferred to nuclei isolation buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl₂, 10 mM Tris-HCl, dithiothreitol, 0.1% Triton). Then it was mechanically homogenized with with a Dounce homogenizer and filtered through a 40 μm strainer, and centrifuged at 1,000 × g for 8 min at 4 °C. After removing the supernatant, the nuclei pellet was resuspended in 0.5% BSA, filtered again, stained with SYTOX Green, and single nuclei were sorted by FACS into ice-cold methanol and immediately stored at −80 °C until library preparation.
FACS-sorted single nuclei from three mice per genotype were pooled and loaded onto a 10x Genomics Chromium Controller using the Chromium Single Cell 3′ Reagent Kit (Next GEM v3.1, Dual Index), targeting ~10,000 nuclei per library. Libraries were quantified and quality-checked and sequenced on an Illumina HiSeq X Ten in paired-end mode (R1 28 bp, i7 10 bp, i5 10 bp, R2 90 bp).

value: Colon

value: Wild type


title: JCC300 Surface Protein reaction 3

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

institute: The Peter Doherty Institute for Infection and Immunity

description:
Library name: 1943812_JCC300_ON_3_Surface
IAV Acute,IBV Acute/Convalescent,Vaccine D7

data_processing:
Cellranger multi pipeline  3.1.0
Assembly: refdata-cellranger-GRCh38-3.0.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0
Supplementary files format and content: Cell ranger features matrix output: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: Cell ranger VDJ filtered contigs files
Library strategy: CITE-seq

source_name: B cells/Tfh

extract_protocol:
Sorted B cells and Tfh cells were encapsulated in gel beads in emulsion (GEMs) using a 10x Genomics Chromium Controller. Reverse transcription and cDNA amplification according to the 10x Genomics protocol CG000186 Chromium Single Cell VDJ Feature Barcoding technology Rev D.
Gene expression and Feature Barcode libraries were prepared according to 10x Genomics protocol 10x Genomics protocol CG000186 Chromium Single Cell VDJ Feature Barcoding technology Rev D.

value: B cells/Tfh


title: KPB25L-UV Tumor, Untreated, CP-3821

description:
Library name: KPB25L-UV_CP-3821
Column name in raw_counts_All_Samples.txt: KPB25L-UV_CP-3821


title: CD90posCD55pos, biol rep1

value: bone and bone marrow

value: Tnfsf11-tTA; LC1; R26-tdTomato


title: JCC300 Surface Protein reaction 4

description:
Library name: 1943813_JCC300_ON_4_Surface
IAV Acute/Convalscent,IBV Acute,Vaccine D7


title: KPB25L-UV Tumor, Untreated, CP-3820

description:
Library name: KPB25L-UV_CP-3820
Column name in raw_counts_All_Samples.txt: KPB25L-UV_CP-3820

value: Untreated


title: JCC300 Surface Protein reaction 2

description:
Library name: 1943811_JCC300_ON_2_Surface
IAV Convalescent,Vaccine D0


title: ID WT mESC ctcf AID Rep2

description:
Library name: ID_WT_mESC_ctcf_AID_Rep2
mESCs expressing transgene WT CTCF with degradation of the endogenous CTCF

value: Embryo


title: 4T1 Tumor, Carboplatin + Paclitaxel, CP-4071

description:
Library name: 4T1_CP-4071
Column name in raw_counts_All_Samples.txt: 4T1_CP-4071


title: RNA-seq, WAPL-AID cells, auxin-24h, rep3

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

description:
Library name: RSRS42
RSRS42

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: CD90negCD55pos, biol rep1


title: RNA-seq, WAPL-AID cells, untreated, rep3

description:
Library name: RSRS41
RSRS41


title: CD90negCD55neg, biol rep2


title: CD90negCD55neg, biol rep1


title: JCC300 BCR reaction 4

description:
Library name: 1943809_JCC300_ON_4_BCR
IAV Acute/Convalscent,IBV Acute,Vaccine D7

