title: D18-CD137

description: single cell RNA

source_name: Purified BM CD8+ T cells

extract_protocol:
At the indicated time points, CD8+ T cells were isolated from the BM using mouse CD8+ T cell isolation kit (Miltenyi Biotec) and FACSaria™ Fusion (BD biosciences).
Single-cell libraries (3′ gene expression) were generated using the Chromium Controller Instrument and Chromium Single Cell 3′ Library & Gel Bead Kit v3 according to the manufacturer’s protocol (10× Genomics).  Single-cell library size and quality were confirmed on the Fragment Analyzer (Agilent). KAPA Quantification Kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify libraries.
The libraries were sequenced on a NextSeq 550 (Illumina) in pair-end sequencing 28 bp (read1) × 91 bp (read2) and a single index 8 bp in length.

treatment_protocol: C57BL/6 mice were injected with Vk12653 Multiple myeloma cells. After 10 days, mice were treated with anti-CD137 (100 µg, 3H3, BioXcell, twice a week) or with control IgG (100 µg, HRPN,BioXcell).

value: from n=5 D28 VK12653 bearing mice


title: D18-Ig

status: Public on Jun 30 2023

type: SRA

city: Toulouse

first: Liliana

middle: Elisa

last: Lucca

address: 2 Avenue Hubert Curien

department: Immunology

country: France

institute: CRCT

description: single cell RNA

library_source: transcriptomic

data_processing:
fastq files were generated from Illumina BCL files with the 'mkfastq' pipeline of cellranger v3.0.2
Assembly: mm10
Supplementary files format and content: a matrix of expression was generated by joining the outputs of the 'count' pipeline of cellranger v3.0.2, filtering cells with less than 30,000 UMIs per cell and less than 25% mitochondrial reads. Data were than transformed using the sctransform function of Seurat v3.0

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissu

tag: treatment

value: Control IgG

tag: treatment kinetic


title: D11-CD137

description: single cell RNA

value: from n=5 D21 VK12653 bearing mice


title: Primary MEF cells, population B, control (no TAT-CRE)

city: Cambridge

first: Anne

last: Ferguson-Smith

address: 20 Downing Place

department: Genetics

country: United Kingdom

institute: Cambridge University

library_source: genomic

data_processing:
tcBS-seq reads were trimmed by Trim Galore (v0.6.0).
tcBS-seq reads were aligned to mm10 using Bismark.
tcBS-seq reads with map quality score less than 10 were excluded and were further filtered by M-bias: for MEF DNMT3A/3B DKO and control data, we excluded the first two bp on Read 1and the first four and last two bp on Read 2.
tcBS-seq read data was extracted using bismark_methylation_extractor and analysed in R (v3.6.1).
Assembly: mm10
Supplementary files format and content: CpG_combine* files are tab delimited with the following four columns:   chromosome, genomic locus (bp), unmethylated read counts, methylated read counts

molecule: genomic DNA

source_name: MEF-B

growth_protocol: Primary MEFs were established from Dnmt3aflox/flox3bflox/flox E13.5 embryos and grown at 37°C and 5% CO2 in high glucose DMEM GlutaMAX™ (ThermoFisher, cat no. 31966021) supplemented with 10% FBS (Gibco, 11550356) and 1% penicillin/streptomycin solution and passaged with trypsin/EDTA.

extract_protocol:
DNA extraction was performed with the Qiagen AllPrep DNA/RNA Mini Kit (cat no. 80204).
Target capture bisulfite-sequencing (tcBS-seq) libraries were generated using the SureSelectXT Methyl-seq Library Preparation Kit with the following specifications. 1µg of DNA was sonicated to an average size of 200bp with the Covaris E220 (Duty Factor = 30%, PIP = 100, Cycles per Burst = 1000, Treatment Time = 95, Bath Temperature = 7°C, with intensifier fitted) using 50µl microTUBEs (cat no. 520166) and 24-place rack (cat no. 500308). Following end repair, dA tailing, and adaptor ligation, libraries were hybridised to single-stranded RNA probes homologous to 297,000 regions in the mouse genome (SureSelectXT Methyl-Seq Capture Probes, cat no. 931052). After purification, the libraries were bisulfite converted using Zymo Research’s Methylation-Gold Kit (cat no. D5005) and PCR amplified for 8 cycles. The PCR amplified bisulfite-treated libraries were then purified, indexed by PCR amplification (6 cycles), and purified again. All purification steps took place using Ampure XP beads (Beckman Coulter, cat no. A63881). The final libraries were then quality checked and quantified for multiplexing using the Bioanalyzer High-Sensitivity DNA kit (Agilent, 5067-4626) and Qubit dsDNA HS Assay kit (Thermo Scientific, Q32854). The multiplexed libraries were sequenced as 150 bp paired-end reads on the Illumina Novaseq 6000 SP.

treatment_protocol: To induce the knockout of DNMT3A/3B, 1x106 cells were plated and the next day washed with PBS and media was replaced with 5ml of DMEM:PBS (1:1) with 50µl TAT-CRE recombinase (2-3µg/µl) and incubated at 37°C for 8 hours. Following the TAT-CRE recombinase treatment, cells were washed three times with PBS and the original growth media was replaced. The TAT-CRE recombinase treatment was carried out again 48 hours following the start of the initial treatment. Cells were collected for protein and DNA/RNA extraction 72 hours after the second TAT-CRE recombinase treatment.

tag: cell line

value: MEF-B

tag: cell type

value: Primary mouse embryonic fibroblasts (MEFs)


title: RNA-Seq BSC, Ctrl, rep4

city: Boston

first: Xingbin

last: Ai

state: MA

address: 55 Fruit St

department: Pediatrics

country: USA

institute: MASSACHUSETTS GENERAL HOSPITAL

description: BSC, Ctrl, rep4

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the STAR algorithm with default settings.
The number of fragments overlapping predefined genomic genes is counted. Only read pairs that have both ends aligned are counted.
Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
The gene annotations were obtained from Subread R package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene.
Genes with the same Entrez gene identifiers were also merged into one gene.
Assembly: hg38
Supplementary files format and content: csv

organism: Homo sapiens

source_name: Lung

extract_protocol:
Total RNA isolation using a RNeasy kit (QIAGEN, Cat# 74104).
For each sample, 2 µg of total RNA was used in library construction using TruSeq Stranded mRNA Library kit (Illumina, Cat# 20020594).

tag: tissue

value: Lung

value: Basal stem cell


title: SHP77 (sRNA-Seq)

city: Hefei

first: fengmei

last: chao

state: Anhui

address: East Huanhu road

country: China

institute: Anhui Provincial Cancer Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include Normalized_Value/Count values for each Sample

molecule: polyA RNA

source_name: Small cell lung cancer cells

growth_protocol: The cells were cultured on 10cm cell culture dish in 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol
Total RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). Libraries were sequenced on the Illumina HiSeq 2500 with single-end 50bp following the manufacturer's protocols.

value: Small cell lung cancer cells

tag: cell source

value: Derived from a non-encapsulated primary lung tumor

value: untreated

tag: phenotype

value: Chemoresistance


title: RNA-Seq BSC, Ctrl, rep3

description: BSC, Ctrl, rep3


title: RNA-Seq BSC, Ctrl, rep6

description: BSC, Ctrl, rep6


title: Primary MEF cells, population A, control (no TAT-CRE)

source_name: MEF-A

value: MEF-A


title: RNA-Seq BSC, Ctrl, rep2

description: BSC, Ctrl, rep2


title: D11-Ig

description: single cell RNA


title: D4-Ig

description: single cell RNA

value: from n=5 D14 VK12653 bearing mice


title: D4-CD137

description: single cell RNA


title: RNA-Seq BSC, Ctrl, rep1

description: BSC, Ctrl, rep1


title: Immortalised MEF cells, subclonal population 2-5

data_processing:
RNA-sequencing data was trimmed by Trim Galore (v0.6.0)
RNA-sequencing data was aligned (mm10) and quantified using Salmon (v1.5.2) using the mm10 reference annotation (Ensembl release 102, Nov 2020).
RNA-sequencing data transcript quantification was processed using the R/Bioconductor package DESeq2 (v1.24.0), to obtain normalised counts using the “regularised log” (rlog) transformation.
Assembly: mm10
Supplementary files format and content: all_clonal_MEF_gene_expression_data is a tab delimited file with the following 3 columns: gene id (from ensembl release 102), cell line, and rlog transformation of normalised read counts (from DESeq2 v1.24.0 via Salmon v1.5.2)

growth_protocol: Mouse embryonic fibroblasts (MEFs) were established from E13.5 C57BL/6J mouse embryos. MEFs were grown at 37°C and 5% CO2 in high glucose DMEM GlutaMAX™ (ThermoFisher, cat no. 31966021) supplemented with 10% FBS (Gibco, 11550356) and 1% penicillin/streptomycin solution and passaged with trypsin/EDTA. MEFs were immortalised by serial passaging the cells through crisis phase. Isolation of single immortalised MEF cells was performed by flow cytometry (MoFlo Astrios Cell Sorter) to 96-well plates. The isolated single cells were grown into clonal cell lines by successive passaging from 96-well, 48-well, 24-well, 12-well, and 6-well plates to 10cm dishes where they were grown to 75% confluency to yield 1-2 million cells per clonal line for DNA/RNA extraction. The parental lines, from which the clonal lines were derived, were also grown to 75% confluency on 10cm dishes to yield 1-2 million cells for DNA/RNA extraction.

extract_protocol:
RNA extraction was performed with the Qiagen AllPrep DNA/RNA Mini Kit (cat no. 80204).
Libraries were generated using the NEBNext® rRNA Depletion Kit (NEB, cat no. E6310) and Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, cat no. E7760) with the following specifications. RNA Integrity Number (RIN) was determined using the Agilent RNA 6000 Pico Kit (cat no. 5067-1513) on the Agilent 2100 Bioanalyzer and its associated software. 1μg of RNA was hybridised to probes for rRNA depletion, treated with RNase H and DNase I, and purified before being fragmented at 94°C with incubation times ranging from 8 to 15 minutes depending on the RIN. The fragmented RNA was then reverse-transcribed to cDNA in two steps and purified. Following end repair and adapter ligation, the cDNA libraries were purified, PCR enriched for 9 cycles, and purified again. All purification steps took place using Ampure XP beads (Beckman Coulter, cat no. A63881). The final libraries were quality checked and quantified for multiplexing using the Bioanalyzer High-Sensitivity DNA kit (Agilent, 5067-4626), Qubit dsDNA HS Assay kit (Thermo Scientific, Q32854), and the KAPA Library Quantification Kit optimised for Roche® LightCycler 480 (Roche, 07960298001). The multiplexed libraries were sequenced as 150 bp paired-end reads on the Illumina Novaseq 6000 S1.

value: Immortalised mouse embryonic fibroblasts (MEFs)


title: Immortalised MEF cells, subclonal population 2-7


title: Immortalised MEF cells, subclonal population 2-4


title: Immortalised MEF cells, subclonal population 2-3


title: RNA-Seq BSC, CDH, rep12

description: BSC, CDH, rep12


title: D1-CD137

description: single cell RNA

value: from n=5 D11 VK12653 bearing mice


title: Immortalised MEF cells, subclonal population 2-1


title: Immortalised MEF cells, subclonal population 2-2


title: RNA-Seq BSC, CDH, rep11

description: BSC, CDH, rep11


title: AML patient leukemic blasts (sort purified)

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

data_processing:
Sequencing output of the library was run through CellRanger mkfastq, version 2.1.1 (10x GENOMICS).
The resulting fastq files were run through CellRanger count, version 2.1.1, to obtain bam alignment files. GRCh38 was used as a reference.
To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in terms of number of genes, number of UMIs, and percentage of mitochondrial genes using the R package scater (ver.1.8.0; nmads = 3). Normalization of cell-specific biases and removal of technical noise were performed using scran package (ver. 1.8.2).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including either UMI counts or normalized logcounts for individual genes (rows) in individual cells (QCed; columns). Gene symbols and ENSEMBL gene IDs were in the first and second column, respectively. Barcodes in the first row consist of cellular barcodes and library IDs.

source_name: peripheral blood mononuclear cells

growth_protocol: Cryopreserved human AML cells were thawed and were sort purified to obtain viable (7AAD negative) CD45+CD33+ human leukemic blasts.

