title: chALL7 H3K27ac

description: Library name: chALL7_H3K27ac


title: NGS4406 LIB5455000 NCI-H2122 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 1

status: Public on Aug 12 2025

type: SRA

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: NGS4406_R8074_LIB5455000_SAM24414225

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

organism: Homo sapiens

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

tag: cell line

tag: cell type

value: Epithelial, Rounded

tag: treatment

tag: batch


title: PPP_10umol/L_24h_3

city: Warthausen

first: Rakesh

last: Santhanam

address: Goetheweg 10

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

description: Library name: LIB2024_066_045_001

data_processing:
Sequencing reads were processed with a pipeline built upon the implementation of the ENCODE’ “Long RNA-seq” pipeline: Filtered reads were mapped against the Homo sapiens (humans) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. For quantification of transcript levels, the annotation files from Ensembl version 86 were used, which corresponds to GENCODE 25
Assembly: hg38/GRCh38
Supplementary files format and content: tab delimited text file include raw counts for each sample

source_name: Adipose

growth_protocol: hMADS cells were cultured in DMEM low glucose (1 g/L) with L- GlutaMAX (Gibco, 11885084) supplemented with 10% fetal bovine serum (FBS) (Gibco, 11500064), 1% Pen/Strep (Gibco, 15070063), 15 mM HEPES (Gibco, 15630056) and 2.5 ng/ml bFGF-2 (Peprotech, 100-18B-50UG). Tissue culture-treated surfaces were used for seeding the hMADS cells. The cells were induced to differentiate at day 2 post confluence (designated as day 0) in Omental Adipocyte Differentiation Medium (Zenbio, OM-DM°500mL)

extract_protocol:
RNA was extracted utilizing RNeasy kit (Qiagen, 74104) following the manufacturer’s protocol. RNA concentration was measured was quantitatively  assessed using the fluorescence Broad Range Quant-iT RNA Assay Kit (Thermo Fisher Scientific) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively. Total RNA input of 250 ng was employed for library preparation with the NEBNext. UltraExpress RNA Library Prep Kit for Illumina
RNA- seq libraries were eluted in 30 µL EB Buffer (Qiagen) and were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Libraries were assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 96-channel Fragment Analyzer (Agilent). Libraries were normalized on the MicroLab STAR (Hamilton)

treatment_protocol: The 9-day old differentiated hMADS cells were starved overnight with starvation medium consisting of DMEM without glucose supplementation with 0.5% BSA (37 °C, 5% CO2). On the following day, for western blot assays, cells were incubated with compounds for 15 min (37 °C, 5% CO2). Insulin was added into corresponding samples and incubated for another 15 min (37 °C, 5% CO2). When the incubation time was finished, cells were washed with PBS and lysed as previously described. For mRNA expression determination, cells were pre- incubated with compounds for 30 min. Insulin was added to the corresponding samples and incubated for another 24 h (37 °C, 5% CO2). When the incubation was finished, the cells were washed with PBS and lysed with RLT buffer supplemented with 1% 2-mercaptoethanol for mRNA isolation and RT-qPCR.

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)

value: adipocyte stem cell


title: E23_rabbit_striatum, scRNAseq

city: San Francisco

first: Alex

last: Pollen

state: CA

country: USA

institute: University of California San Francisco

description: Library name: E23_rabbit_striatum

library_source: transcriptomic single cell

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: GRCr8 (rat), mOrycun1.1 (rabbit), mMonDom1.pri (opossum), SugarGlider_lib1_testN_pseudohap (Sugar glider), ASM1176430v1.1 (ferret), SusScrofa11.1 (pig)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: striatum, LGE, MGE

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells from pig, ferret, opossum, rat, and rabbit were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's protocol

value: striatum, LGE, MGE

value: WT, E23

value: developing brain


title: NGS4277 LIB5452742 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452742_SAM24411573

value: Epithelial


title: NGS4277 LIB5452744 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452744_SAM24411575


title: neural progenitor cells, C3, Pan troglodytes, IgG, NPC_Rep3

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

description: Library name: NPC_C3_IgG_R3

library_source: genomic

data_processing:
Adapters were trimmed with cutadapt v2.5 (Martin, 2011) and sequencing quality was determined with fastqc v0.11.5 (Andrews et al., 2010). Reads 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).. Peak calling with macs2 was performed with matched IgG samples as the background set and the following parameters: --nomodel --shift -100 --extsize 200. Peak calling was also performed for all mapped reads for each TF of interest using macs2 to get the set of consensus peaks.
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: peak bed files
Library strategy: CUT&Tag

molecule: genomic DNA

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 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 and piNs at D28 were scraped off of tissue culture plates into NE1 lysis buffer (20mM HEPES pH 7.9, 10mM KCl, 0.1% Triton X-100, 3mM MgCl2, 0.5mM Spermidine, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) and nutated at 4°C for 10min to isolate nuclei. Nuclei were pelleted at 4°C at 200rpm for 10min and then resuspended in 1ml WB150 (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) for counting. For each library, 500,000 nuclei were aliquoted into a total volume of 1ml WB150. 20µl Concanavalin A bead (Bangs Laboratories, cat # BP531) slurry was prepared per library by washing beads twice in binding buffer (20µM HEPES-KOH pH7.9, 10µM KCl, 1µM CaCl2, 1µM MnCl2) and resuspending in 10µl binding buffer. Beads were added to the nuclei suspension and incubated for 10min at room temperature. Using a magnet, the supernatant was removed, and beads were resuspended in 50µl antibody buffer (WB150 supplemented with 0.1% Triton X-100 and 2mM EDTA) with 1µl primary antibody (rabbit anti-FOSL2: Cell Signaling Technology, cat #19967; rabbit anti-MAZ: Abcam, cat #ab85725; rabbit IgG: Cell Signaling Technology, cat #2729S; rabbit anti-H3K27Ac: abcam, cat #ab4729; rabbit anti-FOS: Cedarlane, cat# 226003) for overnight incubation at 4°C.
The next day, the primary antibody solution was removed and beads were resuspended in 100µl of antibody buffer with 1.2µl of secondary antibody (goat anti-rabbit: Fisher Scientific, cat #NBP172763; goat anti-mouse: Abcam, cat #ab46540). Beads were incubated at room temperature for 1h and then washed 3X with 1ml WB150. Beads were resuspended in 100µl WB300 (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50mL) containing 2.5µl proteinAG-Tn5 (Epicypher Inc, cat #15-1017) and incubated at room temperature for 1h. Then, beads were washed 3X with 1ml WB300 and incubated in tagmentation buffer (WB300 supplemented with 10mM MgCl2) at 50°C for 1h at 500rpm. DNA was extracted with Phenol/Chloroform, ethanol precipitated with 0.02mg/ml GlycoBlue (Life Technologies, cat #AM9515), and resuspended in 22µl H2O.
For library preparation, 20µl of DNA was PCR amplified with 5X KAPA Hifi Buffer (Roche, cat #KK2101), 0.3mM dNTP (Roche, cat #KK2101), 1µl KAPA HiFi Polymerase (Roche, cat #KK2101), and primers with Illumina adapters in a 50µl reaction at 72°C for 5min, 98°C for 30s, 14 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1min, and 72°C for 5min. DNA was purified using double-sided size selection (0.5X, then 1.2X) with Ampure XP beads (Thermo Fisher, cat #NC0110018). Briefly, 25µl of SPRI beads were added to the PCR reaction, incubated at room temperature for 8 min, and allowed to adhere to the magnet for 8 min. The supernatant was moved to a new tube and 65µl of SPRI beads were added. After 8 min incubation at room temperature, beads were allowed to adhere to the magnet for 8 min, the supernatant was discarded, and beads were washed twice with 200µl 80% EtOH for 30s each. Beads were resuspended in 53µl 10mM Tris-HCl, pH 7.5 and placed on the magnet, and the supernatant was moved to a new tube. The supernatant was then further cleaned by adding 55µl beads, incubated at room temperature for 8 min, washed twice with 200µl 80% EtOH for 30s each, and then eluted in 20µl 10mM Tris-HCl, pH 7.5. Libraries were quantified with the KAPA Library Quantification Kit (Roche, cat #07960140001).

value: neural progenitor cells

tag: target

value: IgG


title: chALL4 MLLT1

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: chALL4_MLLT1

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1. Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20. Reads were aligned to the reference genome hg38 using bowtie2 version 2.5.1 with with default parameters. and blacklisted regions (https://github.com/Boyle-Lab/Blacklist) were removed using bedtools. BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM  --minMappingQuality 10 --maxFragmentLength 2000 --minFragmentLength 1 --samFlagInclude 3 --samFlagExclude 4. Peak calling was performed using lanceotron v1.2.6 with the following parameters: -c 0.5
Assembly: hg38
Supplementary files format and content: Bigwigs and Peaks

