title: CRE2_J2

status: Public on Feb 27 2026

type: SRA

city: Worcester

first: Sithara Raju

last: Ponny

state: MA

address: 55 N Lake Ave

department: Program in Molecular Medicine

country: USA

institute: UMass Chan Medical School

description:
Library name: Sample 10
10X Genomics

library_source: transcriptomic single cell

data_processing:
Alignment, filtering, barcode counting,UMI counting and aggregation was done using Cell Ranger Software
All further analysis was done using Seurat
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
The liver was diced with scissors and gently pushed with a 10 ml plunger through a 100 μm cell strainer. The cells were washed with 2% FBS-PBS and centrifuged at 1,700 rpm (6 min). The cells were re-suspended with 33.8 % Isotonic Percoll and centrifuged at 2,000 rpm (12 min). The pellet (leukocytes) was collected. Red blood cells were removed with ACK lysing buffer. The cells were then washed with PBS.
Single cell capture and library preparation were performed according to the Chromium Single Cell 3’ Reagent Kits V3 User Guide. Cells were loaded on a multiple-channel microfluidics chip of the Chromium Controller (10X Genomics) with a targeted cell recovery of 8,000. Libraries were constructed with Single Cell 3’ Reagent Kits V3. Illumina sequencing libraries were prepared with the amplified cDNA and assessed with High sensitivity DNA Assay Kits (Agilent Bioanalyzer system) and Qubit dsDNA High Sensitivity Assay Kits.

tag: tissue

value: Liver

tag: strain

tag: genotype

value: J1 J2 lf/lf


title: GFP2_J2

description:
Library name: Sample 8
10X Genomics


title: CRE1_J2

description:
Library name: Sample 9
10X Genomics


title: FLPO1_J2

description:
Library name: Sample 11
10X Genomics


title: mK4-F7-rep3

city: Freiburg

first: Gwang-Jin

last: Kim

address: Albertstrasse 25

country: Germany

institute: University of Freiburg

library_source: transcriptomic

data_processing:
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-33-26).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format.

growth_protocol: mk4 cells were rown under standard serum conditions (10%FBS)

extract_protocol: none provided by the submitter

treatment_protocol: mk4 FOXD2 mutant cells (cloneF7) was generated using crispr cas. Control cells likwise underwent CRISPR/cas  gene targeting, however a non targeting  guide RNA was used.

tag: sample type

value: mutant

value: FOXD2 homozygous frameshift mutation


title: mK4-F7-rep1


title: mK4-F7-rep4


title: mK4-ctrl-rep5

value: control

value: Foxd2 wildtype genotype


title: mK4-ctrl-rep3


title: mK4-F7-rep2


title: GFP1_J2

description:
Library name: Sample 7
10X Genomics


title: mK4-ctrl-rep1


title: Synovialo sarcoma

city: Paris

first: Mathilde

last: Filser

address: 26 rue d'Ulm

department: Genetics Department

country: France

institute: Institut Curie

description: Library name: SQK_LSK114_P19

library_source: genomic

data_processing:
Nanopore sequencing bioinformatics analysis relied on the custom bioinformatics pipeline NanoCliD, available on github (https://github.com/InstituteCurieClinicalBioinformatics/NanoCliD). Methylation calling was performed using Nanopolish 0.14.0 for R9 flow cells and f5c for R10 flow cells. The Guppy 5.0.17 data processing toolkit for R9 flow cells and then the Dorado one for R10 flow cells facilitated the conversion of FAST5 files to FASTQ files. Sequences were aligned to the reference genome hg19 with Minimap 2.24-r1122. Structural variants were identified using a combination of Sniffles2, SVIM and cuteSV. The resulting BAM files were then manually inspected using the Integrative Genomics Viewer (IGV) to highlight relevant fusions and rearrangements. The NanoDx pipeline was integrated into NanoCliD for tumor classification. CpG sites identified during Nanopore sequencing were cross-referenced with the 850,000 sites covered by the EPIC array, retaining only common sites. A random forest algorithm was then applied to generate a methylation profile, allowing tumor classification into subgroups based on CpG sites overlapping those from Illumina arrays and comparison with either Capper’s or Koelsche’s classifier. The classification score, reflecting the sample's passage through the algorithm’s decision trees, was determined by counting the class assigned by each tree. Additionally, Uniform Manifold Approximation and Projection (UMAP) and tdistributed Stochastic Neighbor Embedding (t-SNE) were generated for each sample to aid visualization.
Assembly: hg19
Supplementary files format and content: Methylation calls tables (tsv format)

molecule: genomic DNA

organism: Homo sapiens

source_name: Fresh frozen tumor

extract_protocol:
DNA were extracted from frozen tumor samples using the standard phenol-chloroform procedure. Remaining of the DNA was extracted using the Maxwell automat. The quality and quantity of DNA were assessed using Nanodrop (Thermo Fisher Scientific) and Qubit (Thermo Fisher Scientific). The extracted DNA was quantified using the Qubit Fluorometer (Quant-iT dsDNA BR Assay Kit; Thermo Fisher Scientific) and qualified using TapeStation (Genomic DNA screenTape; Agilent) following the manufacturer’s instructions.
DNA libraries were prepared from 2 µg of genomic DNA, quantified using the Qubit assay. Two libraries, P6 and P7, were generated from 343 ng and 987 ng of DNA, respectively, based on available quantities. The library preparation process is efficient, requiring approximately half a day to complete. The main steps include mechanical DNA fragmentation using Covaris® g-tubes to achieve a target fragment size of 20 kb, followed by end repair, adapter ligation, and library purification. Initially, libraries were prepared using the ligation sequencing kit LSK-SQK110 and later with LSK-SQK114 (Oxford Nanopore Technologies) due to a chemistry update during the study, following the manufacturer’s guidelines. Sequencing was performed in two batches using R9 or R10 flow cells. First, half of the library was loaded onto a MinION MK1B device for approximately 24 hours of sequencing. Once data acquisition reached a plateau and most flow cell pores became saturated, sequencing was paused. The flow cell was then washed with a nuclease mix to recover as many active pores as possible before loading the remaining half of the library for an additional 24 hours of sequencing.

value: Fresh frozen tumor

tag: cell type

value: tumor cell


title: mK4-ctrl-rep4


title: Extra-renal malignant rhabdoid tumor

description: Library name: SQK_LSK114_20


title: FLPO2_J2

description:
Library name: Sample 12
10X Genomics


title: Ewing's sarcoma

description: Library name: SQK_LSK114_P17


title: Poorly differentiated carcinoma

description: Library name: SQK_LSK114_P16


title: mK4-ctrl-rep2


title: Suspicion of Ewing's sarcoma

description: Library name: SQK_LSK114_P14


title: Mesenchymal or neuro-ectodermal tumor

description: Library name: SQK_LSK114_P10


title: Poorly differentiated tumor with small, round, blue cells

description: Library name: SQK_LSK114_P11


title: Focal chondroid areas

description: Library name: SQK_LSK114_P8


title: Pilocytic astrocytoma

description: Library name: SQK_LSK114_P7


title: Dysembryoplastic neuroepithelial tumor

description: Library name: SQK_LSK114_P9


title: Dermatofibrosarcoma protuberans

description: Library name: SQK_LSK114_P18


title: Rhabdomyosarcoma

description: Library name: SQK_LSK114_P13


title: High-grade neuroepithelial tumor

description: Library name: SQK_LSK114_P5


title: Embryonal tumor INI-conserved

description: Library name: SQK_LSK114_P12


title: Low-grade glioneuronal lesion

description: Library name: SQK_LSK114_P6


title: Mesenchymal chondrosarcoma or Ewing like tumor

description: Library name: SQK_LSK114_P15


title: Embryonal tumor

description: Library name: SQK_LSK114_P3


title: Desmoplastic medulloblastoma

description: Library name: SQK_LSK114_P2


title: Caco2_Propionate_H3K9pr_r2_CNR

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University

description: Library name: Sample 8

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: BSgenome.Hsapiens.UCSC.hg19 (version 1.4.3) and TxDb.Hsapiens.UCSC.hg19.knownGene (version 3.4.0)
Assembly: hg19
Supplementary files format and content: counts, bigwigs
Library strategy: CUT&Run

growth_protocol: HCT-116 cells were grown in DMEM medium or human plasma like media (HPLM) with 10% fetal bovine serum and 1% penicillin/streptomycin. When cells were grown in HPLM, cells were washed in PBS and cultured in HPLM for at least three days prior to experiments. Caco-2 cells were grown in Eagle's Minimum Essential Medium supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 20% FBS, and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNA isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated or digested chromatin for ChIP-seq and Cut&Run, respectively.
Libraries were generated using NEBNext Ultra II kits following the manufacturer's protocol.

treatment_protocol: HCT-116 and Caco-2 cells were treated with different short chain fatty acids (SCFAs) or inhibitors for 6 or 24 hours prior to RNA isolation. For ChIP-seq or Cut&Run experiments, cells were treated with 5 mM butyrate or 5 mM propionate for 24 hours prior to fixation.

tag: cell line

value: Colorectal carcinoma

value: Wild type

tag: treatment

value: 5 mM propionate for 24 hours


title: Basophils_1

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

data_processing:
Raw FASTQ data were processed as previously described. RNAseq data analysis was performed as previously described in the R programming environment (R Core Team, Vienna, Austria). Importantly, mean–variance modelling at the observation level transformation (VOOM), followed by linear models and empirical bayes in limma R package were applied to obtain differentially expressed genes between groups. Differential gene expression was calculated as a log2-fold change in expression between in vitro better and poor / non-responders to omalizumab treatment.
Assembly: GRCh37
Supplementary files format and content: counts.txt; gene ids, counts

molecule: polyA RNA

source_name: Peripheral venous blood basophils

growth_protocol: 12 mL of venous blood was collected into the K2EDTA tubes (BD Vacutainer, BD, New Jersey, USA). Blood plasma was separated by centrifugation at 300×g, 20 min, room temperature (RT), next, white blood cells (WBCs) were isolated by gradient centrifugation (1.200×g, 10 min, RT) using density medium (1.094 g/mL, mixed from High Density Spin Medium and Density Diluent Medium, both pluriSelect, Leipzig, Germany) and SepMate50 tubes (Stem Cell Technologies, Vancouver, Canada). The basophils were isolated using fluorescence activated cell sorting (FACS Aria Fusion, BD Biosciences, New Jersey, USA) as a CD45+CD123+HLA-DRneg population. Single cells (singlets) were separated from doublets and cellular debris using the FSC-A / FSC-H gating. The following conjugated primary antibodies were used: Mouse IgG anti-human CD45-PE (#1P-160-T100), Mouse IgG anti-human CD123-APC (#1A-700-T100) and Mouse IgG anti-human HLA-DR-FITC (#1F-474-T100, all EXBIO, Prague, Czechia). Antibody concentrations recommended by the manufacturer were used.

extract_protocol:
RNA was isolated from sorted basophils (the in vitro testing) using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) and from PAX RNA tubes (the clinical cohort) using the PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland), following the manufacturers’ recommendations. RNA concentration was determined using the Synergy2 microplate reader (Biotek, Winooski, VT, USA), and RNA integrity was assessed using the Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany) or by gel electrophoresis.
For RNA sequencing (RNAseq), cDNA libraries were prepared using the Stranded mRNA Prep Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Paired-end RNA sequencing (2×74 bp) was performed on a NextSeq 550 system (Illumina) using a NextSeq 500/550 Mid Output Kit v2.5 (Illumina).

