title: K562 cells, sg-LSD1, GFI1 ChIP

city: Freiburg im Breisgau

first: Heike L.

last: Pahl

address: Breisacher Str. 117

country: Germany

institute: University Hospital Freiburg

description: Library name: K562_sg-LSD1_GFI1_ChIP

data_processing:
SPI1, GFI1 and LSD1 ChIP-seq analysis was performed using the following tools and versions: trim-galore v0.6.1, bowtie2 v2.5.4, Picard v3.1.0, macs2 v2.2.9.1, homer v5.1, deeptools v3.5.5. First, low quality reads and adapter sequences were trimmed using Trim Galore! and the filtered reads were mapped against GRCh38 using bowtie2 with the parameters “-X 1000 --very-sensitive”. Duplicate reads were removed using Picard. High-confidence peaks (p < 10-5) were called with the MACS2 callpeak function using “-f BAMPE --keep-dup all” and blacklisted for low-mappability regions using the GRCh38 ENCODE blacklists. Motif analysis was performed on 50bp region surrounding the peak summits with the HOMER findMotifsGenome.pl script. Coverage scores were calculated with deeptools bamCoverage using a bin size of 1 and were normalized to CPM (counts per million) and blacklisted as well. H3K4me1 RELACS ChIP-Seq data was processed on the European usegalaxy.eu servers and mapped to the mm10 genome. The same tools and parameters as for regular ChIP-seq analysis were used, except for bowtie2 which was run in “--local” mode and duplicate read removal, which was performed using deeptools alignmentSieve. The coverage scores were computed for 25bp bins and normalized to RPKM (reads per million mapped reads).
Assembly: GRCh38, mm10
Supplementary files format and content: Coverage tracks as bigWig-files, blacklisted peaks as .narrowpeak file

extract_protocol:
For SPI1, GFI1 and LSD1 ChIP-seq, 10 million cells (per ChIP) were fixed with 1.5mM DSG and 1% formaldehyde before quenching with 125 mM glycine. After cell lysis and nuclei extraction, chromatin was sheared using a Covaris S220 to generate 100-500 bp fragments. Samples were immunoprecipitated with 5μg antibody either against GFI1 (R&D Systems, AF3540), SPI1 (Invitrogen, PA5-17505) or LSD1 (Schuele Laboratory, 20752). For H3K4me1 RELACS ChIP-seq, CD117+ bone marrow cells from LSD1 ei and LSD1 ei ctrl mice were isolated using CD117 MicroBeads (Miltenyi Biotec, 130097146) and LS columns (Miltenyi Biotec, 130042401) according to the manufacturer’s instructions. 1-3 million CD117+ cells from Lsd1 ei and Lsd1 ei ctrl mice were fixed with 1% formaldehyde before quenching with 125 mM glycine and snap freezing in liquid nitrogen. Nuclei extraction, chromatin preparation and immunoprecipitation were performed as described in Arrigoni et. al (Communications Biology, 2018). For immunoprecipitation an antibody against H3K4me1 (Diagenode, C15410194) was used.
For SPI1, GFI1 and LSD1 ChIP-seq,  Libraries were generated using an NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645). For H3K4me1 RELACS ChIP-seq, library preparation was performed as described in Arrigoni et. al (Communications Biology, 2018).


title: K562 cells, sg-LSD1, Input

status: Public on Aug 12 2025

type: SRA

description: Library name: K562_sg-LSD1_Input

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, 2hrKCl, piN_Rep1

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

country: USA

institute: Boston Children's Hospital

description:
Library name: C1C1a_B7-1_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

data_processing:
ATAC-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was aligned to a composite human-chimpanzee genome (hg38 and panTro6) using bwa mem v0.7.17 (Li and Durbin, 2009). Reads with poor alignment or quality were removed (samtools view -F 3844 -q 10) and de-duplicated with samtools v1.3.1 (Li et al., 2009). Bam files were converted to bed files using bedtools v2.26.0 (Quinlan and Hall, 2010), and peaks were called with macs2 v2.1.1.20160309 with the parameters --nomodel --extsize 200 (Zhang et al., 2008). We used reads from diploids and autotetraploids that mapped to the incorrect species as the background for peak calling.
Aligned reads and peaks were then filtered by mapping reads and peaks called in panTro6 to hg38 and vice versa using pslMap from UCSC v363 (Zhu et al., 2007). To generate the chain file used in pslMap, we downloaded panTro6.hg38.all.chain.gz from the UCSC Genome Browser (Navarro Gonzalez et al., 2021) and filtered for orthologous chains as previously described (Turakhia et al., 2020). Reads and peaks were then filtered for those that map uniquely and where the orthologous regions have <5-fold change and <5kb difference in size. Peaks in hg38 coordinates that overlapped ENCODE blacklist regions (Amemiya et al., 2019) or alternate chromosomes were also filtered out. This resulted in reads and peaks in hg38 and panTro6 coordinates for each sample. For allotetraploids, reads and peaks that initially mapped to hg38 were represented separately from those that initially mapped to panTro6.
Reads from diploids and autotetraploids that mapped to the incorrect species were similarly filtered to generate a background mis-mapping file for chimpanzee samples in both hg38 and panTro6 coordinates and for human samples in both hg38 and panTro6 coordinates. We called peaks using macs2 for the background mis-mapping files in hg38 coordinates to identify genomic regions where there were high levels of mis-mapping.
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: bigwig files where reads were first mapped to a composite hg38-panTro6 genome, the appropriate reads were extracted (ex. reads that mapped to panTro6 from a chimpanzee sample), and then those reads were filtered and mapped to hg38
Supplementary files format and content: background_mismapping bigwigs are reads from human samples that incorrectly mapped to panTro6 and reads from chimpanzee samples that incorrectly mapped to hg38 (see data processing steps)
Supplementary files format and content: peak bed files

organism: Pan troglodytes

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. Cells were split on D7 using Accutase (Millipore, cat #SCR005) and then harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

extract_protocol:
NPCs at D14 of differentiation or piNs at D28 were lyzed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20) and collected into conical tubes at a final volume of 500µl lysis buffer. The cell suspension was incubated at 4°C for 10min to release nuclei and then pelleted at 830rcf for 10min. Nuclei were resuspended in 1ml lysis buffer and counted. 50,000 nuclei were then pelleted at 830rcf for 10min and resuspended in 50µl of transposition mix (1X TD buffer [10mM Tris-HCl pH7.6, 5mM MgCl2, 10% dimethyl formamide], 0.33X PBS, 0.001% Digitonin, 0.1% Tween-20, 100nM Tn5 transposase [made in house]). The resuspended nuclei were incubated at 37°C for 30min. DNA was then purified and eluted in 21µl H2O using the DNA Clean and Concentrator-5 Kit (Zymo Research, cat #D4014).
20µl of the eluent was PCR amplified with 1X NEBNext High Fidelity PCR Master Mix (New England Biolabs, cat #M0541L) and primer sequences containing Illumina adapters for 72°C for 5min, 98°C for 30s, and then 5 cycles of 98°C for 10s, 63°C for 30s, and 72°C for 1min.  Libraries were purified using the DNA Clean and Concentrator-5 Kit and quantified with the KAPA Library Quantification Kit (Roche, cat #07960140001).

tag: cell type

value: patterned induced neurons

tag: ploidy

tag: kcl treatment

value: N

tag: batch


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, minusKCl, piN_Rep1

description:
Library name: C1_B2_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: minusKCl


title: NGS4790 BP043201 NCI-H226 G03498025-0.1uM

city: Mississauga

first: James

middle: R

last: Hawley

state: Ontario

address: 7070 Mississauga Road

department: Computational Sciences

country: Canada

institute: Roche Canada

description: Library name: NGS4790_R9111_LIB5467375_SAM24428350

library_source: transcriptomic

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 — pairmax-rna = 200000—clip-overlap) (PMID: 27008021). Transcript annotation was based on the Ensembl genes database (release 77). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated. Differential gene expression was performed with DESeq2. A pre-filter was applied so that only genes with at least a median RPKM value of 10 in one were analyzed. P-values for other genes were simply set to 1 and log fold changes were set to 0 for visualization purposes, but such genes were not included in the multiple testing correction. Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding. Counts were transformed to log2 counts per million, quantile-normalized, and precision-weighted with the “voom” function of the limma package.
Assembly: GRCh38
Supplementary files format and content: gzipped tab-separated value file

molecule: total RNA

source_name: Lung

growth_protocol: All cell lines used in this study were obtained from American Type Culture Collection (ATCC). They were maintained in RPMI 1640 supplemented with 10% FBS (Sigma-Aldrich Corporation) and 2 mM L-glutamine (Gibco Life Sciences) in a humidified incubator maintained at 37 °C with 5% CO2. Cell line authentication was conducted for Short Tandem Repeat (STR) Profiling using the Promega PowerPlex 16 System (Promega Corporation). This was performed once when receiving new cell lines and compared to external STR profiles of cell lines (when available) to determine cell line ancestry. Cell line authentication was routinely conducted by SNP-based genotyping using Fluidigm multiplexed assays at the Genentech cell line core facility. Cells were assessed with a Vi-CELL Cell Viability Analyzer (Beckman Coulter); viability of at least 90% was required for experiments and screening.

extract_protocol:
For treatment, cells were seeded at 1-2 × 10^5 cells/well on tissue culture treated 6-well plates, and were treated after 12-24 h with experimental compounds. Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini Kit (catalog number 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific). For analysis by RNA Fluidigm, 100 ng RNA was subjected to a complementary DNA (cDNA) synthesis reaction using the Applied Biosystems High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, Cat. No. 4368814), as per the manufacturer’s protocol. A preamplification reaction was then performed with Taqman PreAmp Master Mix (Thermo Fisher Scientific). After amplification, samples were diluted 1:4 with Tris-EDTA, and qPCR was conducted on Fluidigm 96.
RNA integrity was confirmed using a Bioanalyzer 2100 (Agilent Technologies). About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M single-end 50-base pair reads.