source_name: KMT2A::AFF1 ALL patient

extract_protocol:
TOPMentation
Briefly, protein A-coupled magnetic beads (10 µl) were incubated with 1 µl of the appropriate antibody for 4 h with rotation at 4 °C in PBS with 0.5% BSA and 1× protease inhibitor cocktail. The antibodies used are detailed in Supplementary Table 1. Cells were single-fixed (1% formaldehyde for 10 min) for histone modifications or double-fixed (2 mM disuccinimidyl glutarate for 30 min, then 1% formaldehyde for 30 min) for transcription/chromatin factors. Fixed samples were lysed in 120 µl of lysis buffer (50 mM Tris-HCl pH 8.0, 0.5% SDS, and 10 mM EDTA, 1× protease inhibitor cocktail) and sonicated using a Covaris ME220 (Woburn, MA) to generate 200–300 bp fragments. The sonicated chromatin was then incubated with Triton-X100 at a final concentration of 1% for 10 min at room temperature to neutralize the SDS in the lysis buffer. The chromatin was pre-cleared for 30 min at 4 °C with rotation using 5 µl protein A-coupled beads to reduce non-specific binding. The antibody-incubated beads were washed in 150 µl Binding Wash Buffer (PBS with 0.5% FCS), and the pre-cleared chromatin was then added to the antibody-coated beads before incubation overnight at 4 °C with rotation. Immunoprecipitated chromatin was washed three times with RIPA buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na deoxycholate). Beads were transferred to a second tube between the first and second wash to remove non-immunoprecipitated fragments that adhered to the tube. The beads were then washed once with Tris-EDTA and once with 10 mM Tris-HCl pH 8.0. The chromatin was then tagmented by resuspending beads in 29 µl Tagmentation Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 10% dimethylformamide) and adding 1 µl of transposase (Illumina). Samples were incubated at either 37 °C or 50oC for 5 min 5 mins (dependent on the activity of the transposase lot), and the reaction was terminated by adding 150 µl RIPA buffer. Beads were washed with 10 mM Tris-HCl pH 8.0 to remove any detergent and resuspended in 22.5 µl ddH2O. In order to amplify the tagmented chromatin, 25 µl NEBNext Ultra II Q5 Master Mix (NEB) and indexed amplification primers (125 nM final concentration) were added, and libraries were prepared using the following thermal profile: 72 °C 5 min, 95 °C 5 min, (98 °C 10 s, 63 °C 30 s, 72 °C 3 min) × 12 cycles, 72 °C 5 min. Library clean-up was performed using Agencourt AMPure XP beads at a 1:1 ratio. Samples were sequenced by paired-end sequencing on a NextSeq 500 or on a NovaSeq6000 S4 flow cell.

tag: disease state

value: acute lymphoblastic leukemia (ALL)

value: KMT2A::AFF1 ALL patient

tag: chip antibody


title: neural progenitor cells, C3, Pan troglodytes, IgG, NPC_Rep2

description: Library name: NPC_C3_IgG_R2


title: chALL4 H3K27ac

description: Library name: chALL4_H3K27ac


title: NGS4277 LIB5452740 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452740_SAM24411571


title: neural progenitor cells, C2, Pan troglodytes, IgG, NPC_Rep2

description: Library name: NPC_C2_IgG_R2


title: EX00013861_10nmol/L_24h_5

description: Library name: LIB2024_066_041_001


title: neural progenitor cells, C2, Pan troglodytes, IgG, NPC_Rep3

description: Library name: NPC_C2_IgG_R3


title: chALL4 H3K4me3

description: Library name: chALL4_H3K4me3


title: PPP_10umol/L_24h_1

description: Library name: LIB2024_066_043_001


title: EX00013861_10nmol/L_24h_6

description: Library name: LIB2024_066_042_001


title: NGS4277 LIB5452745 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452745_SAM24411576


title: NGS4277 LIB5452741 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452741_SAM24411572


title: NGS4277 LIB5452743 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452743_SAM24411574


title: NGS4277 LIB5452739 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452739_SAM24411570


title: chALL4 H3K27me3

description: Library name: chALL4_H3K27me3


title: neural progenitor cells, C1, Pan troglodytes, IgG, NPC_Rep2

description: Library name: NPC_C1_IgG_R2


title: neural progenitor cells, C3, Pan troglodytes, MAZ, NPC_Rep3

description:
Library name: NPC_C3_MAZ_R3
consensus_peaks.MAZ.hg38.bed

value: MAZ


title: chALL4 H3K4me1

description: Library name: chALL4_H3K4me1


title: NGS4277 LIB5452738 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452738_SAM24411569


title: EX00013861_10nmol/L_24h_3

description: Library name: LIB2024_066_039_001


title: EX00013861_10nmol/L_24h_4

description: Library name: LIB2024_066_040_001


title: neural progenitor cells, C1, Pan troglodytes, MAZ, NPC_Rep3

description:
Library name: NPC_C1_MAZ_R3
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, C2, Pan troglodytes, MAZ, NPC_Rep3

description:
Library name: NPC_C2_MAZ_R3
consensus_peaks.MAZ.hg38.bed


title: EX00013861_10nmol/L_24h_2

description: Library name: LIB2024_066_038_001


title: neural progenitor cells, C1, Pan troglodytes, IgG, NPC_Rep3

description: Library name: NPC_C1_IgG_R3


title: NGS4277 LIB5452737 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452737_SAM24411568


title: EX00013861_10nmol/L_24h_1

description: Library name: LIB2024_066_037_001


title: NGS4277 LIB5452736 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452736_SAM24411567


title: chALL4 KMT2A-N

description: Library name: chALL4_KMT2A-N


title: NGS4277 LIB5452735 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452735_SAM24411566


title: DMSO_0.1%_24h_6

description: Library name: LIB2024_066_036_001


title: chALL4 SSRP1

description: Library name: chALL4_SSRP1


title: neural progenitor cells, C3, Pan troglodytes, MAZ, NPC_Rep2

description:
Library name: NPC_C3_MAZ_R2
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, C2, Pan troglodytes, MAZ, NPC_Rep2

description:
Library name: NPC_C2_MAZ_R2
consensus_peaks.MAZ.hg38.bed


title: DMSO_0.1%_24h_4

description: Library name: LIB2024_066_034_001


title: neural progenitor cells, C1, Pan troglodytes, MAZ, NPC_Rep2

description:
Library name: NPC_C1_MAZ_R2
consensus_peaks.MAZ.hg38.bed


title: chALL4 H3K79me2

description: Library name: chALL4_H3K79me2


title: neural progenitor cells, C3, Pan troglodytes, FOSL2, NPC_Rep3

description:
Library name: NPC_C3_FOSL2_R3
consensus_peaks.FOSL2.hg38.bed


title: chALL4 PAF1

description: Library name: chALL4_PAF1


title: NGS4277 LIB5452729 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452729_SAM24411560


title: neural progenitor cells, C2, Pan troglodytes, FOSL2, NPC_Rep3

description:
Library name: NPC_C2_FOSL2_R3
consensus_peaks.FOSL2.hg38.bed


title: DMSO_0.1%_24h_3

description: Library name: LIB2024_066_033_001


title: chALL3 H3K27me3

description: Library name: chALL3_H3K27me3


title: DMSO_0.1%_24h_2

description: Library name: LIB2024_066_032_001


title: chALL4 RING1B

description: Library name: chALL4_RING1B


title: NGS4277 LIB5452728 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452728_SAM24411559


title: neural progenitor cells, C1, Pan troglodytes, FOSL2, NPC_Rep3

description:
Library name: NPC_C1_FOSL2_R3
consensus_peaks.FOSL2.hg38.bed


title: DMSO_0.1%_24h_1

description: Library name: LIB2024_066_031_001


title: chALL3 H3K4me3

description: Library name: chALL3_H3K4me3


title: NGS4277 LIB5452724 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452724_SAM24411555


title: chALL3 H3K4me1

description: Library name: chALL3_H3K4me1


title: EX00014762_10umol/L_4h_6

description: Library name: LIB2024_066_030_001


title: neural progenitor cells, C3, Pan troglodytes, FOSL2, NPC_Rep2

description:
Library name: NPC_C3_FOSL2_R2
consensus_peaks.FOSL2.hg38.bed


title: NGS4277 LIB5452723 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452723_SAM24411554


title: chALL4 RUNX1

description: Library name: chALL4_RUNX1


title: NGS4277 LIB5452734 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452734_SAM24411565


title: DMSO_0.1%_24h_5

description: Library name: LIB2024_066_035_001


title: chALL3 H3K27ac

description: Library name: chALL3_H3K27ac


title: EX00014762_10umol/L_4h_5

description: Library name: LIB2024_066_029_001


title: NGS4277 LIB5452730 NCI-H358 G03498025 1uM + G03427947 1uM, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452730_SAM24411561


title: NGS4277 LIB5452722 NCI-H358 G03427947 1uM + DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452722_SAM24411553


title: chALL3 PAF1c

description: Library name: chALL3_PAF1c


title: neural progenitor cells, C1, Pan troglodytes, FOSL2, NPC_Rep2

description:
Library name: NPC_C1_FOSL2_R2
consensus_peaks.FOSL2.hg38.bed


title: EX00014762_10umol/L_4h_2

description: Library name: LIB2024_066_026_001


title: chALL3 KMT2A-N

description: Library name: chALL3_KMT2A-N


title: NGS4277 LIB5452718 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452718_SAM24411549


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep1

description:
Library name: H1C1b_F10-1_2hrKCl_H3K27Ac_Rep1
The raw data are being made available for controlled access in dbGaP.

organism:
Pan troglodytes
Homo sapiens

value: patterned induced neurons

tag: kcl treatment


title: NGS4277 LIB5452719 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452719_SAM24411550


title: EX00014762_10umol/L_4h_1

description: Library name: LIB2024_066_025_001


title: chALL2 KMT2A-N

description: Library name: chALL2_KMT2A-N


title: NGS4277 LIB5452721 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4277_R7888_LIB5452721_SAM24411552


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H2C2a_G11-1_2hrKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, H3K27Ac, piN_Rep1

description:
Library name: H2C2a_G6-2_minusKCl_H3K27Ac_Rep1
The raw data are being made available for controlled access in dbGaP.