treatment_protocol: Freshly isolated WBCs from the discovery and validation cohorts were seeded in RPMI-1640 media (Gibco, ThermoFisher Scientific, Waltham, MA, USA) supplemented with 10% of the respective donor's own blood plasma and 1% penicillin / streptomycin (Sigma-Aldrich, St. Louis, MO, USA) at a density of 2.5×10^6 cells/mL. One half of the cells were treated with 3.32 µg/mL omalizumab (Xolair, Novartis, Basel, Switzerland) for 24 hours at standard cell culture conditions: 37°C, 5% CO2, >95% relative humidity. The specific concentration of omalizumab used was calculated from the manufacturer's recommended dose for subcutaneous administration to patients.

value: Peripheral venous blood basophils

tag: patients

value: Basophils

value: Omalizumab

tag: phenotype

value: poor response

tag: library type

value: mRNA


title: Ependymoma

description: Library name: SQK_LSK114_P1


title: Caco2_Propionate_H3K27pr_r1_CNR

description: Library name: Sample 10


title: Caco2_Propionate_IgG_CNR

description: Library name: Sample 14


title: Caco2_Propionate_H3K9pr_r1_CNR

description: Library name: Sample 7


title: Basophils_3


title: Caco2_Propionate_H3K27pr_r2_CNR

description: Library name: Sample 11


title: Caco2_Propionate_H3K27pr_r3_CNR

description: Library name: Sample 12


title: Basophils_4

value: good response


title: KO_E18.5_rep1

city: Boston

first: Maria

last: Loscertales

address: 185 Cambridge st

institute: MGH

description:
Library name: Sample5
Embryonic day 18.5 mouse lung tissue from Svep1-/- embryos, total RNA extracted for bulk RNA-seq.
OC105

data_processing:
Raw FASTQ files were quality-checked using FastQC (v0.11.9) and trimmed for adapters and low-quality bases using Trimmomatic (v0.39).
FASTQ files were aligned to version GRCm39 of the mouse reference genome using STAR (v2.7.10a) with default parameters.
BAM files resulting from the alignments were summarized to genes using featureCounts (v2.0.3) based on GENCODE vM31 annotation.
Raw counts were normalized using DESeq2 (v1.40.0) to generate normalized expression values for each sample.
Differentially expressed genes were identified using DESeq2 with default parameters, considering adjusted p-value ≤ 0.05.
Assembly: ersion GRCm39 of the mouse reference genome
Supplementary files format and content: Tab-delimited text files include normalized counts for each sample, with gene identifiers in rows and sample IDs in columns.

source_name: Lung

growth_protocol: Timed pregnant C57BL/6 mice carrying Svep1 heterozygous embryos were maintained under standard housing conditions. Embryos were collected at embryonic day 18.5 (E18.5). Whole lungs were dissected immediately after euthanasia and processed for RNA extraction.

extract_protocol:
Total RNA was isolated from whole embryonic lungs using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were assessed prior to library preparation.
libraries werRNA-seq libraries were prepared from poly(A)-selected RNA using a standard Illumina-compatible library preparation kit according to the manufacturer’s instructions. Libraries were indexed, pooled, and sequenced using paired-end Illumina sequencing.e prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: No experimental treatment was applied. Samples represent native developmental conditions at embryonic day 18.5DMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.

value: Lung

value: whole lung cells

value: embryonic lung tissue


title: WT_E18.5_rep4

description:
Library name: Sample4
Embryonic day 18.5 mouse lung tissue from Svep1+/+ embryos, total RNA extracted for bulk RNA-seq.
OC104


title: Caco2_Propionate_H3K9pr_r3_CNR

description: Library name: Sample 9


title: WT_E18.5_rep2

description:
Library name: Sample2
Embryonic day 18.5 mouse lung tissue from Svep1+/+ embryos, total RNA extracted for bulk RNA-seq.
OC101


title: Caco2_Butyrate_H3K9bu_r1_CNR

description: Library name: Sample 1

value: 5 mM butyrate for 24 hours


title: KO_E18.5_rep3

description:
Library name: Sample7
Embryonic day 18.5 mouse lung tissue from Svep1-/- embryos, total RNA extracted for bulk RNA-seq.
OC109


title: Caco2_Butyrate_H3K27bu_r3_CNR

description: Library name: Sample 6


title: KO_E18.5_rep4

description:
Library name: Sample8
Embryonic day 18.5 mouse lung tissue from Svep1-/- embryos, total RNA extracted for bulk RNA-seq.
OC109


title: WT_E18.5_rep3

description:
Library name: Sample3
Embryonic day 18.5 mouse lung tissue from Svep1+/+ embryos, total RNA extracted for bulk RNA-seq.
OC102


title: Caco2_Butyrate_H3K9bu_r3_CNR

description: Library name: Sample 3


title: Basophils_2


title: Caco2_Propionate_H3K4me3_CNR

description: Library name: Sample 13


title: Caco2_Butyrate_H3K9bu_r2_CNR

description: Library name: Sample 2


title: Caco2_Butyrate_H3K27bu_r1_CNR

description: Library name: Sample 4


title: WT_E18.5_rep1

description:
Library name: Sample1
Embryonic day 18.5 mouse lung tissue from Svep1+/+ embryos, total RNA extracted for bulk RNA-seq.
OC100


title: Caco2_Butyrate_H3K27bu_r2_CNR

description: Library name: Sample 5


title: Retina, Isl1 cKO, E13.5, Rep2

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

description: Library name: Retina_Isl1KO_E13_5_Rep2

data_processing:
The Trimmomatic software (github.com/usadellab/Trimmomatic) was used to filter and trim minority low quality sequencing reads from the data set
The quality of sequence reads in FASTQ files was evaluated using FastQC analysis
High quality sequence reads were aligned to the mouse mm10 reference transcriptome using HISAT2. The HISAT2 outputs were transformed with SAMtools and then fed into StringTie for transcript quantification
Subsequently, the count tables or matrices were input into the DESeq2 statistical package for determination of differential transcript expression between samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retina

extract_protocol:
Total RNA was extracted from fresh frozen tissue
The strand-specific RNA sequencing library was prepared using the Illumina NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., Ipswich, MA), and PolyA selection for mRNA was used to remove rRNA.

treatment_protocol: E13.5 retinae were dissected and flash frozen in Trizol and sent to Azenta Life Sciences for mRNA isolation and library preparation

value: retina


title: KO_E18.5_rep2

description:
Library name: Sample6
Embryonic day 18.5 mouse lung tissue from Svep1-/- embryos, total RNA extracted for bulk RNA-seq.
OC106


title: Retina, Isl1 cKO, E13.5, Rep1

description: Library name: Retina_Isl1KO_E13_5_Rep1


title: Retina, control, E13.5, Rep2

description: Library name: Retina_control_E13_5_Rep2

value: control


title: Retina, control, E13.5, Rep1

description: Library name: Retina_control_E13_5_Rep1


title: NHEK cells treated with PDSO after UVB irradiation, biol rep 1

city: Kunming

first: Liping

last: Qu

state: Yunnan

address: No. 53 Keyi Road, Kunming City

country: China

institute: Yunnan Botanee Bio-technology Group Co., Ltd.

description: Library name: UVB_PDSO_1

data_processing:
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, followed by sequencing using the Illumina Novaseq X Plus platform. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of thereference genome, and use HISAT2 to align paired-end clean reads to the reference genome. The mapped reads of each sample were assembled by StringTie (v2.2.3) (Mihaela Pertea.et al. 2015) in a reference-based approach. featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis for two groups was performed using the DESeq2 R package(1.42.0). The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression: padj <= 0.05 ＆ |log2(foldchange)| >= 0.58. (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were implemented by the clusterProfiler (4.8.1).
Assembly: hg38
Supplementary files format and content: gene_fpkm.txt

source_name: normal human epidermal keratinocytes (NHEK)

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: NHEK Cells were seeded into 6-well plates at a density of 5 ×105 cells/well and cultured for 24 h. Prior to UVB irradiation, cells were treated with 120 μg/ml PDSO for 2 h. Subsequently, the culture medium was replaced with PBS solution and cells were exposed to 30 mJ/cm2 of UVB irradiation. After irradiation, the PBS was aspirated immediately and fresh DMEM medium containing 120 μg/ml PDSO was introduced. Cells were cultured for an additional 24 h and then  lysed to extract total RNA.

value: keratinocytes

value: wild type

value: UVB irradiation and PDSO treatment


title: NHEK cells irradiated with UVB radiation, biol rep 3

description: Library name: UVB_3

value: normal human epidermal keratinocytes (NHEK)

value: UVB irradiation


title: NHEK cells treated with PDSO after UVB irradiation, biol rep 2

description: Library name: UVB_PDSO_2


title: NHEK cells irradiated with UVB radiation, biol rep 2

description: Library name: UVB_2


title: NHEK cells treated with PDSO after UVB irradiation, biol rep 3

description: Library name: UVB_PDSO_3


title: normal NHEK cells, biol rep 2

description: Library name: Control_2


title: normal NHEK cells, biol rep 1

description: Library name: Control_1


title: NHEK cells irradiated with UVB radiation, biol rep 1

description: Library name: UVB_1


title: normal NHEK cells, biol rep 3

description: Library name: Control_3


title: 11-H2-WT-d3

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

description:
Library name: Sample 11
Parse Biosciences WT Evercode

data_processing:
Raw Parse Evercode WT sequencing data was processed per sublibrary by the Parse Evercode pipeline (split-pipe version 1.3.0), aligning to human and influenza A genonome (custom GRCh38_H3N2) using the GRCh38 primary assembly with Ensembl v112 annotations and influenza A virus Perth H3N2 genome (Genbank Accessions: KJ609203-KJ609210)
The matrix table of gene counts from the Parse Evercode pipeline was used as an input for integration and clustering analyses using the R-based Seurat package (version 5.1.0, R version 4.3.1)
Assembly: GRCH38_H3N2
Supplementary files format and content: Raw counts from barcodes called as cells are made available in matrix format.

source_name: air liquid interface culture

growth_protocol: Human bronchial epithelial cells were grown in Pneumacult Ex-Plus media, then plated on collagen-coated transwell inserts ad allowed to differentiate in Pneumacult Basal ALI media for 3 weeks (Stemcell)

extract_protocol:
ALI cultures were trypsinized for 30 minutes and dead cells were depleted using an Annexin V dead cell depletion kit (Stemcell)
Library preparation was performed with Parse Evercode WT kit

treatment_protocol: Samples were collected after 1 and 3 days post infection

value: air liquid interface culture

value: human bronchial epithelial cells

tag: donor

value: Donor 2

tag: infection condition

tag: days post_infection

value: 3 DPI


title: 12-H2-DX-d3

description:
Library name: Sample 12
Parse Biosciences WT Evercode

value: PA-X deficient A/Perth/16/2009 H3N2


title: 5-H1-WT-d3

description:
Library name: Sample 5
Parse Biosciences WT Evercode

value: Donor 1


title: 6-H1-DX-d3

description:
Library name: Sample 6
Parse Biosciences WT Evercode


title: 10-H2-M-d3

description:
Library name: Sample 10
Parse Biosciences WT Evercode

value: Mock


title: 7-H2-M-d1

description:
Library name: Sample 7
Parse Biosciences WT Evercode

value: 1 DPI


title: 1-H1-M-d1

description:
Library name: Sample 1
Parse Biosciences WT Evercode


title: 4-H1-M-d3

description:
Library name: Sample 4
Parse Biosciences WT Evercode


title: 2-H1-WT-d1

description:
Library name: Sample 2
Parse Biosciences WT Evercode


title: 9-H2-DX-d1

description:
Library name: Sample 9
Parse Biosciences WT Evercode


title: 3-H1-DX-d1

description:
Library name: Sample 3
Parse Biosciences WT Evercode


title: Donor SAMN38872001 Vehicle Treated ROS Positive

city: Indianapolis

first: Amelia

middle: K

last: Linnemann

state: IN

address: 1210 Waterway Blvd. Suite 4000

department: Pediatrics

institute: Indiana University School of Medicine

description: Library name: SAMN2001_Veh_Pos_S6_L006

data_processing:
Reads were mapped to reference genome using STAR v2.7.10a
Quality of RNA-seq data was evaluated by NGSUtils,bamutils v0.5.9
Low quality mapped reads were excluded and featureCounts v1.5.1 was used to quantify gene level expression
Differential gene expression analysis was performed using edgeR v3.30.3
Assembly: HG38
Supplementary files format and content: excel file with raw counts, log2 FPKM, and fold change