data_processing:
Cellranger multi pipeline  3.1.0
Assembly: refdata-cellranger-GRCh38-3.0.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0
Supplementary files format and content: Cell ranger features matrix output: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: Cell ranger VDJ filtered contigs files

source_name: B cells

value: B cells


title: MeRIP_HCT116_TGFP_MT_rep1_Input

description: Library name: MeRIP_HCT116_TGFP_MT_rep1_Input

data_processing:
All sequencing FASTQ files were trimmed using the Trim_Galore program. In the summary of the trimming process for FASTQ files from MeRIP samples, we observed that in several samples, the first read from our paired-end sequencing exhibited lower sequencing quality. To minimize bias, only the second sequencing reads were used for downstream analysis. The second read FASTQ files were first aligned to the human ribosomal RNA sequence using the HISAT2 aligner program (v2.2.1) [58], reads that did not align to the ribosomal RNA were then re-aligned to the human hg38 genome. Duplicates were marked and subsequently removed using the Picard program.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
MeRIP was performed following the manufacturer's protocol (Magna MeRIP Kit, Merck, Cat# 17-10499). Briefly, 300 ug of total RNA was isolated using the RNeasy Mini Kit.
MeRIP was performed following the manufacturer's protocol (Magna MeRIP Kit, Merck, Cat# 17-10499). Briefly, 300 ug of total RNA was isolated using the RNeasy Mini Kit. The RNA was fragmented to approximately 100 nucleotides by heating at 94°C for 4 minutes. Immunoprecipitation was carried out using Magna ChIP Protein A/G Magnetic Beads (Cat# CS203152) and an anti-m6A antibody (Cat# MABE1006). The RNA, beads, and antibody mixture were incubated for 1 hour at room temperature to facilitate binding. Following immunoprecipitation, RNA was eluted from the beads using the provided elution buffer. The eluted RNA was subsequently purified using the RNeasy Mini Kit. For library preparation, 100 ng of input RNA and immunoprecipitated (IP) RNA were used. Libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (Cat. #E7760L) together with the NEBNext® Multiplex Oligos for Illumina® (Index Primer Set 1; Cat. #E7335S/L). The resulting cDNA libraries were sequenced using a paired-end 100-bp run configuration on the NextSeq 2000 platform.

value: Colorectal cancer

value: human colorectal cancer cell line

value: wild type

value: Mock treated


title: KPB25L-UV Tumor, Untreated, CP-3819

description:
Library name: KPB25L-UV_CP-3819
Column name in raw_counts_All_Samples.txt: KPB25L-UV_CP-3819


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep3

description:
Library name: RSRS40
RSRS40

value: WAPL-AID, NIPBL-FKBP, RAD21-Halo,Tir1


title: Pink1 KO, colon, single-nucleus RNA-seq

description:
Library name: Sample 2
10x Genomics Chromium single-cell 3' RNA-seq

value: Pink1 knockout


title: JCC300 BCR reaction 3

description:
Library name: 1943808_JCC300_ON_3_BCR
IAV Acute,IBV Acute/Convalescent,Vaccine D7


title: MeRIP_HCT116_TGFP_MT_rep1_IP

description: Library name: MeRIP_HCT116_TGFP_MT_rep1_IP


title: JCC300 Surface Protein reaction 1

description:
Library name: 1943810_JCC300_ON_1_Surface
IBV Convalescent,Vaccine D28


title: KPB25L Tumor, Untreated, CP-3804

description:
Library name: KPB25L_CP-3804
Column name in raw_counts_All_Samples.txt: KPB25L_CP-3804

value: mammary tumor


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, untreated, rep3

description:
Library name: RSRS39
RSRS39


title: CD90posCD55neg, biol rep1


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep3

description:
Library name: RSRS38
RSRS38

value: PDS5A-AID, PDS5B-AID, NIPBL-FKBP, RAD21-Halo,Tir1


title: 2225 Tumor, Carboplatin + Paclitaxel, CP-3751

description:
Library name: 2225_CP-3751
Column name in raw_counts_All_Samples.txt: 2225_CP-3751