value: minusKCl


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H2C2a_G6-2_2hrKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: chALL3 H3K79me2

description: Library name: chALL3_H3K79me2


title: NGS4277 LIB5452720 NCI-H358 G03498025 1uM + DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452720_SAM24411551


title: chALL3 RUNX1

description: Library name: chALL3_RUNX1


title: BI02997598_10umol/L_4h_6

description: Library name: LIB2024_066_024_001


title: BI02997598_10umol/L_4h_5

description: Library name: LIB2024_066_023_001


title: neural progenitor cells, C2, Pan troglodytes, FOSL2, NPC_Rep2

description:
Library name: NPC_C2_FOSL2_R2
consensus_peaks.FOSL2.hg38.bed


title: EX00014762_10umol/L_4h_4

description: Library name: LIB2024_066_028_001


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H2C2a_G11-1_minusKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: NGS4277 LIB5452717 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 2

description: Library name: NGS4277_R7888_LIB5452717_SAM24411548


title: NGS4277 LIB5452716 NCI-H358 DMSO 0.02%, 48 hrs, Replicate 1

description: Library name: NGS4277_R7888_LIB5452716_SAM24411547


title: EX00014762_10umol/L_4h_3

description: Library name: LIB2024_066_027_001


title: chALL2 H3K4me3

description: Library name: chALL2_H3K4me3


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H2C2a_G6-2_minusKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: chALL2 H3K79me2

description: Library name: chALL2_H3K79me2


title: BI02997598_10umol/L_4h_4

description: Library name: LIB2024_066_022_001


title: HJ-23-1

city: JiangSu

first: Zhang Meiqi

last: Zhang

address: 59 Cangwu Road, Haizhou District, Lianyungang City

country: China

institute: 江苏海洋大学

data_processing:
Raw data quality assessed with FastQC.
Quality trimming using Trimmomatic.
Alignment with HISAT2.
Redundancy and insertion fragment distribution analysis with RSeQC.Uniformity and genome structure distribution analysis with Qualimap.
Gene coverage and sequencing distribution analysis with BEDTools.
Assembly: HISAT2
Supplementary files format and content: The counts matrices provide gene expression counts across different samples. RSEM quantification files contain estimated expression levels for each gene and transcript. Quality control reports from FastQC are also included to visualize and assess the sequencing data quality.

source_name: Colorectal Carcinoma

growth_protocol: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 30µM HJ-23 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: Colorectal Carcinoma

value: Colorectal cells

tag: genotype

value: WT

value: HJ-25, 30 μM, 24 hours


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H1C1b_F10-1_2hrKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: chALL2 H3K4me1

description: Library name: chALL2_H3K4me1


title: BI02997598_10umol/L_4h_3

description: Library name: LIB2024_066_021_001

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, H3K27Ac, piN_Rep3

description:
Library name: H1C1b_F10-1_minusKCl_H3K27Ac_Rep3
The raw data are being made available for controlled access in dbGaP.


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep2

description:
Library name: H2C2a_G6-2_2hrKCl_H3K27Ac_Rep2
The raw data are being made available for controlled access in dbGaP.


title: DMSO-1

extract_protocol:
One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer.
Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: DMSO, 0.1%, 24 hours


title: DMSO-2


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, H3K27Ac, piN_Rep2

description:
Library name: H2C2a_G6-2_minusKCl_H3K27Ac_Rep2
The raw data are being made available for controlled access in dbGaP.


title: chALL2 H3K27ac

description: Library name: chALL2_H3K27ac


title: BI02997598_10umol/L_4h_1

description: Library name: LIB2024_066_019_001

value: adipocyte stem cell


title: chALL1 KMT2A-N

description: Library name: chALL1_KMT2A-N


title: EX00013861_10nmol/L4h_6

description: Library name: LIB2024_066_018_001


title: chALL1 H3K79me2

description: Library name: chALL1_H3K79me2


title: chALL1 H3K4me3

description: Library name: chALL1_H3K4me3


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, H3K27Ac, piN_Rep2

description:
Library name: H1C1b_F10-1_minusKCl_H3K27Ac_Rep2
The raw data are being made available for controlled access in dbGaP.


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep2

description:
Library name: H1C1b_F10-1_2hrKCl_H3K27Ac_Rep2
The raw data are being made available for controlled access in dbGaP.


title: Whole BM, ei, Mouse 1

city: Freiburg im Breisgau

first: Heike L.

last: Pahl

address: Breisacher Str. 117

institute: University Hospital Freiburg

description:
Library name: EPIG_A07_1033
10x Genomics

data_processing:
Raw sequencing data were processed and aligned to the murine genome GRCm39 using the CellRanger pipeline (10x Genomics, version v9.0.0).
We applied sample-specific quality control and excluded low-quality cells with mitochondrial read fractions exceeding 5 median absolute deviations (MAD) above the median. This approach preserved cell type composition across samples, including those where cells with low transcriptional complexity (erythrocytes and neutrophils) were abundant. We detected residual ambient RNA from red blood cells lysis and neutrophils and removed these reads by applying SoupX to the count matrices.  We identified doublets using the R-Bioconductor package scDblFinder.
Subsequent data analysis was performed using Scanpy  and Seurat V5.
Assembly: GRCm39
Supplementary files format and content: CellRanger H5 files and Rdata file containing Seurat objects

organism: Mus musculus

source_name: Whole Bone Marrow  (BM) Cells

extract_protocol:
Whole BM cells were harvested by flushing of femora and tibiae and viably frozen. Viably frozen cells were thawed at 37 ºC, resuspended in ice-cold PBS, washed twice and counted with a LUNA automated cell counter (Logos Biosystems).
Single cell capture, reverse transcription and library preparation were carried out on the Chromium platform (10x Genomics) with the single cell 3ʹ reagent v2 protocol according to the manufacturer’s recommendations using 1,000 cells as input per reaction channel. The cDNA libraries were paired end sequenced (26 bp and 74 bp) on the Illumina HiSeq 4000 system.

value: Whole Bone Marrow  (BM) Cells

value: LSD1 ei

tag: host strain


title: Whole BM, ei ctrl, Mouse 3

description:
Library name: EPIG_A07_1030
10x Genomics

source_name: Whole Bone Marrow (BM) Cells

value: Whole Bone Marrow (BM) Cells

value: LSD1 ei ctrl


title: Whole BM, ei, Mouse 2

description:
Library name: EPIG_A07_1034
10x Genomics


title: EX00013861_10nmol/L4h_4

description: Library name: LIB2024_066_016_001


title: Whole BM, ei ctrl, Mouse 2

description:
Library name: EPIG_A07_1032
10x Genomics


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep1

description:
Library name: H2C2a_G11-1_2hrKCl_H3K27Ac_Rep1
The raw data are being made available for controlled access in dbGaP.


title: chALL1 H3K27ac

description: Library name: chALL1_H3K27ac

value: acute lymphoblastic leukemia (ALL)


title: EX00013861_10nmol/L4h_5

description: Library name: LIB2024_066_017_001


title: chALL1 H3K4me1

description: Library name: chALL1_H3K4me1

value: KMT2A::AFF1 ALL patient


title: Whole BM, ei ctrl, Mouse 1

description:
Library name: EPIG_A07_1031
10x Genomics


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, H3K27Ac, piN_Rep1

description:
Library name: H2C2a_G11-1_minusKCl_H3K27Ac_Rep1
The raw data are being made available for controlled access in dbGaP.


title: EX00013861_10nmol/L4h_3

description: Library name: LIB2024_066_015_001


title: SEM_B9

description: Library name: SEM_B9

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1. Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20. Reads were aligned to the reference genome hg38 using bowtie2 vbowtie2-align-s version 2.5.1 with with default parameters. Duplicate reads were removed using Picard MarkDuplicates v3.1.1 with with default parameters. BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM. Peak calling was performed using lanceotron v1.2.6 with the following parameters: -c 0.5
Assembly: hg38
Supplementary files format and content: BigWig

source_name: SEM

extract_protocol:
ATAC-seq
ATAC-seq was conducted on 5 × 104 live cells using Nextera Tn5 transposase (Illumina) as previously described123. Libraries were sequenced by paired-end sequencing with a 75-cycle high-output Nextseq 500 kit (Illumina)

value: KMT2A::AFF1 ALL cell line

value: SEM


title: BI02997598_10umol/L_4h_2

description: Library name: LIB2024_066_020_001


title: SEM_C6

description: Library name: SEM_C6


title: Whole BM, ko BMT, Mouse 2

description:
Library name: EPIG_A07_1017
10x Genomics

value: LSD1 ko BMT


title: EX00013861_10nmol/L4h_2

description: Library name: LIB2024_066_014_001


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, H3K27Ac, piN_Rep1

description:
Library name: H2C2a_G6-2_2hrKCl_H3K27Ac_Rep1
The raw data are being made available for controlled access in dbGaP.

value: patterned induced neurons


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, IgG, piN_Rep1

description:
Library name: H2C2a_G6-2_2hrKCl_IgG_Rep1
The raw data are being made available for controlled access in dbGaP.

value: IgG


title: Forskolin_10umol/L_4h_6

description: Library name: LIB2024_066_012_001


title: Whole BM, ko ctrl BMT, Mouse 2

description:
Library name: EPIG_A07_1015
10x Genomics

value: LSD1 ko ctrl BMT


title: SEM_B11

description: Library name: SEM_B11


title: Whole BM, ko BMT, Mouse 1

description:
Library name: EPIG_A07_1016
10x Genomics


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H2C2a_G11-1_2hrKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: RS411_C10

description: Library name: RS411_C10


title: Whole BM, ko ctrl BMT, Mouse 1

description:
Library name: EPIG_A07_1014
10x Genomics


title: Forskolin_10umol/L_4h_4

description: Library name: LIB2024_066_010_001


title: EX00013861_10nmol/L4h_1

description: Library name: LIB2024_066_013_001


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, IgG, piN_Rep1

description:
Library name: H2C2a_G6-2_minusKCl_IgG_Rep1
The raw data are being made available for controlled access in dbGaP.

value: minusKCl


title: Whole BM, ko, Mouse 2

description:
Library name: EPIG_A07_1007
10x Genomics

value: LSD1 ko


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, IgG, piN_Rep1

description:
Library name: H2C2a_G11-1_minusKCl_IgG_Rep1
The raw data are being made available for controlled access in dbGaP.