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x GENOMICS) according to the manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 (10x GENOMICS) according to the manufacturer's protocol.

tag: Sex

value: male

tag: cell population

value: 7AAD negative, CD45+CD33+ Leukemic blasts

tag: disease state

value: AML


title: RNA-Seq BSC, CDH, rep10

description: BSC, CDH, rep10


title: RNA-Seq BSC, CDH, rep9

description: BSC, CDH, rep9


title: RNA-Seq BSC, Ctrl, rep5

description: BSC, Ctrl, rep5


title: sfGFP-B112, 6HR, Rep3

city: Berkeley

first: Anthony

last: Harris

state: CA

address: 622 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

description:
sfGFP_B112_6HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue

data_processing:
Sequencing reads were mapped to a reference genome using HISAT2, samtools, and Stringtie
Mapped reads were visualized to IGV_2.12.3.app
Counts and TPM tables were generated from sequencing reads using pseudoalignment with kallisto
Assembly: SK1 Reference Genome from Saccharomyces Genome Resequencing Project at Sanger Institute
Supplementary files format and content: Excel tables include counts and TPMs for each sample.

organism: Saccharomyces cerevisiae

growth_protocol:
(Mitotic) – SK1 cells were grown overnight in rich media (YPD) at 30˚C before being back diluted to 0.2 OD600 and allowed to grow to log phase (0.5 OD600) at 30˚C.
(Meiotic) – SK1 cells were grown overnight first in rich media (YPD), then in presporulation media, before being transferred to sporulation media (SPO) at 1.85 OD600 all at 30˚C.

extract_protocol:
RNA was harvested using phenol chloroform precipitation and DNA was cleared using TURBO DNA-free kit (Thermo Fisher) according to manufacturer’s protocol.
RNA libraries were prepared for RNA-Seq using NEXTFLEX Rapid Direction RNA-seq kit (PerkinElmer) according to the provided manual.

treatment_protocol:
(Mitotic Depletion) Log phase cells were treated with ß-estradiol (40µM; t = -30min). This expressed OsTIR in cells with 4xLexO-OsTIR. Then, 30 min later auxin was added to cells (200µM; t = 0). This initiated Ume6 depletion in 4xLexO-OsTIR cells.
(Meiotic Depletion) Cells transferred to SPO were allowed to normalize for 30 min (t = 0.5 h). All cells were treated with ß-estradiol (5nM) and Auxin (200µM), but Ume6 depletion only occurred in 8xLexO-OsTIR containing cells. Cells were incubated in SPO for an additional 1.5 h before IME1 and IME4 were induced by CuSO4 (50µM).

tag: genotype

value: sfGFP-B112; UME6(T99N)-3V5-aGFP

tag: time

tag: condition

value: Meiotic


title: RNA-Seq BSC, CDH, rep8

description: BSC, CDH, rep8


title: Immortalised MEF cells, subclonal population 1-7


title: sfGFP-B112, 4HR, Rep3

description:
sfGFP_B112_4HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: RNA-Seq BSC, CDH, rep6

description: BSC, CDH, rep6


title: sfGFP-B112, 2HR, Rep3

description:
sfGFP_B112_2HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Immortalised MEF cells, subclonal population 1-5


title: RNA-Seq BSC, CDH, rep5

description: BSC, CDH, rep5


title: sfGFP-B112, 0HR, Rep3

description:
sfGFP_B112_0HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Immortalised MEF cells, subclonal population 1-4


title: D1-Ig

description: single cell RNA

value: Control IgG


title: Immortalised MEF cells, subclonal population 2-6


title: Immortalised MEF cells, subclonal population 1-3


title: RNA-Seq BSC, CDH, rep4

description: BSC, CDH, rep4


title: sfGFP-B112, 4HR, Rep2

description:
sfGFP_B112_4HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: sfGFP-B112, 6HR, Rep2

description:
sfGFP_B112_6HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Immortalised MEF cells, subclonal population 1-1


title: sfGFP-B112, 2HR, Rep2

description:
sfGFP_B112_2HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: D0-NI

description: single cell RNA

value: from n=5 naive mice


title: Immortalised MEF cells, subclonal population 1-2


title: Hep3B NaB Curcumin and piperine treatment

city: Istanbul

first: Fikrettin

last: Sahin

state: Other (Not found in list)

address: Kayisdagi Cd

country: Turkey

institute: Yeditepe University

data_processing:
Tuxedo Protocol
Quality control and read statics were determined by FastQC program
The reads were mapped to GRCh38 using STAR (default settings)
Transcript assembly was done by Cufflinks
Differential expression analysis were performed using Cuffdiff software
Assembly: GRCh38
Supplementary files format and content: GTF format  assembled transcripts FPKM values

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using  NebNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Hepatocellular carcinoma cell line

value: WT

value: NaB curcumin and piperine


title: RNA-Seq BSC, CDH, rep2

description: BSC, CDH, rep2

value: Lung

value: Basal stem cell


title: RNA-Seq BSC, CDH, rep7

description: BSC, CDH, rep7


title: ATAC-Seq BSC, Ctrl, rep6

description: BSC, Ctrl, rep6

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the BWA v0.7.12 algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads are removed.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
BSCs were cryopreserved in 50% FBS/40% SAGM/10%DMSO solution prior to ATAC-seq by Active Motif (Carlsbad, CA, USA). Cells were thawed in a 37℃ water bath, pelleted, and tagmented using Nextera Library Prep Kit (Illuminutesa, Cat# FC-130-1064). Tagmented DNA was purified using the MinutesElute PCR purification kit (Qiagen, Cat# 13323).
The DNA was then amplified with 10 cycles of PCR, purified using Agencourt AMPure SPRI beads (Beckman Coulter).


title: sfGFP-B112, 6HR, Rep1

description:
sfGFP_B112_6HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Hep3B curcumin and piperine treatment

value: Curcumin and piperine


title: Immortalised MEF cells, parental population 1


title: RNA-Seq BSC, CDH, rep1

description: BSC, CDH, rep1


title: sfGFP-B112, 0HR, Rep2

description:
sfGFP_B112_0HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Immortalised MEF cells, subclonal population 1-6


title: Hep3B NaB treatment

value: NaB


title: ATAC-Seq BSC, Ctrl, rep5

description: BSC, Ctrl, rep5


title: sfGFP-B112, 4HR, Rep1

description:
sfGFP_B112_4HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: OD5

city: Melbourne

first: Conor

middle: Friend

last: McGuinness

state: VIC

address: 305 Grattan St

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
FASTQ files were demultiplexed and adapters trimmed using cutadapt (Martin, 2011)
Poor quality reads from FASTQ files were trimmed using Trimmomatic (Bolger et al., 2014).
Files were then aligned individually using bwa mem with standard parameters (Li and Durbin, 2009).
Mutations were called using the GATK4 MuTect2 pipeline for tumour only samples (Van der Auwera and O’Connor, 2020). The MarkDuplicates step was omitted due to the nature of RADseq data likely resulting in a high likelihood of false positive detection of duplicates, due to reads generated from the same cut site sharing identical mapping coordinates.
Assembly: mm10
Supplementary files format and content: gzip vcf files containing final variants after pipeline
Library strategy: RAD-seq

source_name: SSM3 derivative

growth_protocol: SSM3 cells were cultured in 90% DMEM + 10% FBS, 50μM β-mercaptoethanol, 5μg/mL bovine insulin, 10ng/mL transferrin, 0.3μM hydrocortisone at 8% CO2. Monoclonal isolates were derived by limiting dilution.

extract_protocol:
DNA was isolated using a commercial kit (Quick DNA Miniprep kit, Zymo Research, USA) and eluted in Type I water.
The RADseq libraries were constructed according to the methods outlined in Elshire et al., (2011) with modifications as outlined in Dodds et al. (2015). RADseq libraries were prepared using a PstI- MspI double-digest, and included negative control samples (no DNA). Libraries underwent a Pippin Prep (SAGE Science, Beverly, Massachusetts, United States) to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Raw fastq files were quality checked using a custom qc pipeline (available at https://github.com/AgResearch/DECONVQC). As one of the qc steps raw fastq files were quality checked using FastQC v0.10.1

treatment_protocol: 0D5 cells were seeded at 800000 cells/well of a 6cm dish. 24 hours after plating, media was replaced with SSM3 media, and cells were transfected with a mixture containing 2μg pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B(kindly donated by Vincent Caval), co-transfected with 2000μg pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and 1000μg of a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis, with 17.325μL of FuGene in a total volume of 325μL of transfection mixture. Control cells were co-transfected with pcDNA3.1-IRES-GFP (Addgene plasmid # 51406 ; http://n2t.net/addgene:51406 ; RRID:Addgene_51406 ) and the mCherry reporter construct above

value: SSM3 derivative

value: Mouse mammary luminal

value: Parental cell line


title: DT1D12

value: GFP transfected


title: sfGFP-B112, 2HR, Rep1

description:
sfGFP_B112_2HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Hep3B control

value: control


title: DT1C2


title: ATAC-Seq BSC, Ctrl, rep4

description: BSC, Ctrl, rep4


title: sfGFP-B112, 0HR, Rep1

description:
sfGFP_B112_0HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: ATAC-Seq BSC, Ctrl, rep3

description: BSC, Ctrl, rep3


title: sfGFP-IME1, 6HR, Rep3

description:
sfGFP_IME1_6HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: sfGFP-IME1; UME6(T99N)-3V5-aGFP