value: Carboplatin + Paclitaxel


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, untreated, rep3

description:
Library name: RSRS37
RSRS37


title: MeRIP_HCT116_TGFP_MT_rep2_IP

description: Library name: MeRIP_HCT116_TGFP_MT_rep2_IP


title: MeRIP_HCT116_TGFP_MT_rep2_Input

description: Library name: MeRIP_HCT116_TGFP_MT_rep2_Input


title: KPB25L Tumor, Untreated, CP-3806

description:
Library name: KPB25L_CP-3806
Column name in raw_counts_All_Samples.txt: KPB25L_CP-3806


title: JCC300 BCR reaction 2

description:
Library name: 1943807_JCC300_ON_2_BCR
IAV Convalescent,Vaccine D0


title: JCC300 BCR reaction 1

description:
Library name: 1943806_JCC300_ON_1_BCR
IBV Convalescent,Vaccine D28


title: KPB25L Tumor, Untreated, CP-3805

description:
Library name: KPB25L_CP-3805
Column name in raw_counts_All_Samples.txt: KPB25L_CP-3805


title: 2225 Tumor, Carboplatin + Paclitaxel, CP-3750

description:
Library name: 2225_CP-3750
Column name in raw_counts_All_Samples.txt: 2225_CP-3750


title: JCC300 TCR reaction 4

description:
Library name: 1943805_JCC300_ON_4_TCR
IAV Acute/Convalscent,IBV Acute,Vaccine D7

source_name: Tfh

value: Tfh


title: MeRIP_HCT116_TGFP_MT_rep3_Input

description: Library name: MeRIP_HCT116_TGFP_MT_rep3_Input


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep2

description:
Library name: RSRS34
RSRS34


title: 2225 Tumor, Carboplatin + Paclitaxel, CP-3749

description:
Library name: 2225_CP-3749
Column name in raw_counts_All_Samples.txt: 2225_CP-3749


title: JCC300 TCR reaction 2

description:
Library name: 1943803_JCC300_ON_2_TCR
IAV Convalescent,Vaccine D0


title: T11-APOBEC Tumor, Untreated, CP-3597

description:
Library name: T11-APOBEC_CP-3597
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-3597


title: T11 Tumor, Untreated, CP-3584

description:
Library name: T11_CP-3584
Column name in raw_counts_All_Samples.txt: T11_CP-3584


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep2

description:
Library name: RSRS32
RSRS32


title: T11-APOBEC Tumor, Untreated, CP-3599

description:
Library name: T11-APOBEC_CP-3599
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-3599


title: JCC300 Gene Expression reaction 3

description:
Library name: 1943800_JCC300_ON_3_Gex
IAV Acute,IBV Acute/Convalescent,Vaccine D7

value: B cells/Tfh


title: RNA-seq, WAPL-AID cells, untreated, rep2

description:
Library name: RSRS35
RSRS35


title: JCC300 Gene Expression reaction 4

description:
Library name: 1943801_JCC300_ON_4_Gex
IAV Acute/Convalscent,IBV Acute,Vaccine D7


title: JCC300 TCR reaction 1

description:
Library name: 1943802_JCC300_ON_1_TCR
IBV Convalescent,Vaccine D28


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, untreated, rep2

description:
Library name: RSRS33
RSRS33


title: JCC300 Gene Expression reaction 2

description:
Library name: 1943799_JCC300_ON_2_Gex
IAV Convalescent,Vaccine D0


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, untreated, rep2

description:
Library name: RSRS31
RSRS31


title: MeRIP_HT29_METTL3KD1_MT_rep1_IP

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep1_IP

value: METTL3 knock-down


title: MeRIP_HT29_METTL3KD1_MT_rep2_IP

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep2_IP


title: RNA-seq, WAPL-AID cells, auxin-24h, rep2

description:
Library name: RSRS36
RSRS36


title: RNA-seq, WAPL-AID cells, untreated, rep1

description:
Library name: RSRS29
RSRS29


title: JCC300 TCR reaction 3

description:
Library name: 1943804_JCC300_ON_3_TCR
IAV Acute,IBV Acute/Convalescent,Vaccine D7