title: Forskolin_10umol/L_4h_3

description: Library name: LIB2024_066_009_001

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)


title: Whole BM, ko ctrl, Mouse 2

description:
Library name: EPIG_A07_1006
10x Genomics

value: LSD1 ko ctrl


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H2C2a_G6-2_2hrKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H2C2a_G11-1_minusKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: RS411_A6

description: Library name: RS411_A6


title: RS411_A8

description: Library name: RS411_A8


title: Forskolin_10umol/L_4h_2

description: Library name: LIB2024_066_008_001

value: adipocyte stem cell


title: Whole BM, ko, Mouse 1

description:
Library name: EPIG_A07_1005
10x Genomics

value: Whole Bone Marrow  (BM) Cells


title: Forskolin_10umol/L_4h_5

description: Library name: LIB2024_066_011_001


title: SEM_B4

description: Library name: SEM_B4


title: Forskolin_10umol/L_4h_1

description: Library name: LIB2024_066_007_001


title: RS411_A4

description: Library name: RS411_A4


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H2C2a_G6-2_minusKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: iALL9

description: Library name: iALL9


title: DMSO_0.1%_4h_6

description: Library name: LIB2024_066_006_001


title: RRBS_PGCs_E13.5f_Uhrf2L1/L1_rep2

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

data_processing:
Reads were trimmed to remove low quality bases with Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired) and aligned to the mm10 genome with BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1).
Methylation scores were calculated using methratio.py in BSMAP v2.74 (parameters -z -u -g) and CpGs were filtered at a minimum of 8 X sequencing depth.
Assembly: mm10
Supplementary files format and content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Primordial germ cells

extract_protocol:
Genomic DNA samples were prepared by proteinase K digestion, phenol/chloroform/Isoamyl alcohol (25:24:1) extraction and precipitation with ethanol.
RRBS libraries were prepared as described in Bender et al. (2021), Methods Mol Biol 2214:207-220. Briefly, between 5 and 100 ng genomic DNA were digested with MspI (Thermo Fisher Scientific) for 5 h at 37°C, end-repaired and A-tailed with 5 U Klenow fragment exo- (Thermo Fisher Scientific) for 40 min at 37°C and ligated to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (Thermo Fisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel, purified with the MinElute gel extraction kit (Qiagen) and bisulfite converted with the EpiTect bisulfite kit (Qiagen) with two consecutive rounds of conversion. Final libraries were amplified with PfU Turbo Cx hotstart DNA polymerase (Agilent) with 14-18 PCR cycles and purified with AMPure XP beads (Beckman Coulter).

value: Primordial germ cells

value: Uhrf2 L1/L1

tag: developmental stage

tag: Sex

value: Female


title: Whole BM, ko ctrl, Mouse 1

description:
Library name: EPIG_A07_1004
10x Genomics


title: DMSO_0.1%_4h_5

description: Library name: LIB2024_066_005_001


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H1C1b_F10-1_minusKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: RRBS_PGCs_E13.5f_Uhrf2L1/L1_rep1


title: DMSO_0.1%_4h_4

description: Library name: LIB2024_066_004_001


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, IgG, piN_Rep1

description:
Library name: H1C1b_F10-1_2hrKCl_IgG_Rep1
The raw data are being made available for controlled access in dbGaP.


title: DMSO_0.1%_4h_3

description: Library name: LIB2024_066_003_001


title: chALL7

description: Library name: chALL7

value: acute lymphoblastic leukemia (ALL)

value: KMT2A::AFF1 ALL patient


title: RRBS_PGCs_E13.5f_Uhrf2L1_WT_rep1

value: WT


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, IgG, piN_Rep3

description:
Library name: H1C1b_F10-1_2hrKCl_IgG_Rep3
The raw data are being made available for controlled access in dbGaP.


title: chALL3

description: Library name: chALL3


title: DMSO_0.1%_4h_2

description: Library name: LIB2024_066_002_001


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, IgG, piN_Rep2

description:
Library name: H1C1b_F10-1_2hrKCl_IgG_Rep2
The raw data are being made available for controlled access in dbGaP.


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, IgG, piN_Rep2

description:
Library name: H2C2a_G6-2_minusKCl_IgG_Rep2
The raw data are being made available for controlled access in dbGaP.


title: DMSO_0.1%_4h_1

description: Library name: LIB2024_066_001_001


title: RRBS_PGCs_E13.5m_Uhrf2L1/L1_rep1

value: Male


title: RRBS_PGCs_E13.5m_Uhrf2L1/L1_rep2


title: chALL1

description: Library name: chALL1


title: Whole Genome Sequencing of RS4;11 cells

description: Library name: gDNA-RS411

data_processing:
FastQ files were quality checked using FastQC and the reads were trimmed using Trim Galore with the parameter --2colour 20. The trimmed reads were then mapped to hg38 reference genome using Bowtie2, PCR duplicates were removed using picard MarkDuplicates (v3.0.0) and blacklisted regions were removed using bedtools. Variant calling was performed using bcftools (v1.17) the variants were split at multiallelic sites and then filtered for quality and non-heterozygous SNP variants removed. SNPs were then annotated using dbSNP (build 151).
Assembly: hg38
Supplementary files format and content: VCF containing identified SNVs and INDELS

extract_protocol:
Genomic DNA was extracted from 5x106 cells using a Monarch Genomic DNA extraction kit (NEB)
2 ng of genomic DNA was incubated at 55°C for 15 minutes with 0.4 ul TDE1 (Illumina) before purification (Qiagen MinElute PCR purification kit). Indexing and sample purification was performed in the same manner as for TOPmentation. Libraries were sequenced on a NovaSeq X (2x150 bp).

value: pre-B cell


title: RRBS_PGCs_E13.5m_Uhrf2L1_WT_rep2


title: chALL2

description: Library name: chALL2


title: SEM H3K79me3

description: Library name: SEM_H3K79me3

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1. Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20. Reads were aligned to the reference genome hg38 using bowtie2 version 2.5.1 with with default parameters. and blacklisted regions (https://github.com/Boyle-Lab/Blacklist) were removed using bedtools. BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM  --minMappingQuality 10 --maxFragmentLength 2000 --minFragmentLength 1 --samFlagInclude 3 --samFlagExclude 4. Peak calling was performed using lanceotron v1.2.6 with the following parameters: -c 0.5
Assembly: hg38
Supplementary files format and content: Bigwigs

extract_protocol:
ChIP-seq
Briefly, 10^7 cells were single-fixed (1% formaldehyde for 10 min) for histone modifications or double-fixed (2 mM disuccinimidyl glutarate for 30 min, then 1% formaldehyde for 30 min) for transcription/chromatin factors, then lysed with 120 µl SDS lysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) and sonicated using a Covaris ME220 (Woburn, MA) to generate 200–300 bp fragments. Insoluble material was pelleted, then the supernatant was diluted 10× and pre-cleared for 30 min at 4 °C with rotation using 5 µl protein A- and G-coupled dynabeads (ThermoFisher Scientific). An input sample was taken, then 2 µg antibody was added to the sample before incubation overnight at 4 °C with rotation. The antibodies used are detailed in Supplementary Table 3. Protein A- and G-coupled dynabeads were used to isolate antibody-chromatin complexes, after which the beads were washed three times with RIPA buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP40 and 0.7% sodium deoxycholate) and once with Tris-EDTA. Samples were eluted with SDS lysis buffer, RNase A- and proteinase K-treated and crosslinks were reversed at 65 °C overnight. DNA was purified by PCR purification column (Qiagen) and analyzed by qPCR, relative to input. PCR primer sequences are given in Supplementary Table 4. For ChIP-seq, libraries were generated using the Ultra II library preparation kit (NEB), then sequenced by paired-end sequencing with a 75-cycle high-output Nextseq 500 kit (Illumina).

value: SEM


title: RRBS_PGCs_E13.5m_Uhrf2L1_WT_rep1


title: Whole Genome Sequencing of SEM cells

description: Library name: gDNA-SEM


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, IgG, piN_Rep2

description:
Library name: H1C1b_F10-1_minusKCl_IgG_Rep2
The raw data are being made available for controlled access in dbGaP.

value: patterned induced neurons

value: IgG


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, IgG, piN_Rep1

description:
Library name: H2C2a_G11-1_2hrKCl_IgG_Rep1
The raw data are being made available for controlled access in dbGaP.


title: RRBS_PGCs_E13.5f_Uhrf2L1_WT_rep2


title: chALL1 Enhancer Capture Sub-library 6

description: Library name: chALL1-enhancer-capture-sublibrary-6

data_processing:
MCC analysis was performed using the MCC pipeline 31 (https://github.com/jojdavies/Micro-Capture-C).
Assembly: hg38
Supplementary files format and content: BigWig of the MES1 enhancer viewpoint

source_name: KMT2A::AFF1 ALL

extract_protocol:
MCC protocol
Briefly, 5x106 chALL1 blast cells were fixed with 2% formaldehyde for 10 min, then quenched with glycine and washed with PBS. Cells were permeabilized with 0.005% digitonin (Sigma Aldrich) for 15 min, then snap-frozen. Thawed cells were pelleted and resuspended in reduced-calcium MNase buffer (10 mM Tris-HCl pH 7.5, 1 mM CaCl2), then split into 3 aliquots. Cells were treated with a titration of different micrococcal nuclease (NEB) concentrations (typically 10-30 Kunitz U in an 800 µl volume) for 1 h at 37 °C in a Thermomixer (Eppendorf) at 550 rpm. The reaction was stopped with the addition of ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA) to 5 mM and 200 µl was removed to assess the extent of digestion. The remaining cells were pelleted, washed with PBS/EGTA, then processed for end repair, phosphorylation and ligation. Cell pellets were resuspended in DNA ligase buffer, supplemented with 400 µM dNTPs and 5 mM EDTA, before addition of DNA Polymerase I large (Klenow) fragment (NEB) to 100 U/µl, T4 polynucleotide kinase (NEB) to 200 U/µl and T4 DNA ligase (Thermo Scientific) to 300 U/µl. The reaction was incubated for 2 h at 37 °C, then for 8 h at 20 °C, at 550 rpm, then cooled to 4 °C overnight. Both the digested and ligated chromatin were decrosslinked at 65 °C in the presence of proteinase K, then DNA was purified using the Qiagen DNeasy Blood and Tissue Kit. Digestion and ligation efficiencies were assessed by TapeStation (Agilent D1000). Library preparation, indexing and capture were performed as described for NG Capture-C.