treatment_protocol: For single agent treatments with pan-TEAD experimental compounds or in combination with KRAS G12C, KRAS G12D or EGFR experimental compounds, cells were seeded at 1000 cells/well on tissue culture treated flat bottom 96-well plates. 12-24 h post plating, cells were treated with multipoint titration ranges as indicated of the desired chemical compounds using the HP D300 drug dispenser. Cell growth was assessed using CellTiter-Glo Luminescent Cell Viability Assays (Promega Corporation), and luminescence was read by a 2104 EnVision Multilabel Plate Reader (PerkinElmer). All cell viability data was collected and calculated for at least 5 replicates per time point, per condition. IC50 values for the inhibitors were determined by fitting the nonlinear regression curves generated by GraphPad Prism. To assess colony formation, cells were seeded at 1.5 × 103 cells/well in 40 mL 0.29% soft agar on a base layer of 40 mL 0.6% soft agar and treated with 40 mL 3× concentrated experimental compound. On day 7, 40 mL 4× concentrated experimental compound/well was added. Colonies were imaged and counted on days 7, 10, and 14 using a GelCount colony counter (Oxford Optronix) per the manufacturer’s instructions.

tag: tissue

value: Lung

value: Epithelial


title: NGS4790 BP043201 NCI-H226 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467367_SAM24428342


title: NGS4790 BP043201 NCI-H2461 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467351_SAM24428326


title: HeLa enDR3, RNA-seq, replicate 3

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description:
Library name: HeLa_enDR3_Rep_3
RNA-seq

data_processing:
Raw sequencing reads were mapped to human genome reference assembly GRCh38/hg38 using STAR (version 2.7.10a) in the paired-end mode and counted using featureCounts from the Subread package (v1.6.4). Duplicate reads were removed. DESeq2 (v1.24.0) R package was used to obtain differentially expressed genes. bigWig signal files (counts per million normalized) were generated using deeptools (version 3.5.1). Duplicate reads were removed.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cervical cancer

growth_protocol: Cells were cultured in HyClone DMEM with high glucose, 4 mM L-glutamine, and sodium pyruvate (Cytiva) supplemented with 10% FBS (Gibco) at 37°C in an atmosphere of 5% CO2

extract_protocol:
Total cellular RNA was isolated using TRI Reagent (Sigma). DNA contamination was removed by digestion with TURBO DNase (Thermo Scientific). The RNA was then purified by phenol:chloroform extraction, precipitated with ethanol, suspended in water, and measured in a NanoDrop ND2000 spectrophotometer (Thermo Scientific). A total of 2 mg of purified total RNA was ribodepleted in cytoplasmic rRNA using the Ribo-Zero rRNA Removal Kit (Illumina) according to the manufacturer’s instructions.
The KAPA RNA HyperPrep Kit (Kapa Biosciences) was used to prepare the strand-specific libraries according to the manufacturer’s instructions. To estimate the number of cycles for library amplification, the KAPA Library Quantification Kit (Kapa Biosciences) was used according to the manufacturer’s instructions. The final amplification products (cDNA libraries), in addition to purification with the KAPA RNA HyperPrep Kit, were purified from short fragments on AMPure XP (Beckman Coulter) and then analyzed on the 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent). cDNA libraries were prepared in three biological replicates.

treatment_protocol: No treatment

value: Cervical cancer

value: HeLa Flp-In T-Rex

value: Epithelial cells

tag: genotype

value: enDR3-mEGFP-expressing cells


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, 30minKCl, piN_Rep1

description:
Library name: C1_B2_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: K562 cells, sg-NT, LSD1 ChIP

description: Library name: K562_sg-NT_LSD1_ChIP

value: sg-NT


title: K562 cells, sg-NT, Input

description: Library name: K562_sg-NT_Input


title: NGS4790 BP043201 NCI-H2373 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467350_SAM24428325


title: THP1 cells, GFI1 ChIP

description: Library name: THP1_GFI1_ChIP


title: THP1 cells, Input

description: Library name: THP1_Input


title: NGS4790 BP043201 NCI-H290 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467349_SAM24428324


title: THP1 cells, SPI1 ChIP

description: Library name: THP1_SPI1_ChIP


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, minusKCl, piN_Rep1

description:
Library name: C1_B12_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4790 BP043201 VMRC-LCD G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467347_SAM24428322

value: VMRC-LCD


title: NGS4790 BP043201 NCI-H2803 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467344_SAM24428319


title: NGS4790 BP043201 NCI-H2461 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467343_SAM24428318


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, 2hrKCl, piN_Rep1

description:
Library name: C1_B2_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, 30minKCl, piN_Rep1

description:
Library name: C1_B12_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: neural progenitor cells, C1C1c, Pan troglodytes, 4N, NPC_Rep2

description:
Library name: C1C1c_2_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw

value: neural progenitor cells


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, 2hrKCl, piN_Rep1

description:
Library name: C1_B12_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: neural progenitor cells, C1C1c, Pan troglodytes, 4N, NPC_Rep1

description:
Library name: C1C1c_1_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: neural progenitor cells, C1C1a, Pan troglodytes, 4N, NPC_Rep2

description:
Library name: C1C1a_2_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: CG_DTAG13_D25_REP1 + CG_DTAG13_D25_REP2 + CG_DTAG13_D25_REP3 ATAC

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 3 samples in this scATAC-seq library
214127

library_source: genomic single cell

data_processing:
Raw sequencing data were processed with the cellranger-arc-2.0.2 software (10x Genomics; localcores=12 --localmem=90)
Downstream analysis, quality control and data integration was was performed in R mainly using Seurat v4.2.0 and Signac v1.11.0 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: compressed matrix files of CellRanger-arc outputs
Supplementary files format and content: rds and h5ad file containting Seurat objects of full Multiome (scRNA-seq/ATAC-seq) data and MK subset after QC, normalization, and dimensionality reduction. Please refer to Supplementary Table 1 of the associated manuscript for an overview of the processed data.
Supplementary files format and content: Excel sheet of the type of the features in Multiome CellPlex samples. Please refer to Supplementary Table 1 of the associated manuscript for an overview of the processed data.
Supplementary files format and content: compressed tab-separated value file of the scATAC-seq fragments and corresponding index file
Assembly: GRCh38-2020-A (10X Genomics)

source_name: Blood

growth_protocol: hiPSC line (Gibco A18945) was used  and routinely cultured under hypoxic conditions (37 °C, 3% O2, 5% CO2) on plates coated with hESC-qualified Matrigel (Corning) in TeSR E8 or mTeSR-Plus medium (STEMCELL Technologies). Cells were passaged every 3–4 days mostly at a split ratio of 1:6 using StemPro Accutase (Thermo Fisher Scientific), and medium was exchanged every 1-2 days

extract_protocol:
Multi-omic scRNA/ATAC-seq
Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ v3.1 workflow following the manufacturer’s instructions.
Cells were cryopreserved in CryoStor CS10. Vials were thawed in a water bath at 37°C and warm DMEM was added dropwise. Cells were washed once with DMEM and resuspended in PBS+10% FBS. Cells were counted and biological replicates were barcoded with distinct CELLPLEX labels and the same number of cells from each sample was pooled. Samples were then processed for multi-omic scRNA/ATAC-seq analysis using the 10x Genomics Single Cell Multiome ATAC + Gene Expression v1 workflow.

treatment_protocol:
Parental hiPSCs (WT genotype) were genetically engineered by in trans paired nicking to carry CBFA2T3::GLIS2 (CG genotype) in one endogenous CBFA2T3 allele.
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.

value: Blood

value: hiPSC Gibco A18945

value: hematopoietic

value: CG


title: NGS4790 BP043201 NCI-H290 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467341_SAM24428316


title: K562 cells, sg-NT, GFI1 ChIP

description: Library name: K562_sg-NT_GFI1_ChIP


title: CG_DTAG13_D25_REP1 + CG_DTAG13_D25_REP2 + CG_DTAG13_D25_REP3 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 3 samples in this scRNA-seq library. (Note: The processing of this library using CellRanger failed and was not included in the analysis. Nevertheless, the raw data is uploaded for transparency.)
212459

library_source: transcriptomic single cell

molecule: polyA RNA


title: NGS4790 BP043199 SK-N-F1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467329_SAM24428304

source_name: Adrenal

value: Adrenal

value: Neuroblast


title: CG_UNTREATED_LONGTERM_REP1 + CG_UNTREATED_LONGTERM_REP2 + CG_UNTREATED_LONGTERM_REP3 ATAC

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint LONGTERM. We pooled 3 samples in this scATACseq library
214128

value: UNTREATED


title: CG_UNTREATED_LONGTERM_REP1 + CG_UNTREATED_LONGTERM_REP2 + CG_UNTREATED_LONGTERM_REP3 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint LONGTERM. We pooled 3 samples in this scRNA-seq library
212460


title: neural progenitor cells, C1C1a, Pan troglodytes, 4N, NPC_Rep1

description:
Library name: C1C1a_1_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw

value: N


title: CG_UNTREATED_D25_REP1 + CG_UNTREATED_D25_REP2 + CG_UNTREATED_D25_REP3 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 3 samples in this scRNA-seq library
212458


title: NGS4790 BP043199 NCI-H2804 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467328_SAM24428303

value: Lung


title: CG_UNTREATED_D25_REP1 + CG_UNTREATED_D25_REP2 + CG_UNTREATED_D25_REP3 ATAC

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 3 samples in this scATAC-seq library
214126


title: neural progenitor cells, C3, Pan troglodytes, 2N, NPC_Rep2

description:
Library name: C3_2_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw

value: Y


title: CG_DTAG13_D13_REP1 + CG_DTAG13_D13_REP2 + CG_DTAG13_D13_REP3 ATAC

description:
Multiome (scATAC-seq) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 3 samples in this scATAC-seq library
214125


title: NGS4790 BP043199 JL-1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467326_SAM24428301

source_name: Pleura

value: Pleura

value: Epithelial


title: NGS4790 BP043201 NCI-H2373 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467342_SAM24428317


title: neural progenitor cells, C3, Pan troglodytes, 2N, NPC_Rep1

description:
Library name: C3_1_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: CG_UNTREATED_D13_REP1 + CG_UNTREATED_D13_REP2 + CG_UNTREATED_D13_REP3 ATAC