source_name: Pancreatic Islet

extract_protocol:
Qiagen RNAeasy mini kit with on-column DNAse treatment
cDNA libraries were prepped using SMART-seq ultra-low input RNA kit: Clontech SMART-Seq v4 Ultra Low Input RNA Kit; Illumina Nextera XT DNA Lib Kit

value: Pancreatic Islet


title: Donor SAMN38872001 Vehicle Treated ROS Negative

description: Library name: SAMN2001_Veh_Neg_S5_L006


title: Donor SAMN38872001 IFN⍺ Treated ROS Positive

description: Library name: SAMN2001_IFNa_Pos_S8_L006


title: 8-H2-WT-d1

description:
Library name: Sample 8
Parse Biosciences WT Evercode


title: Donor SAMN38891395 Vehicle Treated ROS Positive

description: Library name: SAMN1395_Veh_Pos_S10_L006


title: Donor SAMN38891395 Vehicle Treated ROS Negative

description: Library name: SAMN1395_Veh_Neg_S9_L006


title: Donor SAMN38872001 IFN⍺ Treated ROS Negative

description: Library name: SAMN2001_IFNa_Neg_S7_L006


title: Ependymoma or astroblastoma

description: Library name: SQK_LSK114_P4

value: Fresh frozen tumor

value: tumor cell


title: Donor SAMN38891395 IFN⍺ Treated ROS Positive

description: Library name: SAMN1395_IFNa_Pos_S12_L006


title: Donor SAMN38891395 IFN⍺ Treated ROS Negative

description: Library name: SAMN1395_IFNa_Neg_S11_L006


title: Donor SAMN39461369 IFN⍺ Treated ROS Positive

description: Library name: SAMN1369_IFNa_Pos_S4_L006


title: Donor SAMN39461369 Vehicle Treated ROS Positive

description: Library name: SAMN1369_Veh_Pos_S2_L006


title: Donor SAMN39461369 Vehicle Treated ROS Negative

description: Library name: SAMN1369_Veh_Neg_S1_L006


title: MOLM-13, A485, H3K27me3, rep1

city: Mainz

first: Aarón

last: Gallego Crespo

state: Rhineland-palatinate

address: Langenbeckstraße 1

department: III. Medical Department

institute: University Medical Center of the Johannes Gutenberg University

description: Library name: Sample 10

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology.
ChIP-Seq reads were trimmed using Trim Galore v0.6.5 for adapters removal.
Trimmed reads were aligned to the human reference genome (GRCh38/hg38) using the aligner Bowtie2 v2.5.1 (Parameters: bowtie2 --very-sensitive -k 1). Uniquely mapped and properly paired reads were retained using Picard v2.6.0 for reads deduplication.
Peaks were called with MACS2 v2.2.7.1.
BigWig files were created using DeepTools v3.5.1 for coverage visualization
Assembly: hg38
Supplementary files format and content: Bigwig files

growth_protocol: RPMI 10% FCS and 1% Pen/Strep; cells were cultured at 37°C with 5% CO2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Crosslinking was terminated with 125mM Glycine for 5 minutes. Cell pellets were washed twice with ice-cold PBS and snap-frozen in liquid nitrogen
ChIP libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit for Illumina. ChIP DNA was amplified using 11 cycles according to the manufacturers instruction. Amplified ChIP libraries were finally size selected using AMPure Beads (Beckman-Coulter) and analyzed via Tapesation (High Sensiticity, Agilent).

treatment_protocol: 24 Hours of Treatment with A-485 or DMSO

value: Acute Myeloid Leukemia


title: Donor SAMN39461369 IFN⍺ Treated ROS Negative

description: Library name: SAMN1369_IFNa_Neg_S3_L006


title: MOLM-13, A485, H3K27me3, rep2

description: Library name: Sample 12


title: MOLM-13, DMSO control, H3K27me3, rep2

description: Library name: Sample 11

value: DMSO


title: MOLM-13, DMSO control, H3K27me3, rep1

description: Library name: Sample 9


title: MOLM-13, dCBP, H3K27ac, rep1

description: Library name: Sample 5

value: dCBP


title: MOLM-13, both (A485+dCBP), H3K27ac, rep1

description: Library name: Sample 7

value: both


title: MOLM-13, A485, H3K27ac, rep2

description: Library name: Sample 4


title: MOLM-13, DMSO control, H3K27ac, rep2

description: Library name: Sample 3


title: MOLM-13, dCBP, H3K27ac, rep2

description: Library name: Sample 6


title: MOLM-13, both (A485+dCBP), H3K27ac, rep2

description: Library name: Sample 8


title: Mini_Sublibrary2_CRISPR

description: Library name: Mini_CRISPR2

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology. Sequencing depths were 20,000 reads per cell for the transcriptomics libraries and 2,000 reads per cell for the CRISPR libraries
For processing the transcriptomic FASTQ files, Parses' proprietary pipeline (Trailmaker) was used, the individual sgRNAs were then assigned using the CRISPR FASTQ files via the split-pipe pipeline (v 1.4.1).
Downstream analysis was performed using Seurat (v 5.3).
Assembly: hg38
Supplementary files format and content: Tab-delimited txt files with raw count matrix separately for all Mega and Mini Kit Samples
Supplementary files format and content: Xlsx files with loading tables separately for Mega and Mini Kit Samples

source_name: Blood cells

growth_protocol: Cells were grown in RPMI with 10% FCS and 1% Pen/Strep

extract_protocol:
Cells were fixed and stored at -80°C according to a proprietary protocol from Parse Biosciences (Evercode Cell Fixation v3)
We used a combinatorial barcoding approach from Parse Biosciences (Seattle, USA). Samples were processed according to Parse Biosciences Manual (Evercode WT Mini and Mega v3 with CRISPR Detect), (sub-)libraries were prepared for transcriptomics and seperately for sgRNA detection, each library was tested on Agilents TapeStation before submitting for sequencing. Each library is pooled due to combinatorial barcoding, and cell identidies are determined during analysis using an individual sample processing sheet.

treatment_protocol: 24 Hours with A-485 or DMSO

value: Blood cells


title: Mini_Sublibrary1_CRISPR

description: Library name: Mini_CRISPR1


title: Mini_Sublibrary2_WT

description: Library name: Mini_WT2


title: MOLM-13, A485, H3K27ac, rep1

description: Library name: Sample 2


title: Mini_Sublibrary1_WT

description: Library name: Mini_WT1


title: MOLM-13, DMSO control, H3K27ac, rep1

description: Library name: Sample 1


title: Mega_Sublibrary1_CRISPR

description: Library name: Mega_CRISPR1


title: Mega_Sublibrary2_CRISPR

description: Library name: Mega_CRISPR2


title: Mega_Sublibrary3_CRISPR

description: Library name: Mega_CRISPR3


title: Mega_Sublibrary4_WT

description: Library name: Mega_WT4


title: Mega_Sublibrary4_CRISPR

description: Library name: Mega_CRISPR4


title: Mega_Sublibrary3_WT

description: Library name: Mega_WT3


title: Mega_Sublibrary2_WT

description: Library name: Mega_WT2


title: Brunello Plasmid

description: Library name: Sample17

library_source: other

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology. Sequencing conditions were 150PE aiming for 10 Mio reads
Adapter sequences were trimmed prior further analysis using Cutadapt
Downstream processing of raw FASTQ files was done using the MaGeCK algorithm and the MaGeCK Flute pipeline. We used the minimum likelihood algorithm (MLE) and also applied MaGeCK Flutes cell cycle correction to corresponding samples. Samples for each cell line were analyzed together.
ß-score differences were calculated among the different conditions, then z-score normalized and p-values were generated from the z-scores.
Assembly: hg38
Supplementary files format and content: Tab-delimited txt files with raw counts for each sample per cell line
Supplementary files format and content: Tab-delimited txt files with normalized counts for each sample per cell line
Library strategy: CRISPR Screen

molecule: other

source_name: Plasmid Pool

growth_protocol: Cells were grown in RPMI with 10% FCS and 1% Pen/Strep in large T-175 flasks

extract_protocol:
For DNA extraction we used Qiagens QIAamp DNA Blood Maxi Kit (#51194), for each DNA extraction we used pellets from 100Mio cells
sgRNA amplification and library construction were performed using a single step PCR with customized primers. For each sample 24 seperate PCRs with 10µg DNA per sample were performed using Agilents Herculase II PCR Kit. PCR products were size selected using AMPure beads and a TapeStation (Agilent) was used for Quality control.

treatment_protocol: 60 Mio cells were treated with their respective IC50 dose of A-485/DMSO in T-175 flasks for 48 hours