title: RNA-seq, WAPL-AID cells, auxin-24h, rep1

description:
Library name: RSRS30
RSRS30


title: MeRIP_HT29_METTL3KD1_MT_rep1_Input

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep1_Input


title: T11 Tumor, Untreated, CP-3583

description:
Library name: T11_CP-3583
Column name in raw_counts_All_Samples.txt: T11_CP-3583


title: T11-APOBEC Tumor, Untreated, CP-3598

description:
Library name: T11-APOBEC_CP-3598
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-3598


title: JCC300 Gene Expression reaction 1

description:
Library name: 1943798_JCC300_ON_1_Gex
IBV Convalescent,Vaccine D28


title: MeRIP_HCT116_TGFP_MT_rep3_IP

description: Library name: MeRIP_HCT116_TGFP_MT_rep3_IP


title: T11 Tumor, Untreated, CP-3582

description:
Library name: T11_CP-3582
Column name in raw_counts_All_Samples.txt: T11_CP-3582


title: MeRIP_HT29_METTL3KD1_MT_rep3_IP

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep3_IP


title: MeRIP_HT29_METTL3KD1_MT_rep2_Input

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep2_Input


title: MeRIP_HT29_METTL3KD1_MT_rep3_Input

description: Library name: MeRIP_HT29_METTL3KD1_MT_rep3_Input


title: scRNAseq_GF_MULTI_7

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description: Library name: Barcode_7

data_processing:
CellRanger v 7.0.0 count is used for processing cDNA samples.
kb_kite (kallisto and bustools) with default parameters is used along with hashdrops for demultiplexing
Hashdrops was used for demultiplexing the data
Colon relevant data is subsetted for downstream data analysis, where data was SCT normalized on individual batches and then used FASTMNN for integrating the data.
Assembly: mm10
Supplementary files format and content: matrix files, barcodes.tsv, features.tsv

extract_protocol:
The colons were opened and washed with PBS. Epithelial cells were isolated by incubating the tissue in 15 mM EDTA for 45 minutes at 37°C, followed by manual shaking. Crypts were dissociated into single cells by incubation in a dissociation buffer containing Dispase II (2 U/mL) and DNase I (30 μg/mL) for 30 minutes at 37°C. Cells were pooled by condition and sorted at a 1:1 ratio of proliferative epithelial cells (EPCAM⁺, CD44⁺, CD45⁻) and differentiated epithelial cells (EPCAM⁺, CD44⁻, CD45⁻) using fluorescence-activated cell sorting (FACS).
The library was prepared using the 10X Chromium Single Cell 3’ Library Kit according to the manufacturer’s protocol.

value: Colon

value: Epithelium

value: Germ-free C57BL/6J


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, untreated, rep1

description:
Library name: RSRS27
RSRS27

value: Mouse Embryonic Stem Cells

value: untreated


title: MeRIP_HT29_TGFP_MT_rep1_Input

description: Library name: MeRIP_HT29_TGFP_MT_rep1_Input

value: Colorectal cancer


title: MOLM-13 cells, RIP, rep 2

city: SEVILLA

first: Gonzalo

last: Millán-Zambrano

address: Avenida Américo Vespucio, 24

country: Spain

institute: CSIC

description: Library name: sample8

data_processing:
Reads were aligned using STAR v2.7.11b
Quantification of the reads was performed using StringTie v2.2.3
Assembly: hg38
Supplementary files format and content: CSV containing gene counts per sample

source_name: peripherial blood

growth_protocol: MOLM-13 cells were cultured in RPMI 1640-Glutamax supplemented with 10% FBS and 1% penicillin/streptomycin. They were grown at 37ºC in a humidified incubator with 5% CO2.

