title: RNA_CUACC1_BRM014_rep2

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: mRNA in CU-ACC1 treated with 1 μM BRM014 for 72 hours

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT2 v2.1.0.
Fragments with read qualities greater than 10 were considered for further analysis. Of these, reads mapping to the coding strand of exonic regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser.
The table of all counts was processed using DESeq2, using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including total numbers of reads overlapping each transcript for each sample.

growth_protocol: H295R cells were cultured in DMEM: F12 medium (ATCC) supplemented with 2.5% of Nu-serum (Corning), 1% ITS (Corning) and 1% penicillin/streptomycin (PS). CU-ACC1 cells were maintained in F medium [3:1 (v/v) F12:DMEM], 5% FBS, 0.4 µg/mL hydrocortisone (Sigma-Aldrich), 5 µg/mL insulin (Sigma-Aldrich), 8.4 ng/mL cholera toxin (Sigma-Aldrich), 10 ng/mL epidermal growth factor (Invitrogen), 24 µg/mL adenine (Sigma-Aldrich) and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted from cells at 80% confluency using TRIzol reagent and mRNA enriched by poly(dT) capture. RNA was fragmented, converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 µM BRM014 or an equivalent volume of DMSO for 72 hours.


title: OTX2-dTAG_PS_HA_Rep2

status: Public on Jul 21 2025

type: SRA

city: New York

first: Ly-sha

last: Ee

address: 413 E 69th Street

country: USA

institute: Weill Cornell Medicine

description: Library name: u56_HA_7H1

library_source: genomic

data_processing:
Reads were trimmed using bbmap (v38.95) with parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2 (v2.3.5.1) with parameters --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 5 -X 999 (Langmead and Salzberg, 2012)
Reads with a MAPQ score less than 5 were removed with samtools (v1.14) (Li, et al., 2009).
PCR duplicates were removed with Picard (v2.26.10) using parameter VALIDATION_STRINGENCY=LENIENT. Fragments between 20 and 120bp were isolated using a custom awk script
Bigwigs were generated from bam files using bedtools (v2.30) normalizing to sequencing depth using the formula: (effective_genome_size / read_count * read_length) with 1870000000 as the effective genome size (Quinlan and Hall, 2010)
Bam files were converted to bed files with bedtools (v2.30) with parameter -bedpe. MACS (v2.2.6) was used to call peaks on individual and merged replicates using parameters -g 1870000000 --nomodel --seed 123 –keep-dup all (Zhang, et al., 2008)
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeak, bed
Supplementary files format and content: txt
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: 7H1 OTX2-dTAG-EGFP

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs (PS) followed by 100ng/ml Activin A, 100nM LDN for 24hrs (DE)

extract_protocol:
CUT&RUN on OTX2-HA was performed on 500,000 EpiSCs, PS or DE cells per sample using BioMag Plus Concanavalin A beads (ConA beads, PolySciences NC1358578), 1:100 anti-HA (CST C29F4 #3724) or anti-IgG (EpiCypher 130042), and ProteinA/G MNase (EpiCypher). Fragmented DNA was isolated by phenolchloroform extraction and EtOH precipitation
CUT&RUN libraries were constructed using the Takara Thruplex Library Prep and Unique Dual Index kits. Cycles for PCR amplification were determined individually for each sample by qPCR. Libraries were size selected using SPRI beads (Beckman Coulter)

treatment_protocol: Live DE cells were sorted for CUT&RUN with DAPI on BD-Influx

tag: cell line

value: 7H1 OTX2-dTAG-EGFP

tag: cell type

value: Primitive Streak

tag: genotype

value: BL6/129 hybrid


title: RNA_CUACC1_BRM014_rep1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: WT

tag: treatment


title: RNA_CUACC1_DMSO_rep2

description: mRNA in CU-ACC1 treated with DMSO for 72 hours

value: DMSO


title: OTX2-dTAG_PS_IgG

description: Library name: u54_IgG

source_name: 7H2 OTX2-dTAG-EGFP

value: 7H2 OTX2-dTAG-EGFP


title: OTX2-dTAG_PS_HA_Rep1

description: Library name: u55_HA_7H

source_name: 7H OTX2-dTAG-EGFP

value: 7H OTX2-dTAG-EGFP


title: OTX2-dTAG_EPI_K4me1_DMSO_Rep1

description: Library name: EPI_K4me1_DM_7H

data_processing:
Reads were trimmed using bbmap (v38.95) with parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hist= 1 mink=11.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2 (v2.3.5.1) with parameters --local --very-sensitive-local --no-mixed--no-discordant --phred33 -I 5 -X 999 (Langmead and Salzberg, 2012)
Reads with a MAPQ score less than 5 were removed with samtools (v1.14) (Li, et al., 2009).
PCR duplicates were removed with Picard (v2.26.10) using parameter
VALIDATION_STRINGENCY=LENIENT. Bigwigs were generated from bam files using bedtools (v2.30) normalizing to sequencing depth using the formula: (effective_genome_size / read_count * read_length) with 1870000000 as the effective genome size (Quinlan and Hall, 2010)
Assembly: Bam files were converted to bed files with bedtools (v2.30) with parameter - bedpe. MACS (v2.2.6) was used to call peaks on individual and merged replicates using parameters -g 1870000000 --nomodel --seed 123 -keep-dup all (Zhang, et al., 2008)
Supplementary files format and content: BigWig, narrowPeak
Supplementary files format and content: Bed
Library strategy: CUT&Tag

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. PS and DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs followed by 100ng/ml Activin A, 100nM LDN for 24hrs

extract_protocol:
CUT&TAG on H3K27ac and H3K4me1 was performed on 100,000-400,000 EpiSCs, PS or DE cells per sample using BioMag Plus Concanavalin A beads (ConA beads, PolySciences NC1358578), 1:100 anti-H3K27ac (EpiCypher) or anti-H3K4me1 (Abcam8895), and ProteinA/G Tn5 (EpiCypher).
Tagmented DNA was amplified using Non-Hot Start 2X PCR Master Mix (EpiCypher). Cycles for PCR amplification were determined individually for each sample by qPCR. Libraries were size selected using SPRI beads (Beckman Coulter)

treatment_protocol: Live DE cells were sorted for CUT&TAG with magnetic-assisted sorting.

value: Epiblast stem cells


title: RNA_H295R_BRM014_rep2

description: mRNA in H295R treated with 1 μM BRM014 for 72 hours


title: RNA_H295R_BRM014_rep1


title: RNA_H295R_DMSO_rep2

description: mRNA in H295R treated with DMSO for 72 hours


title: PS_DMSO_Rep2

description: Library name: PS_7H1_DM

data_processing:
Fastq files were processed and DESeq2 was used to generate real normalized counts as described in Medina Cano et al., Development 2022
Assembly: mm10
Supplementary files format and content: xlsx

molecule: polyA RNA

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs followed by 100ng/ml Activin A, 100nM LDN for 24hrs (DE1) or 48hrs (DE2)

extract_protocol:
EpiSCs, Primitive Streak (PS), DE1 and DE2 stage cells were harvested with Accutase following 21hrs of DMSO or dTAG13 treatment. Total RNA was extracted using Trizol and chloroform precipitation and purified with the Zymo RNA Clean & Concentrator kit.
PolyA-enriched libraries were prepared by Novogene

treatment_protocol: dTAG13 or DMSO vehicle added at EpiSC, PS, or DE1 stage for 21hrs to deplete OTX2.