value: Plasmid Pool


title: Mega_Sublibrary1_WT

description: Library name: Mega_WT1


title: OCIAML3, A485, rep2

description: Library name: Sample12

source_name: Blood Cells

value: Blood Cells


title: OCIAML3, DMSO for Inobrodib samples, rep2

description: Library name: Sample14


title: OCIAML3, A485, rep1

description: Library name: Sample11


title: OCIAML3, DMSO for A485 samples, rep2

description: Library name: Sample10


title: OCIAML3, DMSO for A485 samples, rep1

description: Library name: Sample9


title: MOLM13, Inobrodib, rep2

description: Library name: Sample8

value: Inobrodib


title: MOLM13, A485, rep2

description: Library name: Sample4


title: MOLM13, DMSO for Inobrodib samples, rep2

description: Library name: Sample6


title: MOLM13, Inobrodib, rep1

description: Library name: Sample7


title: OCIAML3, 1 µM A485, RUNX1, rep2

description: Library name: Sample 95


title: MOLM13, DMSO for A485 samples, rep1

description: Library name: Sample1


title: OCIAML3, DMSO control, RUNX1, rep1

description: Library name: Sample 92


title: MOLM13, A485, rep1

description: Library name: Sample3


title: OCIAML3, 1 µM A485, RUNX1, rep1

description: Library name: Sample 93


title: MOLM13, DMSO for Inobrodib samples, rep1

description: Library name: Sample5


title: OCIAML3, DMSO for Inobrodib samples, rep1

description: Library name: Sample13


title: OCIAML3, Inobrodib, rep1

description: Library name: Sample15


title: OCIAML3, DMSO control, RUNX1, rep2

description: Library name: Sample 94


title: MOLM13, DMSO for A485 samples, rep2

description: Library name: Sample2


title: OCIAML3, DMSO control, MEF2D, rep2

description: Library name: Sample 86


title: OCIAML3, DMSO control, CREBBP, rep2

description: Library name: Sample 54


title: OCIAML3, 1 µM A485, ARID1A, rep2

description: Library name: Sample 67


title: OCIAML3, Inobrodib, rep2

description: Library name: Sample16


title: OCIAML3, 1 µM A485, CEBPB, rep2

description: Library name: Sample 75


title: OCIAML3, DMSO control, CEBPB, rep2

description: Library name: Sample 74


title: OCIAML3, 1 µM A485, P300, rep2

description: Library name: Sample 51


title: OCIAML3, 1 µM A485, CREBBP, rep2

description: Library name: Sample 55


title: OCIAML3, DMSO control, P300, rep2

description: Library name: Sample 50


title: OCIAML3, DMSO control, ARID1A, rep2

description: Library name: Sample 66


title: OCIAML3, 1 µM A485, MEF2D, rep2

description: Library name: Sample 87


title: MOLM13, 1 µM A485, IRF8, rep2

description: Library name: Sample 47


title: MOLM13, DMSO control, IRF8, rep2

description: Library name: Sample 46


title: MOLM13, 1 µM A485, IRF8, rep1

description: Library name: Sample 45


title: MOLM13, 1 µM A485, MEF2D, rep2

description: Library name: Sample 43


title: MOLM13, DMSO control, MEF2D, rep2

description: Library name: Sample 42


title: MOLM13, DMSO control, MEF2D, rep1

description: Library name: Sample 40


title: MOLM13, DMSO control, RUNX1, rep2

description: Library name: Sample 38


title: MOLM13, 1 µM A485, RUNX1, rep2

description: Library name: Sample 39


title: MOLM13, 1 µM A485, RUNX1, rep1

description: Library name: Sample 37


title: MOLM13, DMSO control, RUNX1, rep1

description: Library name: Sample 36


title: MOLM13, 1 µM A485, CEBPB, rep2

description: Library name: Sample 19


title: MOLM13, 1 µM A485, STAT1,  rep1

description: Library name: Sample 21


title: MOLM13, 1 µM A485, IRF2BP2, rep2

description: Library name: Sample 12


title: MOLM13, DMSO control, CEBPA, rep2

description: Library name: Sample 15


title: MOLM13, 1 µM A485, ARID1A, rep1

description: Library name: Sample 25


title: MOLM13, DMSO control, PU1, rep2

description: Library name: Sample 34


title: MOLM13, DMSO control, ARID1A, rep2

description: Library name: Sample 26


title: MOLM13, DMSO control, IRF2BP2, rep2

description: Library name: Sample 11


title: MOLM13, DMSO control, CEBPB, rep2

description: Library name: Sample 18


title: MOLM13, 1 µM A485, STAT1, rep2

description: Library name: Sample 23


title: MOLM13, 1 µM A485, ARID1A, rep2

description: Library name: Sample 27


title: MOLM13, 1 µM A485, IRF2BP2, rep1

description: Library name: Sample 10


title: MOLM13, 1 µM A485, FLI1, rep2

description: Library name: Sample 31


title: MOLM13, 1 µM A485, MEF2D, rep1

description: Library name: Sample 41


title: MOLM13, DMSO control, ARID1A, rep1

description: Library name: Sample 24


title: MOLM13, DMSO control, STAT1, rep2

description: Library name: Sample 22


title: MOLM13, DMSO control, STAT1, rep1

description: Library name: Sample 20


title: MOLM13, DMSO control, IRF8, rep1

description: Library name: Sample 44


title: MOLM13, 1 µM A485, PU1, rep2

description: Library name: Sample 35


title: MOLM13, 1 µM A485, CEBPA, rep2

description: Library name: Sample 16


title: MOLM13, DMSO control, FLI1, rep2

description: Library name: Sample 30


title: 53BP1-KO murine BCPs + p210 (60days), rep.5

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

country: United Kingdom

institute: Imperial College London

description: Library name: BB42_BCR_D60_RNAseq_rep1

data_processing:
Salmon (v1.10.1) was used to quantify transcript count from RNA-Seq. A full decoy index was generated using whole genome and transcript sequences obtained from GENCODE genes database, with the hg38 (release 43) and mm39 (release 32) genomes, respectively.
Trimmed fastq files were processed using Salmon (v1.10.1) with the following parameters: ‑‑gcbias, ‑‑writeUnmappedNames.
GenomicFeatures(v1.46.5) was used to generate transcript-to-gene objects in R, using GTF files obtained from the GENECODE gene database.
Salmon quantification file was subsequently analysed using DESeq2 (v1.34.0).
Assembly: hg38 or mm39
Supplementary files format and content: quant.sf

source_name: bone marrow

growth_protocol: Cell lines were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax, primary murine cells were grown on at a density 0.5-3mio/ml in IMDM media with 20% FBS, 1% Pen/Strep and 1X Glutamax and 10ng/ml mIL3.

extract_protocol:
Cells were washed with PBS, counted and subjected RNA isolation using Qiagen RNAeasy kit. RNA was snap frozen and sent for mRNA sequencing at Novogene.
Libraries were generated by Novogene.

treatment_protocol: Where indicated, cells were treated with 0.5 uM A-485 (48h), 0.25 uM dCBP1 (24h) or DMSO (24h or 48h)

value: bone marrow

value: primary

value: B-cell precursor

value: TRP53BP1-/- +BCR::ABL1(p210) retrovirus

value: no treatment


title: MOLM13, 1 µM A485, CREBBP, rep2

description: Library name: Sample 8


title: 53BP1-KO murine BCPs + p210 (60days), rep.6

description: Library name: BB42_BCR_D60_RNAseq_rep2


title: MOLM13, DMSO control, IRF2BP2, rep1

description: Library name: Sample 9


title: 53BP1-KO murine BCPs + p210 (60days), rep.3

description: Library name: BB40_BCR_D60_RNAseq_rep1


title: MOLM13, DMSO control, CREBBP, rep2

description: Library name: Sample 7


title: 53BP1-KO murine BCPs + p210 (60days), rep.2

description: Library name: BB39_BCR_D60_RNAseq_rep2


title: MOLM13, 1 µM A485, CREBBP, rep1

description: Library name: Sample 6


title: 53BP1-KO murine BCPs + p210 (60days), rep.1

description: Library name: BB39_BCR_D60_RNAseq_rep1


title: MOLM13, DMSO control, CREBBP, rep1

description: Library name: Sample 5


title: MOLM13, 1 µM A485, P300, rep2

description: Library name: Sample 4


title: 53BP1-KO murine BCPs + p210 (7days), rep.3

description: Library name: BB66_BCR_D7_RNAseq


title: 53BP1-KO murine BCPs + p210 (7days), rep.5

description: Library name: BB68_BCR_D7_RNAseq


title: 53BP1-KO murine BCPs + p210 (7days), rep.1

description: Library name: BB39_BCR_D7_RNAseq


title: 53BP1-KO murine BCPs + EV, rep.3

description: Library name: BB66_EV_D7_RNAseq


title: MOLM13, 0.5 µM Inobrodib, 2h, rep2

description: Library name: Sample 31

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology.
Adapters sequences were trimmed from raw reads using Trim Galore v0.6.5.
Trimmed reads were aligned to the human reference genome (GRCh38/hg38) and both total and nascent mRNA were deconvoluted using the tools software SLAM-DUNK v0.6.5.
Assembly: hg38
Supplementary files format and content: Tab-delimited txt files with raw counts for total RNA per each experimental timepoint
Supplementary files format and content: Tab-delimited txt files with raw counts for nascent RNA per each experimental timepoint

growth_protocol: MOLM13 cells were grown to reach 80% confluency in RPMI 1640 with 10% FCS and 1% penicillin/streptomycin at 37°C, 5% CO2

extract_protocol:
RNA was isolated using the RNeasy Kit from Qiagen and chemically modified using the SLAMSeq Anabolic Kinetics Module from Lexogen.
DNA libraries were constructed using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit with UDI from Lexogen.

treatment_protocol: Cells were incubated over 2h/12h/24h with 1µM A485, 0.5µM Inobrodib, 0.25µM dCBP-1 or DMSO in RPMI 1640 with 10% FCS at 37°C, 5% CO2. After 1h/11h/23h, 100µM S4U was added to the medium.

tag: time


title: MOLM13, 1 µM A485, P300, rep1

description: Library name: Sample 2


title: MOLM13, DMSO control, P300, rep1

description: Library name: Sample 1


title: E13_5_retina_Isl1_Rep2

description: Library name: E13_5_retina_Isl1_Rep2

data_processing:
Raw data were pre-processed for quality control using FastQC
Qualified peaks were aligned to the mouse mm10 reference transcriptome using the Bowtie2. Peaks were called using MACS2 and SEACR
Peak annotation and functional analyses were performed using ChIP seeker and visualized by IGV
Assembly: mm10
Supplementary files format and content: bed file
Library strategy: CUT&Tag

source_name: Retina

extract_protocol:
E13.5 retinae were isolated and nuclei extracted immediately by incubating in NE Buffer for 10 min on ice. The nuclei were incubated with activated concanavalin A-coated magnetic beads at room temperature for 10 min. The nuclei-beads were collected using magnetic stand and resuspended in 50 μl ice cold antibody buffer. 0.5 μg antibody against ISL1 (rabbit, AB4326, Millipore; rabbit, ab20670, Abcam) was added to each sample and mixed on a rotator at 4°C overnight or at room temperature for 2 h. The antibody-bound nuclei-beads were isolated and resuspended in 50 μl of ice cold Digitonin 150 Buffer. 0.5 μg of anti-rabbit IgG secondary antibody (EpiCypher #13-0047 and #13-0048) was added and samples were incubated for 30 min at room temperature on a rotator. After two washes in ice cold Digitonin 150 Buffer, nuclei-beads were resuspended in 50 μl of ice cold Digitonin 300 Buffer, 2.5 μl of CUTANA pAG-Tn5 solution (EpiCypher #15-1017) was added, and nuclei-beads were incubated for 1 h at room temperature on a rotator. The samples were again washed twice in ice cold Digitonin 300 Buffer, resuspended in 125 μl of cold Tagmentation Buffer, and incubated at 37°C for 1 h. Then, 2.5 μl of 0.5 M EDTA, 1.25 μl of 10% SDS and 1.1 μl of 20 mg/ml Proteinase K were added to each sample and samples were incubated at 70°C for 10 min or 55°C for 30 min. After this, DNA fragments were purified and collected in 30 μl of ddH2O using Cycle Pure Kit (Omega, D6492-02).
21 μl of DNA fragments were transferred to a PCR tube, to which 2 μl of barcoded i5 and i7 primers and 25 μl CUTANA High Fidelity 2x PCR Master Mix (EpiCypher, #15-1018) were added. PCR was performed using the following conditions: 72°C for 5 min, 98°C for 30 s, and 20 cycles of 10 s at 98°C and 10 s at 63°C, followed by an extra 1 min extension at 72°C. The PCR product was analyzed on an Agilent Fragment Analyzer. Combined DNA libraries were cleaned up using AMPure XP beads (#A63880, Beckman Coulter). Each pooled DNA library of 10 samples was resuspended in 40–80 μl water and quantified using a NanoDrop (Thermo FIsher Scientific). Library fragments were sent for sequencing commercially at Azenta Life Sciences. Sequencing was performed on Hiseq 4000 (Illumina) with 2 x 150 paired-end reads and a depth of 10 million reads per sample.

value: Retina

value: wild type

tag: cut&tag antibody


title: 53BP1-KO murine BCPs + EV, rep.4

description: Library name: BB67_EV_D7_RNAseq


title: MOLM13, 1 µM A-485, 2h, rep3

description: Library name: Sample 29


title: 53BP1-KO murine BCPs + p210 (7days), rep.2

description: Library name: BB42_BCR_D7_RNAseq


title: E13_5_retina_Isl1_Rep1

description: Library name: E13_5_retina_Isl1_Rep1


title: MOLM13, 0.25 µM dCBP-1, 2h, rep3

description: Library name: Sample 35


title: 53BP1-KO murine BCPs + EV, rep.1

description: Library name: BB39_EV_D7_RNAseq


title: MOLM13, 0.5 µM Inobrodib, 2h, rep3

description: Library name: Sample 32


title: MOLM13, 0.25 µM dCBP-1, 2h, rep2

description: Library name: Sample 34


title: MOLM13, 0.25 µM dCBP-1, 2h, rep1

description: Library name: Sample 33


title: 53BP1-KO murine BCPs + EV, rep.2

description: Library name: BB42_EV_D7_RNAseq


title: EV_D7_rep3

data_processing:
Trimmed fastq files were aligned to the human genome, hg38, using bowtie2 (v2.4.4), using the additional parameter: --no-unal.
SAM files generated by bowtie2 were converted to BAM format using samtools (v1.14) view -S -b.
Bam files were processed using samtools fixmate ‑m, samtools sort -o, samtools markdup -r, samtools collate -o, samtools sort -o
To generate a file for visualisation on a genome browser, the final bam files were processed by deeptools (v3.5.1) suite.
To generate bigwig files, bamCoverage was used with the following parameters: --normalizeUsing RPKM, --extendReads, --effectiveGenomeSize 2913022398 (for hg38), or 2654621783 (for mm39).
Assembly: hg38 or mm39
Supplementary files format and content: RPKM normalised bedGraph files for track visualisation by genome browsers.