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 3 samples in this scATAC-seq library
214124


title: NGS4790 BP043199 NCI-H2591 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467325_SAM24428300


title: CG_UNTREATED_D13_REP1 + CG_UNTREATED_D13_REP2 + CG_UNTREATED_D13_REP3 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 3 samples in this scRNA-seq library
212456


title: neural progenitor cells, C2, Pan troglodytes, 2N, NPC_Rep2

description:
Library name: C2_2_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: WT_UNTREATED_D25_REP1 + WT_DTAG13_D25_REP1 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 2 samples in this scRNA-seq library
212455

value: WT


title: NGS4790 BP043199 SK-N-F1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467321_SAM24428296


title: neural progenitor cells, C2, Pan troglodytes, 2N, NPC_Rep1

description:
Library name: C2_1_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: WT_UNTREATED_D13_REP1 + WT_DTAG13_D13_REP1 ATAC

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 2 samples in this scATAC-seq library.
214122


title: WT_UNTREATED_D25_REP1 + WT_DTAG13_D25_REP1 ATAC

description:
Multiome (scATAC-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D25. We pooled 2 samples in this scATAC-seq library
214123


title: NGS4790 BP043199 JL-1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467318_SAM24428293


title: D25_plusdTAG_13_CMO

description: scRNA-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells wild type and harboring CG allele at timepoint D25. We multiplexed 4 samples in this scRNA-seq GEX library

data_processing:
Raw sequencing data were processed with the CellRanger v7.0.0 software (10x Genomics, parameters: CHEM=SC3Pv3  CPUs=8  localmem=64  --nosecondary) for cell-level demultiplexing and alignment to the human reference transcriptome.
Downstream analysis, quality control and data integration was was performed in R mainly using Seurat v4.2.0 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: Compressed matrix files of filtered CellRanger outputs
Supplementary files format and content: Comma-separated values tables of cell demulteplixing from CellPlex.
Supplementary files format and content: rds and h5ad file containting Seurat objects of the full scRNA-seq data and the megkaryocyte subset after applying QC, normalization, and dimensionality reductions.
Supplementary files format and content: Comma-separated values table of the sample barocode and feature type in scRNA-seq CellPlex. Please refer to Supplementary Table 1 of the associated manuscript for an overview of the processed data.
Assembly: GRCh38-2020-A (10X Genomics)

extract_protocol:
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.
Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ v3.1 workflow following the manufacturer’s instructions.
For the 2020 batch, fresh cells were processed directly. For the 2022 batch, cells were cryopreserved in CryoStor CS10. Vials were thawed in a water bath at 37°C and warm DMEM was added dropwise. Cells were washed once with DMEM and resuspended in PBS+10% FBS. Cells were counted and biological replicates were barcoded with distinct CELLPLEX labels and the same number of cells from each sample was pooled.

treatment_protocol: Parental hiPSCs (WT genotype) were genetically engineered by in trans paired nicking to carry CBFA2T3::GLIS2 (CG genotype) in one endogenous CBFA2T3 allele.

value: hiPSC (Gibco A18945)


title: neural progenitor cells, C1, Pan troglodytes, 2N, NPC_Rep1

description:
Library name: C1_1_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: neural progenitor cells, C1, Pan troglodytes, 2N, NPC_Rep2

description:
Library name: C1_2_ATAC
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: D13_plusdTAG_13_CMO

description: scRNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We multiplexed 4 samples in this scRNA-seq GEX library


title: NGS4790 BP043199 NCI-H2591 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467317_SAM24428292


title: NGS4790 BP043199 NCI-H2804 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467320_SAM24428295


title: WT_UNTREATED_D13_REP1 + WT_DTAG13_D13_REP1 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 2 samples in this scRNA-seq library.
212454


title: D115_CMO

description: scRNA-seq profiling of hiPSC-derived long-term lines CG_A9_HEM22 and CG_A9_HEM23/1 at timepoint D115 and CG_E5_HEM32/1 at D72. We multiplexed 3 samples in this scRNA-seq GEX library


title: Gala_mdagg-4_R2

city: Beaucouzé

first: Matthieu

last: Gaucher

address: 42 rue Georges Morel

department: SPE

country: France

institute: INRAE

description: Library name: Sample 8

data_processing:
The sequenced reads (ranging from 33.3 to 42.5 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: GDDH13 v1.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios of each transgenic line/control comparison

organism: Malus domestica

source_name: leaf

growth_protocol: In vitro apple plants were micropropagated and then placed into rooting conditions. The in vitro rooted plants were transferred to the greenhouse and grown under natural light, 22°C, 80% relative humidity for 8 weeks.

extract_protocol:
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol

treatment_protocol: ASM (0,2 g/l) was sprayed to runoff on entire plants with a hand sprayer, and sampling for RNAseq analysis occurred 3 days after treatment

value: leaf

value: Gala

value: Acibenzolar-S-methyl


title: NGS4790 BP043199 NCI-H2052 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467308_SAM24428283


title: CG_DTAG13_D13_REP1 + CG_DTAG13_D13_REP2 + CG_DTAG13_D13_REP3 GEX

description:
Multiome (scRNA-seq modality) profiling of hematopoietic differentiation of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We pooled 3 samples in this scRNA-seq library
212457

value: Blood


title: Gala_mdagg-4_R1

description: Library name: Sample 7


title: D13_CMO

description: scRNA-seq profiling of hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We multiplexed 4 samples in this scRNA-seq GEX library


title: D25_GEX

description: scRNA-seq profiling of hiPSC-derived hematopoietic cells wild type and harboring CG allele at timepoint D25. We multiplexed 4 samples in this scRNA-seq GEX library


title: Gala_mdagg-3_R2

description: Library name: Sample 6


title: D115_GEX


title: D13_GEX


title: Gala_mdagg-3_R1

description: Library name: Sample 5


title: D25_CMO


title: mut_25

description: scRNA-seq profiling of hiPSC-derived hematopoietic cells harboring CG allele at timepoint D25


title: mut_13

description: scRNA-seq profiling of hiPSC-derived HSPCs harboring CG allele at timepoint D13


title: wt_25

description: scRNA-seq profiling of hiPSC-derived hematopoietic cells at timepoint D25


title: [RNA-Seq] CG_UNTREATED_D13_REP4

description: RNA-seq profiling of hiPSC-derived HSPCs harboring CG allele at timepoint D13

data_processing:
Raw sequence data were processed using the nf-core/rnaseq pipeline v3.5.
Downstream analysis, quality control and differential analysis was was performed in R mainly using Rsubread v.2.12.3 and DESeq2 v1.38.3 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: Comma-separated values tables contatining RNA-seq Salomn and htseq counts of all the samples included in the analysis pipeline. Please refer to Supplementary Table 1 of the associated manuscript for an overview of the processed data.
Assembly: GRCh38 human genome reference

extract_protocol:
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.
Suspension cells enriched for hematopoietic stem and progenitor cells (HSPCs) were harvested from supernatants on differentiation day 12 or 13 (on average 1.5x105 per well of a 12-well plate). Additional cell samples were collected on day 22 or 25 of differentiation or after long-term liquid culture (day 72-115). M-07e (ACC 104) and MOLT 4 (ACC 362) cell lines were obtained from German Collection of Microorganisms and Cell Cultures GmbH (DSMZ) and cultured in RPMI 1640 GlutaMax containing 10% fetal bovine serum, 1x Penicillin/Streptomycin (all from Thermo Fisher Scientific), and M-07e additionally with 10 ng/ml IL3
total RNA was isolated from live cells using TRIzol reagent (Thermo Scientific). 500 ng RNA were used for strand-specific library prep using the NEBnext Ultra II kit and sequenced on an Illumina NovaSeq (2x150 cycles paired-end setup)


title: [RNA-Seq] CG_DTAG13_D13_REP4

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs harboring CG allele at timepoint D13


title: [RNA-Seq] CG_DTAG13_D13_REP3


title: NGS4790 BP043199 NCI-H2722 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467301_SAM24428276


title: Gala_wt_R2

description: Library name: Sample 2


title: NGS4790 BP043199 NCI-H2052 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467300_SAM24428275


title: Gala_wt_R1

description: Library name: Sample 1


title: NGS4790 BP043199 HCC845 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467307_SAM24428282

value: Epithelial, Fibroblast


title: [RNA-Seq] CG_UNTREATED_D13_REP3

value: hematopoietic


title: NGS4790 BP043199 HCC845 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467299_SAM24428274


title: [RNA-Seq] CG_DTAG13_D13_REP2

value: CG


title: D25_plusdTAG_13_GEX

description: scRNA-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells wild type and harboring CG allele at timepoint D25. We multiplexed 4 samples in this scRNA-seq GEX library


title: D13_plusdTAG_13_GEX

description: scRNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs lines wild type and harboring CG allele at timepoint D13. We multiplexed 4 samples in this scRNA-seq GEX library


title: [RNA-Seq] WT_DTAG13_D13_REP2

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs at timepoint D13


title: [RNA-Seq] CG_UNTREATED_D13_REP2


title: NGS4790 BP043199 NCI-H2691 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467298_SAM24428273