title: DT1B5


title: HepG2 curcumin and piperine treatment


title: HepG2 NaB Curcumin and piperine treatment


title: ATAC-Seq BSC, Ctrl, rep1

description: BSC, Ctrl, rep1


title: ATAC-Seq BSC, Ctrl, rep2

description: BSC, Ctrl, rep2


title: HepG2 NaB treatment


title: HepG2 control


title: B2F11

value: hAPOBEC3B transfected


title: DT1A4


title: ATAC-Seq BSC, CDH, rep2

description: BSC, CDH, rep2


title: sfGFP-IME1, 4HR, Rep3

description:
sfGFP_IME1_4HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: Meiotic


title: B2A4


title: Patient_3_PreDose

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
rMATS_patient3_10mg_2hr_H3B_vs_patient_Si_Cl_preDose.tar.gz
Patient_peripheal_blood_RNAseq_raw_gene_counts.txt

data_processing:
Adapter sequences were trimmed by cutadapt before fastq files were aligned to a hg19 genome using STAR (version 2.7.3a). Reads were dedupulicated. Read coverage tracks were generated by STAR and then samples were normalized samples by sequencing depth.
Gene counts were generated using featurecounts function of the Rsubread package (version 2.0.1) (Liao et al., 2019), aligning reads to the Ensembl (GRCh37.87) basic transcript annotations.
Alternative splicing was quantified using rMATS (Shen et al., 2014) considering junction-spanning reads only.
Assembly: hg19
Supplementary files format and content: Read coverage bigWig tracks, normalized by read depth
Supplementary files format and content: Raw gene counts generated by featureCounts in tad-delimited text value
Supplementary files format and content: rMATS output files in directory, tar and gzipped.

source_name: Peripheral blood

extract_protocol:
RNA extraction was performed using a Qiagen RNeasy Mini Kit.
50ng of RNA was used as input for library preparation with the KAPA mRNA HyperPrep kit. Libraries were sequenced on the Illumina NOVASeq in PE100 mode to a depth of 100M reads per sample at the Dana-Farber Cancer Institute.

value: Peripheral blood

value: Predose


title: ATAC-Seq BSC, CDH, rep1

description: BSC, CDH, rep1


title: sfGFP-IME1, 6HR, Rep2

description:
sfGFP_IME1_6HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Patient_3_10mg_2hr_H3B8800


title: B1F1


title: sfGFP-IME1, 0HR, Rep3

description:
sfGFP_IME1_0HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: sfGFP-IME1, 4HR, Rep2

description:
sfGFP_IME1_4HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: MDS_73413

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

country: Spain

institute: Center for Applied Medical Research

description:
HSC isolated from an MDS patient.
Low input 3’ end RNA-Seq

data_processing:
Illumina Casava software used for basecalling (NextSeq 500).
The reads in the FASTQ files were aligned to the GRCh38/hg38 human genome (GENECODE 25) with Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2B with default parameters.
To assign reads to genes we applied featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: DataRaw_ReadCounts.txt: Tab-delimited text file including raw counts for each Sample.

source_name: MDS HSC

extract_protocol:
Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific).
Protocol reproduced from: Jaitin, D. A. et al. (2014) ‘Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.’, Science, 343(6172), pp. 776–9.

tag: disease diagnosis

value: MDS

value: HSC


title: Patient_2_PreDose

description:
rMATS_patient2_20mg_4hr_H3B_vs_patient_Ma_Ar_preDose.tar.gz
Patient_peripheal_blood_RNAseq_raw_gene_counts.txt


title: MDS_20793


title: D0-PBS

description: single cell RNA

value: from n=5 D10 VK12653 bearing mice


title: sfGFP-IME1, 2HR, Rep3

description:
sfGFP_IME1_2HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Patient_2_20mg_4hr_H3B8800


title: B1D9


title: MDS_20750


title: A2H1

value: hAPOBEC3A transfected


title: sfGFP-IME1, 0HR, Rep2

description:
sfGFP_IME1_0HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: sfGFP-IME1, 2HR, Rep2

description:
sfGFP_IME1_2HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Patient_1_7mg_4hr_H3B8800

description:
rMATS_patient1_7mg_4hr_H3B_vs_patient_Ra_Ly_preDose.tar.gz
Patient_peripheal_blood_RNAseq_raw_gene_counts.txt


title: A1H7


title: B1B8


title: MDS_19954


title: A1A2_CL


title: Cohesin_WT_AML_PDX_E7107_rep2

description:
rMATS_Cohesin_WT_AML_PDX_b1_Vehicle_b2_E7107.tar.gz
Cohesin_WT_AML_PDX_RNAseq_raw_gene_counts.txt

data_processing:
Adapter sequences were trimmed by cutadapt before fastq files were aligned to a combined mm10 and hg19 genome using STAR (version 2.7.3a). Reads were dedupulicated and filtered for those uniquely aligned to the hg19 genome. Read coverage tracks were generated by STAR and then samples were normalized samples by sequencing depth.
Gene counts were generated using featurecounts function of the Rsubread package (version 2.0.1) (Liao et al., 2019), aligning reads to the Ensembl (GRCh37.87) basic transcript annotations.
Alternative splicing was quantified using rMATS (Shen et al., 2014) considering junction-spanning reads only.
Assembly: hg19
Supplementary files format and content: Read coverage bigWig tracks, normalized by read depth
Supplementary files format and content: Raw gene counts generated by featureCounts in tad-delimited text value
Supplementary files format and content: rMATS output files in directory, tar and gzipped.

source_name: hCD45+ STAG2-wt PDX

growth_protocol: Three weeks after transplant, PDX mice were bled, and a complete blood count was performed with an Element HT5 analyzer (Heska). Mice were assigned to treatment groups based on platelet counts and treatment began 4 weeks post-injection for 3 days.

extract_protocol:
Four hours post injection on day 3, mice were sacrificed and single-cell suspensions were made from bone marrow, cells were washed and red blood cells were lysed. Samples were stained and sorted for viable, human CD45+ cells directly into RLT lysis buffer supplemented with b-Mercaptoethanol on a BD FACSAria II cell sorter. RNA extraction was performed using a Qiagen RNeasy Mini Kit.
50ng of RNA was used as input for library preparation with the KAPA mRNA HyperPrep kit. Libraries were sequenced on the Illumina NOVASeq in PE100 mode to a depth of 100M reads per sample at the Dana-Farber Cancer Institute.

treatment_protocol: E-7107 (4mg/kg in 10% Ethanol, 5% Tween80 in sterile saline solution) or an equivalent volume of Vehicle, was delivered daily via tail vein injection.

value: hCD45+ PDX cells isolated from mouse

value: 5day  E-7107 (4mg/kg in 10% Ethanol, 5% Tween80 in sterile saline solution)


title: sfGFP-IME1, 6HR, Rep1

description:
sfGFP_IME1_6HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: sfGFP-IME1, 4HR, Rep1

description:
sfGFP_IME1_4HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: MDS_18355


title: Patient_1_PreDose


title: sfGFP-IME1, 2HR, Rep1

description:
sfGFP_IME1_2HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Cohesin_WT_AML_PDX_STAG2_E7107_rep1


title: RBMS1 Knockdown, rep3

city: Riyadh

first: Sameer

last: Mohammad

address: Ali Al Arini, Ar Rimayah, P.O. Box 3660, Mail code 1515

country: Saudi Arabia

institute: KAIMRC, KSAU-HS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (version 0.6.7)
Trimmed sequence reads were mapped to GRCm38 using STAR (version 2.7.10a)
Gene-level counts were generated from the aligned reads using Salmon (version 1.9.0)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include gene count values for each Sample

growth_protocol: RBMS1KD and scrambled control 3T3-L1 cells differentiated into adipocytes using adipogenic cocktail (IBMX, Insulin, Dexamethasone and roziglitazone)

extract_protocol:
The RNeasy mini kit was purchased from Qiagen, (Maryland, USA) and utilized to isolate RNA from cell adipocytes.
The library was created using the Illumina Stranded Total RNA Prep protocol.
The library was amplified using PCR and cleaned with Agencourt AMPureXP (Beckman, CA,USA). The final library was then normalized, pooled, and loaded into an SP flow cell for up to 400 million reads of coverage. On an Illumina NovaSeq 6000 platform, the library was sequenced (200 cycles).

treatment_protocol: Cells harvested on day 7 of differentiated and used to RNA sequencing

value: Fibroblast

value: Adipogenic Differentiation

value: Day 7


title: MDS_17786


title: RBMS1 Knockdown, rep2


title: MDS_NAV


title: sfGFP-IME1, 0HR, Rep1

description:
sfGFP_IME1_0HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: RBMS1 Knockdown, rep1


title: MDS_15891


title: MDS_19957


title: Cohesin_WT_AML_PDX_Vehicle_rep1

value: 5day Vehicle


title: B112, 6HR, Rep3

description:
B112_6HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: STAG2-mutant_AML_PDX_RNAseq_E7107_rep2

description: rMATS output files in directory, tar and gzipped.

data_processing:
Adapter sequences were trimmed by cutadapt before fastq files were aligned to a combined mm10 and hg19 genome using STAR (version 2.7.3a). Reads were depulicated and filtered for those uniquely aligned to the hg19 genome. Read coverage tracks were generated by STAR and then samples were normalized samples by sequencing depth.
Gene counts were generated using featurecounts function of the Rsubread package (version 2.0.1) (Liao et al., 2019), aligning reads to the Ensembl (GRCh37.87) basic transcript annotations.
Alternative splicing was quantified using rMATS (Shen et al., 2014) considering junction-spanning reads only. To quantify splicing changes in E-7107 treated in vivo samples, bam files from the three replicate samples of the E-7107 treated arm were merged to obtain one replicate with sufficient read coverage for splicing analysis. As the E-7107 treated arm had dramatic depletion of the human cells,  fewer reads were obtained mapping to human cells in those samples. The vehicle treated samples had sufficient coverage in each replicate and were kept separate. The same read coverage and significance filters as described above were used to determine significantly-regulated splicing changes.
Assembly: hg19
Supplementary files format and content: Read coverage bigWig tracks, normalized by read depth
Raw gene counts generated by featureCounts in tad-delimited text value

source_name: hCD45+ STAG2-mutant PDX

growth_protocol: Three weeks after transplant, PDX mice were bled, and a complete blood count was performed with an Element HT5 analyzer (Heska). Mice were assigned to treatment groups (n=3 per group) based on platelet counts and treatment began 4 weeks post-injection for 5 days.

extract_protocol:
Four hours post injection on day 5, mice were sacrificed and single-cell suspensions were made from bone marrow, cells were washed and red blood cells were lysed. Samples were stained and sorted for viable, human CD45+ cells directly into RLT lysis buffer supplemented with b-Mercaptoethanol on a BD FACSAria II cell sorter. RNA extraction was performed using a Qiagen RNeasy Mini Kit.
50ng of RNA was used as input for library preparation with the KAPA mRNA HyperPrep kit. Libraries were sequenced on the Illumina NOVASeq in PE100 mode to a depth of 100M reads per sample at the Dana-Farber Cancer Institute.