growth_protocol: Cell lines were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax. Ph+B-ALL cells from patient BAL08 were expanded ex vivo on sub-lethally irradiated OP9 cells (0.5x106 OP9 cells/10 cm dish, mitotically inactivated by 13.6 Gy, 25 × 106 B-ALL cells/plate) grown in aMEM media with 20% FBS, 1% Pen/Strep and 1X Glutamax. After ~20 days of co-culture, cells were checked for viability and B-ALL phenotype by flow cytometry and then split to new OP9-coated plates for respective experiments.

extract_protocol:
ChIP-Seq for H3K27ac was done as described in Boulianne et al using anti-Histone H3 (acetyl K27) antibody – ChIP Grade (ab4729) (Abcam) and polyclonal rabbit IgG (isotype control) (sc2027) (Santa Cruz Biotechnologies), with the exception that initial cross-linking was performed at RT. For HA-ChIP-Seq, three lots of 2 x 10^7 cells per sample were separately, sequentially double-crosslinked consisting of a 30 min RT incubation with 2 mM Disuccinimidyl Glutarate (DSG) in PBS followed by a 30 min RT incubation with 1% formaldehyde (prepared in PBS) (rotating during incubation and washes in between), with the remainder done as described in Boulianne et al3 but using 0.8 ug anti-HA-tag antibody (Cell Signalling #3724) per 2 x 10^7 cells.
ChIP-Seq libraries were generated from ChIP immunoprecipitated DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (NEB) and sequenced either at Novogene or at the in-house sequencing facility of the MRC London Institute of Medical Sciences at Imperial College London.

treatment_protocol: Where indicated cells were treated with DMSO or Ponatinib (100nM for human cells, 10nM for mouse cells), 250nM dTAGV-1, or 2.5uM AK-2292. Treatment was for 24h, except for samples labeled BV173_parental_* and BV173_STAT5_2A_NTAG_* that were treated for 48h.

value: primary cells

value: B-cell precursors


title: MOLM13, 1 µM A-485, 2h, rep2

description: Library name: Sample 28

value: Acute Myeloid Leukemia


title: EV_D7_rep2

value: DMSO


title: MOLM13, 0.5 µM Inobrodib, 2h, rep1

description: Library name: Sample 30


title: MOLM13, DMSO control, P300, rep2

description: Library name: Sample 3


title: 53BP1-KO murine BCPs + p210 (7days), rep.4

description: Library name: BB67_BCR_D7_RNAseq


title: EV_D7_rep1


title: MOLM13, DMSO control, 2h, rep3

description: Library name: Sample 26


title: EV_D7_input


title: MOLM13, DMSO control, 2h, rep2

description: Library name: Sample 25


title: MOLM13, 1 µM A-485, 2h, rep1

description: Library name: Sample 27


title: BCR_D60_rep3


title: MOLM13, DMSO control, 2h, rep1

description: Library name: Sample 24


title: BCR_D7_input


title: MOLM13, 0.25 µM dCBP-1, 12h, rep3

description: Library name: Sample 23


title: BCR_D60_rep2


title: MOLM13, 0.5 µM Inobrodib, 12h, rep3

description: Library name: Sample 20


title: MOLM13, 0.25 µM dCBP-1, 12h, rep2

description: Library name: Sample 22


title: BCR_D60_rep1


title: EV_D3_H3K27ac_rep3


title: MOLM13, 1 µM A-485, 12h, rep2

description: Library name: Sample 17


title: MOLM13, 1 µM A-485, 12h, rep1

description: Library name: Sample 16


title: EV_D3_H3K27ac_rep1


title: MOLM13, 0.25 µM dCBP-1, 12h, rep1

description: Library name: Sample 21


title: MOLM13, 0.5 µM Inobrodib, 12h, rep1

description: Library name: Sample 18


title: EV_D3_IgG


title: BA_p190_PON_H3K27ac_rep1

value: Ponatinib


title: EV_D3_H3K27ac_rep2


title: MOLM13, DMSO control, 12h, rep2

description: Library name: Sample 14


title: BA_p190_DMSO_IgG


title: BA_p190_PON_H3K27ac_rep2


title: MOLM13, 0.5 µM Inobrodib, 12h, rep2

description: Library name: Sample 19


title: BA_p190_DMSO_H3K27ac_rep3


title: MOLM13, DMSO control, 12h, rep1

description: Library name: Sample 13


title: BA_p190_PON_H3K27ac_rep3


title: BA_p190_DMSO_H3K27ac_rep2


title: MOLM13, DMSO control, 12h, rep3

description: Library name: Sample 15


title: MOLM13, 0.25 µM dCBP-1, 24h, rep3

description: Library name: Sample 12


title: MOLM13, 0.25 µM dCBP-1, 24h, rep2

description: Library name: Sample 11


title: BA_p190_DMSO_H3K27ac_rep1


title: MOLM13, 0.25 µM dCBP-1, 24h, rep1

description: Library name: Sample 10


title: BM_+d55_p190_+PON_(C57BL6)_rep2

treatment_protocol: Where indicated, cells were treated with DMSO or Ponatinib (100nM for human cells, 10nM for mouse cells), 250nM dTAGV-1, or 2.5uM AK-2292. Treatment was for 24h, except for samples indicated that were treated for 48h.

value: BCR::ABL1 retrovirus


title: MOLM13, 0.5 µM Inobrodib, 24h, rep3

description: Library name: Sample 9

value: Blood cells


title: BM_+d59_p190_+PON_(C57BL6)_rep1


title: MOLM13, 0.5 µM Inobrodib, 24h, rep2

description: Library name: Sample 8


title: BM_+d55_p190_+DMSO_(C57BL6)_rep2


title: MOLM13, 1 µM A-485, 24h, rep3

description: Library name: Sample 6


title: MOLM13, 0.5 µM Inobrodib, 24h, rep1

description: Library name: Sample 7


title: BM_+d3_p190_(C57BL6)_rep2


title: MOLM13, 1 µM A-485, 24h, rep1

description: Library name: Sample 4


title: MOLM13, DMSO control, 24h, rep3

description: Library name: Sample 3


title: MOLM13, 1 µM A-485, 24h, rep2

description: Library name: Sample 5


title: BM_+d3_p190_(C57BL6)_rep1


title: MOLM13, DMSO control, 24h, rep1

description: Library name: Sample 1


title: TOM-1 +0.25uM dCBP1 (24h), rep.2

description: Library name: R082_sample


title: SUP-B15 +0.5uM A-485 (48h), rep.2

description: Library name: R030_sample


title: BM_+d3_EV_(C57BL6)_rep2

value: normal


title: MOLM13, DMSO control, 12h, rep1

description: Library name: Sample 3

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology.
PRO-Seq reads were trimmed using Cutadapt v2.10, removing adapters and discarding reads with < 14 bp length
PRO-Seq reads were aligned to the human reference genome (GRCh38/hg38) with BWA v0.7.17. Uniquely mapped and properly paired reads were retained using SAMtools v1.17.
Peaks were called with MACS2 v2.2.7.1.
BigWig files were created using DeepTools v3.5.1 for coverage visualization. Signal was normalized using D. melanogaster spike-in DNA (reference assembly dm6).
Assembly: hg38
Supplementary files format and content: BigWig files including all paired-end reads per sample
Supplementary files format and content: BigWig files specific for forward strand reads per sample
Supplementary files format and content: BigWig files specific for reverse strand reads per sample
Library strategy: PRO-Seq

source_name: Blood

growth_protocol: MOLM13 cells were grown to reach 80% confluency in RPMI 1640 with 10% FCS and 1% penicillin/streptomycin at 37°C, 5% CO2.

extract_protocol:
Harvested cells were washed with PBS, nuclei were isolated using a Dounce homogenizer. RNA was extracted after run-on reaction and chemically modified.
The modified RNA was enriched, reverse transcribed and libraries were PCR amplified with 17 cycles on a thermocycler. The resulting library was purified with Ampure XP beads from Beckman Coulter.

treatment_protocol: Cells were incubated over 12h with 1µM A485 or DMSO in RPMI 1640 with 10% FCS at 37°C, 5% CO2.

value: Blood


title: TOM-1 +0.25uM dCBP1 (24h), rep.1

description: Library name: R081_sample


title: TOM-1 +DMSO (dCBP1 exp), rep2

description: Library name: R080_sample


title: BM_+d59_p190_+DMSO_(C57BL6)_rep1


title: MOLM13, DMSO control, 12h, rep2

description: Library name: Sample 4


title: MOLM13, 1 µM A485, 12h, rep2

description: Library name: Sample 2


title: TOM-1 +DMSO (dCBP1 exp), rep1

description: Library name: R079_sample


title: MOLM13, 1 µM A485, 12h, rep1

description: Library name: Sample 1


title: SUP-B15 +0.25uM dCBP1 (24h), rep.1

description: Library name: R085_sample


title: bamP-GFP sorted cells, Control KD, Rep 2

city: Toronto

first: Thomas

last: Hurd

state: Ontario

address: 661 University Avenue

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
Library name: Ctrl KD Rep2
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep2_CtrlKD_TPM and Rep2_CtrlKD_NumReads

data_processing:
bcl2fastq2 v2.20 was used to generate untrimmed reads in FASTQ format
Adaptor sequences were trimmed using default settings of Trim Galore v0.6.7 (RRID:SCR_011847) which is a wrapper around Cutadapt v2.10 (RRID:SCR_011841).
Residual rRNA sequences were removed using RiboDetector v0.2.7 using default settings for paired-end reads (Deng, Z. et al., 2022) or with SortMeRNA 4.3.6 and rRNA sequences documented by SILVA (Kopylova et al. 2012; Quast et al. 2013).
Transcript level read counts were obtained using Salmon v1.9.0 (RRID:SCR_017036) by indexing to dmel r6.54 chromosome and transcripts fasta sequences hosted on FlyBase (Gramates et al., 2022).
Assembly: dmel r6.54
Supplementary files format and content: csv file with TPM and Raw read count for each transcript in each sample.
Supplementary files format and content: csv file with TPM and Raw read count for each gene in each sample.