value: KMT2A::AFF1 ALL


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, IgG, piN_Rep5

description:
Library name: H2C2a_G11-1_2hrKCl_IgG_Rep5
The raw data are being made available for controlled access in dbGaP.


title: RRBS_PGCs_E13.5f_Uhrf2_KO_rep1


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, IgG, piN_Rep2

description:
Library name: H2C2a_G6-2_2hrKCl_IgG_Rep2
The raw data are being made available for controlled access in dbGaP.


title: SEM H3K4me3

description: Library name: SEM_H3K4me3


title: SEM H3K36me2

description: Library name: SEM_H3K36me2


title: chALL1 Enhancer Capture Sub-library 5

description: Library name: chALL1-enhancer-capture-sublibrary-5


title: SEM ERG

description: Library name: SEM_ERG


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, FOS, piN_Rep1

description:
Library name: H2C2a_G6-2_2hrKCl_FOS_Rep1
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed

value: FOS


title: RRBS_PGCs_E13.5m_Uhrf2_WT_rep2


title: chALL1 Enhancer Capture Sub-library 4

description: Library name: chALL1-enhancer-capture-sublibrary-4


title: RRBS_E8.5_Uhrf2_KO_rep2

source_name: Whole embryo

value: Whole embryo


title: RRBS_E8.5_Uhrf2_KO_rep1


title: chALL1 Enhancer Capture Sub-library 3

description: Library name: chALL1-enhancer-capture-sublibrary-3


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, FOS, piN_Rep1

description:
Library name: H2C2a_G6-2_minusKCl_FOS_Rep1
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed

value: minusKCl


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, IgG, piN_Rep5

description:
Library name: H2C2a_G11-1_minusKCl_IgG_Rep5
The raw data are being made available for controlled access in dbGaP.


title: SEM CTCF

description: Library name: SEM_CTCF


title: chALL1 Enhancer Capture Sub-library 2

description: Library name: chALL1-enhancer-capture-sublibrary-2


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H2C2a_G11-1_2hrKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: chALL1 Enhancer Capture Sub-library 1

description: Library name: chALL1-enhancer-capture-sublibrary-1


title: RS411 KMT2A

description: Library name: RS411_KMT2A


title: RRBS_E8.5_Uhrf2_WT_rep2


title: RS411 H3K79me2

description: Library name: RS411_H3K79me2


title: RRBS_E8.5_Uhrf2_WT_rep1


title: chALL4

description: Library name: chALL4


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H2C2a_G6-2_2hrKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: RRBS_PGCs_E13.5m_Dnmt1_cKO_rep2

value: Dnmt1 D/D (cKO)


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H2C2a_G6-2_minusKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: RS411 H3K4me1

description: Library name: RS411_H3K4me1


title: RRBS_PGCs_E13.5m_Dnmt1_cKO_rep1


title: RS411 H3K4me3

description: Library name: RS411_H3K4me3


title: CUT&TAG for H3K27ac in HSPC-derived leukemia sample 2 replicate 1

description: Library name: HSPC-derived-leukemia-sample-2-rep1_H3K27ac

data_processing:
CUT&TAG analysis was performed using the SeqNado pipeline (https://github.com/alsmith151/SeqNado). In brief, Following QC of FASTQ files by FastQC (v0.12.1;1), reads were trimmed using trim_galore with Cutadapt (v0.6.10 ;2). Trimmed reads were then mapped to the hg38 reference genome using Bowtie 2 (v2.5.1)3. PCR duplicates were removed using picard MarkDuplicates (v3.0.0; 4). Problematic genomic regions present in the ENCODE Blacklist 5 were removed from the aligned files, and further QC of the aligned files was performed using samtools (v1.17)6. As many of the factors that were immunoprecipitated have a mix of both sharp and broad modalities, we used the deep learning-based peak caller LanceOtron (v1.0.8)7 (with a peak score cut-off value of 0.5) to call peaks. Due to the limited material available, replicates were not performed and therefore an IDR-based method was not used. BigWigs were generated using the deepTools (v3.5.1) bamCoverage command (https://github.com/deeptools/deepTools), with the flags –extendReads –normalizeUsing RPKM, and visualized in the UCSC genome browser8.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

source_name: Bone Marrow

extract_protocol:
CUT&TAG protocol
3-6x105 FACS sorted bone marrow cells  were pelleted at 300 x g for 10 mins at RT before resuspending in 1 ml NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, 1× Complete Protease Inhibitor [EDTA-free]) and incubating on ice for 10 mins. Nuclei were pelleted at 500 x g for 10 mins at 4oC  before resuspending in 0.1% formaldehyde and incubating at RT for 2 mins, followed by quenching with 78 mM Glycine and pelleting the nuclei at 500 x g for 10 mins  at 4oC. Nuclei were resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× Roche Complete Protease Inhibitor [EDTA-free]) and counted by trypan blue staining. Concanavalin A (Con A)  beads were activated by washing (2x) with 1 ml Concanavalin Activation Buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂). For each antibody/sample combination, 5 ul of activated ConA beads were added to  5x104 . Nuclei were incubated with 0.5 ul of primary antibody (antibodies listed in Supplementary Table 3) in 25 ul of antibody buffer (0.1% BSA, 2 mM EDTA in Wash Buffer) for either 1 hr at RT or overnight at 4oC. Nuclei were then incubated with 25 ul of 1:100 secondary antibody (typically Guinea Pig anti-Rabbit IgG) for 30 mins at RT. Nuclei were washed with 200 ul Wash Buffer and incubated with 25 ul 1:20 pAG-Tn5 (EpiCypher) in WB-300 (300 mM NaCl in Wash Buffer) for 1hr at RT. Nuclei were washed (x2) with 200 ul of WB-300 to remove unbound pAG-Tn5 and then incubated at 37oC for 1hr in 50 ul Tagmentation buffer  (10 mM MgCl₂ in WB-300). Tagmentation was halted  by washing with 50 ul TAPS Wash Buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA) before lysing the nuclei with 5 ul SDS-ProK Buffer (1% SDS, 10 mM TAPS pH 8.5, Thermolabile Proteinase K) and incubating for 1 hr at 37oC and 1hr at 58oC. SDS was neutralised with 15 ul 6% Triton and tagmented DNA amplified with NEBNext Ultra II Q5 Master Mix and indexed primers (thermal profile: 58 °C 5 min, 72 °C 5 min, 98 °C 5 min, [98 °C 10 sec, 60 °C 10 sec, 72 °C 1 min] ×12). Libraries were cleaned with Agencourt AMPure XP beads and sequenced on NovaSeqX.

value: Bone Marrow

value: KMT2A::AFF1 Blasts


title: CUT&TAG for H3K27ac in HSPC-derived leukemia sample 1 replicate 2

description: Library name: HSPC-derived-leukemia-sample-1-rep2_H3K27ac


title: RRBS_PGCs_E13.5m_Dnmt1_Het(D/+)_rep2

value: Primordial germ cells

value: Dnmt1 D/+


title: SEM ELF1

description: Library name: SEM_ELF1

value: acute lymphoblastic leukemia (ALL)


title: RS411 H3K27ac

description: Library name: RS411_H3K27ac


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H1C1b_F10-1_minusKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: RRBS_PGCs_E13.5m_Dnmt1_Het(D/+)_rep1


title: CUT&TAG for H3K27ac in HSPC-derived leukemia sample 1 replicate 1

description: Library name: HSPC-derived-leukemia-sample-1-rep1_H3K27ac


title: RS411 AFF1

description: Library name: RS411_AFF1


title: chALL1 Sub-library 6

description: Library name: chALL1_E-H12

data_processing:
MCC analysis was performed using the MCC pipeline (https://github.com/jojdavies/Micro-Capture-C).
Assembly: hg38
Supplementary files format and content: Average BigWig for selected viewpoints


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, FOS, piN_Rep1

description:
Library name: H1C1b_F10-1_2hrKCl_FOS_Rep1
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: RRBS_PGCs_E13.5m_Dnmt1_Het(2lox/-)_rep2

value: Dnmt1 2lox/-


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H1C1b_F10-1_2hrKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: SEM TET2

description: Library name: SEM_TET2


title: chALL1 Sub-library 5

description: Library name: chALL1_E-H11


title: RRBS_PGCs_E13.5f_Dnmt1_Het(2lox/-)_rep1

value: Female


title: CUT&TAG for H3K27ac in HSPC-derived leukemia sample 2 replicate 2

description: Library name: HSPC-derived-leukemia-sample-2-rep2_H3K27ac


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, FOS, piN_Rep3

description:
Library name: H2C2a_G11-1_minusKCl_FOS_Rep3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: patterned induced neurons, H2C2a_G6-2, 2hrKCl, Homo sapiens, FOS, piN_Rep2

description:
Library name: H2C2a_G6-2_2hrKCl_FOS_Rep2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: chALL1 Sub-library 4

description: Library name: chALL1_E-H10


title: patterned induced neurons, H2C2a_G6-2, minusKCl, Homo sapiens, FOS, piN_Rep2

description:
Library name: H2C2a_G6-2_minusKCl_FOS_Rep2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: chALL1 Sub-library 3

description: Library name: chALL1_C9B-D11


title: RRBS_PGCs_E13.5m_Dnmt1_WT_rep1

value: WT

value: Male


title: SEM RUNX3

description: Library name: SEM_RUNX3

value: SEM


title: patterned induced neurons, H1C1b_F10-1, 2hrKCl, Homo sapiens, FOS, piN_Rep2

description:
Library name: H1C1b_F10-1_2hrKCl_FOS_Rep2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed

value: patterned induced neurons


title: patterned induced neurons, H1C1b_F10-1, minusKCl, Homo sapiens, FOS, piN_Rep2

description:
Library name: H1C1b_F10-1_minusKCl_FOS_Rep2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: SEM RUNX2

description: Library name: SEM_RUNX2


title: RNAseq_E8.5_Uhrf2_KO_rep3

data_processing:
The reads were mapped to the mouse mm10 genome using TopHat2 v2.0.13 with a RefSeq transcriptome index and default parameters.
Bigwig files were generated using bam2wig.py from the RSeQC package v2.4 (parameters -u -t 5000000000).
Assembly: mm10
Supplementary files format and content: We provide bigWig files for visualization of RNA-seq tracks.