title: MDS_68400


title: Scrambled control, rep3

value: WT


title: B112, 2HR, Rep3

description:
B112_2HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: MDS_71766


title: B112, 0HR, Rep3

description:
B112_0HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: Scrambled control, rep1


title: Scrambled control, rep2


title: STAG2-mutant_AML_PDX_RNAseq_Vehicle_rep2


title: STAG2-mutant_AML_PDX_RNAseq_E7107_rep3


title: MOS19

description:
HSC isolated from an aged healthy donor.
Low input 3’ end RNA-Seq

source_name: aged healthy donor HSC

value: Healthy

tag: age

value: Aged


title: B112, 6HR, Rep2

description:
B112_6HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue

tag: strain


title: MOS17


title: B112, 4HR, Rep2

description:
B112_4HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: k923_KO_LA

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing:
Sequenced reads were aligned to the mouse genome (mm10) using STAR (2.7.9a) (PMID: 23104886). Differential expression analysis was performed with DESeq2 (1.30.1) (PMID: 25516281). Pathway enrichment analysis was carried out with Metascape (PMID: 30944313).
Assembly: mm10
Supplementary files format and content: Gene counts table constructed of raw output from STAR.

source_name: left atria

extract_protocol:
Total RNA was extracted from murine cardiac tissue using the Direct-zol RNA Miniprep kit (Zymo Research, R2051).
RNA-seq libraries were generated with an mRNA enrichment protocol (KAPA mRNA HyperPrep, 08098115702). All RNA-seq libraries were sequenced on an Illumina NovaSeq.

value: left atria

value: Cardiac

value: Zfhx3 KO


title: Cohesin_WT_AML_PDX_Vehicle_rep2


title: STAG2-mutant_AML_PDX_RNAseq_Vehicle_rep3


title: B112, 2HR, Rep2

description:
B112_2HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: Meiotic


title: MOS11


title: STAG2-mutant_AML_PDX_RNAseq_Vehicle_rep1


title: k921_KO_RA

source_name: right atria

value: right atria


title: B112, 4HR, Rep3

description:
B112_4HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: STAG2-mutant_AML_PDX_RNAseq_E7107_rep1


title: MOS7

value: HSC


title: MOS4


title: k921_KO_LA


title: B112, 0HR, Rep2

description:
B112_0HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: k918_KO_RA


title: U937_SMC3-2_6hr-30nM-H3B

data_processing:
Adapter sequences were trimmed by cutadapt before fastq files were aligned to the hg19 genome using STAR (version 2.7.3a). Read coverage tracks were generated from deduplicated BAM files by STAR and then samples were normalized samples by sequencing depth. Gene counts were generated using featurecounts function of the Rsubread package (version 2.0.1) (Liao et al., 2019) and differentially expressed genes calculated using DESeq2 (version 1.26.0) (Love et al., 2014), normalizing samples by sequencing depth.
Assembly: hg19
Supplementary files format and content: Read coverage tracks, normalized by read depth

source_name: U937 cells

growth_protocol: Cells were grown in RPMI+10%FBS+1%P/S/G

extract_protocol:
1 million cells were collected in 350ul of Trizol and flash frozen. RNA was extracted with Zymogen Direct-Zol columns.
100ng of input RNA was used for library preparation with the KAPA RNA hyper prep kit with RiboErase treatment according to manufacturer’s instructions. Libraries were sequenced on the Illumina NOVASeq in PE100 mode to a depth of 100M reads per sample.

treatment_protocol: Cells were treated with H3B-8800 at 10nM, 30nM or DMSO for 6 hours.

value: SMC3-het, clone2


title: k918_KO_LA


title: k923_KO_RA


title: MOS2


title: U937_SMC3-1_6hr-10nM-H3B

value: SMC3-het, clone1


title: MOS6


title: U937_SMC3-2_6hr-10nM-H3B


title: Immortalised MEF cells, parental population 2

value: Immortalised mouse embryonic fibroblasts (MEFs)


title: h926_het_RA

value: Zfhx3 Het


title: D197

description:
HSC isolated from a young healthy donor.
Low input 3’ end RNA-Seq

source_name: young healthy donor HSC

value: Young


title: U937_SMC3-2_DMSO

value: 6h DMSO


title: B112, 0HR, Rep1

description:
B112_0HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: B112, 4HR, Rep1

description:
B112_4HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: IME1, 6HR, Rep3

description:
IME1_6HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: IME1; UME6(T99N)-3V5-aGFP


title: D196


title: U937_SMC3-1_DMSO


title: h917_het_LA


title: IME1, 4HR, Rep3

description:
IME1_4HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: B112, 6HR, Rep1

description:
B112_6HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: U937_SMC3-1_6hr-30nM-H3B


title: h916_het_RA


title: MOS3


title: D219


title: IME1, 2HR, Rep3

description:
IME1_2HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: B112, 2HR, Rep1

description:
B112_2HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: h916_het_LA


title: D218


title: IME1, 0HR, Rep3

description:
IME1_0HR_Rep3
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: h926_het_LA


title: D217


title: U937_A2-3_6hr-10nM-H3B

value: STAG2-KO2, clone 3


title: IME1, 6HR, Rep2

description:
IME1_6HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: U937_A2-1_6hr-30nM-H3B

value: STAG2-KO2, clone 1


title: w914_wt_LA

value: WT


title: h917_het_RA


title: IME1, 4HR, Rep2

description:
IME1_4HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: U937_A2-2_6hr-10nM-H3B

value: STAG2-KO2, clone 2


title: w913_wt_RA


title: D212

value: Healthy


title: IME1, 2HR, Rep2

description:
IME1_2HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: D214


title: w913_wt_LA

value: left atria

value: Cardiac


title: U937_A2-3_6hr-30nM-H3B


title: IME1, 0HR, Rep2

description:
IME1_0HR_Rep2
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: Meiotic


title: U937_A2-2_6hr-30nM-H3B


title: D209


title: U937_A2-3_DMSO


title: IME1, 6HR, Rep1

description:
IME1_6HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: w911_wt_RA

value: right atria


title: U937_A2-2_DMSO


title: D208

value: HSC


title: RNA-Seq BSC, CDH, rep3

description: BSC, CDH, rep3

value: Lung

value: Basal stem cell


title: w911_wt_LA


title: w914_wt_RA


title: D207


title: IME1, 4HR, Rep1

description:
IME1_4HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: U937_A2-1_DMSO


title: D216


title: input control adult mouse cortex animal no. 9

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

institute: McGill University

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FASTQ files were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Trimmed FASTQ files were aligned to hg38 reference genome using bowtie239 v2.4.5 with default parameters.
SAM files were converted to BAM format and unmapped reads were removed with samtools v1.16.1
BAM files were sorted and duplicates were marked with Picard tools v2.18.29 and indexed with samtools.
Significant peaks were identified with the callpeak function from macs2 v2.2.7.1 using the respective input sequencing data for each sample as control and precompiled values for the mappable human genome size.
Assembly: mm39
Supplementary files format and content: narrowPeak (except for input samples)

source_name: cortex

growth_protocol: Surgically excised cerebral cortices of wild-type adult (14 weeks) C57BL/6J female mice were purchased from the Jackson Laboratory and shipped frozen.

extract_protocol:
Chromatin immunoprecipitation of mouse cortices was performed with the ChIP-IT High Sensitivity® Kit (Active Motif, cat. no 53040) according to the manufacturer’s protocol. Frozen mouse cortices were cut into ~1 mm cubes in 10 mL Complete Tissue Fixation Solution in a 100-mm petri dish and incubated, with rotation, at room temperature for 15. The reaction was quenched with 515 µL Stop Solution followed by incubation at room temperature for 5 minutes. The cross-linked tissues were then homogenized by passing the suspension 20 times through a 20-guage needle attached to a sterile plastic syringe. The tissues were pelleted by centrifugation at 1,250 x g for 3 min at 4  °C and pellets were washed twice with 10 mL ice-cold PBS Wash Buffer. Washed pellets were resuspended in 5 mL Chromatin Prep Buffer supplemented with 5 µL protease inhibitor cocktail (PIC) and 5 µL 100 µM PMSF,  incubated on ice for 10 minutes, and homogenized again to lyse cell membranes. Nuclei were pelleted by centrifugation as before, resuspended in 1 mL ChIP buffer, incubated for 10 min on ice, and sonicated in a Bioruptor (Diagenode) sonicator in 200 µL aliquots, each receiving 6 10-min rounds of sonication at high power (30 sec on / 30 sec off). Sonicated samples were clarified by centrifugation for 2 minutes at 4  °C at 16,000 x g and stored at -80 °C. Input DNA was prepared as follows: 25 µL was removed and purified according to the manufacturer’s protocol (briefly, RNAse A treatment, Proteinase K treatment, addition of NaCl and reverse cross-linking at 65 °C for 16 hours, and purification by phenol:chloroform and ethanol extraction) and quantified using a NanoDrop spectrophotometer. 30 µg sheared chromatin was immunoprecipitated overnight at 4 °C by dilution in 200 µL ChIP Buffer supplemented with 5 µL PIC and incubation with 4 µg antibody with 5 µL Blocker. 30 µL washed Protein G agarose beads were added to the reaction and incubated for 3 h. The reactions were then diluted by the addition of 600 µL ChIP buffer and added to ChIP filtration columns, washed 5 times with Wash Buffer AM1, and eluted in 100 µL Elution Buffer AM4. ChIP DNA was purified in the same manner as input DNA and in 36 µL elution volume for ChIP-sequencing.
Libraries were generated from 25 µL of fragmented DNA (range 100-300 bp) using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies (IDT). Size selection was carried out using SparQ beads (QIAGEN) prior to PCR amplification (12 cycles). Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average fragment size was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized, pooled, and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 175 pM (HEK293 cells) or 200pM (mouse cortices) on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

tag: animal

value: animal no. 9

value: cortex

value: female

value: 14 weeks

tag: chip antibody

value: wild-type


title: IME1, 2HR, Rep1

description:
IME1_2HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue

value: IME1; UME6(T99N)-3V5-aGFP


title: D204

value: Young


title: U937_A1-2_6hr-30nM-H3B

value: STAG2-KO1, clone 2

tag: treatment


title: IME1, 0HR, Rep1

description:
IME1_0HR_Rep1
gene_count_matrix_Ume6T99N_TransAD_Rescue


title: input control adult mouse cortex animal no. 7

value: animal no. 7


title: U937_A2-1_6hr-10nM-H3B

tag: cell line

value: STAG2-KO2, clone 1


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6(T99N)-3V5-aGFP


title: U937_A1-1_6hr-30nM-H3B

value: STAG2-KO1, clone 1


title: U937_A1-2_6hr-10nM-H3B


title: input control adult mouse cortex animal no. 5

value: animal no. 5


title: TDG ChIP-seq adult mouse cortex animal no. 9

value: TDG (Proteintech 13370-1-AP)