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Total RNA was extracted from sorted cells according to manufacturer’s protocol using TRI-Reagent, chloroform, GlycoBlue, 2-propanol and ethanol, and eluted in nuclease-free water. Purified RNA was treated with Turbo DNAse. An additional ethanol precipitation was carried out according to Green and Sambrook 2020 and resuspended in nuclease-free water.
Purified RNA concentration was measured by Qubit 4 Fluorometer and quality was measured by Agilent 2100 Bioanalyzer by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children. Ribosomal RNA (rRNA)-depleted cDNA library preparation was performed by TCAG using QIAseq FastSelect –rRNA Fly Kit (Qiagen, 333262) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760) without poly(A) selection with 18 ng of RNA.

treatment_protocol: Ovaries were dissociated in cell dissociation buffer (ThermoFisher Scientific, 13150016) with collagenase (0.25 mg/mL; Gibco, 17018029) and elastase (0.4 mg/mL; BioShop Canada, ELA292) at 37°C for 30 min with shaking. Dissociated cells were run through 70 µm (Genesee Scientific, 25-376) and 30 µm (Miltenyi Biotec, 130-041-407) cell strainers and resuspended in PBS with 1% BSA prior to sorting. Propidium iodide (3 µM; BioShop Canada, PPI777) was used to measure identify and sort for live cells. The BD FACSymphony S6 SE cell sorter was used to isolated GFP positive cells.

value: Ovary

value: germ cell

value: Control knockdown


title: SUP-B15 +0.25uM dCBP1 (24h), rep.2

description: Library name: R086_sample

value: bone marrow

value: B-cell precursor


title: MOLM13, DMSO control, 24h, rep2

description: Library name: Sample 2


title: BM_+d3_EV_(C57BL6)_rep1

value: primary

value: no treatment


title: bamP-GFP sorted cells, Control KD, Rep 3

description:
Library name: Ctrl KD Rep3
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep3_CtrlKD_TPM and Rep3_CtrlKD_NumReads


title: bamP-GFP sorted cells, Control KD, Rep 1

description:
Library name: Ctrl KD Rep1
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep1_CtrlKD_TPM and Rep1_CtrlKD_NumReads


title: BV173_24h_Asciminib_H3K27ac

description: Library name: C211_sample

data_processing:
Trimmed fastq files were aligned to the human genome, hg38, using bowtie2 (v2.4.4), using the additional parameter: --no-unal.
SAM files generated by bowtie2 were converted to BAM format using samtools (v1.14) view -S -b.
Bam files were processed using samtools fixmate ‑m, samtools sort -o, samtools markdup -r, samtools collate -o, samtools sort -o
To generate a file for visualisation on a genome browser, the final bam files were processed by deeptools (v3.5.1) suite.
To generate bigwig files, bamCoverage was used with the following parameters: --normalizeUsing RPKM, --extendReads, --effectiveGenomeSize 2913022398 (for hg38)
Assembly: hg38
Supplementary files format and content: RPKM normalised bedGraph files for track visualisation by genome browsers.

growth_protocol: Cell lines were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax.

extract_protocol:
ChIP-Seq for H3K27ac was done as described in Boulianne et al using anti-Histone H3 (acetyl K27) antibody – ChIP Grade (ab4729) (Abcam) and polyclonal rabbit IgG (isotype control) (sc2027) (Santa Cruz Biotechnologies), with the exception that initial cross-linking was performed at RT and 1mio cells were used for crosslinking instead of 15mio. ChIP-Seq for MYC (CST #13987, D3N8F) and STAT5 (CST #94205 D206Y) and the IgG control (Abcam #171870) related to these libraries was done with 60mio cells and using double fixation with 2 mM DSG (30min) followed by 1% formaldehyde (30min).
ChIP-Seq libraries were generated from ChIP immunoprecipitated DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (NEB) and sequenced either at Novogene or at the in-house sequencing facility of the MRC London Institute of Medical Sciences at Imperial College London.

treatment_protocol: Where indicated cells were treated for 24h with DMSO or Ponatinib (100nM), Asciminib (1uM) or MYC degrader 1

value: 24h + 1uM Asciminib


title: bamP-GFP sorted cells, Atx2 KD, Rep 2

description:
Library name: Atx2 KD Rep2
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep2_Atx2KD_TPM and Rep2_Atx2KD_NumReads

value: Atx2 knockdown


title: bamP-GFP sorted cells, Atx2 KD, Rep 3

description:
Library name: Atx2 KD Rep3
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep3_Atx2KD_TPM and Rep3_Atx2KD_NumReads


title: bamP-GFP sorted cells, Atx2 KD, Rep 1

description:
Library name: Atx2 KD Rep1
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep1_Atx2KD_TPM and Rep1_Atx2KD_NumReads


title: BV173_24h_DMSO_H3K27ac_(Asciminib_exp)

description: Library name: C210_sample

value: B-cell precursors

value: 24h +DMSO


title: SUP-B15_24h_DMSO_H3K27ac_(Asciminib_exp)

description: Library name: C208_sample


title: TOM-1_24h_Asciminib_H3K27ac

description: Library name: C207_sample


title: SUP-B15 +DMSO (dCBP1 exp), rep2

description: Library name: R084_sample

value: DMSO


title: Kc167, Cul4 mouse ab, ChIP in controll, bio rep3

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

description: Library name: Kc167_mock_Cul4ms_R3

data_processing:
All samples were sequenced with Novaseq (Illumina) using 50 bp single-end sequencing at the NHLBI DNA Sequencing and Genomics Core Facility.
FASTQ files of sequenced single-end 50 bp reads were trimmed using cutadapt v3.4 (Martin, 2011) with arguments ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA’, ‘--nextseq-trim 20’, ‘--minimum-length 25’ and ‘--overlap 6’.
Bowtie2 v2.4.2 (Langmead and Salzberg, 2012) with default arguments was used to map the trimmed reads to the Flybase r6-35 genome assembly.
Then, multimapping reads were removed using samtools v1.12 (Li et al., 2009) view command with the argument -q 20. Picard MarkDuplicates v2.25.2 (http://broadinstitute.github.io/picard/index.html) was applied to remove duplicates from mapped, uniquely mapping reads.
Peaks were called by MACS2 v2.2.7.1 (Zhang et al., 2008) (https://github.com/taoliu/MACS) by providing replicate IPs and inputs as multiple BAMs with arguments ‘-f BAM’, ‘--gsize=dm’, ‘-q 0.000000001’, ‘--mfold 3 100’.
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

source_name: embryo

growth_protocol: Kc167 is grown in CCM3 media

extract_protocol:
2–3×107 cells were fixed by adding 1% formaldehyde directly to cells in culture medium for 10 min at RT with gentle agitation. 0.125 M glycine was used to quench formaldehyde with gentle agitation for 5 min. Cells were centrifugated at 500 x g for 5 min and washed twice with ice-cold PBS. Chromatin preparation and chromatin immunoprecipitation (ChIP) were performed following earlier described methods (Bag et al., 2019).
Libraries were prepared according to the manufacturer’s protocol (NEB; Ultra II for DNA Library Prep Kit; E7645).

treatment_protocol: Cells were incubated with dsRNA for 4 d at 25°C before harvest.

value: embryo

value: hemocyte

value: mcherry dsRNA


title: Kc167, Cul4 mouse ab, ChIP in controll, bio rep2

description: Library name: Kc167_mock_Cul4ms_R2


title: bamP-GFP sorted cells, Atx2 KD, Rep 4

description:
Library name: Atx2 KD Rep4
Column name in Salmon_TxLevel_TPM_NumReads_NOT_normalized_SC.csv and Salmon_GeneLevel_TPM_NumReads_NOT_normalized_SC.csv: Rep4_Atx2KD_TPM and Rep4_Atx2KD_NumReads


title: Kc167, Cul4 mouse ab, ChIP in controll, bio rep1

description: Library name: Kc167_mock_Cul4ms_R1


title: LAMA84_24h_Ponatinib_H3K27ac

description: Library name: C174_sample

value: myeloid precursors

value: 24h +100nM Ponatinib


title: TOM-1_24h_DMSO_H3K27ac_(Asciminib_exp)

description: Library name: C206_sample


title: SUP-B15 +DMSO (dCBP1 exp), rep1

description: Library name: R083_sample


title: Kc167, Input, ChIP in control, bio rep3


title: SUP-B15_24h_Asciminib_H3K27ac

description: Library name: C209_sample


title: Kc167, Su(Hw), ChIP in control, bio rep1


title: APV245 cella, control shRNA, 5

city: Sakai

first: Noriomi

last: Matsumura

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kindai University

description:
Library name: Sample16
Column name in shRNA1_count_GEO.csv: K20-S97

data_processing:
FastQC v0.11.9, Trim Galore v0.6.6, STAR v2.7.0f, samtools v1.11, Subread v1.6.4, and R v4.0.4.
Sequence reads were trimmed for adapter sequences and low-quality bases using Trim Galore v0.6.6 with paired-end mode (parameters: --paired). Quality control was performed using FastQC v0.11.9 before and after trimming.
Trimmed sequence reads were mapped to the Mus musculus reference genome (mm10/GRCm38) using STAR v2.7.0f with Ensembl release 102 annotation (parameters: --chimOutType SeparateSAMold --outSAMtype BAM SortedByCoordinate --outBAMcompression 1). Post-alignment processing was performed using samtools v1.11 to generate BAM indices.
Read count extraction was performed using featureCounts (Subread v1.6.4) with Ensembl release 102 annotation (parameters: -p -T 5 -t exon -g gene_name). Normalization to FPKM values was performed using R v4.0.4 based on gene length and total library size.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: APV245 cells

growth_protocol: APV245 cells were maintained in DMEM high glucose supplenented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries fpr RNA-seq prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacture's protcols.

value: APV245 cells

value: tumor cells

value: WT (control shRNA)

tag: batch


title: KCL22_24h_Ponatinib_H3K27ac

description: Library name: C170_sample

value: bone marrow


title: LAMA84_24h_DMSO_H3K27ac

description: Library name: C173_sample


title: APV245 cella, control shRNA, 4

description:
Library name: Sample15
Column name in shRNA1_count_GEO.csv: K19-S96


title: APV245 cella, control shRNA, 3

description:
Library name: Sample14
Column name in shRNA1_count_GEO.csv: K18-S95


title: Kc167, Su(Hw), ChIP in control, bio rep3


title: APV245 cella, control shRNA, 2

description:
Library name: Sample13
Column name in shRNA1_count_GEO.csv: K17-S94


title: APV245 cella, control shRNA, 1

description:
Library name: Sample12
Column name in shRNA1_count_GEO.csv: K16-S93


title: Kc167, Su(Hw), ChIP in control, bio rep2


title: K562_24h_Ponatinib_H3K27ac

description: Library name: C172_sample


title: KCL22_24h_DMSO_H3K27ac

description: Library name: C169_sample


title: APV245 cells, IL6 shRNA1, 4

description:
Library name: Sample4
Column name in shRNA1_count_GEO.csv: K14-S91

value: IL6 knockdown


title: APV245 cells, IL6 shRNA1, 5

description:
Library name: Sample5
Column name in shRNA1_count_GEO.csv: K15-S92


title: K562_24h_DMSO_H3K27ac

description: Library name: C171_sample


title: APV245 cells, IL6 shRNA1, 3

description:
Library name: Sample3
Column name in shRNA1_count_GEO.csv: K13-S90


title: Kc167, Input, ChIP in control, bio rep1


title: Kc167, Input, ChIP in control, bio rep2


title: APV245 cells, IL6 shRNA1, 2

description:
Library name: Sample2
Column name in shRNA1_count_GEO.csv: K12-S89


title: APV245 cells, IL6 shRNA1, 1

description:
Library name: Sample1
Column name in shRNA1_count_GEO.csv: K11-S88


title: Kc167, Cul4, ChIP in control, bio rep3


title: SUP-B15_MYC

description: Library name: C149_sample


title: SUP-B15_IgG

description: Library name: C152_sample


title: Kc167, Cul4, ChIP in control, bio rep2


title: Kc167, Cul4, ChIP in control, bio rep1


title: SUP-B15_STAT5

description: Library name: C150_sample


title: whole blood_Boxe_T1_QUAPRICE_DES_CLOTINS

type: RNA

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Horse_60K_2016_01_22 021322 GE 8x60K (AMID 081421)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 081421_D_F_20160126). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 6 out of 44 microarrays. At this step, 42342 spots out of 62976 were selected.  The mean signal of the 32 first samples and 12 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30458 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Equus caballus

source_name: whole blood

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Venous blood (10 ml) was collected from horses using EDTA tubes (BD Vacutainer®). In order to stabilized intracellular RNA, 0.8 ml of venous blood was transferred in a tube containing 0.8 ml of Lysis Buffer DL (Macherey-Nagel, Düren, Germany). After homogenization, the samples were maintained at -20°C until RNA extraction. Total RNA was extracted using the NucleoSpin® RNA Blood kit (Macherey-Nagel, Düren, Germany). The manufacturer’s protocol was modified to obtained sufficient ARN quantities for the Microarray gene expression analyses: extraction was carried out from 1.6 ml of the mix blood and Lysis Buffer DL. Twenty µl of proteinase K was then added to complete blood lysis. To adjust RNA binding conditions, 0.8 ml of 70% ethanol was added. The following steps were not modified, except the elution that was carried out with 40 µl of RNase free water. Total RNA quality was assessed using RNA Pico chips on a Bioanalyser 2100 (Agilent, Boeblingen, Germany) and and its concentration was measured on a Nano Drop One Spectrophotometer (ThermoScientific, Illkirch, France).