title: PS_dTAG_Rep3

description: Library name: PS_7H2_13


title: PS_dTAG_Rep2

description: Library name: PS_7H1_13


title: GFP control 3

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
Sequencing reads were adapter trimmed using Trimgalore and aligned to hg38 using STAR. The read counts for Refseq genes were quantified using htseq-count. Differential expression analysis was performed using DEseq2.
Assembly: hg38
Supplementary files format and content: tab delimited file includes raw counts

extract_protocol:
RNA was extracted using miRNeasy Cell/Tissue advanced kit following manufacturer's recommendation. All the steps were performed in a benchtop PCR hood and all the equipments were treated with RNase away.
KAPA Hyper Prep Kit (catalog no. KK8504, KAPA Biosystems) and KAPA Dual-indexed Adapter Kit (catalog no. KK8722 KAPA Biosystems) were used to construct the CUT&RUN DNA library for sequencing on an Illumina platform following the manufacturer's instructions. After adaptor ligation, 2× volume of AMPure XP beads was used to recover the small fragments. After 12–14 cycles of PCR amplification, the product was cleaned up with AMPure XP beads. 3% gel purification was performed if the PCR dimers were too much.

value: GFP control


title: RNA_H295R_DMSO_rep1


title: PS_DMSO_Rep1

description: Library name: PS_7H_DM


title: PS_dTAG_Rep1

description: Library name: PS_7H_13


title: KYSE450, shSOX2, rep1

city: Shanghai

first: Yiting

last: Zhong

address: 130 Dong'an Road

country: China

institute: Fudan University

data_processing:
For RNA-seq analysis of gene expression profiling, three biological replicates were analyzed for each sample. The resulting RNA-seq data were analyzed for Pearson's correlation coefficients and shown to have an excellent consistency. Raw RNA-seq reads were processed by FastQC, aligned by STAR (v2.6.0c) to the human genome build hg19 and yeast genome build sacCer3 (spike-in control) with the default parameters, and converted to matrix by featureCounts (v2.0.3). Downstream analysis was performed by R package DESeq2. Differentially expressed genes were called using the fold change cutoff ≥ 3 and P-value < 0.05. The heatmaps were plotted by R package pheatmap and the expression counts were normalized by Z-score. GO analysis was performed using R package clusterProfiler.
Assembly: hg19
Supplementary files format and content: txt

growth_protocol: The ESCC and non-small cell lung cancer cells were cultured in RPMI1640 medium (Invitrogen) and supplemented with 10% fetal bovine serum (Sigma, F8318) and 1% penicillin/streptomycin. C33A cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% Fetal Bovine Serum (Sigma, F8318) and 1% penicillin/streptomycin solution (Invitrogen) at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol:
For RNA-seq analysis , equivalent numbers of cells from each group were used for preparation of RNAs. Total RNA was isolated from each sample using RNAiso Plus (TARAKA).The same amount of spike-in yeast RNAs (10%) was added to each RNA sample.  RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
RNA libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China),and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: For stable cell line generation, lentiviruses were produced by Lipofectamine 2000 (Invitrogen) transfection of HEK293T cells (Invitrogen) with pLKO shRNA-carrying plasmids and helper plasmids pMD2.G and psPAX2. Viral supernatants were collected 48 h after transfection, and filtered through a 0.45-μm filter. The stable cell lines were obtained by puromycin selection for 1 week.

tag: tissue

value: Human esophageal squamous cancer

value: SOX2 knockdown


title: KYSE450, shSOX2, rep3


title: KYSE450, shSOX2, rep2


title: EPI_DMSO_Rep3

description: Library name: EPI_7H2_DM


title: KYSE450, shVec, rep3

value: control


title: GFP control 1


title: KYSE450, shVec, rep2


title: KYSE450, shVec, rep1


title: EPI_DMSO_Rep2

description: Library name: EPI_7H1_DM


title: EPI_dTAG_Rep2

description: Library name: EPI_7H1_13


title: EPI_DMSO_Rep1

description: Library name: EPI_7H_DM


title: KYSE450, shSOX2, ChIP input

data_processing:
The ChIP-seq reads were aligned to the human genome build hg19 and mouse genome build mm10 using the bowtie2 (v2.3.4.1) with the default parameters and duplicate reads were removed by picard MarkDuplicates. The human ChIP-seq reads were multiplied by a scale factor which, when multiplied, equalized Mus musculus mapped reads and visualized in UCSC genome browser. The ChIP-seq peaks of SOX2 in control and SOX2 knockdown cells were called by MACS2 (v2.1.2) with the parameters --fix-bimodal -p 0.05 because SOX2 signals were weak, and the ChIP-seq peaks of H4ac, H3K27ac and H3K4me3 were called with the parameters -B -q 0.01 --nomodel -extsize 150. The differential ChIP-seq peaks were called with -p 1e-7, and further filtered to acquire at least 1.5-fold changed peaks. The genome distribution of SOX2 ChIP-seq peaks was calculated by R package ChIPseeker and plotted by EXCEL. The motifs of SOX2 binding sites were identified by Homer. The heatmaps and the emission profiles were plotted by Deeptools. Super-enhancers were identified using ROSE based on the ranking of H3K27ac intensities. The Veen Diagram and density plot were plotted by R package VennDiagram and ggplot2.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
The cells were crosslinked with 1% formaldehyde for 10 min and then quenched by adding 125 mM glycine. Chromatin samples were sonicated in lysis buffer (high salt buffer with 0.1% SDS and protease inhibitors).
ChIP-seq libraries were prepared using a Vazyme kit (Vazyme, ND607)


title: EPI_dTAG_Rep3

description: Library name: EPI_7H2_13


title: RNA_CUACC1_DMSO_rep1


title: PS_DMSO_Rep3

description: Library name: PS_7H2_DM


title: EPI_dTAG_Rep1

description: Library name: EPI_7H_13


title: DE2_DMSO_Rep3

description: Library name: DE2_7H2_DM

value: Definitive Endoderm


title: KYSE450, shSOX2, H3K27ac,ChIP


title: KYSE450, shSOX2, H4ac,ChIP


title: DE2_dTAG_Rep3

description: Library name: DE2_7H2_13


title: DE2_DMSO_Rep2

description: Library name: DE2_7H1_DM


title: KYSE450, shSOX2, H3K4me3,ChIP


title: KYSE450, shSOX2, SOX2,ChIP


title: KYSE450, WT, H3K27ac,ChIP


title: DE2_DMSO_Rep1

description: Library name: DE2_7H_DM


title: KYSE450, WT, SOX2,ChIP


title: KYSE450, WT, H3K4me3,ChIP


title: DE2_dTAG_Rep1

description: Library name: DE2_7H_13


title: DE1_dTAG_Rep3

description: Library name: DE1_7H2_13


title: DE1_DMSO_Rep3

description: Library name: DE1_7H2_DM


title: H11_MV411_colonies_rep3, RNA

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Following demultiplexing, squencing runs with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element countreateds from unique and ambiguously aligned reads (bam files) using TEcountreated with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single countreated table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Countreateds for individual samples are contained in column 14 onwards.

source_name: Peripheral blood

growth_protocol:
Cell lines were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium.  HL-60 cells were maintained in Iscove's Modified Dulbecco's media supplemented with 4mM GlutaMAX and 10% Fetal Bovine Serum (FBS). MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.
Treated cells were seeded in MethoCult Optimum (H4034; STEMCELL Technologies Inc.) at 500 cells/well in 6-well plates. Cells were then cultured at 37°C, 5% CO2 for 14 days to allow colony formation. Wells containing colonies were imaged using Cytation3 (Biotek). Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C.