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: D202

description:
HSC isolated from a young healthy donor.
Low input 3’ end RNA-Seq

value: Healthy

tag: cell type

value: HSC


title: U937_A1-1_6hr-10nM-H3B


title: D200


title: D199


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: TDG ChIP-seq adult mouse cortex animal no. 5

tag: tissue


title: TDG ChIP-seq adult mouse cortex animal no. 7


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: U937_A1-2_DMSO

value: 6h DMSO


title: U937_A1-1_DMSO


title: MBD3 ChIP-seq adult mouse cortex animal no. 9

value: animal no. 9

value: cortex

value: MBD3 (Abcam ab157464)


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: D198


title: MBD3 ChIP-seq adult mouse cortex animal no. 7

value: female

value: 14 weeks

value: wild-type


title: U937_WT-3_6hr-30nM-H3B

value: nontargeting guide 2, clone 1


title: U937_WT-2_6hr-30nM-H3B

value: nontargeting guide 1, clone 2


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: THP-1-libA T7 Control

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

data_processing: Cells were transfected with MS2-P65-HSF-Hygro lentivirus and selected with 500 μg/mL hygromycin B (Invitrogen) for 120 h. Then, the sgRNA-dCas9-VP64-blasticidin lentivirus was added to the infected cells and passaged for 2 days. The cells were treated with 4 μg/mL blasticidin (Sigma-Aldrich) for 5 days, and the uninfected control cells were completely killed. After setting aside as a Day 0 baseline for sequencing, the THP-1 cells were then divided into two groups, one that was free to grow and the other that was given constant low doses of IDA treatment. The screening process lasted 7 days.

source_name: AML cells

extract_protocol:
sgRNA assays data analysis was performed as previously described (Julia Joung et al., 2017). In brief, genomic DNA quality was assessed by Uv absorption spectrum, Qubit DNA quantification and Agilent 4150 Tapestation System after extraction from the samples. The genomic DNA library was prepared using the CRISPR2 "Self-balancing library preparation technique" and "Non-bias sgRNA fragment capture technique" developed by Gikegiin. After the completion of PCR library construction, 0.4x and 0.8x AMPure Beads were used to purify product DNA to remove residual primer, template and other sequencing interferences. Agilent 4150 TapeStation High Sensitive D1000 Assay was used to evaluate library quality. The mixed library was sequenced by Illumina HiSeq X and decomposed into each sample data using index sequence. SgRNA reads were obtained from one-way reads and then compared with sgRNA library sequences. Data containing sgRNA are obtained in turn. After illumina sequencing, all the data were visualized using R version 4.0.2 (R development core team).
RNA libraries were prepared for sequencing using standard Illumina protocols
sgRNA  sequencing

treatment_protocol: For CRISPR-PoolTM SAM Screening, cells were transfected with MS2-P65-HSF-Hygro lentivirus and selected with 500 μg/mL hygromycin B (Invitrogen) for 120 h. Then, the sgRNA-dCas9-VP64-blasticidin lentivirus was added to the infected cells and passaged for 2 days. The cells were treated with 4 μg/mL blasticidin (Sigma-Aldrich) for 5 days, and the uninfected control cells were completely killed. After setting aside as a Day 0 baseline for sequencing, the THP-1 cells were then divided into two groups, one that was free to grow and the other that was given constant low doses of IDA treatment. The screening process lasted 7 days.

value: THP-1 cells

value: AML


title: THP-1-libB T7 Control


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6(T99N)-3V5-aGFP


title: THP-1-libB T0


title: D201

value: Young


title: RNA polymerase II phospho serine 5 ChIP-seq adult mouse cortex animal no. 9

value: RNA pol II phosphoSer5 (Abcam ab5408)


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: U937_WT-2_6hr-10nM-H3B


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: RNA polymerase II phospho serine 5 ChIP-seq adult mouse cortex animal no. 7

value: animal no. 7


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: H3K4me1 ChIP-seq adult mouse cortex animal no. 9

value: H3K4me1 (Abcam ab176877)


title: U937_WT-1_6hr-10nM-H3B

value: nontargeting guide 1, clone 1


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


description:
sfGFP-IME1, Ume6(T99N)-3v5-aGFP,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: MBD3 ChIP-seq adult mouse cortex animal no. 5

value: animal no. 5


title: H3K4me1 ChIP-seq adult mouse cortex animal no. 7

value: cortex


title: U937_WT-2_DMSO

value: 6h DMSO


title: RNA polymerase II phospho serine 5 ChIP-seq adult mouse cortex animal no. 5

value: female


title: U937_WT-1_DMSO


title: BaP_THP1cocultured with A459_rep3

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 human whole genome using CLC Software (Genomics Workbench v.11)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated directly by the CLC Software (Genomics Workbench v. 11)
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: cell line

extract_protocol:
Total RNA was harvested using QIAGEN® – RNA purification kit. TruSeq stranded mRNA Sample Preparation kit was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA Sample Preparation protocol

tag: cell composition

value: Non differentiated THP1

tag: culture conditions

value: Submerged

value: BaP 48h but cocultured


title: Control_THP1cocultured with A459_rep3

value: no treatment but cocultured


title: BaP_THP1cocultured with A459_rep2


title: sfGFP-IME1,  Ume6(T99N)-3v5,  4HR,  Rep3

description:
sfGFP-IME1, Ume6(T99N)-3v5,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6(T99N)-3V5


title: H3K27ac ChIP-seq adult mouse cortex animal no. 9

value: animal no. 9

tag: Sex

value: 14 weeks

value: H3K27ac (Abcam ab4729)

value: wild-type


title: decidualized hESCs, 12-2DD4

first: Tingting

last: Zhou

address: 157 Jingliu Road

institute: Shandong

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.   The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hESCs, 12-2DD4

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: human endometrial stromal cells

tag: cell state

value: induced decidualization


title: Control_THP1cocultured with A459_rep2


title: U937_WT-3_6hr-10nM-H3B

value: nontargeting guide 2, clone 1


title: Control_THP1cocultured with A459_rep1


title: BaP_THP1cocultured with A459_rep1


title: H3K27ac ChIP-seq adult mouse cortex animal no. 7

value: animal no. 7


title: THP-1-libA T0

value: THP-1 cells

value: AML


title: sfGFP-IME1,  Ume6(T99N)-3v5,  2HR,  Rep3

description:
sfGFP-IME1, Ume6(T99N)-3v5,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: U937_WT-3_DMSO

value: 6h DMSO


title: H3K27ac ChIP-seq adult mouse cortex animal no. 5

value: animal no. 5

value: cortex

value: female


title: BaP-48h_THP1_rep3

value: Non differentiated THP1

value: Submerged

value: BaP 48h


title: decidualized hESCs, NCDD4

source_name: hESCs, NCDD4

value: si-NC


title: BaP-48h_THP1_rep2


title: sfGFP-IME1,  Ume6(T99N)-3v5,  0HR,  Rep3

description:
sfGFP-IME1, Ume6(T99N)-3v5,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6(T99N)-3V5


title: decidualized hESCs, 12-2CD4

source_name: hESCs, 12-2CD4


title: sfGFP-IME1,  Ume6(T99N)-3v5,  6HR,  Rep3

description:
sfGFP-IME1, Ume6(T99N)-3v5,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: H3K4me1 ChIP-seq adult mouse cortex animal no. 5

value: 14 weeks

value: H3K4me1 (Abcam ab176877)

value: wild-type


title: decidualized hESCs, NCCD4

source_name: hESCs, NCCD4

value: human endometrial stromal cells

value: induced decidualization


title: BaP-48h_THP1_rep1


title: APOBEC-seq of input DNA from adult mouse cortex animal no. 7

data_processing:
Base calling was performed with RTA v3.4.4.
The program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FASTQ files were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Reads were aligned to mouse (GRCm39) reference genomes using bismark v0.23.1 with default parameters.
Bismark alignments were processed by Bismark deduplication and methylation extractor scripts.
Assembly: GRCm39
Supplementary files format and content: Bismark deduplicated coverage files.
Library strategy: APOBEC-seq

extract_protocol:
Chromatin immunoprecipitation of mouse cortices was performed with the ChIP-IT High Sensitivity® Kit (Active Motif, cat. no 53040) according to the manufacturer’s protocol. Frozen mouse cortices were cut into ~1 mm cubes in 10 mL Complete Tissue Fixation Solution in a 100-mm petri dish and incubated, with rotation, at room temperature for 15. The reaction was quenched with 515 µL Stop Solution followed by incubation at room temperature for 5 minutes. The cross-linked tissues were then homogenized by passing the suspension 20 times through a 20-guage needle attached to a sterile plastic syringe. The tissues were pelleted by centrifugation at 1,250 x g for 3 min at 4  °C and pellets were washed twice with 10 mL ice-cold PBS Wash Buffer. Washed pellets were resuspended in 5 mL Chromatin Prep Buffer supplemented with 5 µL protease inhibitor cocktail (PIC) and 5 µL 100 µM PMSF,  incubated on ice for 10 minutes, and homogenized again to lyse cell membranes. Nuclei were pelleted by centrifugation as before, resuspended in 1 mL ChIP buffer, incubated for 10 min on ice, and sonicated in a Bioruptor (Diagenode) sonicator in 200 µL aliquots, each receiving 6 10-min rounds of sonication at high power (30 sec on / 30 sec off). Sonicated samples were clarified by centrifugation for 2 minutes at 4  °C at 16,000 x g and stored at -80 °C. Input DNA was prepared as follows: 25 µL was removed and purified according to the manufacturer’s protocol (briefly, RNAse A treatment, Proteinase K treatment, addition of NaCl and reverse cross-linking at 65 °C for 16 hours, and purification by phenol:chloroform and ethanol extraction) and quantified using a NanoDrop spectrophotometer. 30 µg sheared chromatin was immunoprecipitated overnight at 4 °C by dilution in 200 µL ChIP Buffer supplemented with 5 µL PIC and incubation with 4 µg antibody with 5 µL Blocker. 30 µL washed Protein G agarose beads were added to the reaction and incubated for 3 h. The reactions were then diluted by the addition of 600 µL ChIP buffer and added to ChIP filtration columns, washed 5 times with Wash Buffer AM1, and eluted in 100 µL Elution Buffer AM4. ChIP DNA was purified in the same manner as input DNA and in 36 µL elution volume for ChIP-sequencing.
Libraries were generated from 200 ng fragmented input or 3.5-200 ng ChIP DNA using the NEBNext® Enzymatic Methyl-seq Kit (NEB, cat. no. E7120L) with some modifications to the manufacturer’s protocol. End prep and ligation of EM-seq adapter ligation were performed as per the manufacturer’s protocol except that the NEBNext EM-seq Adapter was substituted with 5hmC Adapter provided as a gift by NEB: this is critical as methylated NEBNext Em-seq Adapters included with the kit are not resistant to APOBEC-conversion alone. Cleanup after adapter ligation was performed with NEBNext Sample Purification Beads as per manufacturer’s protocol but elution volume was reduced to 17 µL for compatibility with the modified protocol. The TET2 oxidation step of the NEBNext® Enzymatic Methyl-seq Kit protocol was then skipped and 16 µL eluant was used directly for the APOBEC conversion (denaturation and deamination) steps. Denaturation with formamide, deamination with APOBEC, cleanup, PCR amplification, and final cleanup steps were performed according to the manufacturer’s protocol. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x150 cycles (HEK293 cells) or 2x100 cycles (mouse cortices) (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