tag: group

value: Boxe

tag: aggressiveness

tag: unresponsiveness

tag: alert

tag: stereotypies

tag: animal

tag: horse type

value: Mare

tag: age

tag: washbatch


title: SUP-B15_24h_MYCdegr1_rep2

description: Library name: C148_sample

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: 24h +25nM MYC degrader 1


title: Kc167, CP190, ChIP in control, bio rep2


title: whole blood_Pasture_T0_AMOUR_DE_VOUGON

value: Pasture

tag: time

value: Geldings


title: SUP-B15_24h_MYCdegr1_rep1

description: Library name: C144_sample

value: B-cell precursors


title: SUP-B15_24h_DMSO_rep1_(MYCdegr_exp)

description: Library name: C143_sample

value: 24h +DMSO


title: whole blood_Boxe_T1_PLUTON_DE_LUSSE


title: whole blood_Pasture_T1_AMOUR_DE_VOUGON


title: Kc167, CP190, ChIP in control, bio rep1

value: embryo


title: whole blood_Boxe_T0_PLUTON_DE_LUSSE


title: Kc167, Su(Hw), ChIP in eff kd cell, bio rep3

value: hemocyte

value: eff dsRNA


title: whole blood_Pasture_T0_TONTOUTA_VIENNOISE


title: whole blood_Pasture_T1_ZORRO

value: ZORRO


title: whole blood_Pasture_T1_TONTOUTA_VIENNOISE


title: 53BP1-KO murine BCPs + p210 (60days), rep.4

description: Library name: BB40_BCR_D60_RNAseq_rep2

value: primary

value: B-cell precursor

value: TRP53BP1-/- +BCR::ABL1(p210) retrovirus

value: no treatment


title: BV173_IgG

description: Library name: C095_sample

value: bone marrow


title: whole blood_Boxe_T1_AREZZO_DE_RIVERLAND


title: Kc167, CP190, ChIP in control, bio rep3

value: mcherry dsRNA


title: whole blood_Boxe_T0_QUAPRICE_DES_CLOTINS

value: Boxe


title: SUP-B15_24h_DMSO_rep2_(MYCdegr_exp)

description: Library name: C147_sample


title: Kc167, Su(Hw), ChIP in eff kd cell, bio rep2


title: whole blood_Boxe_T0_AREZZO_DE_RIVERLAND


title: whole blood_Pasture_T0_ZORRO


title: BV173_MYC

description: Library name: C127_sample


title: whole blood_Pasture_T1_VEGAS_DU_PRE_MARAS


title: whole blood_Boxe_T0_VELOURS_DE_LA_ROQUE


title: whole blood_Pasture_T0_VEGAS_DU_PRE_MARAS


title: BV173_STAT5

description: Library name: C094_sample


title: BV173_24h_MYCdegr1_rep2

description: Library name: C146_sample


title: Kc167, Input, ChIP in eff kd cell, bio rep3


title: whole blood_Boxe_T1_VELOCE_DE_RIVERLAND

value: Mare


title: Kc167, Su(Hw), ChIP in eff kd cell, bio rep1


title: Kc167, Input, ChIP in eff kd cell, bio rep2


title: BV173_24h_MYCdegr1_rep1

description: Library name: C142_sample

value: 24h +25nM MYC degrader 1


title: whole blood_Boxe_T1_VELOURS_DE_LA_ROQUE


title: whole blood_Pasture_T1_RIESLING_D_AMOUR

value: Pasture


title: Kc167, Cul4, ChIP in eff kd cell, bio rep3


title: Kc167, Cul4, ChIP in eff kd cell, bio rep2


title: whole blood_Pasture_T0_STARTER_DE_COSE

value: Geldings


title: whole blood_Boxe_T0_VELOCE_DE_RIVERLAND


title: whole blood_Pasture_T1_STARTER_DE_COSE


title: whole blood_Pasture_T0_RIESLING_D_AMOUR


title: Kc167, Input, ChIP in eff kd cell, bio rep1


title: BV173_24h_DMSO_rep1_(MYCdegr_exp)

description: Library name: C141_sample

value: B-cell precursors


title: whole blood_Boxe_T1_RACONTEUR

value: RACONTEUR


title: whole blood_Pasture_T0_VALDOR_DU_LOUVET


title: whole blood_Pasture_T1_VALDOR_DU_LOUVET


title: Healthy Human bone marrow  B-cells (#3)

description: Library name: C183_sample

value: primary BM B-cells

value: wild type


title: Kc167, Cul4, ChIP in eff kd cell, bio rep1

value: embryo

value: hemocyte

value: eff dsRNA


title: Healthy Human bone marrow  B-cells (#2)

description: Library name: C182_sample


title: BV173_24h_DMSO_rep2_(MYCdegr_exp)

description: Library name: C145_sample

value: 24h +DMSO


title: Kc167, CP190, ChIP in eff kd cell, bio rep3


title: whole blood_Pasture_T1_ALOES_DES_SAULES


title: Healthy Human bone marrow B-cells (#1)

description: Library name: C181_sample


title: Kc167, CP190, ChIP in eff kd cell, bio rep2


title: whole blood_Boxe_T0_RACONTEUR


title: whole blood_Pasture_T1_PALOMA_DU_MONCEL


title: whole blood_Pasture_T0_ALOES_DES_SAULES


title: Kc167, CP190, ChIP in eff kd cell, bio rep1


title: whole blood_Pasture_T0_PALOMA_DU_MONCEL


title: BV173_ETV5_shRNA_13938_C911_ctrl_Ponatinib_H3K27ac_rep2

description: Library name: C122_sample

extract_protocol:
ChIP-Seq for H3K27ac was done as described in Boulianne et al using anti-Histone H3 (acetyl K27) antibody – ChIP Grade (ab4729) (Abcam) and polyclonal rabbit IgG (isotype control) (sc2027) (Santa Cruz Biotechnologies), with the exception that initial cross-linking was performed at RT and 1mio cells were used for crosslinking instead of 15mio.
ChIP-Seq libraries were generated from ChIP immunoprecipitated DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (NEB) and sequenced either at Novogene or at the in-house sequencing facility of the MRC London Institute of Medical Sciences at Imperial College London.

treatment_protocol: Where indicated cells were treated for 24h with DMSO or Ponatinib (100nM), or 2.5uM AK-2292.

value: ETV5 RNAi control + 24h Ponatinib


title: whole blood_Boxe_T0_NOBLE_ESPOIR


title: whole blood_Pasture_T0_PERSANE_ROSE


title: whole blood_Boxe_T1_NOBLE_ESPOIR


title: Kc167, Su(Hw), ChIP in cul4 kd cell, bio rep3

value: cul4 dsRNA


title: whole blood_Pasture_T1_HERA

value: HERA


title: BV173_ETV5_shRNA_13938_C911_ctrl_Ponatinib_H3K27ac_rep1

description: Library name: C121_sample

value: bone marrow


title: whole blood_Pasture_T1_PERSANE_ROSE


title: whole blood_Pasture_T0_HERA


title: BV173_ETV5_shRNA_13938_C911_ctrl_AK-2292_H3K27ac_rep2

description: Library name: C120_sample

value: ETV5 RNAi control + 24h AK-2292


title: BV173_ETV5_shRNA_13938_C911_ctrl_DMSO_IgG_ctrl

description: Library name: C123_sample

value: ETV5 RNAi control + 24h DMSO


title: whole blood_Boxe_T1_AZERTY_DE_RIVERLAND

value: Boxe


title: whole blood_Boxe_T0_AZERTY_DE_RIVERLAND


title: Kc167, Su(Hw), ChIP in cul4 kd cell, bio rep2


title: Kc167, Su(Hw), ChIP in cul4 kd cell, bio rep1


title: BV173_ETV5_shRNA_13938_C911_ctrl_AK-2292_H3K27ac_rep1

description: Library name: C119_sample


title: Kc167, Input, ChIP in cul4 kd cell, bio rep3


title: whole blood_Pasture_T0_CHIC_LADY_DU_BRIO

value: Pasture

value: Mare


title: whole blood_Pasture_T1_CHIC_LADY_DU_BRIO


title: whole blood_Pasture_T1_TOO_MUCH_DE_BUISSY


title: whole blood_Pasture_T0_TOO_MUCH_DE_BUISSY


title: Kc167, Input, ChIP in cul4 kd cell, bio rep2


title: S3

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

description: Library name: Sample 6

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.8 and MultiQC v1.7 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.0 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Mycobacterium tuberculosis H37Ra reference genome (ASM1614v1; GCA_000016145.1) using HISAT2 v2.1.0 aligner.
The PCR and optical duplicates were marked and removed using Picard v2.20.3 tools.
Gene expression values were obtained as read counts using ensembl annotation file (Mycobacterium tuberculosis H37Ra) and featureCounts v1.6.4 software.
Assembly: ASM1614v1 (GCF_000016145.1)
Supplementary files format and content: Sum of all raw reads counts was used to normalize read count value for each gene and presented in tab-delimited text format

organism: Mycobacterium tuberculosis

source_name: Bacterial Cells

growth_protocol: Culturing of bacteria in 7H9 medium comtaining 1X OADS, 0.5% glycerol, 0.05% Tyloxapol, 50µg/ml L-leucine and 24µg/ml pantothenate with shaking at 200rpm at 37 degree Celsius.

extract_protocol:
Extraction of total RNA by bead-beating lysis of bacteria in Trizol followed by Chlorform extraction and ethanol precipitation.
Library was prepared using RibominusTM Transcriptome Isolation Kit (Yeast and Bacteria) and NEBNext Ultra II RNA-Seq kit for illumina.