extract_protocol:
Total RNA samples were extracted using the RNeasy Micro kit (Qiagen).
RNA-seq libraries were generated from > 200 ng total RNA using the TruSeq Stranded Total RNA Library Prep kit with Ribo-Zero depletion (Illumina) according to the manufacturer’s instructions.


title: chALL1 Sub-library 1

description: Library name: chALL1_A-D12


title: RNAseq_E8.5_Uhrf2_KO_rep2


title: chALL1 Sub-library 2

description: Library name: chALL1_B9B-D10


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, FOS, piN_Rep5

description:
Library name: H2C2a_G11-1_2hrKCl_FOS_Rep5
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed


title: E83_pig_striatum, scRNAseq

description: Library name: E83_pig_striatum

organism: Sus scrofa

source_name: striatum

value: striatum

value: WT, E83

value: developing brain


title: patterned induced neurons, H2C2a_G11-1, 2hrKCl, Homo sapiens, FOS, piN_Rep1

description:
Library name: H2C2a_G11-1_2hrKCl_FOS_Rep1
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed

value: FOS


title: RNAseq_E8.5_Uhrf2_KO_rep1

value: Whole embryo


title: SEM RBBP5

description: Library name: SEM_RBBP5


title: E83_pig_cortex, scRNAseq

description: Library name: E83_pig_cortex

source_name: cortex

value: cortex


title: RNAseq_E8.5_Uhrf2_WT_rep3


title: patterned induced neurons, H2C2a_G11-1, minusKCl, Homo sapiens, FOS, piN_Rep5

description:
Library name: H2C2a_G11-1_minusKCl_FOS_Rep5
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOS.hg38.bed

value: minusKCl


title: neural progenitor cells, H2C2f, Homo sapiens, IgG, NPC_Rep1

description:
Library name: NPC_H2C2f_IgG_R0
The raw data are being made available for controlled access in dbGaP.

value: neural progenitor cells

value: IgG


title: RNAseq_E8.5_Uhrf2_WT_rep2


title: RRBS_PGCs_E13.5m_Dnmt1_WT_rep2

value: Primordial germ cells


title: SEM PU1

description: Library name: SEM_PU1

value: acute lymphoblastic leukemia (ALL)


title: SEM SMYD2

description: Library name: SEM_SMYD2


title: neural progenitor cells, H2C2f, Homo sapiens, IgG, NPC_Rep3

description:
Library name: NPC_H2C2f_IgG_R3
The raw data are being made available for controlled access in dbGaP.


title: RNAseq_E8.5_Uhrf2_WT_rep1


title: SEM POL2SER2

description: Library name: SEM_POL2SER2


title: Infested 2h R1

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

description:
Library name: Inf_2h_R1
Differential_expression.xlsx, tab 2h vs Control

data_processing:
The preprocessing step was carried out with Trimmomatic version (v) 0.35 (Bolger, Lohse and Usadel, 2014) to remove adapters and filter reads by quality. The filtered high-quality reads were aligned to the most recent version (NBI v1.1) of the Gossypium hirsutum genome downloaded from CottonGen.org using the TopHat2 v2.2 (Trapnell et al., 2012) software with its default parameter values. The abundance estimation of the transcripts was performed using the Cufflinks package v.2.2.1 and the fragments per kilobase of transcript per million mapped reads (FPKM) normalized values and the differential expression analysis were carried out using the Cuffdiff from Cufflinks package (Trapnell et al., 2012) with its default parameter values. Genes with FDR value ≤ 0.05 and absolute fold change (log2FC)  > 1  were considered differentially expressed genes (DEGs).
Assembly: Gossypium hirsutum (NBI v1.1)
Supplementary files format and content: Spreadsheets containing differential expression test and FPKM

organism: Gossypium hirsutum

source_name: Floral buds

growth_protocol: Cotton (Gossypium hirsutum variety “BRS 372”) plants were grown under controlled temperature (27 ± 2 °C) and natural photoperiod in Embrapa Genetic Resources and Biotechnology in Brasilia (DF, Brazil). Three-month-old plants containing flower buds with approximately 6 mm were selected for the experiments.

extract_protocol:
RNA extraction was conducted using InviTrap Spin Plant RNA Mini Kit (Stratec, Birkenfeld, Germany), starting with an input of 100 mg of grounded tissue, according to the manufacturer's instructions.
The 12 first-strand paired-end (2 x 150 bp) libraries were prepared with NEB Next® Ultra Directional RNA Library Prep Kit for Illumina (San Diego, CA, USA), with rRNA removal-Ribo-ZeroTM Magnetic Kit and were sequenced using an Illumina HiSeq 4000 platform PE150.

treatment_protocol: An egg of A. grandis that was ready to hatch, containing an active embryo, was inoculated in a cotton flower bud previously drilled with a needle. The orifice resulting from drilling was sealed with vaseline to prevent dehydration of the egg. The hatching of larvae occurred after about 2 h of egg inoculation (de Moura, Freitas, et al., 2022). Control flower buds and infested flower buds were collected after 2 h and 12 h of infestation immediately frozen in liquid nitrogen and kept at -80 oC until RNA isolation. The control samples consisted of drilled cotton flower buds sealed with vaseline in which no egg was inoculated. Each biological replicate consisted of a pool of five flower buds from different plants and the bioassay was performed with three biological replicates for each condition.

value: Floral buds

value: BRS 372

value: Floral buds infested with boll weevil collected after 2h of infestation, replicate 1


title: RNAseq_PGCs_E13.5f_Uhrf2_KO_rep4

extract_protocol:
Total RNA samples were extracted using the RNeasy Micro kit (Qiagen).
RNA-seq libraries were generated from 1 to 10 ng total RNA using the Ovation RNA Seq System V2 (NuGEN) according to the manufacturer’s instructions.

value: Female


title: neural progenitor cells, H2C2f, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H2C2f_IgG_R2
The raw data are being made available for controlled access in dbGaP.


title: Infested 2h R3

description:
Library name: Inf_2h_R3
Differential_expression.xlsx, tab 2h vs Control

value: Floral buds infested with boll weevil collected after 2h of infestation, replicate 3


title: neural progenitor cells, H2C2a, Homo sapiens, IgG, NPC_Rep3

description:
Library name: NPC_H2C2a_IgG_R3
The raw data are being made available for controlled access in dbGaP.


title: RNAseq_PGCs_E13.5f_Uhrf2_KO_rep3


title: SEM MLLT1

description: Library name: SEM_MLLT1

value: SEM


title: SEM POL2SER5

description: Library name: SEM_POL2SER5


title: RNAseq_PGCs_E13.5f_Uhrf2_KO_rep2


title: Infested 2h R2

description:
Library name: Inf_2h_R2
Differential_expression.xlsx, tab 2h vs Control

value: Floral buds infested with boll weevil collected after 2h of infestation, replicate 2


title: neural progenitor cells, H1C1f, Homo sapiens, IgG, NPC_Rep3

description:
Library name: NPC_H1C1f_IgG_R3
The raw data are being made available for controlled access in dbGaP.


title: SEM SPT16

description: Library name: SEM_SPT16


title: Control 2h R2

description:
Library name: Ctrl_2h_R2
Differential_expression.xlsx, tab 2h vs Control

value: Control for 2h replicate 2


title: RNAseq_PGCs_E13.5f_Uhrf2_KO_rep1


title: neural progenitor cells, H1C1f, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H1C1f_IgG_R2
The raw data are being made available for controlled access in dbGaP.


title: SEM MED26

description: Library name: SEM_MED26


title: SEM MED1

description: Library name: SEM_MED1


title: Infested 12h R3

description:
Library name: Inf_12h_R3
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds infested with boll weevil collected after 12h of infestation, replicate 3


title: RNAseq_PGCs_E13.5f_Uhrf2_WT_rep4

value: WT


title: Infested 12h R2

description:
Library name: Inf_12h_R2
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds infested with boll weevil collected after 12h of infestation, replicate 2


title: RNAseq_PGCs_E13.5f_Uhrf2_WT_rep3


title: neural progenitor cells, H2C2f, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H2C2f_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed

value: MAZ


title: SEM LEO1

description: Library name: SEM_LEO1


title: Infested 12h R1

description:
Library name: Inf_12h_R1
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds infested with boll weevil collected after 12h of infestation, replicate 1


title: neural progenitor cells, H2C2a, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H2C2a_IgG_R2
The raw data are being made available for controlled access in dbGaP.

value: neural progenitor cells


title: SEM LEDGF

description: Library name: SEM_LEDGF


title: RNAseq_PGCs_E13.5f_Uhrf2_WT_rep1


title: SEM KSRP

description: Library name: SEM_KSRP


title: SEM MENIN

description: Library name: SEM_MENIN


title: neural progenitor cells, H2C2f, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H2C2f_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: Control 2h R1

description:
Library name: Ctrl_2h_R1
Differential_expression.xlsx, tab 2h vs Control

value: Control for 2h replicate 1


title: RNAseq_PGCs_E13.5m_Uhrf2_KO_rep4

value: Primordial germ cells

value: Male


title: SEM KMT2A-N

description: Library name: SEM_KMT2A-N

value: acute lymphoblastic leukemia (ALL)


title: neural progenitor cells, H2C2a, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H2C2a_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: RNAseq_PGCs_E13.5m_Uhrf2_KO_rep3


title: SEM RUNX1

description: Library name: SEM_RUNX1


title: neural progenitor cells, H2C2a, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H2C2a_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, H1C1f, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H1C1f_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: RNAseq_PGCs_E13.5m_Uhrf2_KO_rep2


title: SEM H3K9me3

description: Library name: SEM_H3K9me3


title: Biol rep1, 2-week-old caa39 aerial parts.