title: NGS4790 BP043199 MSTO-211H G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467304_SAM24428279

value: Fibroblast


title: NGS4790 BP043199 NCI-H2691 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467306_SAM24428281


title: [RNA-Seq] CG_UNTREATED_LONGTERM_REP2

description: RNA-seq profiling of hiPSC-derived long-term line CG_A9_HEM23/1 at timepoint D101


title: Gala_mdagg-2_R2

description: Library name: Sample 4


title: CH157-MN Treatment Rep5

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

description: Library name: CH_TR_5

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Assembly: hg38
Supplementary files format and content: The processed data file was saved in text format, which contains gene ENSEMBL ID, sample names, gene symbol, gene location, gene length, gene biotype and gene description.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). cDNA library construction and bulk RNA sequencing were performed at Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

value: Meningioma

value: Humanzied SSTR2-MMAF ADC (100 nM)


title: [RNA-Seq] WT_UNTREATED_D13_REP2

description: RNA-seq profiling of hiPSC-derived HSPCs at timepoint D13

value: UNTREATED


title: CH157-MN Treatment Rep4

description: Library name: CH_TR_4


title: NGS4790 BP043199 NCI-H2731 G03498025-0

description: Library name: NGS4790_R9111_LIB5467302_SAM24428277

value: Lung


title: wt_13

description: scRNA-seq profiling of hiPSC-derived HSPCs at timepoint D13


title: NGS4790 BP043199 MSTO-211H G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467296_SAM24428271


title: Gala_mdagg-2_R1

description: Library name: Sample 3


title: [RNA-Seq] CG_UNTREATED_LONGTERM_REP1

description: RNA-seq profiling of hiPSC-derived long-term line CG_A9_HEM22 at timepoint D81


title: CH157-MN Treatment Rep3

description: Library name: CH_TR_3


title: NGS4790 BP043199 NCI-H2731 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467294_SAM24428269


title: CH157-MN Treatment Rep2

description: Library name: CH_TR_2


title: NGS4790 BP043199 NCI-H2722 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467293_SAM24428268


title: [RNA-Seq] CG_DTAG13_D22_REP2

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells harboring CG allele at timepoint D22


title: L_SC, replicate 4, RNA_seq

city: Shan Dong

first: Weijia

last: Li

address: Shandong Province, Jinan City, Lixia District, Shandong University, Baotu Spring Campus

country: China

institute: Shandong University

description:
Library name: L_SC4
FPKM.L_SC4

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-4.7). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: immune cell


title: [RNA-Seq] CG_UNTREATED_D22_REP2

description: RNA-seq profiling of hiPSC-derived hematopoietic cells harboring CG allele at timepoint D22


title: CH157-MN Control Rep5

description: Library name: CH_CT_5

value: PBS


title: NGS4790 BP043199 NCI-H226 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467279_SAM24428254

value: Epithelial


title: L_SC, replicate 3, RNA_seq

description:
Library name: L_SC3
FPKM.L_SC3

value: WT


title: [RNA-Seq] CG_DTAG13_D22_REP1

value: hiPSC (Gibco A18945)


title: NGS4790 BP043199 NCI-H2369 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467278_SAM24428253


title: [RNA-Seq] CG_UNTREATED_D22_REP1


title: CH157-MN Control Rep4

description: Library name: CH_CT_4


title: NGS4790 BP043199 NCI-H226 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467271_SAM24428246


title: [RNA-Seq] WT_DTAG13_D22_REP1

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells at timepoint D22


title: NGS4790 BP043199 NCI-H2369 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467270_SAM24428245


title: CH157-MN Control Rep2

description: Library name: CH_CT_2


title: L_Con, replicate 3, RNA_seq

description:
Library name: L_Con3
FPKM.L_Con3

value: Control


title: L_SC, replicate 1, RNA_seq

description:
Library name: L_SC1
FPKM.L_SC1


title: [RNA-Seq] WT_UNTREATED_D22_REP1

description: RNA-seq profiling of hiPSC-derived hematopoietic cells at timepoint D22


title: [RNA-Seq] CG_DTAG13_D22_REP3


title: NGS4790 BP043199 VMRC-LCD G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467259_SAM24428234

value: VMRC-LCD


title: L_Con, replicate 4, RNA_seq

description:
Library name: L_Con4
FPKM.L_Con4


title: [RNA-Seq] CG_DTAG13_D13_REP1

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs harboring CG allele at timepoint D13

value: Blood


title: CH157-MN Control Rep1

description: Library name: CH_CT_1


title: L_Con, replicate 2, RNA_seq

description:
Library name: L_Con2
FPKM.L_Con2


title: CH157-MN Treatment Rep1

description: Library name: CH_TR_1


title: L_Con, replicate 1, RNA_seq

description:
Library name: L_Con1
FPKM.L_Con1


title: NGS4790 BP043199 NCI-H2461 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467255_SAM24428230


title: [RNA-Seq] CG_UNTREATED_D13_REP1

description: RNA-seq profiling of hiPSC-derived HSPCs harboring CG allele at timepoint D13


title: L_SC, replicate 2, RNA_seq

description:
Library name: L_SC2
FPKM.L_SC2


title: SC shCTCF-1, replicate 1, ChIP-seq input

city: Tianjin

first: xueying

address: 94 Weijin Road, Nankai District

institute: Nankai University

description: Library name: Sample31

data_processing:
For MeRIP-seq, raw sequencing reads underwent quality control using FastQC v0.11.9. Trim Galore v0.6.10 was utilized for adaptor and low-quality base trimming, employing the parameters "--paired --length 20 -q 20 --stringency 3". The resulting reads were mapped to the human genome (hg38) using HISAT2 v2.2.1. m6A peaks were identified using exomePeak v2.16.0. Enriched motifs within the m6A peaks were analyzed using HOMER v4.11. Each peak was annotated using HOMER v4.11. Differentially methylated genes were defined as genes possessing at least one differential m6A peak with a false discovery rate (FDR) < 0.05. For ChIP-seq, quality control on raw sequencing reads was performed by FastQC v0.11.9. Adaptor sequences and low-quality bases were trimmed using Trim Galore v0.6.10 with the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired". The reads were aligned to the hg38 human genome using Bowtie v2.5.1. SAM files were converted to BAM format, sorted, and indexed using samtools v1.16.1. Duplicate reads were marked and removed using MarkDuplicates from the picard v2.27.5 software. Peak calling was performed using MACS2 v2.2.7.1 with the parameters "-f BAM -g hs -B -q 0.05". Differential peak analysis was conducted using DiffBind v3.10.1. For RNA-seq, raw sequencing reads were subjected to quality control analysis using FastQC v0.11.9. Trim Galore v0.6.10 was employed to remove adaptor sequences and low-quality bases, utilizing the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1". The sequencing reads were then aligned to the human genome (hg38) using HISAT2 v2.2.1. Gene expression quantification was performed on the transcriptome using the featureCounts function of Rsubread v2.0.3. Differentially expressed genes (DEGs) were identified using the edgeR package v3.42.4 in R. Genes with a log2 (fold change) > 0.75 or log2 (fold change) < -0.75 and a false discovery rate (FDR) < 0.01 were considered as DEGs.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Schwann cell

extract_protocol:
The experiments were performed following the method described in a previous study (Liu, Y., Shi, M., He, X., Cao, Y., Liu, P., Li, F., Zou, S., Wen, C., Zhan, Q., Xu, Z. et al. (2022). LncRNA-PACERR induces pro-tumour macrophages via interacting with miR-671-3p and m6A-reader IGF2BP2 in pancreatic ductal adenocarcinoma. J Hematol Oncol 15, 52. 10.1186/s13045-022-01272-w.).
For MeRIP-seq, Total RNA (30 μg) was purified using DynabeadsTM Oligo(dT)25 (Thermo Fisher, USA) in two rounds to isolate poly(A) RNA. Subsequently, the purified poly(A) RNA was fragmented using the Magnesium RNA Fragmentation Module (NEB, USA, catalog number E6150S) at 86°C for 7 minutes. The fragmented RNA was then incubated with an m6A-specific antibody (Synaptic Systems, Germany, catalog number 202003) in IP buffer (50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630) at 4°C for 2 hours. Next, the IP RNA was reverse transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, USA, catalog number 1896649). PCR amplification was performed with the following conditions: initial denaturation at 95°C for 3 minutes, followed by 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp. The cDNA library was subjected to paired-end sequencing (PE150) using the Illumina HiSeq X Ten platform (LC-Bio Technology Co., Ltd., Hangzhou, China). For ChIP-seq, the ChIP-seq library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech Co., Ltd, ND607) according to the manufacturer's instructions. The generated DNA library was sequenced using the Illumina HiSeq X Ten sequencing system in paired-end mode. For RNA-seq, Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The RNA content and purity of each sample were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). The integrity of the RNA was evaluated using the Bioanalyzer 2100 (Agilent, CA, USA) to ensure the RNA Integrity Number (RIN) value greater than 7.0, and further validated by denaturing agarose gel electrophoresis. Two rounds of purification were performed using Dynabeads Oligo(dT)25-61005 (Thermo Fisher, CA, USA) to purify poly(A) RNA from 1 μg of total RNA. Subsequently, the poly(A) RNA was fragmented using the Magnesium RNA Fragmentation Module (NEB, USA, catalog number e6150) at 94°C for 5-7 minutes. The fragmented RNA was then reverse transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, USA, catalog number 1896649). The fragmented RNA was used as a template for cDNA synthesis, which was subsequently converted into U-labeled second-strand DNA using E. coli DNA polymerase I (NEB, USA, catalog number m0209), RNase H (NEB, USA, catalog number m0297), and dUTP Solution (Thermo Fisher, USA, catalog number R0133). A base A was added to the end of each strand to prepare for ligation to the index adapters. Each adapter contained a T-overhang, which allowed the adapter to be ligated to the A-tailed fragment DNA. Single or dual index adapters were ligated to the fragments, followed by size selection using AMPureXP beads. After treatment with thermosensitive UDG enzyme (NEB, USA, catalog number m0280) to remove the U-labeled second-strand DNA, PCR amplification was performed. The amplification conditions included an initial denaturation step at 95°C for 3 minutes, followed by 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp. Finally, according to the supplier's recommended protocol, paired-end sequencing (PE150) was performed on an Illumina Novaseq™ 6000 platform.