extract_protocol:
2 and 15 million cells (RNA-seq samples and RIP-seq samples, respectively) were collected and processed using TRIzol (15596026) and total RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research, R2050).
RNA libraries were prepared and sequenced at the CABIMER Genomics Facility (CABIMER, Sevilla). The used kit for library preparation was the Stranded Total RNA Preparation Ribo-Zero kit (Illumina), and sequencing was performed with the NovaSeq 6000 SP reagent kit (Illumina) with 2 × 50 bp paired-end reads in a Novaseq 6000 system (Illumina).

treatment_protocol: For the sake of this experiment, cells were grown for 4 days upon 200 ng/µL DOX treatment.

value: peripherial blood

value: acute myeloid leukemia cells

value: shCONTROL

value: 200 ng/uL doxycycline, 4 days


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep1

description:
Library name: RSRS26
RSRS26


title: MeRIP_HT29_TGFP_MT_rep1_IP

description: Library name: MeRIP_HT29_TGFP_MT_rep1_IP

value: human colorectal cancer cell line

value: wild type

value: Mock treated


title: scRNAseq_GF_MULTI_6

description: Library name: Barcode_6


title: MOLM-13 cells, shBCLAF1, rep 3

description: Library name: sample6


title: scRNAseq_GF_cDNA_7

description: Library name: cDNA_7


title: MOLM-13 cells, RIP, rep 1

description: Library name: sample7


title: RNA-seq, WAPL-AID_NIPBL-FKBP cells, auxin-24h_dTAG-24h, rep1

description:
Library name: RSRS28
RSRS28

value: WAPL-AID, NIPBL-FKBP, RAD21-Halo,Tir1


title: scRNAseq_GF_cDNA_6

description: Library name: cDNA_6


title: MOLM-13 cells, RIP, rep 3

description: Library name: sample9


title: scRNAseq_Abx_MULTI_repeat_3

description: Library name: Barcode_3

value: wild type C57BL/6J

value: Antibiotic


title: MeRIP_HT29_TGFP_MT_rep2_Input

description: Library name: MeRIP_HT29_TGFP_MT_rep2_Input


title: MeRIP_HT29_TGFP_MT_rep2_IP

description: Library name: MeRIP_HT29_TGFP_MT_rep2_IP


title: RNA-seq, PDS5AB-AID_NIPBL-FKBP cells, untreated, rep1

description:
Library name: RSRS25
RSRS25

value: PDS5A-AID, PDS5B-AID, NIPBL-FKBP, RAD21-Halo,Tir1


title: RNA-seq,Tir1-control, untreated, rep3

description:
Library name: RSRS21
RSRS21


title: RNA-seq, PDS5AB-AID cells, auxin-24h, rep3

description:
Library name: RSRS19
RSRS19

value: PDS5A-AID, PDS5B-AID,Tir1


title: scRNAseq_Abx_MULTI_repeat_1

description: Library name: Barcode_1

value: Colon

value: Epithelium


title: MOLM-13 cells, shBCLAF1, rep 1

description: Library name: sample4


title: MeRIP_HT29_TGFP_MT_rep3_Input

description: Library name: MeRIP_HT29_TGFP_MT_rep3_Input


title: scRNAseq_Abx_MULTI_repeat_2

description: Library name: Barcode_2


title: MOLM-13 cells, shBCLAF1, rep 2

description: Library name: sample5


title: CutRun_HT29_METTL3KD1_MT_rep1_H3K4me3

description: Library name: CutRun_HT29_METTL3KD1_MT_rep1_H3K4me3

data_processing:
The trimmed fastq files were aligned to the human hg38 genome using the Bowtie2 aligner program (v.2.3.4.2) with parameters set as: -I 10 -X 700 –local –very-sensitive- local –no-mixed –no-discordant –no-unal. Duplicates were marked and then removed using picard program. To perform spike-in normalization, the same fastq files were aligned to the sacCer3 yeast genome using Bowtie2 with the parameters setting as: -I 10 -X 700 –local –very- sensitive-local –no-mixed –no-discordant –no-unal –no-overlap –no-dovetail. The spike-in normalization factor was calculated as the ratio between 20,000 and the total reads aligned to the yeast genome. Genome coverage of each sample was generated from the alignment files using the genomecov command in the bedtools suite (v.2.28.0) with the scale parameter setting as the spike-in normalization factor to normalize the library. Peaks were called from Human genome aligned BAM files using MACS2 with the following parameters: -q 0.01 -B –SPMR –keep-dup all.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