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

institute: Aix-Marseille Université

data_processing:
Quality Check FASTQC v 0.11.9
Alignment against transcriptome Araport11_cdna_20160703_representative_gene_model, Bowtie 2 v 2.4.4
Read count
Differential expression with SARTools 1.7.4 (edgeR 3.36.0)
Assembly: Araport11_cdna_20160703_representative_gene_model

organism: Arabidopsis thaliana

source_name: Aerial part

growth_protocol: Growth in a controlled environment at 120 μmol m-2 s-1 illumination with a 16 h (long days) photoperiod at 22°C day / 20°C night, and 55% day / 75% night relative humidity during 2 weeks.

extract_protocol:
For each biological repetition, RNA samples were obtained by pooling RNAs from 4 plants. Aerials parts were collected on plants at developmental growth stage 1.04 (Boyes et al., 2001). Total RNA was extracted using TRI Reagent (MRC) and purified using RNA clean and concentrator-25 (Zymo Research) according to the supplier’s instructions.
DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: No treatment

value: Aerial part

tag: ecotype

value: The predominant cell types originate from various leaf tissues such as mesophyll, epidermis or vascular tissues.

value: no


title: RNAseq_PGCs_E13.5m_Uhrf2_KO_rep1


title: iALL2

description: Library name: iALL2

value: KMT2A::AFF1 ALL patient


title: RNAseq_PGCs_E13.5f_Uhrf2_WT_rep2

value: Female


title: neural progenitor cells, H2C2f, Homo sapiens, MAZ, NPC_Rep1

description:
Library name: NPC_H2C2f_MAZ_R0
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: SEM MLLT3

description: Library name: SEM_MLLT3

value: SEM


title: neural progenitor cells, H1C1f, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H1C1f_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: Control 12h R3

description:
Library name: Ctrl_12h_R3
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds

value: BRS 372

value: Floral buds control treatment for 12h, replicate 3


title: SEM H3K79me2

description: Library name: SEM_H3K79me2


title: Biol rep2, 2-week-old ess aerial parts.

value: ess


title: neural progenitor cells, H2C2f, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H2C2f_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: SEM H3K4me1

description: Library name: SEM_H3K4me1


title: Control 12h R2

description:
Library name: Ctrl_12h_R2
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds control treatment for 12h, replicate 2


title: RNAseq_PGCs_E13.5m_Uhrf2_WT_rep4

value: WT


title: Control 2h R3

description:
Library name: Ctrl_2h_R3
Differential_expression.xlsx, tab 2h vs Control

value: Control for 2h replicate 3


title: Biol rep1, 2-week-old ess aerial parts.


title: RNAseq_PGCs_E13.5m_Uhrf2_WT_rep3


title: Biol rep2, 2-week-old WT aerial parts.


title: SEM H3K36me3

description: Library name: SEM_H3K36me3


title: RNAseq_PGCs_E13.5m_Uhrf2_WT_rep2


title: Control 12h R1

description:
Library name: Ctrl_12h_R1
Differential_expression.xlsx, tab 12h vs Control

value: Floral buds control treatment for 12h, replicate 1


title: Biol rep2, 2-week-old caa39 aerial parts.


title: SEM H3K27me3

description: Library name: SEM_H3K27me3


title: neural progenitor cells, H2C2f, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H2C2f_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed

value: neural progenitor cells


title: neural progenitor cells, H2C2a, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H2C2a_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: RNAseq_PGCs_E13.5m_Uhrf2_WT_rep1

value: Primordial germ cells

value: Male


title: SEM H3K27ac

description: Library name: SEM_H3K27ac

value: acute lymphoblastic leukemia (ALL)


title: Biol rep1, 2-week-old WT aerial parts.

value: Aerial part

value: The predominant cell types originate from various leaf tissues such as mesophyll, epidermis or vascular tissues.


title: SEM FLI1

description: Library name: SEM_FLI1


title: P40_sugarglider_striatum, scRNAseq

description: Library name: P40_sugarglider_striatum

organism: Petaurus breviceps

value: striatum

value: WT, P40

value: developing brain


title: neural progenitor cells, H1C1f, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H1C1f_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: P40_sugarglider_cortex, scRNAseq

description: Library name: P40_sugarglider_cortex

value: cortex


title: EHEC Serotonin + Indole 3

city: Madison

first: Vanessa

last: Sperandio

state: WI

address: 1550 Linden Dr

department: Medical Microbiology & Immunology

institute: University of Wisconsin - Madison

description: Library name: B3

data_processing:
Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.
Demultiplexing, quality control, and adapter trimming was performed with bcl- convert (v4.2.4)
Assembly: GCA_000008865.2
Supplementary files format and content: tab-delimited tsv  file includes RPKM values for each Sample

organism: Escherichia coli O157:H7

growth_protocol: WT EHEC was grown in low-glucose DMEM until late log phase with either methanol as vehicle, 10 µM serotonin, 500 µM indole or both of them together.

extract_protocol:
RNA was extracted through TRIzol chloroform extraction method. Extracted RNA was treated with InvitroGen Turbo DNA-free kit and purified by SPRi (RNAClean XP).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: Vehicle, 10 µM serotonin, 500 µM indole or both of them together was added to the growth medium in a filution of 1:1000.

tag: strain

value: 10 µM serotonin + 500 µM indole


title: shCnot2n2

city: Hangzhou

first: Yulin

last: Chen

state: Not US or Canada

address: 88 Jiefang Rd, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: shCnot2n2

data_processing:
Sequence reads were cleaned and filtered using NanoFilt (2.8.0, parameter: -q 7 -l 50).
Sequence reads were then mapped to GRCh38 using minimap2 (2.17 -r941, parameter: -ax splice -uf -k14).
Differential expression analysis was performed with edgeR (3.32.1) and poly(A) length was calculated by tailfindr (1.3).
Assembly: GRCh38
Supplementary files format and content: .xls file includes the TPM for all samples
Supplementary files format and content: .txt files include the poly(A) information for each sample

source_name: HeLa

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher Scientific). 200 ng of total RNA was used for library construction.
RNA libraries for sequencing were prepared using cDNA-PCR Sequencing kit (Oxford Nanopore Technologies) following manufacturer's protocols.

value: HeLa


title: SEM EZH2

description: Library name: SEM_EZH2

value: SEM


title: shCnot2n1

description: Library name: shCnot2n1


title: neural progenitor cells, H2C2f, Homo sapiens, FOSL2, NPC_Rep1

description:
Library name: NPC_H2C2f_FOSL2_R0
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: shGfp

description: Library name: shGfp

value: shGfp


title: EHEC Serotonin + Indole 2

description: Library name: B2

value: WT


title: neural progenitor cells, H1C1f, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H1C1f_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: SEM E2A

description: Library name: SEM_E2A


title: Ground-3

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

data_processing:
The sequenced reads were mapped to the mm39 mouse reference genome using Bismark (v0.24.2) after trimming adaptor sequences and low-quality bases by Trim galore.
CT conversion in promoter CpG regions were analyzed by methylKit.
Assembly: mm39
Supplementary files format and content: text file. methylation.closestGene.tsv

source_name: spermatogonia

growth_protocol: GS cells cryopreserved for a 6 months in ISS or on Earth.

extract_protocol:
Genomic DNA was harvested using DNeasy Blood and Tissue Kit (Qiagen).
Genomic DNA libraries for RRBS were prepared using Zymo-Seq RRBS Library Kit (Zymo Research) following manufacturer's protocols.

value: spermatogonia

value: cryopreserved for a 6 months on earth


title: SEM CYCLINT1

description: Library name: SEM_CYCLINT1


title: EHEC Serotonin + Indole 1

description: Library name: B1


title: EHEC Indole 3

description: Library name: I3

value: 500 µM indole


title: Ground-2


title: 15h_ABC141_biorep3

first: Suzana

middle: P

last: Salcedo

state: Wisconsin

address: 2015 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
Library name: Stat_ABC141_3
Column name in raw counts file O_N_6.abc141_kh.sorted_SCJSCESTW.unique.bam

data_processing:
Bowtie2 v. 2.5.2 with the parameter -very-sensitive-local (to enable soft-trimming and maximise the hit rate) was used to align sequencing reads with the reference genome. gDNAx package v1.6.0 was used to assess genomic DNA contamination in RNA-seq data and filter out potential DNA reads (Calvo-Serra & Castelo, 2025). FeatureCounts v2.0.6 was used to count the number of uniquely mapped reads. DESeq2 v1.44.0 was used to reveal genes differentially expressed between exponential and stationary phases, (false discovery rate cutoff = 0.05) (Love et al., 2014). Gene Ontology (GO) term overrepresentation analysis was performed by kegga method of the limma v3.60.6 R package (Phipson et al., 2016).
Assembly: PRJNA1255660
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Acinetobacter baumannii

source_name: bacterial cell

growth_protocol: A. baumannii ABC141 was grown overnight in LB at 37°C under shaking, which corresponds to 15 h of growth and an OD600 between 2.2 and 2.5. This culture was diluted in LB to an OD600 of 0.1 before incubation under shaking at 37°C until reaching an OD600 of 0.5.