value: Schwann cell

tag: sample group

value: SC shCTCF


title: [RNA-Seq] WT_DTAG13_D13_REP1

description: RNA-seq profiling of dTAG-13-treated hiPSC-derived HSPCs at timepoint D13

value: hematopoietic


title: NGS4790 BP043199 NCI-H2373 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467254_SAM24428229


title: SC shNC-2, replicate 1, ChIP-seq input

description: Library name: Sample30

value: SC shNC


title: [RNA-Seq] WT_UNTREATED_D13_REP1

description: RNA-seq profiling of hiPSC-derived HSPCs at timepoint D13


title: NGS4790 BP043199 NCI-H290 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467253_SAM24428228


title: CH157-MN Control Rep3

description: Library name: CH_CT_3

value: Meningioma


title: tumor10_CE456

city: Heidelberg

first: Data

last: Manager

address: Im Neuenheimer Feld 260

department: ODCF

institute: DKFZ

description: Library name: tumor10_CE456

data_processing:
Samples were aligned to the mouse genome GRCm38mm10 using STAR (Version 2.5.3a). Downstream analysis was done using R statistical computing software (Version 4.2). Counts were processed using DESeq2 (Love et al. 2014) (Version 1.38.3).
Assembly: GRCm38mm10
Supplementary files format and content: TSV files with STAR counts

source_name: lung

extract_protocol:
RNA from sorted cells was isolated using the PicoPure RNA Isolation Kit (Life Technologies, #KIT0204) according to the manufacturer's instructions.
RNA-sequencing libraries were generated using the SMART-Seq mRNA library prep (Takara, #634768) and Unique Dual Index Kit (Takara, #634756) following manufacturer's protocol. Input included 1 ng of RNA and 1 ng of cDNA. Quality control was performed by assessing RNA, cDNA, and final library qualities using Tapestation. Libraries were sequenced in a NovaSeq 6k PE 150 S4.

value: lung

value: neoplastic cells

value: Variant 3 Setd2


title: tumor09_CE456

description: Library name: tumor09_CE456


title: SC shNC-1, replicate 1, ChIP-seq input

description: Library name: Sample29


title: [RNA-Seq] CG_UNTREATED_D22_REP3

value: CG

value: UNTREATED


title: pdac28

city: Baltimore

first: Dimitrios

last: Sidiropoulos

state: MD

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics).
Quality check and filtering with Seurat.
Normalization using SCTransform in Seurat.
Dimensional reduction using PCA in Seurat.
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: spatial barcodes
Supplementary files format and content: features.tsv: genes
Supplementary files format and content: matrix.mtx: sequencing counts
Library strategy: Spatial transcriptomics

source_name: pancreas

extract_protocol:
There was no extraction protocol used.
Libraries were constructed using the Visium FFPE Spatial Gene Expression Reagent Kits (10x Genomics).

tag: disease state

value: pancreatic ductal adenocarcinoma

value: pancreas

tag: tissue subtype

value: lymph node

tag: path response

tag: sample type

value: Frozen

tag: treatment arm

value: A


title: NGS4790 BP043199 VMRC-LCD G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467251_SAM24428226

value: Lung

value: VMRC-LCD

value: Epithelial


title: tumor06_CE472

description: Library name: tumor06_CE472

value: Variant 1 Neo


title: NGS4790 BP043199 NCI-H2803 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467256_SAM24428231


title: NGS4790 BP043199 NCI-H2803 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467248_SAM24428223


title: SC shCTCF-2, replicate 1, ChIP-seq

description: Library name: Sample28

value: Schwann cell

value: SC shCTCF


title: SC shCTCF-2, replicate 1, ChIP-seq input

description: Library name: Sample32


title: tumor06_CE456

description: Library name: tumor06_CE456


title: pdac27

value: tumor

value: C


title: tumor05_CE454

description: Library name: tumor05_CE454

value: lung

value: neoplastic cells


title: pdac25


title: SC shCTCF-1, replicate 1, ChIP-seq

description: Library name: Sample27


title: pdac26


title: tumor05_CE450

description: Library name: tumor05_CE450

value: Variant 3 Setd2


title: SC shNC-1, replicate 1, ChIP-seq

description: Library name: Sample25

value: SC shNC


title: SC shNC-2, replicate 1, ChIP-seq

description: Library name: Sample26


title: NGS4790 BP043199 NCI-H2461 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467247_SAM24428222


title: pdac24

value: pancreatic ductal adenocarcinoma


title: NGS4790 BP043199 NCI-H2373 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467246_SAM24428221


title: NGS4790 BP043199 NCI-H290 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467245_SAM24428220


title: tumor04_CE483

description: Library name: tumor04_CE483

value: Variant 1 Setd2


title: NGS4532 BP045309 NCI-H358 DMSO, Replicate 8

description: Library name: NGS4532_R8332_LIB5458095_SAM24418168

value: DMSO


title: pdac23

value: pancreas

value: Frozen


title: sgNC-2, replicate 2, MeRIP-seq input

description: Library name: Sample16

data_processing:
For MeRIP-seq, raw sequencing reads underwent quality control using FastQC v0.11.9. Trim Galore v0.6.10 was utilized for adaptor and low-quality base trimming, employing the parameters "--paired --length 20 -q 20 --stringency 3". The resulting reads were mapped to the human genome (hg38) using HISAT2 v2.2.1. m6A peaks were identified using exomePeak v2.16.0. Enriched motifs within the m6A peaks were analyzed using HOMER v4.11. Each peak was annotated using HOMER v4.11. Differentially methylated genes were defined as genes possessing at least one differential m6A peak with a false discovery rate (FDR) < 0.05. For ChIP-seq, quality control on raw sequencing reads was performed by FastQC v0.11.9. Adaptor sequences and low-quality bases were trimmed using Trim Galore v0.6.10 with the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired". The reads were aligned to the hg38 human genome using Bowtie v2.5.1. SAM files were converted to BAM format, sorted, and indexed using samtools v1.16.1. Duplicate reads were marked and removed using MarkDuplicates from the picard v2.27.5 software. Peak calling was performed using MACS2 v2.2.7.1 with the parameters "-f BAM -g hs -B -q 0.05". Differential peak analysis was conducted using DiffBind v3.10.1. For RNA-seq, raw sequencing reads were subjected to quality control analysis using FastQC v0.11.9. Trim Galore v0.6.10 was employed to remove adaptor sequences and low-quality bases, utilizing the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1". The sequencing reads were then aligned to the human genome (hg38) using HISAT2 v2.2.1. Gene expression quantification was performed on the transcriptome using the featureCounts function of Rsubread v2.0.3. Differentially expressed genes (DEGs) were identified using the edgeR package v3.42.4 in R. Genes with a log2 (fold change) > 0.75 or log2 (fold change) < -0.75 and a false discovery rate (FDR) < 0.01 were considered as DEGs.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MeRIP-seq