value: animal no. 7

value: APOBEC conversion of DNA


title: APOBEC-seq of input DNA from adult mouse cortex animal no. 9

value: animal no. 9


title: sfGFP-IME1,  Ume6(T99N)-3v5,  4HR,  Rep2

description:
sfGFP-IME1, Ume6(T99N)-3v5,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: sfGFP-IME1,  Ume6(T99N)-3v5,  6HR,  Rep2

description:
sfGFP-IME1, Ume6(T99N)-3v5,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1,  Ume6(T99N)-3v5,  2HR,  Rep2

description:
sfGFP-IME1, Ume6(T99N)-3v5,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: APOBEC-seq of input DNA from adult mouse cortex animal no. 5

value: animal no. 5


title: EGFRI

city: Zunyi

first: Juan

middle: Juan

last: Zhao

state: Guizhou

address: 6 Xuefu west Road

institute: Zunyi medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.   FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: human colonic epithelial cell FHC cells

value: colon

value: colonic epithelial cell FHC cells

tag: disease state

value: LPS-induced FHC cells

value: Erlotinib plus miR-7 inhibitor-transfected


title: Control_THP1_rep3

value: Non differentiated THP1

value: Submerged

value: no treatment


title: In2

value: miR-7 inhibitor-transfected


title: APOBEC-seq of RNA polymerase II phospho Serine 5 ChIP DNA from adult mouse cortex animal no. 9

value: cortex

value: female

value: 14 weeks

value: RNA pol II phosphoSer5 (Abcam ab5408)

tag: genotype

value: APOBEC conversion of ChIP DNA


title: sfGFP-IME1,  Ume6(T99N)-3v5,  0HR,  Rep2

description:
sfGFP-IME1, Ume6(T99N)-3v5,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

data_processing:
Sequencing reads were mapped to a reference genome using HISAT2, samtools, and Stringtie
Mapped reads were visualized to IGV_2.12.3.app
Counts and TPM tables were generated from sequencing reads using pseudoalignment with kallisto
Assembly: SK1 Reference Genome from Saccharomyces Genome Resequencing Project at Sanger Institute
Supplementary files format and content: Excel tables include counts and TPMs for each sample.

value: sfGFP-IME1; UME6(T99N)-3V5

tag: time


title: Control_THP1_rep2


title: Control_THP1_rep1


title: APOBEC-seq of RNA polymerase II phospho Serine 5 ChIP DNA from adult mouse cortex animal no. 7

value: animal no. 7

value: wild-type


title: sfGFP-IME1,  Ume6(T99N)-3v5,  6HR,  Rep1

description:
sfGFP-IME1, Ume6(T99N)-3v5,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

tag: condition

value: Meiotic


title: N2

value: colon

value: miR-7 inhibitor Negative Control-transfected


title: In1

value: colonic epithelial cell FHC cells

value: LPS-induced FHC cells


title: sfGFP-IME1,  Ume6(T99N)-3v5,  4HR,  Rep1

description:
sfGFP-IME1, Ume6(T99N)-3v5,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: C57BL/6 mice injected with adapted cells, bio rep 3

city: Seoul

first: Yoo Hyung

last: Kim

address: Jongro-gu 101

country: South Korea

institute: Seoul national University Hospital

data_processing:
HiSeq2000 (Illumina)
FastQC
HISAT2
Cuffnorm
Cuffdiff
Assembly: mm10
Supplementary files format and content: comma-seperated values
Supplementary files format and content: comma-seperated values

source_name: Cancer

extract_protocol:
Rnaeasy mini plus kit (Qiagen)
Total RNA was used to construct cDNA libraries with the TrueSeq RNA library kit

value: Cancer

value: adapted TBP3743

value: Cancer epithelial cell


title: N1


title: sfGFP-IME1,  Ume6(T99N)-3v5,  2HR,  Rep1

description:
sfGFP-IME1, Ume6(T99N)-3v5,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

extract_protocol:
RNA was harvested using phenol chloroform precipitation and DNA was cleared using TURBO DNA-free kit (Thermo Fisher) according to manufacturer’s protocol.
RNA libraries were prepared for RNA-Seq using NEXTFLEX Rapid Direction RNA-seq kit (PerkinElmer) according to the provided manual.


title: APOBEC-seq of H3K4me1 ChIP DNA from adult mouse cortex animal no. 9

value: animal no. 9

value: H3K4me1 (Abcam ab176877)


title: C57BL/6 mice injected with adapted cells, bio rep 2


title: C57BL/6 mice injected with adapted cells, bio rep 1


title: APOBEC-seq of H3K4me1 ChIP DNA from adult mouse cortex animal no. 7

value: cortex

value: female


title: sfGFP-IME1,  Ume6(T99N)-3v5,  0HR,  Rep1

description:
sfGFP-IME1, Ume6(T99N)-3v5,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: BMI1-KO rep2

city: Ann Arbor

first: Filip

last: Bednar

address: 1500 E Medical Center Dr

institute: University of Michigan

data_processing:
Sample reads were aligned with HISAT2 v2.2.0 using prebuilt index of Homo sapiens UCSC reference genome hg38 obtained from http://daehwankimlab.github.io/hisat2/download/
Conversion of the aligned files to BAM format was done with SAMtools v1.10.
Gene assembly and quantification was done with Stringtie 2.1.1
Counts obtained from duplicated genes were averaged
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A matrix of gene counts

source_name: Pancreatic cancer cell line

growth_protocol: A CRISPR/Cas9 strategy was used to delete Bmi1 in human primary pancreatic cancer cells, and clonal lines were created. BMI1 knockout was confirmed using Western blot. Wild type control and Bmi1 knockout cells were grown in vitro in RPMI with 10% FBS.

extract_protocol:
Cells were plated in vitro and allowed to grow for 48 hours. RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) with an on-column DNase treatment using the RNase-Free DNase Set (Qiagen), according to the manufacturer’s instructions.
RNA libraries were prepared using standard procedures per Illumina protocols

treatment_protocol: WT and Bmi1 KO human primary pancreatic cancer cells were plated

value: pancreas

value: knockout


title: APOBEC-seq of H3K4me1 ChIP DNA from adult mouse cortex animal no. 5

value: animal no. 5

value: 14 weeks

value: APOBEC conversion of ChIP DNA


title: sfGFP-IME1, Ume6-3v5,  6HR,  Rep3

description:
sfGFP-IME1, Ume6-3v5,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6-3V5

value: Meiotic


title: BMI1-KO rep1


title: B6129SF1 mice injected with adapted cells, bio rep 2


title: sfGFP-IME1, Ume6-3v5,  4HR,  Rep3

description:
sfGFP-IME1, Ume6-3v5,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: APOBEC-seq of H3K27ac ChIP DNA from adult mouse cortex animal no. 9

value: H3K27ac (Abcam ab4729)

value: wild-type


title: WT rep3

value: wild type


title: B6129SF1 mice injected with adapted cells, bio rep 1

value: Cancer


title: B6129SF1 mice injected with original TBP3743 cells, bio rep 3

value: original TBP3743


title: APOBEC-seq of H3K27ac ChIP DNA from adult mouse cortex animal no. 7

value: animal no. 7


title: WT rep2


title: sfGFP-IME1, Ume6-3v5,  2HR,  Rep3

description:
sfGFP-IME1, Ume6-3v5,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1, Ume6-3v5,  0HR,  Rep3

description:
sfGFP-IME1, Ume6-3v5,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: B6129SF1 mice injected with original TBP3743 cells, bio rep 2

value: Cancer epithelial cell


title: WT rep1


title: APOBEC-seq of RNA polymerase II phospho Serine 5 ChIP DNA from adult mouse cortex animal no. 5

value: RNA pol II phosphoSer5 (Abcam ab5408)


title: APOBEC-seq of H3K27ac ChIP DNA from adult mouse cortex animal no. 5

value: cortex


title: BMI1-KO rep3


title: sfGFP-IME1, Ume6-3v5,  6HR,  Rep2

description:
sfGFP-IME1, Ume6-3v5,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: B6129SF1 mice injected with original TBP3743 cells, bio rep 1


title: sfGFP-IME1, Ume6-3v5,  4HR,  Rep2

description:
sfGFP-IME1, Ume6-3v5,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: B6129SF1 mice injected with adapted cells, bio rep 3

value: adapted TBP3743


title: M-KO-Con3, Male

city: Shijiazhuang

first: zhao

last: Wang

address: 361 Zhongshan East Road, Yuca Street

institute: Hebei medical university

data_processing:
The sequencing data generated by Illumina NovaSeq6000 is rawsequencing data, and the rawsequencing data is controlled by FastQC for sequencing quality.
After quality control, the reference genome was compared with Hisat2 software.
The StringTie software uses official database annotation information to estimate transcript abundance
The Ballgown package of R software was used to calculate Fragments Per Kilobase of gene model Per Million mapped fragments (FPKM) at the gene level, as well as to calculate differences in expression at the gene level to screen differentially expressed genes (DEGs) between samples or between groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: The animals were housed in the experimental animal center and maintained on a 12-hour light and dark cycle with ad libitum food and water.

extract_protocol:
Total RNA was extracted from hippocampal tissues using TRIzol reagent.   1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hippocampus

value: Male

value: Fmr1 knockdown


title: 293-WT_SnxB_3d_Rep3 [Batch 2]

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, Experiment 3, biological replicate-#3

growth_protocol: 293-WT and 293-dKO cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 5x10^4 cells per well.  24 hours post seeding, cells were treated as indicated.