treatment_protocol: Treatment with 50nM inhibitor for 24hrs

tag: strain

value: Mc2 6206 strain of Mycobacterium tuberculosis

value: Bacterial Cells

tag: replicate

value: Replicate S3

value: Treated

value: Drug-treated

value: 24 hours


title: Kc167, Input, ChIP in cul4 kd cell, bio rep1

value: embryo

value: hemocyte


title: BV173_ETV5_shRNA_13938_C911_ctrl_DMSO_H3K27ac_rep1

description: Library name: C117_sample

value: B-cell precursors


title: S2

description: Library name: Sample 5

value: Replicate S2


title: C3

description: Library name: Sample 3

value: Replicate C3

value: Control

value: Untreated


title: S1

description: Library name: Sample 4

value: Replicate S1


title: whole blood_Pasture_T0_BECEBEGE_D_AUR

tag: group

value: Geldings


title: BV173_ETV5_shRNA_13938_DMSO_IgG_ctrl

description: Library name: C116_sample

value: bone marrow

value: ETV5 RNAi + 24h DMSO


title: whole blood_Pasture_T1_BECEBEGE_D_AUR

value: Pasture

tag: aggressiveness


title: BV173_ETV5_shRNA_13938_C911_ctrl_DMSO_H3K27ac_rep2

description: Library name: C118_sample

value: ETV5 RNAi control + 24h DMSO


title: Kc167, Cul4, ChIP in cul4 kd cell, bio rep3

value: cul4 dsRNA


title: BV173_ETV5_shRNA_13938_DMSO_H3K27ac_rep2

description: Library name: C113_sample


title: C2

description: Library name: Sample 2

value: Mc2 6206 strain of Mycobacterium tuberculosis

value: Bacterial Cells

value: Replicate C2


title: MC38_3 scTCR seq

city: Heidelberg

first: Rienk

last: Offringa

state: Baden-Wuerttemberg

address: Im Neuenheimer Feld 280

department: Division of Molecular Oncology of Gastrointestinal Tumors

institute: DKFZ Heidelberg

description: Library name: MC38_3 scTCR seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1
Assembly: mm10-2020-A, vdj_GRCm38_alts_ensembl-5.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TILs from murine MC38 tumors

extract_protocol:
Tumors were harvested, minced into smaller pieces with a scalpel and digested using the human tumor dissociation kit with gentleMACS Octo tissue dissociator (Miltenyi) according to the manufacturer’s instructions (program ‘37C_h_TDK_3’). Following 1 h digestion, tumor cell suspensions were poured through a 100 μm strainer pre-coated with 2.5% BSA/PBS. Next, cells were washed twice over a 70 µm cell strainer and frozen in liquid nitrogen in freezing media (fetal bovine serum + 10% DMSO) until processing for single-cell RNA sequencing.
Library was performed according to the manufacter’s instructions (10x Genomics, v2 chemistry according to the manufacturer’s protocol (#CG000331 Rev E). Briefly, T-cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. For gene expression library construction, 50 ng mass of sample were fragmented, end-repaired and A-tailed. For V(D)J library construction, cDNA was first enriched using T-cell mixes 1 by PCR amplification, followed by SPRIselect reagent size selection. Then, T-cell mix 2 was used for further enrichment by PCR amplification, followed by SPRIselect reagent size selection. Post target enrichment, quality control was checked on Agilent Bioanalyzer High Sensitivity Chip and quantified using Qubit Fluorometer and Qubit dsDNA HS Assay kit. For V(D)J library construction, 50 ng mass of sample were fragmented, end-repaired and A-tailed. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: TILs from murine MC38 tumors

value: T-cells


title: Kc167, Cul4, ChIP in cul4 kd cell, bio rep2

value: embryo

value: hemocyte


title: MC38_2 scTCR seq

description: Library name: MC38_2 scTCR seq


title: SUP-B15_ETV5_shRNA_13938_C911_ctrl_H3K27ac_rep1

description: Library name: C110_sample

value: B-cell precursors

value: ETV5 RNAi control


title: C1

description: Library name: Sample 1

value: Replicate C1

value: Control

value: Untreated

value: 24 hours


title: BV173_ETV5_shRNA_13938_DMSO_H3K27ac_rep1

description: Library name: C112_sample

value: bone marrow

value: ETV5 RNAi + 24h DMSO


title: MC38_3 scRNA seq

description: Library name: MC38_3 scRNA seq


title: Kc167, CP190, ChIP in cul4 kd cell, bio rep3


title: Kc167, Cul4, ChIP in cul4 kd cell, bio rep1


title: MC38_1 scRNA seq

description: Library name: MC38_1 scRNA seq


title: MC38_2 scRNA seq

description: Library name: MC38_2 scRNA seq


title: MC38_1 scTCR seq

description: Library name: MC38_1 scTCR seq


title: CD45-positive immune cells in B16F10 lung metastases tissue, CAR group

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

description:
Library name: scRNA-seq_CAR
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor-bearing lung

extract_protocol:
CD45-positive immune cells in B16F10 lung metastases were isolated by FACS.Meanwhile, 10x Genomics was performed
10x Genomics scRNA-seq library construction  was performed by AZENTA company  for Illumina sequencing

value: Tumor-bearing lung

value: CD45-positve immune cells

value: WT

value: Transfer CAR BMDMs


title: SUP-B15_ETV5_shRNA_13938_H3K27ac_rep2

description: Library name: C109_sample

value: ETV5 RNAi


title: CD45-positive immune cells in B16F10 lung metastases tissue, ECD group

description:
Library name: scRNA-seq_ECD
10x Genomics

value: Transfer ECD BMDMs


title: SUP-B15_ETV5_shRNA_13938_C911_ctrl_H3K27ac_rep2

description: Library name: C111_sample


title: C3/C3 M2/+ Tmem173-/- male 3

city: Ithaca

first: Mumingjiang

last: Munisha

state: NY

address: 618 Tower Rd, CVM 14 T1-010 VRT

institute: Cornell University

description: Library name: MM12

data_processing:
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0,
Unwanted reads were removed with STAR v 2.7.0e using parameters: --outReadsUnmapped Fastx
final reads were mapped to the mouse reference genome Ensembl GRCm38 using STAR v2.7.0e.
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
Assembly: Ensembl GRCm38
Supplementary files format and content: tab-delimited text file for raw counts for each sample

source_name: Placenta

extract_protocol:
Total RNA was isolated from E13.5 placentae using Zymo Quick-RNA mini-prep Kit
1000ng input total RNA with polyA enrichment is used for library prep using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

value: Placenta

tag: Sex

value: Male

tag: Stage


title: Kc167, CP190, ChIP in cul4 kd cell, bio rep1

value: embryo

value: hemocyte

value: cul4 dsRNA


title: C3/C3 M2/+ Tmem173-/- male 2

description: Library name: MM11


title: SUP-B15_ETV5_shRNA_13938_H3K27ac_rep1

description: Library name: C108_sample

value: B-cell precursors


title: C3/C3 M2/+ Tmem173-/- male 1

description: Library name: MM8


title: SUP-B15_DMSO_IgG_ctrl

description: Library name: C107_sample

value: 24h DMSO


title: C3/C3 M2/+ Tmem173-/- female 3

description: Library name: MM10

value: Female


title: S_484_D36_Con

city: Canyon

first: Bradly

middle: Isaiah

last: Ramirez

state: Texas

address: 3201 Russel Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Base calling with Illumina RTA v3
Quality assessed with FastQC 0.11.9-Java-11
Trimming with Trimmomatic 0.39 to remove adapters; phred33; sliding window of 4 bases, minimum quality score 20; minimum length = 28 bases; trimmed leading and trailing bases with quality score less than 3
HISAT2 v2.2.1 used to map and index reads against Bos taurus reference genome ARS-UCD1.3
Reads assembled and quantified with StringTie v2.1.0
Resulting GFFs merged with StringTie v2.1.0
PrepDE3.py3 used to generate read count matrix
Differential expression performed with edgeR v3.38.4 and glmmSeq v0.2.0
Assembly: ARS-UCD1.3
Supplementary files format and content: Tab delineated text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
RNA extracted with Tempus Spin RNA Isolation Kits
RNA libraries were prepared for sequencing using Illumina stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: Samples collected in Tempus blood RNA tubes and stored same day at -80 C until extraction

value: Whole blood

value: Day 36

value: Control

tag: individual id

tag: disease

value: bovine respiratory disease (BRD)


title: SUP-B15_Ponatinib_H3K27ac_rep2

description: Library name: C106_sample

value: bone marrow


title: C3/C3 M2/+ Tmem173-/- female 2

description: Library name: MM9


title: Kc167, CP190, ChIP in cul4 kd cell, bio rep2


title: C3/C3 M2/+ Tmem173-/- female 1

description: Library name: MM7


title: S_470_D14_Con

value: Day 14


title: UTI_13

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

institute: University Hospital Bonn

description: Library name: DE09NGSUKBR124171_1

data_processing:
Adapter trimming was performed using Cutadapt, and reads were aligned to the mouse reference genome (GRCm38) with STAR. Gene-level read counts were obtained with featureCounts using Ensembl annotations.
Assembly: GRCh38
Supplementary files format and content: txt file contains raw counts for each sample

source_name: Kidney

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 3'mRNA Library Prep Kit

treatment_protocol: Female C57BL/6J mice were infected with uropathogenic E. coli strain 536, which was instilled into the bladder twice at a 3-hour interval. Kidneys were harvested 16 hours after the second infection. Control mice received urethral instillation with PBS.

value: Kidney

value: female

value: uropathogenic E. coli strain 536


title: SUP-B15_Ponatinib_H3K27ac_rep1

description: Library name: C105_sample


title: S_441_D17_Con

value: Day 17


title: UTI_12

description: Library name: DE36NGSUKBR124170_1


title: control_20

description: Library name: DE63NGSUKBR124169_1

value: PBS


title: SUP-B15_AK-2292_H3K27ac_rep2

description: Library name: C104_sample


title: UTI_14

description: Library name: DE79NGSUKBR124172_1


title: control_15

description: Library name: DE20NGSUKBR124167_1


title: S_470_D33_Con

value: Day 33


title: SUP-B15_AK-2292_H3K27ac_rep1

description: Library name: C103_sample


title: S_476_D32_Con

value: Day 32


title: S_419_D14_Con


title: S_484_D13_Con

value: Day 13


title: FLPO2_J1

city: Worcester

first: Sithara Raju

last: Ponny

address: 55 N Lake Ave

institute: UMass Chan Medical School

description:
Library name: Sample 6
10X Genomics

data_processing:
Alignment, filtering, barcode counting,UMI counting and aggregation was done using Cell Ranger Software
All further analysis was done using Seurat
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Liver

extract_protocol:
The liver was diced with scissors and gently pushed with a 10 ml plunger through a 100 μm cell strainer. The cells were washed with 2% FBS-PBS and centrifuged at 1,700 rpm (6 min). The cells were re-suspended with 33.8 % Isotonic Percoll and centrifuged at 2,000 rpm (12 min). The pellet (leukocytes) was collected. Red blood cells were removed with ACK lysing buffer. The cells were then washed with PBS.
Single cell capture and library preparation were performed according to the Chromium Single Cell 3’ Reagent Kits V3 User Guide. Cells were loaded on a multiple-channel microfluidics chip of the Chromium Controller (10X Genomics) with a targeted cell recovery of 8,000. Libraries were constructed with Single Cell 3’ Reagent Kits V3. Illumina sequencing libraries were prepared with the amplified cDNA and assessed with High sensitivity DNA Assay Kits (Agilent Bioanalyzer system) and Qubit dsDNA High Sensitivity Assay Kits.

value: Liver

value: J1 J2 lf/lf


title: S_481_D36_Con


title: FLPO1_J1

description:
Library name: Sample 5
10X Genomics


title: control_19

description: Library name: DE90NGSUKBR124168_1


title: CRE2_J1

description:
Library name: Sample 4
10X Genomics


title: CRE1_J1

description:
Library name: Sample 3
10X Genomics


title: SUP-B15_DMSO_H3K27ac_rep1

description: Library name: C101_sample

value: B-cell precursors

value: 24h DMSO


title: BV173_parental_DMSO_IgG_ChIP

value: DMSO


title: CL75-FLPO-1

description:
Library name: Sample 68
CL75

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
TPM and Counts were calculated using Salmon
Assembly: mm10
Supplementary files format and content: excel file include read count values for each Sample
Supplementary files format and content: excel file include TPM values for each Sample

source_name: liver

extract_protocol:
Total RNA was harvested using RNeasy kit with Dnase I treatment.
PolyA enrichment library preperation by Novogene and libraries were pair end sequenced for 150bp on NovaSeq6000 platform.

value: liver

tag: diet

value: HFD


title: GFP2_J1

description:
Library name: Sample 2
10X Genomics


title: BV173_parental_DMSO_H3K27ac_ChIP

value: bone marrow


title: S_479_D34_Con

value: Whole blood

value: Day 34

value: Control

value: bovine respiratory disease (BRD)


title: GFP1_J1

description:
Library name: Sample 1
10X Genomics


title: CL76-FLPO-2

description:
Library name: Sample 69
CL76


title: SUP-B15_DMSO_H3K27ac_rep2

description: Library name: C102_sample


title: CL74-CRE-3

description:
Library name: Sample 67
CL74


title: CL72-CRE-2

description:
Library name: Sample 66
CL72