value: sgNC


title: tumor04_CE479

description: Library name: tumor04_CE479


title: sgNC-1, replicate 1, MeRIP-seq input

description: Library name: Sample15


title: pdac22

value: B


title: NGS4532 BP045309 NCI-H358 DMSO, Replicate 7

description: Library name: NGS4532_R8332_LIB5458094_SAM24418167

value: Lung

value: Epithelial


title: sgM16-2, replicate 2, MeRIP-seq input

description: Library name: Sample14

value: Schwann cell


title: tumor04_CE472

description: Library name: tumor04_CE472

value: Variant 1 Neo


title: pdac21

value: tumor

value: A


title: NGS4532 BP045309 NCI-H358 DMSO, Replicate 6

description: Library name: NGS4532_R8332_LIB5458093_SAM24418166


title: sgM16-1, replicate 1, MeRIP-seq input

description: Library name: Sample13


title: pdac20


title: tumor04_CE454

description: Library name: tumor04_CE454

value: lung


title: NGS4532 BP045309 NCI-H358 DMSO, Replicate 5

description: Library name: NGS4532_R8332_LIB5458092_SAM24418165


title: DPC SC-2, replicate 2, MeRIP-seq input

description: Library name: Sample12

value: DPC SC


title: pdac19

value: C


title: tumor03_CE483

description: Library name: tumor03_CE483

value: neoplastic cells


title: NGS4532 BP045309 NCI-H358 G03502181, Replicate 2

description: Library name: NGS4532_R8332_LIB5458086_SAM24418159


title: DPC SC-1, replicate 1, MeRIP-seq input

description: Library name: Sample11


title: pdac18

value: pancreatic ductal adenocarcinoma


title: tumor03_CE475

description: Library name: tumor03_CE475

value: Variant 1 Setd2


title: pdac17

value: lymph node


title: pdac16

value: pancreas


title: tumor03_CE468

description: Library name: tumor03_CE468


title: NGS4532 BP045309 ES-2 DMSO, Replicate 3

description: Library name: NGS4532_R8332_LIB5458046_SAM24418119

source_name: Ovary

value: Ovary

value: Fibroblast

value: DMSO


title: NGS4532 BP045309 ES-2 DMSO, Replicate 4

description: Library name: NGS4532_R8332_LIB5458047_SAM24418120


title: tumor03_CE467

description: Library name: tumor03_CE467


title: NDPC SC-1, replicate 1, MeRIP-seq input

description: Library name: Sample9

data_processing:
For MeRIP-seq, raw sequencing reads underwent quality control using FastQC v0.11.9. Trim Galore v0.6.10 was utilized for adaptor and low-quality base trimming, employing the parameters "--paired --length 20 -q 20 --stringency 3". The resulting reads were mapped to the human genome (hg38) using HISAT2 v2.2.1. m6A peaks were identified using exomePeak v2.16.0. Enriched motifs within the m6A peaks were analyzed using HOMER v4.11. Each peak was annotated using HOMER v4.11. Differentially methylated genes were defined as genes possessing at least one differential m6A peak with a false discovery rate (FDR) < 0.05. For ChIP-seq, quality control on raw sequencing reads was performed by FastQC v0.11.9. Adaptor sequences and low-quality bases were trimmed using Trim Galore v0.6.10 with the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired". The reads were aligned to the hg38 human genome using Bowtie v2.5.1. SAM files were converted to BAM format, sorted, and indexed using samtools v1.16.1. Duplicate reads were marked and removed using MarkDuplicates from the picard v2.27.5 software. Peak calling was performed using MACS2 v2.2.7.1 with the parameters "-f BAM -g hs -B -q 0.05". Differential peak analysis was conducted using DiffBind v3.10.1. For RNA-seq, raw sequencing reads were subjected to quality control analysis using FastQC v0.11.9. Trim Galore v0.6.10 was employed to remove adaptor sequences and low-quality bases, utilizing the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1". The sequencing reads were then aligned to the human genome (hg38) using HISAT2 v2.2.1. Gene expression quantification was performed on the transcriptome using the featureCounts function of Rsubread v2.0.3. Differentially expressed genes (DEGs) were identified using the edgeR package v3.42.4 in R. Genes with a log2 (fold change) > 0.75 or log2 (fold change) < -0.75 and a false discovery rate (FDR) < 0.01 were considered as DEGs.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MeRIP-Seq

value: NDPC SC


title: NGS4532 BP045309 ES-2 DMSO, Replicate 2

description: Library name: NGS4532_R8332_LIB5458045_SAM24418118


title: pdac15

value: Frozen


title: NGS4532 BP045309 ES-2 DMSO, Replicate 1

description: Library name: NGS4532_R8332_LIB5458044_SAM24418117


title: tumor03_CE454

description: Library name: tumor03_CE454

value: Variant 3 Setd2


title: sgNC-2, replicate 2, MeRIP-seq

description: Library name: Sample8

value: Schwann cell

value: sgNC


title: sgNC-1, replicate 1, MeRIP-seq

description: Library name: Sample7


title: tumor04_CE468

description: Library name: tumor04_CE468

value: Variant 1 Neo


title: pdac14

value: tumor

value: B


title: pdac13

value: A


title: NGS4532 BP045309 ES-2 G03502181, Replicate 1

description: Library name: NGS4532_R8332_LIB5458038_SAM24418111


title: sgM16-2, replicate 2, MeRIP-seq

description: Library name: Sample6


title: tumor03_CE450

description: Library name: tumor03_CE450

value: lung

value: neoplastic cells


title: NGS4532 BP045308 NCI-H358 DMSO, Replicate 7

description: Library name: NGS4532_R8338_LIB5457999_SAM24418072

value: Lung

value: Epithelial


title: pdac12

value: pancreatic ductal adenocarcinoma

value: pancreas

value: lymph node

value: R

value: FFPE

value: C


title: tumor03_CE433

description: Library name: tumor03_CE433

value: Variant 3 Neo


title: sgM16-1, replicate 1, MeRIP-seq

description: Library name: Sample5

value: Schwann cell


title: NGS4532 BP045308 NCI-H358 DMSO, Replicate 6

description: Library name: NGS4532_R8338_LIB5457998_SAM24418071

value: DMSO


title: NDPC SC-2, replicate 2, MeRIP-seq input

description: Library name: Sample10

value: NDPC SC


title: tumor03_CE429

description: Library name: tumor03_CE429


title: tumor03_CE428

description: Library name: tumor03_CE428


title: DPC SC-2, replicate 2, MeRIP-seq

description: Library name: Sample4

value: DPC SC


title: pdac11

value: Tumor


title: pdac10

value: B


title: NGS4532 BP045308 NCI-H358 G03502181, Replicate 2

description: Library name: NGS4532_R8338_LIB5457990_SAM24418063


title: NDPC SC-2, replicate 2, MeRIP-seq

description: Library name: Sample2


title: pdac9


title: DPC SC-1, replicate 1, MeRIP-seq

description: Library name: Sample3


title: NGS4532 BP045308 NCI-H226 DMSO, Replicate 4

description: Library name: NGS4532_R8338_LIB5457951_SAM24418024


title: tumor02_CE479

description: Library name: tumor02_CE479

value: lung

value: Variant 1 Setd2


title: tumor02_CE475

description: Library name: tumor02_CE475

value: neoplastic cells


title: NGS4532 BP045308 NCI-H226 DMSO, Replicate 3

description: Library name: NGS4532_R8338_LIB5457950_SAM24418023

value: Lung

value: Epithelial


title: NDPC SC-1, replicate 1, MeRIP-seq

description: Library name: Sample1


title: tumor02_CE472

description: Library name: tumor02_CE472

value: Variant 1 Neo


title: NGS4532 BP045308 NCI-H226 DMSO, Replicate 2

description: Library name: NGS4532_R8338_LIB5457949_SAM24418022


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G6-2_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt

data_processing:
RNA-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was analyzed as previously described (Song et al., 2021). Briefly, sequencing reads were trimmed for adapter sequences and assessed for sequencing quality using trimgalore v0.6.6 with cutadapt v2.5 (Martin, 2011) and fastqc v0.11.5 (Andrews et al., 2010). Reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to a composite human-chimpanzee genome (hg38 and panTro6). The number of uniquely-mapped reads (MAPQ=255) that overlap each gene was counted using featureCounts from the subread v2.0.0 package (Liao et al., 2014).
For CRISPR inhibition experiments, UMIs were extracted using umi_tools v1.1.2 (Smith et al., 2017) and adapter sequences were trimmed using cutadapt v2.5 (Martin, 2011). Sequencing quality was assessed with fastqc v0.11.5 (Andrews et al., 2010). Reads that map to rDNA (https://www.ncbi.nlm.nih.gov/nuccore/U13369.1) were removed, and remaining reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to either the hg38 or panTro6 genome, as appropriate. Reads were then de-duplicated based on UMIs using umi_tools, and the number of reads that overlap each gene was counted using featureCounts from the subread v2.0.0 package with default parameters (Liao et al., 2014).
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: gene count files

organism:
Pan troglodytes
Homo sapiens

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. On D7, cells were split using Accutase (Millipore, cat #SCR005) and infected with lentivirus (if applicable). Cells were harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

extract_protocol:
NPCs at D14 or piNs at D28 were collected in Trizol and RNA was extracted with the Direct-Zol Miniprep Kit (Zymo Research, cat #R2052) or the Direct-Zol Microprep Kit (Zymo Research, cat #R2062). Cells infected with lentivirus were collected by FACS prior to RNA extraction.
RNA sequencing libraries were made with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio) or with the WatchMaker RNA Library Prep Kit with Polaris Depletion (WatchMaker Genomics) and the Twist UMI Adapter System - TruSeq Comp, 96 Samples Plate A (Twist Biosciences, cat #105041).

treatment_protocol: If applicable, cells were infected with lentivirus.

value: patterned induced neurons

value: N

value: minusKCl


title: BO_17_scRNA

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Cell ranger version 5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Seurat object saved as .rds with full metadata matching manuscript. One file for cancer samples and one file for normal ureter samples.

source_name: normal ureter

extract_protocol:
10x genomics V3.1 kit
10x genomics V3.1 kit gene expression

value: normal ureter


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G6-2_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: pdac8

value: pancreatic ductal adenocarcinoma

value: pancreas

value: FFPE

value: C


title: BN_9_scRNA


title: tumor02_CE467

description: Library name: tumor02_CE467


title: NGS4532 BP045308 NCI-H358 DMSO, Replicate 5

description: Library name: NGS4532_R8338_LIB5457997_SAM24418070

value: DMSO


title: BN_8_scRNA


title: tumor02_CE429

description: Library name: tumor02_CE429

value: Variant 3 Neo


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G6-2_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP045308 NCI-H226 DMSO, Replicate 1

description: Library name: NGS4532_R8338_LIB5457948_SAM24418021


title: BN_7_scRNA


title: NGS4532 BP045308 NCI-H226 G03502181, Replicate 1

description: Library name: NGS4532_R8338_LIB5457942_SAM24418015


title: tumor02_CE433

description: Library name: tumor02_CE433


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G11-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: tumor02_CE428

description: Library name: tumor02_CE428


title: NGS4532 BP045307 NCI-H358 DMSO, Replicate 7

description: Library name: NGS4532_R8338_LIB5457903_SAM24417976


title: BN_6_scRNA


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G11-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: BN_5_scRNA


title: tumor01_CE483

description: Library name: tumor01_CE483


title: tumor01_CE479

description: Library name: tumor01_CE479


title: BN_4_scRNA


title: NGS4532 BP045307 NCI-H358 DMSO, Replicate 5

description: Library name: NGS4532_R8338_LIB5457901_SAM24417974


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G1-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G1-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: tumor01_CE475