extract_protocol:
Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C. Lysates from single colonies (HL-60: 7.5µL; MOLM-13 and MV-4-11: 2.5µL) were used to separate genomic DNA and mRNA by G&T separation and as previously described following 'scTEM-seq for low-input samples' [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
Single colony TEM-seq and parallel RNA-seq analysis was performed as described, with minor modifications. During single colony TEM-seq library preparation, the number of SINE Alu amplification cycles was reduced to 29. For RNA-seq analysis, 15 cycles of cDNA amplification were used. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol: Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. All cell lines were treated with 100nM decitabine (DAC; Selleckchem #S1200), HL-60 cells were treated with 2000nM azacytidine (AZA; Selleckchem # S1782), and MOLM-13 and MV-4-11 cells were treated with 500nM AZA. Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.

value: Peripheral blood

value: macrophage

tag: disease/cancer type

value: Biphenotypic B Myelomonocytic Leukemia

tag: Sex

value: Male

tag: age

tag: batch

tag: paired sample_id

tag: processing protocol

value: RNA-Seq

value: azacytidine


title: H12_MV411_colonies_rep3, RNA


title: H10_MV411_colonies_rep3, RNA


title: H8_MV411_colonies_rep3, RNA

value: decitabine


title: DE1_DMSO_Rep1

description: Library name: DE1_7H_DM

value: BL6/129 hybrid


title: DE2_dTAG_Rep2

description: Library name: DE2_7H1_13

value: 7H1 OTX2-dTAG-EGFP


title: KYSE450, WT, ChIP input


title: DE1_DMSO_Rep2

description: Library name: DE1_7H1_DM

value: DMSO


title: DE1_dTAG_Rep2

description: Library name: DE1_7H1_13


title: H7_MV411_colonies_rep3, RNA


title: M2B226_2

city: Suzhou

first: Cuiping

last: Liu

state: Jiangsu

address: Ganjiang Road 178#

institute: Jiang Su institue of immunology

description: Library name: Sample4

data_processing:
The gene expression analyses were performed with StringTie(v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Csv flie include FPKM values for each sample.

source_name: spleen

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen).The cDNA was synthesized from the extracted RNA using a reverse transcription kit,and labeled with fluorescent dyes.The purified DNA was denatured at high temperature (typically at 95°C for 3 minutes), followed by hybridization of the labeled cDNA to the mouse gene expression microarray chip(Agilent) according to the manufacturer's instructions.The hybridization was then carried out in a hybridization oven at 42°C for 16-20 hours.The microarray chip was washed to remove unbound cDNA using the recommended buffers and then scaned to detect fluorescence signals.
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).

treatment_protocol: Using a fluorescence-activated cell sorter (FACS) to sort CD226+ CD19+ B cells  and CD226−CD19+  B cells from splenocytes of NOD mice

value: spleen

value: sorted B cell

value: B cell

value: NO


title: DE1_dTAG_Rep1

description: Library name: DE1_7H_13

value: 7H OTX2-dTAG-EGFP


title: M2B226_1

description: Library name: Sample3


title: M1B226_2

description: Library name: Sample2


title: H9_MV411_colonies_rep3, RNA


title: H5_MV411_colonies_rep3, RNA


title: H4_MV411_colonies_rep3, RNA

value: untreated


title: M1B226_1

description: Library name: Sample1


title: H6_MV411_colonies_rep3, RNA


title: H3_MV411_colonies_rep3, RNA


title: Molar, Cilk1 KO wild type, E14.5, rep4

city: Seoul

first: Minjae

last: Kyeong

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

description: Library name: Sample5

data_processing:
Initially, Novogene's internal Perl scripts were used to process raw data in FASTQ format. Low-quality reads, adapter-containing reads, and reads with poly-N sequences were removed to obtain clean data  (clean reads). The Q20, Q30, and GC content of the clean data were then calculated. All downstream analyses were based on high-quality clean data.
Hisat2 v2.0.5 was used to align paired-end clean reads to the reference genome and provide an index of the reference genome  (mm10).
The number of reads mapped to each gene was counted using featureCounts v1.5.0-p3.  The length of each gene and the number of reads mapped to it were used to determine its FPKM.
Assembly: mm10
Supplementary files format and content: txt file includes fpkm values for each sample

source_name: Molar

extract_protocol:
Maxillary molar tooth germs from Cilk1+/+, Cilk1−/− and Cilk1−/−; PCS1−MRCS1△/△ littermate mouse embryos were dissected at E14.5  (n = 6 per biological replicate; quadruplicates for the Cilk1+/+ and Cilk1−/− groups, and triplicates for Cilk1−/−; PCS1−MRCS1△/△ group). TRIZOL® RNA extraction technique  (Invitrogen) was used to extract total RNA. The RNA quality was evaluated following RNA ScreenTape®  (Agilent Technologies, Germany).
Novogene  (China) prepared and sequenced the RNA library. Messenger RNA was isolated from total RNA using magnetic beads conjugated with poly-T oligos. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by second-strand synthesis. Once the library was constructed, it underwent amplification, purification, size selection, adapter ligation, end repair, and A-tailing. The quality of the library was assessed using a bioanalyzer for size distribution, a Qubit fluorometer, and real-time PCR for quantification. Finally, the quantified libraries were pooled and sequenced on the Illumina platform.

value: Molar

value: Wild type


title: Molar, Cilk1 KO homozygous, E14.5, rep4

description: Library name: Sample4

value: Cilk1 knockout homozygous


title: H2_MV411_colonies_rep3, RNA

value: Peripheral blood

value: macrophage

value: Biphenotypic B Myelomonocytic Leukemia


title: Molar, Cilk1; PCS1-MRCS1 KO homozygous, E14.5, rep3

description: Library name: Sample3

value: Cilk1;PCS1-MRCS1 knockout homozygous


title: Molar, Cilk1; PCS1-MRCS1 KO homozygous, E14.5, rep2

description: Library name: Sample2


title: G11_MV411_colonies_rep3, RNA

value: Male

value: RNA-Seq

value: azacytidine


title: H1_MV411_colonies_rep3, RNA


title: G12_MV411_colonies_rep3, RNA


title: G10_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 3

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: CHD4cd_ADNPdN_RNAseq_fusion_r3

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 and repeat sensitive settings according to Teissandier et al (Mobile DNA, 2019) (--outFilterType BySJout --outFilterMultimapNmax 100000  --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000  --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300  --seedNoneLociPerWindow 1000--outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax --limitBAMsortRAM 10000000000).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by using samtools and bedtools to calculate per base coverage, then counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
RNA was collected using RNeasy miniprep kit (Qiagen) according to manufacturer's instructions
Libraries were prepared using TruSeq Ilumina total RNA-seq

tag: genetic background

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: RNA-seq in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: CHD4cd_ADNPdN_RNAseq_fusion_r2


title: G9_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4wt-ADNPdN (N-terminal muntant) fusion mESC, replicate 3

description: Library name: CHD4wt_ADNPdN_RNAseq_fusion_r3


title: RNA-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 3

description: Library name: CHD4cd_ADNPwt_RNAseq_fusion_r3


title: G5_MV411_colonies_rep3, RNA

value: decitabine


title: G6_MV411_colonies_rep3, RNA


title: G7_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: CHD4cd_ADNPwt_RNAseq_fusion_r1


title: G2_MV411_colonies_rep3, RNA


title: G3_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: CHD4cd_ADNPwt_RNAseq_fusion_r2