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using Illumina TruSeq Stranded mRNA prep kit or NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Cells were treated with vehicle control (0.1% DMSO) or 1 μM Senexin B for 24 or 72 hours.

value: 293-WT cells

tag: agent

value: 1microM Senexin B

tag: time point

value: 3 days


title: M-KO-Con2, Male


title: M-KO-Con5, Male


title: sfGFP-IME1, Ume6-3v5,  0HR,  Rep2

description:
sfGFP-IME1, Ume6-3v5,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

tag: strain

value: sfGFP-IME1; UME6-3V5

value: Meiotic


title: M-KO-Con4, Male


title: 293-WT_SnxB_3d_Rep1 [Batch 2]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, Experiment 3, biological replicate-#1


title: sfGFP-IME1, Ume6-3v5,  2HR,  Rep2

description:
sfGFP-IME1, Ume6-3v5,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: 293-WT_SnxB_3d_Rep2 [Batch 2]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, Experiment 3, biological replicate-#2


title: 293-WT_Ctrl_3d_Rep3 [Batch 2]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, Experiment-3, biological replicate-#3

value: 0.1percent DMSO (vehicle control)


title: M-KO-Con1, Male


title: 293-WT_Ctrl_3d_Rep2 [Batch 2]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, Experiment-3, biological replicate-#2


title: sfGFP-IME1, Ume6-3v5,  6HR,  Rep1

description:
sfGFP-IME1, Ume6-3v5,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1, Ume6-3v5,  2HR,  Rep1

description:
sfGFP-IME1, Ume6-3v5,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: M-C57-Con4, Male

value: WT


title: M-C57-Con5, Male


title: 293-WT_Ctrl_3d_Rep1 [Batch 2]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, Experiment-3, biological replicate-#1


title: sfGFP-IME1, Ume6-3v5,  0HR,  Rep1

description:
sfGFP-IME1, Ume6-3v5,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: M-C57-Con3, Male


title: 293-WT_SnxB_24h_Rep3 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 2, biological replicate-#3

value: 24 hours


title: sfGFP-IME1, Ume6-3v5,  4HR,  Rep1

description:
sfGFP-IME1, Ume6-3v5,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: 293-WT_SnxB_24h_Rep2 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 2, biological replicate-#2


title: M-C57-Con2, Male


title: sfGFP-IME1,  6HR,  Rep3

description:
sfGFP-IME1,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6


title: X10.DRB

city: Chuo-ku

first: Bunsyo

last: Shiotani

state: Tokyo

address: 5-1-1 Tuskiji

department: Research Institute

country: Japan

institute: National Cancer Center

data_processing:
Single-end sequenced reads were checked by FastQC.
Mapping was performed using Kallisto (ver. 0.46.0).
The expression matrix was constructed and normlized by tximport package (ver. 1.18.0)
Assembly: hg19
Supplementary files format and content: GEO_processed _data_BS.txt

source_name: Lung

growth_protocol: SAECs (human small airway epithelial cells) were immortalized via expression of hTERT, CDK4 mutants, and cyclin D1, and retrovirally established 4-hydroxytamoxifen (4OHT)-induced KRASG12V. SAECs  cell lines were cultured in BronchiaLife™ Epithelial Basal Medium (Lifeline Cell Technology) supplemented with the components of a LifeFactors® Kit (Lifeline Cell Technology). All cells were cultured at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated by an RNeasy mini kit (Qiagen, Germany) from each cell lysate according to the manufacturer's protocol
Strand-specific method to incorporate dUTP during synthesis of 2nd cDNA strand
DNBSEQ 2x150 bp

treatment_protocol: SAEC cells treated with 0.1 μM of 4OHT (Abcam)  for 3 days to induce KRASG12V. 100 μM of DRB was added for 1.5h before harvesting.

value: Lung

value: SAEC

value: human normal lung epithelial cells

value: KRAS-induced with DRB treatment


title: X2.non

value: KRAS-induced


title: sfGFP-IME1,  2HR,  Rep3

first: Anthony

last: Harris

address: 622 Barker Hall

institute: UC Berkeley

description:
sfGFP-IME1,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1,  4HR,  Rep3

description:
sfGFP-IME1,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: 293-WT_SnxB_24h_Rep1 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 2, biological replicate-#1


title: F-KO-Con5, Female

value: hippocampus

value: Female


title: single cell Plasma cell  [96.3]

city: PARIS

first: Marion

last: Espeli

address: 1 avenue Claude Vellefaux, Inserm U1160, Institut de Recherche Saint Louis

institute: Inserm U1160

library_source: transcriptomic single cell

data_processing:
Reads adapters were trimmed using trim_galore, with parameters --paired --nextera --quality 20 --stringency 3 --length 20
Reads were mapped using STAR (v2.4) with default parameters. Only primary alignment and properly mapped read pairs were kept.
Read count were obtained with featureCounts, counts only reads pairs with fragment length < 2000 , excluding chimeric reads.
Assembly: mm10 + ERCC
Supplementary files format and content: full counttable 1 geo
Supplementary files format and content: rawcount2 geo

source_name: Bone marrow

extract_protocol:
RNA was extracted on C1 array in presence of spike-in (Invitrogen) to normalize gene expression
cDNA-seq libraries have been prepared using the Illumina Nextera XT DNA Prep Kit which employs a transposon to shear genomic DNA and simultaneously introduce adapter sequences

value: Bone marrow

value: Plasma cell


title: 293-WT_Ctrl_24h_Rep3 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-2, biological replicate-#3

value: 293-WT cells

value: 72 hours


title: sfGFP-IME1,  0HR,  Rep3

description:
sfGFP-IME1,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [95.3]


title: F-KO-Con3, Female

value: Fmr1 knockdown


title: F-KO-Con4, Female


title: sfGFP-IME1,  6HR,  Rep2

description:
sfGFP-IME1,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: single cell Plasma cell  [94.3]


title: M-C57-Con1, Male

value: Male


title: 293-WT_Ctrl_24h_Rep2 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-2, biological replicate-#2

value: 0.1percent DMSO (vehicle control)


title: F-KO-Con2, Female


title: 293-WT_Ctrl_24h_Rep1 [Batch 3]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-2, biological replicate-#1

value: 24 hours


title: 293-dKO_SnxB_24h_Rep3

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1,  biological replicate-#3

value: 293-dKO cells

value: 1microM Senexin B


title: F-KO-Con1, Female


title: sfGFP-IME1,  2HR,  Rep2

description:
sfGFP-IME1,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6


title: sfGFP-IME1,  0HR,  Rep2

description:
sfGFP-IME1,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: F-C57-Con5, Female

value: WT


title: single cell Plasma cell  [92.3]


title: single cell Plasma cell  [89.3]


title: 293-dKO_SnxB_24h_Rep2

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1,  biological replicate-#2


title: single cell Plasma cell  [81.3]


title: 293-dKO_Ctrl_24h_Rep3

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 24 hrs, Experiment 1, biological replicate-#3


title: sfGFP-IME1,  4HR,  Rep2

description:
sfGFP-IME1,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1,  6HR,  Rep1

description:
sfGFP-IME1,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: sfGFP-IME1,  4HR,  Rep1

description:
sfGFP-IME1,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: 293-dKO_SnxB_24h_Rep1

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1,  biological replicate-#1


title: F-C57-Con3, Female

source_name: hippocampus


title: F-C57-Con4, Female


title: single cell Plasma cell  [86.3]


title: 293-dKO_Ctrl_24h_Rep2

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 24 hrs, Experiment 1, biological replicate-#2


title: F-C57-Con2, Female


title: single cell Plasma cell  [76.3]


title: U937_WT-1_6hr-30nM-H3B

city: Boston

source_name: U937 cells

value: nontargeting guide 1, clone 1


title: sfGFP-IME1,  0HR,  Rep1

description:
sfGFP-IME1,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: F-C57-Con1, Female


title: 293-dKO_Ctrl_24h_Rep1

source_name: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 24 hrs, Experiment 1, biological replicate-#1


title: single cell Plasma cell  [71.2]


title: 293-WT_SnxB_24h_Rep3 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1, biological replicate-#3


title: Ume6(T99N)-3v5-aGFP,  6HR,  Rep3

description:
Ume6(T99N)-3v5-aGFP,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: IME1; UME6(T99N)-3V5-aGFP


title: ATMs, KO 3

city: Nashville

first: Heather

last: Pua

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt Medical Center

description:
Table S1-Normalized gene counts.txt
Table S2-DESeq2 analysis.txt

data_processing:
For pipeline details please see https://github.com/parkdj1/RNASeq-Pipeline
FastQC was used to quality control data
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to mouse genome using Salmon
Read count extraction and normalization were performed using DESeq2
Assembly: mm10
Supplementary files format and content: Normalized counts and log2FC

source_name: obese adipose tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). ~0.5-1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) selection kit by the Vanderbilt Technologies for Advanced Genomics Core

treatment_protocol:
Control mice and mice containing a myeloid-specific deletion of the clusters on high-fat diet for 20 weeks.
Adipose tissue macrophages from obese control or knockout adipose tissue were isolated via F4/80-positive selction

value: obese adipose tissue

value: primary F4/80+ macrophage

value: Mirc11fl/fl  Mirc22fl/fl Lyz2Cre/Cre

value: High-fat diet feeding

value: 20 wks


title: Ume6(T99N)-3v5-aGFP,  4HR,  Rep3

city: Berkeley

description:
Ume6(T99N)-3v5-aGFP,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [68.3]

value: Bone marrow

value: Plasma cell


title: ATMs, KO 4


title: Ume6(T99N)-3v5-aGFP,  2HR,  Rep3

description:
Ume6(T99N)-3v5-aGFP,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: ATMs, KO 2


title: single cell Plasma cell  [63.3]


title: single cell Plasma cell  [66.3]


title: 293-WT_SnxB_24h_Rep1 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1, biological replicate-#1

value: 293-WT cells


title: 293-WT_Ctrl_24h_Rep3 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-1, biological replicate-#3

value: 0.1percent DMSO (vehicle control)

value: 72 hours


title: ATMs, KO 1


title: 293-WT_SnxB_24h_Rep2 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 1, biological replicate-#2

value: 24 hours


title: LiCl only N1

type: genomic

city: Solna Stockholm

first: Christina

last: Neofytou

address: Tomtebodavägen 16, 32B

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: 3mM LiCl treated

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting.

data_processing: DNA samples were sent to Bioinformatics and Expression Analysis (BEA) Core Facility, Karolinska Institute, for methylation array analysis. Single CpG sites were examined for changes in methylation status using Illumina Infinium MethylationEPIC Bead Chip (n=2). Methylation values measured in b (b=1: 100% CpG methylation, b=0: 0% CpG methylation) were compared between conditions to generate a Δb value.