description: Library name: tumor01_CE475


title: NGS4532 BP045307 NCI-H358 G03502181, Replicate 2

description: Library name: NGS4532_R8338_LIB5457894_SAM24417967


title: BN_3_scRNA


title: NGS4532 BP045307 NCI-H226 DMSO, Replicate 3

description: Library name: NGS4532_R8338_LIB5457854_SAM24417927


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G1-1_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP045307 NCI-H226 DMSO, Replicate 4

description: Library name: NGS4532_R8338_LIB5457855_SAM24417928


title: BN_2_scRNA


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_F10-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: tumor01_CE467

description: Library name: tumor01_CE467


title: NGS4532 BP045307 NCI-H226 DMSO, Replicate 1

description: Library name: NGS4532_R8338_LIB5457852_SAM24417925


title: BN_1_scRNA


title: NGS4532 BP045307 NCI-H226 DMSO, Replicate 2

description: Library name: NGS4532_R8338_LIB5457853_SAM24417926


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_F10-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: BN_10_scRNA


title: tumor01_CE450

description: Library name: tumor01_CE450

value: Variant 3 Setd2


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_F10-1_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: BC_9_scRNA

source_name: bladder

value: bladder


title: NGS4532 BP045307 NCI-H358 DMSO, Replicate 6

description: Library name: NGS4532_R8338_LIB5457902_SAM24417975


title: tumor01_CE433

description: Library name: tumor01_CE433

value: lung


title: BC_8_scRNA


title: tumor01_CE429

description: Library name: tumor01_CE429

value: neoplastic cells


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2C2a_G11-1_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP045307 NCI-H226 G03502181, Replicate 1

description: Library name: NGS4532_R8338_LIB5457846_SAM24417919

value: Lung


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_E4-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: tumor01_CE428

description: Library name: tumor01_CE428


title: BC_7_scRNA


title: NGS4532 BP043210 NCI-H358 DMSO, Replicate 7

description: Library name: NGS4532_R8338_LIB5457807_SAM24417880

value: Epithelial


title: NGS4532 BP043210 NCI-H358 DMSO, Replicate 6

description: Library name: NGS4532_R8338_LIB5457806_SAM24417879


title: tumor01_CE468

description: Library name: tumor01_CE468

value: Variant 1 Neo


title: Cite-seq,Tumor_leukocytes8,ADT_HTO

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

description: Library name: sample4_antibody_capture

data_processing:
fastqs were processed using cellranger count pipeline v.6.0.1
resulting counts matrices were processed with Seurat V4 with following QC thresholds: for RNA: nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5; for Hashtags: HTODemux with default settings
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz (compressed raw counts; features.tsv.gz (gene names); barcodes.tsv.gz (cell barcodes)
Supplementary files format and content: libraries_2021-11-24_WT-FoxP3.csv (library type : fastq mapping); feaute-ref.csv (cellranger feature: barcode mapping)
Library strategy: CITE-seq

source_name: tumor

growth_protocol: Py230 cells (ATCC, CRL-3279) were cultured in Ham’s F-12K Medium(Thermo Fisher, 21-127-022) supplemented with 5% FBS, 1% Penicillin-Streptomycin(Gibco, 15140122), and 0.1% MITO+ serum extender (Corning, 355006). A 1:1 ratio of1x106 tumor cells and Cultrex basement membrane extract (R&D, 3632-010-02) orMatrigel Growth Factor Reduced Basement Membrane Matrix (Corning, 356231) wereinjected bilaterally into the fourth (abdominal) mammary pads with a Hamilton syringe(Point style 4, Length 1in, Hamilton)

extract_protocol:
On the day of harvest, the left and right tumors of each transplant tumor mouse were combined into one sample and made into single-cell suspensions. Tumor lysates were resuspended in 100μL staining buffer consisting of PBS, 2% BSA, and 0.01% Tween in 1.5mL low bind tubes. To this, 10μL of TruStain FcX blocking reagent (Biolegend, 101320) was added and then incubated for 10 minutes at 4°C. A pool of all CITE-seq antibodies (~0.75μg/antibody) and flow cytometry antibodies consisting of Ghost Dye BV510, NKp46-FITC, CD45.2-PE, TCRb-PECy7, EpCAM-APC, and CD19-APCCy7 was created and 40μL was then added to each tube. In addition, 1μg of a unique cell hashing antibody was added to each tube, which were all then incubated for 30 minutes at 4°C. Cells were then sorted on the BD FACSDiva 8.0.2. at the Cytometer & Cell Sorting Laboratory at NYU Grossman School of Medicine for cells that were Ghost Dye-, CD45.2+, NKp46-, CD19-, TCRb-, EpCAM- to enrich for myeloid cells.
scRNA-seq and Cell Surface Protein libraries were constructed using the Chromium Single Cell 3′ v3.1 Reagent Kit (10x Genomics, PN-1000268) according to the manufacturer’s protocol.  Briefly, cell populations were stained with BioLegend Typ B oligo-tagged antibodies and counted using a BioRad TC20 Automated Cell Counter. Cells were then pooled and placed in a single channel of a Next GEM Chip G (10x Genomics, PN-1000120), loaded onto the Chromium Controller (10x Genomics) and single cells were encapsulated into emulsion droplets. Reverse transcription and library preparation were performed on a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad).  cDNA was amplified 11 cycles and evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies).  Final Gene Expression and Cell Surface Protein libraries were amplified 15 and 10 cycles respectively and visualized on an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).  Individual libraries were diluted to 2nM and pooled for sequencing. Pools were sequenced across 16% of an S2 100 cycle flowcell  (28bp Read1, 8bp Index1, 91bp Read2) on the NovaSeq 6000 Sequencing System (Illumina).

treatment_protocol: WT and FoxP3DTR py230 tumor bearing mice were treated with DT for 2 weeks before harvesting

value: tumor

value: tumor cells / leukocytes

value: mixed (WT, Foxp3-DTR)

tag: adt

tag: hto

value: TotalseqB-hashtag1 (WT 1); TotalseqB-hashtag2 (WT 2); TotalseqB-hashtag3 (Foxp3-DTR 1); TotalseqB-hashtag4 (Foxp3-DTR 2)


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_E4-1_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt

value: patterned induced neurons

value: N


title: BC_6_scRNA


title: NGS4532 BP043210 NCI-H358 DMSO, Replicate 5

description: Library name: NGS4532_R8338_LIB5457805_SAM24417878


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_A6-2_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt

value: minusKCl


title: Cite-seq,Tumor_leukocytes7,ADT_HTO

description: Library name: sample3_antibody_capture


title: BC_5_scRNA


title: Cite-seq,Tumor_leukocytes6,ADT_HTO

description: Library name: sample2_antibody_capture


title: NGS4532 BP043210 NCI-H358 G03502181, Replicate 2

description: Library name: NGS4532_R8338_LIB5457798_SAM24417871


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_A6-2_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_A6-2_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP043210 NCI-H226 DMSO, Replicate 4

description: Library name: NGS4532_R8338_LIB5457759_SAM24417832


title: BC_4_scRNA


title: Cite-seq,Tumor_leukocytes5,ADT_HTO

description: Library name: sample1_antibody_capture


title: BC_3_scRNA


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1C1b_E4-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: Cite-seq,Tumor_leukocytes4,GEX

description: Library name: sample4_rna


title: neural progenitor cells, H2C2f, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H2C2f_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

value: neural progenitor cells


title: BC_27_scRNA


title: NGS4532 BP043210 NCI-H226 DMSO, Replicate 2

description: Library name: NGS4532_R8338_LIB5457757_SAM24417830

value: DMSO


title: neural progenitor cells, H2C2a, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H2C2a_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: neural progenitor cells, H1C1f, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H1C1f-14_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP043210 NCI-H226 DMSO, Replicate 1

description: Library name: NGS4532_R8338_LIB5457756_SAM24417829


title: Cite-seq,Tumor_leukocytes1,GEX

description: Library name: sample1_rna


title: Cite-seq,Tumor_leukocytes2,GEX

description: Library name: sample2_rna


title: NGS4532 BP043209 ES-2 DMSO, Replicate 8

description: Library name: NGS4532_R8338_LIB5457711_SAM24417784

value: Ovary

value: Fibroblast


title: BC_23_scRNA

value: bladder


title: PDL

city: Tokyo

first: Toshihide

last: Mizoguchi

address: 2-9-18 Kanda-Misakicho, Chiyodaku

department: Oral Health Science Center

country: Japan

institute: Tokyo Dental College

description: Library name: Sample 1

data_processing:
The sequence reads demultiplexed with Illumina bcl2fastq (Illumina) was mapped, demultiplexed, UMI counted and filtered using Cell Ranger 5.0.1. The reference genome sequence was GRCm38.p6.genome with the addition of eGFP and tdTomato sequences, annotated using gencode.vM25.annotation.
Assembly: GRCm38.p6.genome with the addition of eGFP and tdTomato sequences
Supplementary files format and content: Tab-delimited text file include gene expression feature,  barcode sequences and gene-barcode matrix

source_name: periodontal ligament (PDL)