title: RNA-seq in CHD4wt-ADNPdN (N-terminal muntant) fusion mESC, replicate 2

description: Library name: CHD4wt_ADNPdN_RNAseq_fusion_r2


title: G4_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4wt-ADNPdN (N-terminal muntant) fusion mESC, replicate 1

description: Library name: CHD4wt_ADNPdN_RNAseq_fusion_r1


title: F12_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: CHD4wt_ADNPwt_RNAseq_fusion_r2


title: RNA-seq in CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: CHD4wt_ADNPwt_RNAseq_fusion_r1


title: Molar, Cilk1; PCS1-MRCS1 KO homozygous, E14.5, rep1

description: Library name: Sample1


title: F9_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP N-terminal mutant mESC, for fusion exp, replicate 2

description: Library name: ADNPdN_RNAseq_fusion_r2


title: F10_MV411_colonies_rep3, RNA


title: KYSE450, WT, H4ac,ChIP

value: Human esophageal squamous cancer

value: control


title: F11_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP N-terminal mutant mESC, for fusion exp, replicate 1

description: Library name: ADNPdN_RNAseq_fusion_r1


title: RNA-seq in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: CHD4cd_ADNPdN_RNAseq_fusion_r1


title: G8_MV411_colonies_rep3, RNA


title: F8_MV411_colonies_rep3, RNA


title: RNA-seq in CHD4wt-ADNPwt fusion mESC, replicate 3

description: Library name: CHD4wt_ADNPwt_RNAseq_fusion_r3


title: RNA-seq in ADNP WT mESC, for fusion exp, replicate 3

description: Library name: ADNPwt_RNAseq_fusion_r3


title: F6_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP WT mESC, for fusion exp, replicate 2

description: Library name: ADNPwt_RNAseq_fusion_r2


title: F5_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP WT mESC, for fusion exp, replicate 1

description: Library name: ADNPwt_RNAseq_fusion_r1


title: G1_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP N-terminal mutant mESC, replicate 3

description: Library name: ADNPdN_RNAseq_r3


title: F3_MV411_colonies_rep3, RNA


title: F4_MV411_colonies_rep3, RNA


title: F2_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP N-terminal mutant mESC, replicate 1

description: Library name: ADNPdN_RNAseq_r1


title: RNA-seq in ADNP N-terminal mutant mESC, replicate 2

description: Library name: ADNPdN_RNAseq_r2


title: F1_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP PxVxL mutant mESC, replicate 2

description: Library name: ADNPpxvxl_RNAseq_r2


title: E12_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP PxVxL mutant mESC, replicate 1

description: Library name: ADNPpxvxl_RNAseq_r1


title: RNA-seq in ADNP N-terminal mutant mESC, for fusion exp, replicate 3

description: Library name: ADNPdN_RNAseq_fusion_r3


title: E11_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP WT mESC, replicate 3

description: Library name: ADNPwt_RNAseq_r3


title: RNA-seq in ADNP WT mESC, replicate 1

description: Library name: ADNPwt_RNAseq_r1


title: RNA-seq in ADNP KO mESC, replicate 3

description: Library name: ADNPko_RNAseq_r3


title: RNA-seq in ADNP KO mESC, replicate 2

description: Library name: ADNPko_RNAseq_r2


title: E8_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP KO mESC, replicate 1

description: Library name: ADNPko_RNAseq_r1


title: F7_MV411_colonies_rep3, RNA


title: E7_MV411_colonies_rep3, RNA


title: E6_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: CTCF_ChIP_CHD4cd-ADNPdN_fusion_r2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 with repeat sensitive settings based on Teissandier et al (Mobile DNA, 2019)  ( --outFilterMultimapNmax 100000 --outSAMmultNmax 1 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 2000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 100000 --alignWindowsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 1000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000  --outBAMsortingBinsN 100 --limitBAMsortRAM 10000000000  --alignSJDBoverhangMin 999).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (UCSC tools).

extract_protocol:
10^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ahel et al. 2025.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.


title: E5_MV411_colonies_rep3, RNA


title: E3_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: CTCF_ChIP_CHD4cd-ADNPdN_fusion_r1


title: E4_MV411_colonies_rep3, RNA


title: E2_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: CTCF_ChIP_CHD4cd-ADNPwt_fusion_r1


title: E1_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: CTCF_ChIP_CHD4wt-ADNPdN_fusion_r1


title: CTCF ChIP in CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: CTCF_ChIP_CHD4wt-ADNPwt_fusion_r1


title: CTCF ChIP in CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: CTCF_ChIP_CHD4wt-ADNPwt_fusion_r2


title: D11_MV411_colonies_rep3, RNA


title: CTCF ChIP in ADNP wt mESC, for fusion exp., replicate 2

description: Library name: CTCF_ChIP_ADNPwt_fusionExp_r2


title: D9_MV411_colonies_rep3, RNA


title: RNA-seq in ADNP WT mESC, replicate 2

description: Library name: ADNPwt_RNAseq_r2


title: CTCF ChIP in ADNP wt mESC, for fusion exp., replicate 1

description: Library name: CTCF_ChIP_ADNPwt_fusionExp_r1


title: E10_MV411_colonies_rep3, RNA


title: Input for CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: Input_CHD4cd-ADNPdN_fusion_r2


title: Input for CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: Input_CHD4cd-ADNPdN_fusion_r1


title: Input for CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: Input_CHD4cd-ADNPwt_fusion_r2


title: D6_MV411_colonies_rep3, RNA


title: D7_MV411_colonies_rep3, RNA


title: D8_MV411_colonies_rep3, RNA


title: D5_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: CTCF_ChIP_CHD4wt-ADNPdN_fusion_r2


title: Input for CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: Input_CHD4wt-ADNPdN_fusion_r2


title: D3_MV411_colonies_rep3, RNA


title: Input for CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: Input_CHD4cd-ADNPwt_fusion_r1


title: D2_MV411_colonies_rep3, RNA


title: Input for CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: Input_CHD4wt-ADNPwt_fusion_r2


title: D1_MV411_colonies_rep3, RNA


title: Input for CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: Input_CHD4wt-ADNPdN_fusion_r1


title: Input for CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: Input_CHD4wt-ADNPwt_fusion_r1


title: C12_MV411_colonies_rep3, RNA


title: D12_MV411_colonies_rep3, RNA


title: CTCF ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: CTCF_ChIP_CHD4cd-ADNPwt_fusion_r2


title: D10_MV411_colonies_rep3, RNA


title: C11_MV411_colonies_rep3, RNA


title: Input for ADNP wt mESC, for fusion exp., replicate 1

description: Library name: Input_ADNPwt_fusionExp_r1


title: C10_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: POL3_ChIP_CHD4cd-ADNPdN_fusion_r1


title: C9_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: POL3_ChIP_CHD4cd-ADNPdN_fusion_r2


title: C8_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: POL3_ChIP_CHD4cd-ADNPwt_fusion_r2


title: C7_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: POL3_ChIP_CHD4wt-ADNPdN_fusion_r2


title: C6_MV411_colonies_rep3, RNA


title: D4_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: POL3_ChIP_CHD4cd-ADNPwt_fusion_r1


title: C5_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: POL3_ChIP_CHD4wt-ADNPdN_fusion_r1


title: C4_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: POL3_ChIP_CHD4wt-ADNPwt_fusion_r1


title: C3_MV411_colonies_rep3, RNA


title: POL3 ChIP in ADNP wt mESC, for fusion exp., replicate 2

description: Library name: POL3_ChIP_ADNPwt_fusionExp_r2


title: C2_MV411_colonies_rep3, RNA


title: POL3 ChIP in CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: POL3_ChIP_CHD4wt-ADNPwt_fusion_r2