label: Cy5 and Cy3

source_name: iPSC-derived hNSPCs, 2D cultured, 3mM LiCl treated

label_protocol: Illumina protocol was followed

growth_protocol: Human induced pluripotent stem cell (iPSC)-derived hNSPCs were provided by the iPS Core Facility at Karolinska Institutet. Dermal fibroblasts procured from skin biopsies were reprogrammed into iPSCs using virus free synthetic mRNA (Stemgent, StemRNA 3rd Generation Reprogramming Kit Cat#00–0076) and pushed to hNSPC fate development following the Dual-SMAD inhibition protocol45. Neural rosettes were extracted and cultured in medium enriched with epidermal growth factor (EGF) and fibroblast growth factor-2 (FGF2). hNSPC cultures were grown in T12.5, T25 and T75 sterile flasks, coated with 10% Poly-L-Ornithine (Sigma-Aldrich, Cat#P4957) and 0.2% Laminin (Sigma-Aldrich, Cat#L2020), at 37°C in a 5% CO2-humidified incubator. Cells were cultured in Dulbecco’s Modified Eagle Medium: Nutrient mixture F-12 (DMEM/F12), GlutaMAX (Thermo Fisher Scientific, Cat# 10565018) supplemented with 1% Penicillin – Streptomycin (Pen/Strep) (10000 U, Life technologies, Cat# 15140-122), 1% N2 (100x, Life Technologies, Cat# 17502001), 0.1% B27 (50x, Life Technologies, Cat# 12587-010), 0.1% EGF (10ng/ml, R&D Systems, Cat# 236-EG), and 0.1% FGF2 (10ng/ul, R&D Systems, Cat# 233-FB). Growth factor supplementation maintained proliferative activity without differentiation. Half of the medium volume was changed daily, and cultures were split at 60-80% confluence every 3-4 days.

extract_protocol: DNA isolation was performed following the DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: Cells were seeded at 250,000 cells/well on pre-coated 12-well cell culture plates and expanded in medium overnight to approximately 60% confluence. Subsequently, cells were irradiated in an CIX2 Xstrahl X-Ray Irradiator with Aluminum filter at a focus-to-skin distance (FSD) of 40 cm and with an energy of 195kV, 10 mA for 2 minutes and 58 seconds, for a received dose of 4 Gray (4 GY). To allow for assessment of irradiation damage, cells remained in the incubator for 1 hour. Pre-warmed DMEM/F-12 was mixed with the appropriate amount of LiCl powder (Sigma-Aldrich, Cat# L9650-100G), passed through a 0.22 μm filter, and supplemented with 1% Penicillin-Streptomycin, 1% N2, 0.1% B27, 0.1% EGF, and 0.1% FGF2 to produce 3mM Lithium Chloride (LiCl) hNSPC medium.


title: Ume6(T99N)-3v5-aGFP,  6HR,  Rep2

description:
Ume6(T99N)-3v5-aGFP,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [47.3]

source_name: Bone marrow


title: single cell Plasma cell  [50.3]


title: ATMs, fl/fl 4

value: Mirc11fl/fl  Mirc22fl/fl Lyz2+/+


title: 293-WT_Ctrl_24h_Rep1 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-1, biological replicate-#1


title: single cell Plasma cell  [55.2]


title: ATMs, fl/fl 2


title: 293-WT-19M_Rep3

description:
Grown under regular culture condition, no treatment.
S57

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HEK293_dKO_WT_expression_derivatives_GeneCounts.txt: Space-delimited text file includes gene counts for each sample.

source_name: 293-WT-19M cells (WT cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#3

growth_protocol: HEK293 derivatives (dKO-V, dKO-8, dKO-8M, dKO-19, dKO-19M, dKO-V_2, dKO-8_2, dKO-8M_2, dKO-19_2, dKO-19M_2, WT-V, WT-8, WT-8M, WT-19 and WT-19M) were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent).
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit.

treatment_protocol: Cells were cultured in regular culture media and grown to 80~90% confluent before being lysed for RNA extraction.

value: HEK293 (ATCC)

value: No treatment


title: 293-WT_Ctrl_24h_Rep2 [Batch 1]

source_name: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, Experiment-1, biological replicate-#2


title: Ume6(T99N)-3v5-aGFP,  2HR,  Rep2

description:
Ume6(T99N)-3v5-aGFP,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: ATMs, fl/fl 3


title: IR+LiCl N2

description: 3mM LiCl treated + 4 GY irradiated

source_name: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated + 3mM LiCl treated


title: 293-WT-19M_Rep2

description:
Grown under regular culture condition, no treatment.
S56

source_name: 293-WT-19M cells (WT cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: Ume6(T99N)-3v5-aGFP,  0HR,  Rep2

description:
Ume6(T99N)-3v5-aGFP,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Ume6(T99N)-3v5-aGFP,  4HR,  Rep2

description:
Ume6(T99N)-3v5-aGFP,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Control N1

description: Control sample

source_name: iPSC-derived hNSPCs, 2D cultured, control


title: ATMs, fl/fl 1


title: single cell Plasma cell  [47.2]

value: WT


title: 293-WT-19M_Rep1

description:
Grown under regular culture condition, no treatment.
S55

source_name: 293-WT-19M cells (WT cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#1


title: Whole kidney, biol rep 4

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using bbduk from the bbmap package v38.69 (Bushnell 2015) and filtered for a minimum length of 17nt and phred quality of 30.
Alignment steps were performed with STAR v2.7 (Dobin et al. 2013) using samtools v1.9 (Li et al. 2009) for indexing, whereas reads were mapped against the genomic reference GRCm38.p6 provided by Ensembl (Zerbino et al. 2018).
Assignment of features to the mapped reads was done with htseq-count v0.13 (Anders, Pyl, and Huber 2015).
Assembly: GRCm39 Assembly GCA_000001635.9
Supplementary files format and content: CSV file containing gene read counts from featureCount

source_name: Kidney

extract_protocol: Lexogen Quantseq according to manufacturer's protocol

value: Kidney

tag: seks

value: male

tag: laser microdissected

value: No

tag: microvascular compartment

value: Whole kidney


title: IR only N2

description: 4 GY irradiated

source_name: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated

tag: treatment


title: IR+LiCl N1

description: 3mM LiCl treated + 4 GY irradiated

value: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated + 3mM LiCl treated


title: LiCl only N2

description: 3mM LiCl treated

value: iPSC-derived hNSPCs, 2D cultured, 3mM LiCl treated


title: Ume6(T99N)-3v5-aGFP,  6HR,  Rep1

description:
Ume6(T99N)-3v5-aGFP,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

value: IME1; UME6(T99N)-3V5-aGFP


title: Ume6(T99N)-3v5-aGFP,  0HR,  Rep3

description:
Ume6(T99N)-3v5-aGFP,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Control N2

description: Control sample

value: iPSC-derived hNSPCs, 2D cultured, control


title: single cell Plasma cell  [46.3]

value: Bone marrow

tag: cell type

value: Plasma cell


title: Whole kidney, biol rep 3

tag: tissue


title: 293-WT-19_Rep3

description:
Grown under regular culture condition, no treatment.
S54

source_name: 293-WT-19 cells (WT cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#3

tag: cell line


title: Ume6(T99N)-3v5-aGFP,  4HR,  Rep1

description:
Ume6(T99N)-3v5-aGFP,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: Whole kidney, biol rep 2


title: Ume6(T99N)-3v5-aGFP,  2HR,  Rep1

description:
Ume6(T99N)-3v5-aGFP,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [44.2]


title: 293-WT-19_Rep1

description:
Grown under regular culture condition, no treatment.
S52

source_name: 293-WT-19 cells (WT cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#1


title: 293-WT-8M_Rep3

description:
Grown under regular culture condition, no treatment.
S51

source_name: 293-WT-8M cells (WT cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#3


title: Ume6(T99N)-3v5-aGFP,  0HR,  Rep1

description:
Ume6(T99N)-3v5-aGFP,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: Post-capillary venules, biol rep 4

value: Yes

value: Post-capillary venules


title: Ume6(T99N)-3v5,  6HR,  Rep3

description:
Ume6(T99N)-3v5,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Post-capillary venules, biol rep 3


title: single cell Plasma cell  [39.2]


title: 293-WT-8M_Rep2

description:
Grown under regular culture condition, no treatment.
S50

source_name: 293-WT-8M cells (WT cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: 293-WT-8M_Rep1

description:
Grown under regular culture condition, no treatment.
S49

source_name: 293-WT-8M cells (WT cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#1


title: single cell Plasma cell  [35.3]


title: sfGFP-IME1,  2HR,  Rep1

description:
sfGFP-IME1,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

value: sfGFP-IME1; UME6


title: 293-WT-8_Rep3

description:
Grown under regular culture condition, no treatment.
S48

source_name: 293-WT-8 cells (WT cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#3

value: HEK293 (ATCC)


title: single cell Plasma cell  [35.2]


title: single cell Plasma cell  [44.3]


title: IR only N1

description: 4 GY irradiated

value: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated


title: Post-capillary venules, biol rep 1

value: WT


title: Ume6(T99N)-3v5,  2HR,  Rep3

description:
Ume6(T99N)-3v5,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Post-capillary venules, biol rep 2

value: Kidney


title: single cell Plasma cell  [34.3]


title: Ume6(T99N)-3v5,  6HR,  Rep2

description:
Ume6(T99N)-3v5,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Whole kidney, biol rep 1

value: male


title: single cell Plasma cell  [32.3]


title: 293-WT-8_Rep1

description:
Grown under regular culture condition, no treatment.
S46

source_name: 293-WT-8 cells (WT cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#1

value: No treatment


title: single cell Plasma cell  [39.3]

source_name: Bone marrow


title: Ume6(T99N)-3v5,  4HR,  Rep3

description:
Ume6(T99N)-3v5,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Peritubular capillaries, biol rep 3

value: Peritubular capillaries


title: Ume6(T99N)-3v5,  4HR,  Rep2

description:
Ume6(T99N)-3v5,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [30.3]


title: Ume6(T99N)-3v5,  2HR,  Rep2

description:
Ume6(T99N)-3v5,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Peritubular capillaries, biol rep 2


title: single cell Plasma cell  [26.2]


title: 293-WT-V_Rep2

description:
Grown under regular culture condition, no treatment.
S44

source_name: 293-WT-V cells (WT cells transduced with pHIV-Luc-Blast control vector), biological replicate-#2


title: Ume6(T99N)-3v5,  0HR,  Rep2

description:
Ume6(T99N)-3v5,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [25.3]


title: Peritubular capillaries, biol rep 1


title: Glomeruli, biol rep 4

value: Glomeruli


title: Ume6(T99N)-3v5,  0HR,  Rep3

description:
Ume6(T99N)-3v5,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Ume6(T99N)-3v5,  6HR,  Rep1

description:
Ume6(T99N)-3v5,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [25.2]


title: 293-WT-8_Rep2

description:
Grown under regular culture condition, no treatment.
S47

source_name: 293-WT-8 cells (WT cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#2


title: 293-WT-V_Rep1

description:
Grown under regular culture condition, no treatment.
S43

source_name: 293-WT-V cells (WT cells transduced with pHIV-Luc-Blast control vector), biological replicate-#1


title: Peritubular capillaries, biol rep 4


title: Glomeruli, biol rep 3


title: 293-dKO-19M_2_Rep2

description:
Grown under regular culture condition, no treatment.
S41

source_name: 293-dKO-19M_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: single cell Plasma cell  [22.3]


title: Ume6(T99N)-3v5,  2HR,  Rep1

description:
Ume6(T99N)-3v5,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [18.3]


title: Glomeruli, biol rep 2