extract_protocol:
All ｍaxillary molars were extracted using hooked-end forceps under triple anesthesia (medetomidine hydrochloride 0.75 mg/kg [Domitol; Nippon Zenyaku Kogyo Co., Ltd], midazolam 4.0 mg/kg [Dormicum; Sandoz K. K.], and butorphanol 5.0 mg/kg [Vetorphale, Meiji Seika Pharma Co., Ltd.]). After surgery, euthanasia was performed by cervical spine fracture-dislocation under anesthesia. The extracted 6 molars were incubated with 2 mL of collagenase/protease/DNase mixed buffer (2 Wunsch units of Liberase™ [Roche], 0.5 mg/mL Pronase [Roche], 1/2000 benzonase [Sigma-Aldrich], and 5 mM MgCl2 [Sigma-Aldrich]) modified from a previous report 49) at 37 °C, 2000 rpm for 1 h in a shaking incubator (ThermoMixer® C, Eppendorf). The incubation buffer was collected into a tube with a 35-μm filter cap (Falcon, Corning Inc.) containing 1 ml bone buffer (2% fetal bovine serum, 0.5 mM ethylenediaminetetraacetic acid [EDTA, Thermo Fisher Scientific], 25 μg/ml DNase [Worthington Biochemical Corporation], and 5 mM MgCl2 in phosphate-buffered saline), and centrifuged at 4 °C,  280 g for 10 min. The cell pellet was treated with a hemolysis buffer (ACK Lysing Buffer, Thermo Fisher Scientific) containing 1/2000 benzonase (Sigma-Aldrich) and 5 mM MgCl2 for 3 min on ice. The cells were incubated with APC-conjugated rat anti-CD45 antibody (clone: 30-F11, Thermo Fisher Scientific) (1:100) and APC-conjugated rat anti-Ter119 antibody (clone: TER-119, Thermo Fisher Scientific) (1:100) for 30 min on ice. Cell sorting experiments were performed using a FACSMelody (BD Biosciences) equipped with FACSChorus software (BD Biosciences). Dead cells and debris were excluded using FSC, SSC, and SYTOX Red Dead Cell Stain (Thermo Fisher Scientific) staining profiles. CD45, Ter119-negative living stromal cells were collected and used for scRNA-seq analysis. Because our pre-experiment suggested that the frequency of Lepr-cre-Tom+ cells in the sorted stromal population were too low to perform their gene profiling analysis, we added additional CD45, Ter119-negative living Lepr-cre-Tom+ cells to the sorted CD45, Ter119-negative living stromal sample.
Single cell suspension was prepared according to the manufacture’s instruction of 10x Genomics and filtered through a 40-μm cell strainer. Isolated cells were prepared for single cell suspension using a 10x Chromium Controller (10x Genomics). Single Cell 3' Library kit v3.1 were used for cDNA library preparation and the protocol was followed by 10x Genomics. The quality of the libraries was checked using a BioAnalyzer 2100 (Agilent) and LabChip （PerkinElmer）. Sequencing was performed using NovaSeq 6000 (Illumina) with read１:28 bp、index：8 bp、read2：91 bp.

value: periodontal ligament (PDL)

value: LepR-cre; R26-tdTomato; Runx2-GFP


title: BC_26_scRNA


title: neural progenitor cells, H2C2b, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H2C2b_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP043210 NCI-H226 G03502181, Replicate 1

description: Library name: NGS4532_R8338_LIB5457750_SAM24417823

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 — pairmax-rna = 200000—clip-overlap) (PMID: 27008021). Transcript annotation was based on the Ensembl genes database (release 77). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated. Differential gene expression was performed with DESeq2. A pre-filter was applied so that only genes with at least a median RPKM value of 10 in one were analyzed. P-values for other genes were simply set to 1 and log fold changes were set to 0 for visualization purposes, but such genes were not included in the multiple testing correction. Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding. Counts were transformed to log2 counts per million, quantile-normalized, and precision-weighted with the “voom” function of the limma package.
Assembly: GRCh38
Supplementary files format and content: gzipped tab-separated value file

value: Lung


title: neural progenitor cells, H1C1b, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H1C1b_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: CD117 cells, ei ctrl, Mouse 2, H3K4me1 RELACS-ChIP

description: Library name: CD117_ei_ctrl_2_H3K4me1

data_processing:
SPI1, GFI1 and LSD1 ChIP-seq analysis was performed using the following tools and versions: trim-galore v0.6.1, bowtie2 v2.5.4, Picard v3.1.0, macs2 v2.2.9.1, homer v5.1, deeptools v3.5.5. First, low quality reads and adapter sequences were trimmed using Trim Galore! and the filtered reads were mapped against GRCh38 using bowtie2 with the parameters “-X 1000 --very-sensitive”. Duplicate reads were removed using Picard. High-confidence peaks (p < 10-5) were called with the MACS2 callpeak function using “-f BAMPE --keep-dup all” and blacklisted for low-mappability regions using the GRCh38 ENCODE blacklists. Motif analysis was performed on 50bp region surrounding the peak summits with the HOMER findMotifsGenome.pl script. Coverage scores were calculated with deeptools bamCoverage using a bin size of 1 and were normalized to CPM (counts per million) and blacklisted as well. H3K4me1 RELACS ChIP-Seq data was processed on the European usegalaxy.eu servers and mapped to the mm10 genome. The same tools and parameters as for regular ChIP-seq analysis were used, except for bowtie2 which was run in “--local” mode and duplicate read removal, which was performed using deeptools alignmentSieve. The coverage scores were computed for 25bp bins and normalized to RPKM (reads per million mapped reads).
Assembly: GRCh38, mm10
Supplementary files format and content: Coverage tracks as bigWig-files, blacklisted peaks as .narrowpeak file

source_name: Bone Marrow

extract_protocol:
For SPI1, GFI1 and LSD1 ChIP-seq, 10 million cells (per ChIP) were fixed with 1.5mM DSG and 1% formaldehyde before quenching with 125 mM glycine. After cell lysis and nuclei extraction, chromatin was sheared using a Covaris S220 to generate 100-500 bp fragments. Samples were immunoprecipitated with 5μg antibody either against GFI1 (R&D Systems, AF3540), SPI1 (Invitrogen, PA5-17505) or LSD1 (Schuele Laboratory, 20752). For H3K4me1 RELACS ChIP-seq, CD117+ bone marrow cells from LSD1 ei and LSD1 ei ctrl mice were isolated using CD117 MicroBeads (Miltenyi Biotec, 130097146) and LS columns (Miltenyi Biotec, 130042401) according to the manufacturer’s instructions. 1-3 million CD117+ cells from Lsd1 ei and Lsd1 ei ctrl mice were fixed with 1% formaldehyde before quenching with 125 mM glycine and snap freezing in liquid nitrogen. Nuclei extraction, chromatin preparation and immunoprecipitation were performed as described in Arrigoni et. al (Communications Biology, 2018). For immunoprecipitation an antibody against H3K4me1 (Diagenode, C15410194) was used.
For SPI1, GFI1 and LSD1 ChIP-seq,  Libraries were generated using an NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645). For H3K4me1 RELACS ChIP-seq, library preparation was performed as described in Arrigoni et. al (Communications Biology, 2018).

value: Bone Marrow

value: CD117+ cell

value: LSD1 ei ctrl

tag: host strain


title: BC_25_scRNA


title: NGS4532 BP043209 ES-2 DMSO, Replicate 6

description: Library name: NGS4532_R8338_LIB5457709_SAM24417782

tag: cell line


title: BC_21_scRNA

tag: treatment


title: BC_22_scRNA


title: neural progenitor cells, H1C1f, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H1C1f-6_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

tag: cell type


title: neural progenitor cells, H2C2f, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H2C2f_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

tag: ploidy


title: neural progenitor cells, H1C1a, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H1C1a_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: NGS4532 BP043210 NCI-H226 DMSO, Replicate 3

description: Library name: NGS4532_R8338_LIB5457758_SAM24417831

value: Epithelial


title: BC_20_scRNA


title: CD117 cells, ei, Mouse 2, H3K4me1 RELACS-ChIP

description: Library name: CD117_ei_2_H3K4me1

value: LSD1 ei


title: CD117 cells, ei ctrl, Mouse 1, H3K4me1 RELACS-ChIP

description: Library name: CD117_ei_ctrl_1_H3K4me1


title: NGS4532 BP043209 ES-2 DMSO, Replicate 5

description: Library name: NGS4532_R8338_LIB5457708_SAM24417781


title: CD117 cells, ei, Mouse 1,  H3K4me1 RELACS-ChIP

description: Library name: CD117_ei_1_H3K4me1


title: NGS4532 BP043209 ES-2 G03502181, Replicate 2

description: Library name: NGS4532_R8338_LIB5457702_SAM24417775


title: Cite-seq,Tumor_leukocytes3,GEX

description: Library name: sample3_rna

value: tumor

value: tumor cells / leukocytes

value: mixed (WT, Foxp3-DTR)


title: BC_24_scRNA


title: BC_2_scRNA


title: NGS4532 BP043209 ES-2 DMSO, Replicate 7

description: Library name: NGS4532_R8338_LIB5457710_SAM24417783


title: neural progenitor cells, H2C2b, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H2C2b_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

value: N


title: BC_19_scRNA


title: NGS4532 BP043209 ES-2 DMSO, Replicate 4

description: Library name: NGS4532_R8338_LIB5457663_SAM24417736


title: C2C12 cells, siKEAP1siCCNF, biol rep 2

city: Berkeley

first: Andrew

last: Ingersoll

state: CA

address: 1951 Oxford St

department: MCB

institute: University of California, Berkeley

data_processing:
Reads were mapped to the mouse reference genome using HISAT2, counted, and FPKM were calculated
Assembly: GRCm39
Supplementary files format and content: CSV file containing raw counts and FPKM values for each sample

growth_protocol: Cells were grown in DMEM supplemented with 5% FBS at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA kit (Macherey-Nagel)
mRNA was purified from total RNA by polyA enrichment. mRNA was fragmented and cDNA was synthesized. This was followed by end repair, A-tailling, adapter ligation, size selection, amplification and purification.

treatment_protocol: Cells were treated with 30 nM siRNA for 48 hours before harvesting.

value: Myoblast


title: BC_18_scRNA


title: C2C12 cells, siKEAP1siCCNF, biol rep 3


title: neural progenitor cells, H1C1b, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H1C1b_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

value: neural progenitor cells


title: C2C12 cells, siKEAP1siCCNF, biol rep 1


title: neural progenitor cells, H1C1a, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H1C1a_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt


title: C2C12 cells, siCCNF, biol rep 3

value: siCCNF