title: Input for ADNP wt mESC, for fusion exp., replicate 2

description: Library name: Input_ADNPwt_fusionExp_r2


title: C1_MV411_colonies_rep3, RNA


title: POL3 ChIP in ADNP wt mESC, for fusion exp., replicate 1

description: Library name: POL3_ChIP_ADNPwt_fusionExp_r1


title: B10_MV411_colonies_rep3, RNA


title: B9_MV411_colonies_rep3, RNA


title: ADNP ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: ADNP_ChIP_CHD4cd-ADNPdN_fusion_r1


title: B12_MV411_colonies_rep3, RNA


title: B11_MV411_colonies_rep3, RNA


title: ADNP ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: ADNP_ChIP_CHD4wt-ADNPdN_fusion_r2


title: ADNP ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: ADNP_ChIP_CHD4cd-ADNPwt_fusion_r1


title: B8_MV411_colonies_rep3, RNA


title: B7_MV411_colonies_rep3, RNA


title: B6_MV411_colonies_rep3, RNA


title: ADNP ChIP in CHD4wt-ADNPdN (N-terminal mutant) fusion mESC, replicate 1

description: Library name: ADNP_ChIP_CHD4wt-ADNPdN_fusion_r1


title: ADNP ChIP in CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: ADNP_ChIP_CHD4wt-ADNPwt_fusion_r2


title: B5_MV411_colonies_rep3, RNA


title: B4_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP wt mESC, for fusion exp., replicate 2

description: Library name: ADNP_ChIP_ADNPwt_fusionExp_r2


title: B3_MV411_colonies_rep3, RNA


title: B2_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP wt mESC, for fusion exp., replicate 1

description: Library name: ADNP_ChIP_ADNPwt_fusionExp_r1


title: CTCF ChIP Input from ADNP PxVxL mutant mESC

description: Library name: CTCF_Input_ADNPpxvxl


title: A12_MV411_colonies_rep3, RNA


title: CTCF ChIP Input from ADNP wt mESC

description: Library name: CTCF_Input_ADNPwt


title: A11_MV411_colonies_rep3, RNA


title: CTCF ChIP Input from ADNP N-terminal mutant mESC

description: Library name: CTCF_Input_ADNPdN


title: ADNP ChIP in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: ADNP_ChIP_CHD4cd-ADNPwt_fusion_r2


title: ADNP ChIP in CHD4cd (catalytic dead)-ADNPdN (N-terminal mutant) fusion mESC, replicate 2

description: Library name: ADNP_ChIP_CHD4cd-ADNPdN_fusion_r2


title: CTCF ChIP in ADNP N-terminal mutant mESC, replicate 1

description: Library name: CTCF_ChIP_ADNPdN_r1


title: CTCF ChIP in ADNP PxVxL mutant mESC, replicate 2

description: Library name: CTCF_ChIP_ADNPpxvxl_r2


title: ADNP ChIP in CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: ADNP_ChIP_CHD4wt-ADNPwt_fusion_r1


title: CTCF ChIP in ADNP PxVxL mutant mESC, replicate 1

description: Library name: CTCF_ChIP_ADNPpxvxl_r1


title: A9_MV411_colonies_rep3, RNA


title: A7_MV411_colonies_rep3, RNA


title: CTCF ChIP in ADNP wt mESC, replicate 2

description: Library name: CTCF_ChIP_ADNPwt_r2


title: A6_MV411_colonies_rep3, RNA


title: B1_MV411_colonies_rep3, RNA


title: CTCF ChIP in ADNP wt mESC, replicate 1

description: Library name: CTCF_ChIP_ADNPwt_r1


title: A10_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP N-terminal mutant mESC, replicate 3

description: Library name: ADNP_ChIP_ADNPdN_r3


title: A5_MV411_colonies_rep3, RNA


title: A4_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP N-terminal mutant mESC, replicate 1

description: Library name: ADNP_ChIP_ADNPdN_r1


title: ADNP ChIP in ADNP N-terminal mutant mESC, replicate 2

description: Library name: ADNP_ChIP_ADNPdN_r2


title: A2_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP PxVxL mutant mESC, replicate 3

description: Library name: ADNP_ChIP_ADNPpxvxl_r3


title: CTCF ChIP in ADNP N-terminal mutant mESC, replicate 2

description: Library name: CTCF_ChIP_ADNPdN_r2


title: A3_MV411_colonies_rep3, RNA


title: A1_MV411_colonies_rep3, RNA


title: ADNP ChIP in ADNP PxVxL mutant mESC, replicate 2

description: Library name: ADNP_ChIP_ADNPpxvxl_r2


title: H12_MV411_colonies_rep2, RNA


title: H10_MV411_colonies_rep2, RNA


title: ADNP ChIP in ADNP PxVxL mutant mESC, replicate 1

description: Library name: ADNP_ChIP_ADNPpxvxl_r1


title: Paraxial_Mesoderm_and_PS pool

description:
Library name: Paraxial_Mesoderm_PS_pool
10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were processed using CellRanger (10x genomics cloud).
Raw h5 files were processed using CellBender to eliminate background reads, empty beads, and other artifacts (Fleming, et al., 2022). Scanpy (Wolf, et al., 2018) was used for downstream analyses. Cell clusters with high percentage of mitochondrial reads or a relatively low number of reads were eliminated.
Palantir (Setty, et al., 2019) was used for pseudo-time analyses
For differential expression analyses, Wilcoxon testing was performed and only genes with padj<0.05 and log2 fold-change>1 were considered as differentially expressed genes (DEGs). The scores/ranking per gene given by the scanpy.get.rank_genes_groups_df function were used.
Assembly: mm10
Supplementary files format and content: h5ad

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. PS and PM are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs (PS) or additional  48hrs (PM).

extract_protocol:
Cells at indicated stages were dissociated using Accutase to single-cell suspension in PBS-/- with 0.04% BSA. Samples were labeled with Cell Multiplexing Oligos (10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 Dual Index) and live cells sorted using DAPI on a BD Influx Cell Sorter.
Three pools were created for multiplexing in PBS-/- with 0.04% BSA (targeting 10,000 cells/sample)- EpiSCs, DE with DMSO or dTAG13 added at PS stage; Paraxial Mesoderm with DMSO or dTAG13 added at PS stage; and DE with DMSO or dTAG13 added at 24hrs DE differentiation. Single-cell libraries were generated according to the manufacturer's instructions (10x Genomics Chromium Single Cell Gene Expression - Cell Multiplexing).

treatment_protocol: dTAG13 or DMSO vehicle was added at primitive streak (PS) for 48hrs to deplete OTX2 in Paraxial Mesoderm (PM).