1,000,000 cells per condition were immobilized on Concanavalin A-coated magnetic beads, followed by incubation with an anti-H3K4me3 antibody (Abcam, ab8580, 1:100 dilution) overnight at 4°C. After antibody binding, cells were washed with digitonin-containing wash buffer, and Protein A-MNase was added to the mixture and incubated for 1 hour at 4°C.
CUT&RUN assays were performed on CTRL and METTL3KD CRC cells using the Cell Signaling Technology (CST) CUT&RUN Assay Kit (#86652) according to the manufacturer’s protocol. Briefly, 1,000,000 cells per condition were immobilized on Concanavalin A-coated magnetic beads, followed by incubation with an anti-H3K4me3 antibody (Abcam, ab8580, 1:100 dilution) overnight at 4°C. After antibody binding, cells were washed with digitonin-containing wash buffer, and Protein A-MNase was added to the mixture and incubated for 1 hour at 4°C. To initiate chromatin cleavage, 3 µl of 100 mM CaCl₂ was added, and the reaction was allowed to proceed on ice for 30 minutes. The reaction was terminated by adding a chelation buffer containing EDTA and EGTA. The cleaved chromatin fragments were collected in the supernatant following centrifugation and purified using the QIAGEN MinElute Kit. The purified DNA was then used to prepare sequencing libraries with the NEBNext Ultra II DNA Library Prep Kit, following the manufacturer’s protocol. Libraries were sequenced using the Illumina NextSeq 2000 platform to generate paired-end reads.

value: METTL3 knock-down


title: RNA-seq, PDS5AB-AID cells, untreated, rep3

description:
Library name: RSRS17
RSRS17

value: Mouse Embryonic Stem Cells


title: CutRun_HT29_METTL3KD1_MT_rep2_H3K4me3

description: Library name: CutRun_HT29_METTL3KD1_MT_rep2_H3K4me3

value: Colorectal cancer


title: RNA-seq,Tir1-control, untreated, rep2

description:
Library name: RSRS13
RSRS13


title: CutRun_HT29_METTL3KD1_MT_rep3_H3K4me3

description: Library name: CutRun_HT29_METTL3KD1_MT_rep3_H3K4me3


title: MOLM-13 cells, shCONTROL, rep 1

description: Library name: sample1

value: peripherial blood


title: MeRIP_HT29_TGFP_MT_rep3_IP

description: Library name: MeRIP_HT29_TGFP_MT_rep3_IP


title: scRNAseq_Abx_MULTI_1

description: Library name: multi_1


title: RNA-seq, PDS5AB-AID cells, auxin-24h, rep2

description:
Library name: RSRS11
RSRS11


title: scRNAseq_Abx_cDNA3

description: Library name: cDNA_3


title: MOLM-13 cells, shCONTROL, rep 3

description: Library name: sample3

value: acute myeloid leukemia cells


title: RNA-seq, PDS5AB-AID cells, untreated, rep2

description:
Library name: RSRS9
RSRS9


title: scRNAseq_Abx_cDNA2

description: Library name: cDNA_2


title: CutRun_HT29_TGFP_MT_rep2_H3K4me3

description: Library name: CutRun_HT29_TGFP_MT_rep2_H3K4me3


title: MOLM-13 cells, shCONTROL, rep 2

description: Library name: sample2

value: shCONTROL


title: CutRun_HT29_TGFP_MT_rep1_H3K4me3

description: Library name: CutRun_HT29_TGFP_MT_rep1_H3K4me3


title: RNA-seq, PDS5AB-AID cells, auxin-24h, rep1

description:
Library name: RSRS3
RSRS3