extract_protocol:
An ice-cold 5% (v/v) phenol, 95% (v/v) ethanol ultra-pure solution was prepared, and 2/5 volume was added to 28 mL of the exponential or 15 ml of the ON cultures and incubated on ice for 1h. Samples were pelleted by centrifugation at 3220 × g at 4°C for 10 min and cell pellets were subsequently dissolved in 1 mL ice cold TRIzol and transferred into a Phase-Lock-Tube (VWR, #2302830). Four hundred μL of chloroform was added and the solution was shaken without vortexing for 10 s followed by 3 min incubation at RT. Tubes were centrifuged at full speed for 15 min before the aqueous phase was transferred to a new 1.5 mL tube. RNA was precipitated by the addition of 450 μL of isopropanol and incubation for 30 min at RT. After 30 min, the RNA was pelleted by centrifugation at full speed in a microcentrifuge, and the pellet was washed with 350 μL of ethanol (75%), incubated for 10 min and centrifuged for 10 min at full speed in a microcentrifuge. The wash step was repeated three times before discarding the remaining supernatant, air-drying the pellet and resuspending the RNA with 25 μL of RNase-free water, followed by a 5 min incubation at 65°C at 900 rpm agitation. The RNA extractions were stored at -80°C before assessing their quality using a 1/10 dilution of the extraction using the 4200 TapeStation (Agilent Technologies).
Total RNA was sent to Core Unit Systems Medicine (SysMed) sequencing facility for RNA-seq (University of Würzburg, Germany), where DNase I digestion and rRNA depletion (RiboCop) was performed. Library for the sequencing was prepared using the NEBNext Multiplex Small RNA Library Prep kit. Sequencing was performed on the Illumina NextSeq-500 Mid Output KT v2.5 (150 cycles).

value: bacterial cell


title: 15h_ABC141_biorep2

description:
Library name: Stat_ABC141_2
Column name in raw counts file O_N_4.abc141_kh.sorted_SCJSCESTW.unique.bam


title: SEM CDK6

description: Library name: SEM_CDK6


title: Ground-1


title: EHEC Indole 2

description: Library name: I2


title: SEM CFP1

description: Library name: SEM_CFP1


title: Space-3

value: cryopreserved for a 6 months in ISS


title: S. aureus mNenonGreen_FLAG

city: Oeiras

first: Adrian

last: Izquierdo Martinez

state: Lisboa

address: Avenida da República

country: Portugal

institute: ITQB NOVA

description: Library name: mNenonGreen_FLAG

data_processing:
The CLC workbench (Qiagen) software was used to align the ChIP-seq reads to the reference genome (NCBI Reference Sequence GCF_002085525.1) and to export the sequence coverage data to a tabular .txt file for plotting.
Assembly: GCF_002085525.1
Supplementary files format and content: .txt, curves of coverage

organism: Staphylococcus aureus

growth_protocol: S. aureus strains were grown in TSB at 37°C with agitation overnight. The next day the cultures were diluted 1:200 in 50mL of TSB and incubated at 37°C with agitation until they reached the mid-exponential phase (OD600 0.6-0.8)

extract_protocol:
Formaldehyde (Sigma) was added to the cultures to a final concentration of 1% (v/v) and the mixture was incubated at room-temperature with shaking for 30 min. Afterwards, glycine was added to a final concentration of 125mM and further incubated at room-temperature with shaking for 10 min. Samples were resuspended in 300µl IP buffer (50mM Tris/HCl pH 7.5, 5mM EDTA, 150mM NaCl, 25mM sucrose, 1µg mL-1 lysostaphin, Sigma, 0.3 µg mL-1 RNase A, Sigma, and 1 tablet of cOmplete protease inhibitor cocktail, EDTA free, Roche, per 10mL of buffer) and incubated at 37°C for 1h with shaking. Afterwards the samples were cooled on ice, TritonX-100 was added to a final concentration of 1% (v/v) and they were vortexed. Samples were then sonicated using a Bioruptor Plus bath sonicator at 4°C using 50 cycles of alternating 30s on and 90s off in the high-power mode followed by centrifugation at 20000xg for 10min at 4°C.
Libraries were constructed using the NuGEN Ovation ultra low library preparation kit following the manufacturers instructions.

value: anti-Flag M2 (SIGMA)


title: neural progenitor cells, H2C2a, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H2C2a_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed

data_processing:
Adapters were trimmed with cutadapt v2.5 (Martin, 2011) and sequencing quality was determined with fastqc v0.11.5 (Andrews et al., 2010). Reads 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).. Peak calling with macs2 was performed with matched IgG samples as the background set and the following parameters: --nomodel --shift -100 --extsize 200. Peak calling was also performed for all mapped reads for each TF of interest using macs2 to get the set of consensus peaks.
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: peak bed files
Library strategy: CUT&Tag

extract_protocol:
NPCs at D14 and piNs at D28 were scraped off of tissue culture plates into NE1 lysis buffer (20mM HEPES pH 7.9, 10mM KCl, 0.1% Triton X-100, 3mM MgCl2, 0.5mM Spermidine, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) and nutated at 4°C for 10min to isolate nuclei. Nuclei were pelleted at 4°C at 200rpm for 10min and then resuspended in 1ml WB150 (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) for counting. For each library, 500,000 nuclei were aliquoted into a total volume of 1ml WB150. 20µl Concanavalin A bead (Bangs Laboratories, cat # BP531) slurry was prepared per library by washing beads twice in binding buffer (20µM HEPES-KOH pH7.9, 10µM KCl, 1µM CaCl2, 1µM MnCl2) and resuspending in 10µl binding buffer. Beads were added to the nuclei suspension and incubated for 10min at room temperature. Using a magnet, the supernatant was removed, and beads were resuspended in 50µl antibody buffer (WB150 supplemented with 0.1% Triton X-100 and 2mM EDTA) with 1µl primary antibody (rabbit anti-FOSL2: Cell Signaling Technology, cat #19967; rabbit anti-MAZ: Abcam, cat #ab85725; rabbit IgG: Cell Signaling Technology, cat #2729S; rabbit anti-H3K27Ac: abcam, cat #ab4729; rabbit anti-FOS: Cedarlane, cat# 226003) for overnight incubation at 4°C.
The next day, the primary antibody solution was removed and beads were resuspended in 100µl of antibody buffer with 1.2µl of secondary antibody (goat anti-rabbit: Fisher Scientific, cat #NBP172763; goat anti-mouse: Abcam, cat #ab46540). Beads were incubated at room temperature for 1h and then washed 3X with 1ml WB150. Beads were resuspended in 100µl WB300 (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50mL) containing 2.5µl proteinAG-Tn5 (Epicypher Inc, cat #15-1017) and incubated at room temperature for 1h. Then, beads were washed 3X with 1ml WB300 and incubated in tagmentation buffer (WB300 supplemented with 10mM MgCl2) at 50°C for 1h at 500rpm. DNA was extracted with Phenol/Chloroform, ethanol precipitated with 0.02mg/ml GlycoBlue (Life Technologies, cat #AM9515), and resuspended in 22µl H2O.
For library preparation, 20µl of DNA was PCR amplified with 5X KAPA Hifi Buffer (Roche, cat #KK2101), 0.3mM dNTP (Roche, cat #KK2101), 1µl KAPA HiFi Polymerase (Roche, cat #KK2101), and primers with Illumina adapters in a 50µl reaction at 72°C for 5min, 98°C for 30s, 14 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1min, and 72°C for 5min. DNA was purified using double-sided size selection (0.5X, then 1.2X) with Ampure XP beads (Thermo Fisher, cat #NC0110018). Briefly, 25µl of SPRI beads were added to the PCR reaction, incubated at room temperature for 8 min, and allowed to adhere to the magnet for 8 min. The supernatant was moved to a new tube and 65µl of SPRI beads were added. After 8 min incubation at room temperature, beads were allowed to adhere to the magnet for 8 min, the supernatant was discarded, and beads were washed twice with 200µl 80% EtOH for 30s each. Beads were resuspended in 53µl 10mM Tris-HCl, pH 7.5 and placed on the magnet, and the supernatant was moved to a new tube. The supernatant was then further cleaned by adding 55µl beads, incubated at room temperature for 8 min, washed twice with 200µl 80% EtOH for 30s each, and then eluted in 20µl 10mM Tris-HCl, pH 7.5. Libraries were quantified with the KAPA Library Quantification Kit (Roche, cat #07960140001).

value: neural progenitor cells


title: EHEC Indole 1

description: Library name: I1


title: Space-2


title: SEM BRG1

description: Library name: SEM_BRG1

value: acute lymphoblastic leukemia (ALL)


title: OD0.5_ABC141_biorep3

description:
Library name: Expo_ABC141_3
Column name in raw counts file Expo_6.abc141_kh.sorted_SCJSCESTW.unique.bam


title: 15h_ABC141_biorep1

description:
Library name: Stat_ABC141_1
Column name in raw counts file O_N_1.abc141_kh.sorted_SCJSCESTW.unique.bam


title: SEM BRD3

description: Library name: SEM_BRD3


title: OD0.5_ABC141_biorep2

description:
Library name: Expo_ABC141_2
Column name in raw counts file Expo_4.abc141_kh.sorted_SCJSCESTW.unique.bam


title: Space-1


title: SEM JMJD2A

description: Library name: SEM_JMJD2A


title: SEM BRD2

description: Library name: SEM_BRD2


title: patterned induced neurons, C2_C8-1, Pan troglodytes, 2N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: C2_C8-1_minusKCl_1
piN_human-chimp_gene_counts.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

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

tag: ploidy

value: minusKCl


title: EHEC Serotonin 2

description: Library name: S2

value: 10 µM serotonin


title: SEM BIOCAP

description: Library name: SEM_BIOCAP


title: P14_ferret_striatum, scRNAseq

description: Library name: P14_ferret_striatum

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: GRCr8 (rat), mOrycun1.1 (rabbit), mMonDom1.pri (opossum), SugarGlider_lib1_testN_pseudohap (Sugar glider), ASM1176430v1.1 (ferret), SusScrofa11.1 (pig)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

organism: Mustela putorius furo

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells from pig, ferret, opossum, rat, and rabbit were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's protocol

value: striatum

value: WT, P14

value: developing brain


title: patterned induced neurons, C2_C8-1, Pan troglodytes, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: C2_C8-1_6hrKCl_1
piN_human-chimp_gene_counts.txt


title: EHEC Vehicle 3

description: Library name: V3

value: Methanol


title: patterned induced neurons, C2_C8-1, Pan troglodytes, 2N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: C2_C8-1_2hrKCl_1
piN_human-chimp_gene_counts.txt