value: 7H OTX2-dTAG-EGFP

value: Primitive streak, Paraxial Mesoderm

value: BL6/129 hybrid

value: DMSO_dTAG at primitive streak


title: A8_MV411_colonies_rep3, RNA


title: RNA-seq of inhibitory nuclei, replicate 2

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

description:
Library name: INH_rep2
Column name in TPM_all_samples.txt: INH_rep2

data_processing:
For RNA-seq datasets of excitatory and inhibitory nuclei, adapters and bases of low quality were trimmed using fastp software (v0.23.4) and the remaining reads were mapped to the mouse genome (mm10) by hisat2 (v2.2.1) with bowtie2 (v2.3.5) and quantified by stringtie (v2.2.1) to achieve the expression level of each gene. TPM (Transcripts Per Million) values were adopted as the expression levels in this study.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file represents TPMs

source_name: Whole brain (excluding olfactory bulb)

extract_protocol:
The FACS-sorted neuronal nuclei were pelleted and resuspended in 1mL TRIzol. After TRIzol/chloroform phase separation, the aqueous phase was collected in a new 1.5mL tube, an equal volume of 100% ethanol was added. The mixture was loaded onto the RNA Clean&Concentrator-5 columns. After washing once with RNA Wash Buffer, DNase I solution were added into the column and incubated for 15min at room temperature to remove any residual DNA. After washing once with RNA Prep Buffer and twice with RNA Wash Buffer, RNA was eluted from the column with RNase-free H2O. RNA concentrations were quantified with Qubit RNA HS assay kit (Thermo Fisher, cat# Q32852) on Qubit 3.0 Fluorometer (Thermo Fisher, cat# Q33218).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat# E7760S) following the manufacturer’s instructions. Briefly, rRNAs were depleted from the neuronal nuclei RNA samples using NEBNext rRNA Depletion Kit (NEB, cat# E6350S). The rRNA-depleted RNA samples were fragmented, followed by first strand cDNA synthesis and second strand cDNA synthesis. After purification with Ampure XP beads (Beckman Coulter, cat# A63880), the double-stranded cDNA samples were end repaired, dA-tailed and ligated with adaptors. After purification with Ampure XP beads (Beckman Coulter, cat# A63880), PCR amplification for 12 cycles were performed to enrich adaptor-ligated DNA. The PCR products were purified by Ampure XP beads. The concentrations of the RNA-seq libraries were quantified by Qubit dsDNA HS assay kit (Thermo Fisher, cat# Q32854) on Qubit 3.0 Fluorometer (Thermo Fisher, cat# Q33218) and the peak distributions were measured by Agilent DNA D1000 Screen Tape (Agilent, cat# 5067-5582) on 4150 TapeStation System (Agilent, cat# G2992AA). The indexed RNA-seq libraries were pooled and sequenced on Novaseq 6000 platform with paired end 150bp mode.

value: Whole brain (excluding olfactory bulb)

value: FACS-sorted inhibitory nuclei

value: Inhibitory neuron

value: WT


title: H9_MV411_colonies_rep2, RNA

value: Peripheral blood

value: macrophage

value: Biphenotypic B Myelomonocytic Leukemia


title: RNA-seq of inhibitory nuclei, replicate 1

description:
Library name: INH_rep1
Column name in TPM_all_samples.txt: INH_rep1


title: H8_MV411_colonies_rep2, RNA

value: Male

value: RNA-Seq


title: RNA-seq of excitatory nuclei, replicate 2

description:
Library name: EXC_rep2
Column name in TPM_all_samples.txt: EXC_rep2

value: FACS-sorted excitatory nuclei

value: Excitatory neuron


title: RNA-seq of excitatory nuclei, replicate 1

description:
Library name: EXC_rep1
Column name in TPM_all_samples.txt: EXC_rep1


title: H5_MV411_colonies_rep2, RNA

value: decitabine


title: H6_MV411_colonies_rep2, RNA


title: Molar, Cilk1 KO wild type, E14.5, rep3

description: Library name: Sample6

data_processing:
Initially, Novogene's internal Perl scripts were used to process raw data in FASTQ format. Low-quality reads, adapter-containing reads, and reads with poly-N sequences were removed to obtain clean data (clean reads). The Q20, Q30, and GC content of the clean data were then calculated. All downstream analyses were based on high-quality clean data.
Hisat2 v2.0.5 was used to align paired-end clean reads to the reference genome and provide an index of the reference genome (mm10).
The number of reads mapped to each gene was counted using featureCounts v1.5.0-p3.  The length of each gene and the number of reads mapped to it were used to determine its FPKM.
Assembly: mm10
Supplementary files format and content: Comma Separated Values File include fpkm values for each sample

extract_protocol:
Cilk1+/+and Cilk1 KO maxillary molar tooth germs from littermate mouse embryos were dissected at E14.5 (n = 6 per biological replicate, and triplicates per group). TRIZOL® RNA extraction technique (Invitrogen) was used to extract total RNA. The RNA quality was evaluated following RNA ScreenTape® (Agilent Technologies, Germany).
Novogene (China) prepared and sequenced the RNA library. Messenger RNA was isolated from total RNA using magnetic beads conjugated with poly-T oligos. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by second-strand synthesis. Once the library was constructed, it underwent amplification, purification, size selection, adapter ligation, end repair, and A-tailing. The quality of the library was assessed using a bioanalyzer for size distribution, a Qubit fluorometer, and real-time PCR for quantification. Finally, the quantified libraries were pooled and sequenced on the Illumina platform.

value: Molar

value: Wild type


title: Molar, Cilk1 KO wild type, E14.5, rep2

description: Library name: Sample5


title: Molar, Cilk1 KO wild type, E14.5, rep1

description: Library name: Sample4


title: H4_MV411_colonies_rep2, RNA

value: untreated


title: H3_MV411_colonies_rep2, RNA


title: Molar, Cilk1 KO homozygous, E14.5, rep3

description: Library name: Sample3

value: Cilk1 knockout homozygous


title: Molar, Cilk1 KO homozygous, E14.5, rep2

description: Library name: Sample2


title: H2_MV411_colonies_rep2, RNA


title: Molar, Cilk1 KO homozygous, E14.5, rep1

description: Library name: Sample1


title: H1_MV411_colonies_rep2, RNA


title: G12_MV411_colonies_rep2, RNA

value: azacytidine


title: Endometrial tissue, untreated

city: Chengdu

first: Ming

last: Zhang

state: Sichuan

address: Sichuan Agricultural University, Huimin Road, Wenjiang District

department: Animal Reproduction

institute: Sichuan Agricultural University, China

description:
Library name: Sample 1
SeekGene

data_processing:
Seeksoultools software was used for the generation of gene expression matrices and aggregation of sample data. Seurat in R software (version 4.1.1) was applied for further processing of the raw data
Quality control-find clusters-cluster markers-cluster annotation
Cell fate trajectory analysis
Cell communication analysis
Assembly: Mouse mm10
Assembly: Lipopolysaccharides
Supplementary files format and content: The file format is tsv.gz, mtx.gz and fastq.gz. The content of the files related to it’s the file name.

source_name: Endometrium along embryo

extract_protocol:
The mice were killed by cervical dislocation and uterine samples along with embryos were collected. At the time of sample collections, half of the one uterine horn flushed with saline to collect the blastocyst for confirmation of pregnancy and early embryonic growth. Samples from each group were pooled, washed , and dissociated with the help of SeekMate reagent kit A Pro (SeekGene, K01801301). Then samples were filtered using different reagents and cell viability checked using Cell analyzer (Counterstar®)
Library was prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene, Catalog No. K00202). Briefly, appropriate samples, Barcoded hydrogen beads and oil were added to the SeekOne® chip S3. cDNA amplification was done using PCR reaction following the purification and processed it to ligated with the adaptor for sequencing. The index sequenced libraries were filtered using Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400)  and finally generated libraries were sequenced using the Illumina NovaSeq 6000 (PE150 read length).

treatment_protocol: The mice were purchased and kept under controlled enviroment, then synchronized using PMSG and hCG followed by natural mating (1:1 male:female). The vaginal plug was observed on second day to confirm the successful mating. The mice were divided into two groups, control and LPS gorup. The Lipopolysaccharides (LPS) are administered to the LPS group on third day of pregnancy while normal saline to the control group on same time.

value: Endometrium along embryo

value: 8-16 weeks

tag: bacterial strain


title: G11_MV411_colonies_rep2, RNA


title: Transcriptome BCAA 5+3 AML cells biol rep6

city: Boston

first: Christina

last: Mayerhofer

state: MA

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

description:
RNA 24
gene_counts_transcriptome.tsv

data_processing:
RiboSeq data was processed according to the recommendation of the manufacturer (diagenode user guide C05030001) and the original RiboLite publication. First, the UMI was copied from the read to the read identifier with fumi tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools) to allow subsequent deduplication. Trimming was performed by cutadapt with parameters --match-read-wildcards -u 16 -n 4 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -a GAACTCCAGTCAC -e 0.166666 --nextseq-trim 20 -m 18. The reads were then aligned to mouse rRNA (https://www.ncbi.nlm.nih.gov/nuccore/BK000964) using bowtie2 with --seedlen=23. Unaligned reads were aligned to GRCm38 release 102 reference genome using STAR with parameters  --sjdbOverhang 36 -outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. Deduplication of reads was performed using samtools and fumi_tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools). Read distribution was calculated using read_distribution.py from RSeQC package, and metaplots were generated by RiboCode. Finally, featureCounts was used to detect exons in single-end forward stranded mode, and reads were summarized per gene.
Transcriptome RNASeq data was processed according to the recommendation of the manufacturer (Smart-Seq v4, Takara Bio USA) and the original RiboLite publication. Reads were trimmed with cutadapt in paired-end read mode with parameters: -j 4 --trim-n --match-read-wildcards -a CTGTCTCTTATACACATCT -a AAAAAAAAAAA -A CTGTCTCTTATACACATCT -A AAAAAAAAAAA --nextseq-trim 20 -m 10. Reads were then aligned using STAR to GRCm38 release 102 reference genome in paired-end read mode with parameters --sjdbOverhang 99. Finally, featureCounts was used to detect exons in paired-end unstranded mode, and reads were summarized per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: bone marrow

growth_protocol: The MLL-AF9 leukemia cells express GFP under the control of the ubiquitin transporter and luciferase under the control of the β-actin promoter.  Leukemic cells from a terminally ill mouse were harvested and expanded ex vivo in RPMI1640 medium (Lonza) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine (all from Corning), 20 ng/ml recombinant mouse SCF (rmSCF), 10 ng/ml recombinant mouse interleukin 3 (rmIL-3) and 10 ng/ml rmIL-6 (all from R&D Systems).

extract_protocol:
Mice were euthanized at the point of maximum response of chemotherapy and femurs, tibias, pelvis and humeri were isolated and cleaned to remove muscle. Bones were then crushed using a pre-cooled mortar and pestle in ice-cold flow buffer (PBS containing 2% FBS), and the obtained BM cell suspension was passed through a 70 μm cell strainer. Red blood cells were removed by incubating cells for 5 minutes in ACK lysing buffer (Gibco) on ice, the remaining BM cells were washed and resuspended in ice-cold flow buffer. Viable cells (AML cells GFP+) were sorted on a BD FACSAria II (BD Biosciences) with the sample collector cooled to 4°C. After centrifugation, samples were lysed in 20 μl ice-cold lysis buffer (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100; 25 U/ml Turbo DNase) for 10 min on ice. For mRNA 2 μl of the lysate was subjected to the Smart-seq2 protocol. Following addition to 300 μl lysis buffer to the lysate, it was clarified for 10 min at 20,000g at 4°C, then treated with RNase 1 Ambion, AM2295, 1 μl for up to 50k cells, 2 μl for up to 200k cells) and incubated at room temperature for 45 min with gentle mixing. The digested extracts were stopped by the addition of 10 μl SUPERaseIn and were overlaid onto a 700 μl sucrose cushion of 1 M sucrose in 20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX and 20 U/ml SUPERaseIn for 4 h at 260,000g, 4°C in MLA-150 rotor in Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris pH 7.5 and 1% SDS). RPFs were extracted from pellet buffer by using 1 ml Trizol and 200 μl chloroform. The aqueous phase was precipitated by adding 750 μl isopropanol and 20 μg glycogen. Precipitation was carried out at −20 °C overnight, and RPFs were then pelleted by centrifugation for 40 min at 12,000 g, 4 °C. RPF was resuspended in 6 μl nuclease-free water and mixed with 6 μl Gel Loading Buffer II. The 15% (wt/vol) polyacrylamide TBE-urea gel was pre-run for 30 min at 200 V. The RNA samples were denatured for 90 s at 80°C. RPFs were separated by electrophoresis for 65 min at 200 V. To minimize contamination, each sample was run in a separate gel and the electrophoresis was run without RNA or DNA markers. The region from 26 to 34 nt for RPFs was excised according to the light-blue loading dye and further determined on the basis of the relative position of RNA oligo markers to the loading dye on a separate and parallel gel. Extract RNA from the polyacrylamide gel slices by adding 400 μl RNA extraction buffer (300 mM sodium acetate pH 5.5, 1 mM EDTA and 0.25% SDS), snap-frozen at −80°C for 20 min and thawed at 37°C for two rounds and then kept overnight at room temperature with gentle mixing. The liquid was transferred to a clean tube, and 500 μl isopropanol and 20 μg glycogen were added and precipitated overnight. The RPF sample was pelleted by centrifugation for 40 min at 12,000 g, 4°C and resuspended in 6 μl nuclease-free water. The sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP. Barcoded libraries were pooled and sequenced on the Illumina platform with 2x 100bp reads.
For mRNA 2 μl of the lysate (10%) was subjected to the Smart-seq2 protocol. The Ribo-lite/RPF sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP.

treatment_protocol: Recipient male mice (age 8-10 weeks) were injected intravenously (retro-orbital) with 1 million leukemia cells in 200 μl PBS without preconditioning. Disease progression was tracked in luciferase-expressing AML using bioluminescence imaging. When reaching a critical AML burden, mice were treated with 5+3 (cytarabine, 100 mg/kg, once daily for 5 days and doxorubicin, 3 mg/kg, once daily for the first 3 days) or vehicle (PBS) delivered via i.p. injection.

value: bone marrow

value: MLL-AF9 AML

value: Acute myeloid leukemia

value: BCAA 5+3


title: G8_MV411_colonies_rep2, RNA

value: Peripheral blood

value: macrophage

value: Biphenotypic B Myelomonocytic Leukemia


title: G10_MV411_colonies_rep2, RNA

value: Male

value: RNA-Seq


title: Transcriptome BCAA 5+3 AML cells biol rep5

description:
RNA 21
gene_counts_transcriptome.tsv

value: WT


title: G9_MV411_colonies_rep2, RNA


title: Transcriptome BCAA 5+3 AML cells biol rep7

description:
RNA 25
gene_counts_transcriptome.tsv


title: G6_MV411_colonies_rep2, RNA

value: decitabine


title: H7_MV411_colonies_rep2, RNA


title: Transcriptome BCAA 5+3 AML cells biol rep3

description:
RNA 18
gene_counts_transcriptome.tsv


title: Transcriptome BCAA 5+3 AML cells biol rep2

description:
RNA 17
gene_counts_transcriptome.tsv


title: Transcriptome BCAA 5+3 AML cells biol rep4

description:
RNA 19
gene_counts_transcriptome.tsv


title: G5_MV411_colonies_rep2, RNA


title: G4_MV411_colonies_rep2, RNA


title: Transcriptome BCAA 5+3 AML cells biol rep1

description:
RNA 16
gene_counts_transcriptome.tsv


title: G7_MV411_colonies_rep2, RNA


title: G3_MV411_colonies_rep2, RNA


title: Transcriptome BCAA vehicle AML cells biol rep4

description:
RNA 14
gene_counts_transcriptome.tsv

value: BCAA vehicle


title: G2_MV411_colonies_rep2, RNA

value: untreated


title: Transcriptome BCAA vehicle AML cells biol rep3

description:
RNA 13
gene_counts_transcriptome.tsv


title: Transcriptome BCAA vehicle AML cells biol rep2

description:
RNA 12
gene_counts_transcriptome.tsv


title: Transcriptome AA 5+3 AML cells biol rep4

description:
RNA 10
gene_counts_transcriptome.tsv


title: F12_MV411_colonies_rep2, RNA


title: Transcriptome BCAA vehicle AML cells biol rep1

description:
RNA 11
gene_counts_transcriptome.tsv


title: F10_MV411_colonies_rep2, RNA


title: Transcriptome AA 5+3 AML cells biol rep3

description:
RNA 8
gene_counts_transcriptome.tsv


title: Transcriptome AA 5+3 AML cells biol rep2

description:
RNA 7
gene_counts_transcriptome.tsv


title: F9_MV411_colonies_rep2, RNA


title: F7_MV411_colonies_rep2, RNA


title: F8_MV411_colonies_rep2, RNA


title: F6_MV411_colonies_rep2, RNA


title: Transcriptome AA vehicle AML cells biol rep4

description:
RNA 4B
gene_counts_transcriptome.tsv

value: AA vehicle


title: F5_MV411_colonies_rep2, RNA


title: Transcriptome AA vehicle AML cells biol rep3

description:
RNA 3B
gene_counts_transcriptome.tsv


title: F3_MV411_colonies_rep2, RNA


title: Transcriptome  AA vehicle AML cells biol rep2

description:
RNA 2B
gene_counts_transcriptome.tsv


title: Transcriptome BCAA vehicle AML cells biol rep5

description:
RNA 15
gene_counts_transcriptome.tsv


title: F4_MV411_colonies_rep2, RNA


title: G1_MV411_colonies_rep2, RNA


title: F2_MV411_colonies_rep2, RNA


title: F1_MV411_colonies_rep2, RNA


title: Translatome BCAA 5+3 AML cells biol rep7

description:
RFP 25
gene_counts_translatome.tsv

library_source: other

molecule: other


title: F11_MV411_colonies_rep2, RNA

value: azacytidine


title: Transcriptome AA 5+3 AML cells biol rep1

description:
RNA 6
gene_counts_transcriptome.tsv


title: Transcriptome AA vehicle AML cells biol rep1

description:
RNA 1B
gene_counts_transcriptome.tsv


title: Translatome BCAA 5+3 AML cells biol rep6

description:
RFP 24
gene_counts_translatome.tsv


title: Translatome BCAA 5+3 AML cells biol rep4

description:
RFP 19
gene_counts_translatome.tsv


title: E10_MV411_colonies_rep2, RNA


title: Translatome BCAA 5+3 AML cells biol rep3

description:
RFP 18
gene_counts_translatome.tsv


title: Transcriptome AA vehicle AML cells biol rep5

description:
RNA 5B
gene_counts_transcriptome.tsv


title: E11_MV411_colonies_rep2, RNA


title: Translatome BCAA 5+3 AML cells biol rep5

description:
RFP 21
gene_counts_translatome.tsv


title: E9_MV411_colonies_rep2, RNA


title: Translatome BCAA 5+3 AML cells biol rep2

description:
RFP 17
gene_counts_translatome.tsv


title: Translatome BCAA 5+3 AML cells biol rep1

description:
RFP 16
gene_counts_translatome.tsv


title: E8_MV411_colonies_rep2, RNA


title: E6_MV411_colonies_rep2, RNA


title: Translatome BCAA vehicle AML cells biol rep4

description:
RFP 14
gene_counts_translatome.tsv


title: E5_MV411_colonies_rep2, RNA


title: Translatome BCAA vehicle AML cells biol rep3

description:
RFP 13
gene_counts_translatome.tsv


title: E3_MV411_colonies_rep2, RNA


title: E4_MV411_colonies_rep2, RNA


title: Translatome BCAA vehicle AML cells biol rep2

description:
RFP 12
gene_counts_translatome.tsv


title: Translatome AA 5+3 AML cells biol rep4

description:
RFP 10
gene_counts_translatome.tsv


title: E12_MV411_colonies_rep2, RNA


title: Translatome BCAA vehicle AML cells biol rep1

description:
RFP 11
gene_counts_translatome.tsv


title: E2_MV411_colonies_rep2, RNA


title: E1_MV411_colonies_rep2, RNA


title: D12_MV411_colonies_rep2, RNA


title: Translatome AA 5+3 AML cells biol rep1

description:
RFP 6
gene_counts_translatome.tsv


title: Translatome AA 5+3 AML cells biol rep3

description:
RFP 8
gene_counts_translatome.tsv


title: Translatome AA 5+3 AML cells biol rep2

description:
RFP 7
gene_counts_translatome.tsv


title: ETV3 Prog 1 CnR 447

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No

data_processing:
CUT&RUN analysis was performed with custom Snakemake pipelines. Adapters were removed using cutadapt20 v.4.5, aligned to hg38 with bowtie221 v.2.4.2 (--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 700), and duplicates removed  (samtools fixmate -m {input} - |  samtools sort -T {params.tmp} - | samtools markdup - - | samtools view -b -f 0x3 -F 0x400 –). Replicates were combined with samtools merge. Peaks were called with MACS222 (v.2.2.9.1) vs IgG controls (macs2 callpeak -t {input.expt} -c {input.ctrl} -g hs -f BAMPE -q 0.1). Peaks were filtered using the ENCODE exclusion list (ENCFF356LFX).
Assembly: hg38
Supplementary files format and content: Bigwig files scaled to reads per million, and for non-IgG samples, MACS2 peaks called with the default settings vs the IgG controls.
Library strategy: CUT&RUN

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500).

extract_protocol:
CUT&RUN was performed without fixation according mostly to the Epicypher protocol. CUT&RUN was performed on 0.4-1 million primary keratinocytes/experiment using reagents from the EpiCypher kit (EpiCypher, 14-1048), either using antibody to the endogenous TF (the majority) or infected with virus expressing HA-tagged TF (NRF1 and ZNF217). Keratinocytes were washed with PBS, harvested with trypsin, quenched with DMEM, and resuspended in cold PBS + 0.1% BSA to be maintained afterwards at 4°C. Cells were washed twice with PBS + 0.1% BSA, and quantified with a Countess. Nuclei were extracted by resuspending in 100 μL nuclei extraction buffer per 1-2.5 M cells (20 mM HEPES pH 7.5, 10 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 0.1% NP-40, and 1 tablet Roche mini protease inhibitor per 10-15 mL) and incubating for 10 minutes on ice. 5-10 volumes of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 0.05%Triton X-100, and Roche protease inhibitor) were added, cells centrifuged at 600 RCF, and supernatant removed. After an additional wash, cells were quantified using a Countess. 400K-1M nuclei were bound to 10 μL activated Concanavalin A beads (EpiCypher, 21-1401) per sample for 10 min incubation at 4°C. After removing supernatant, beads were incubated with rocking at 4°C for 2 hrs with antibody diluted in 50 μL Antibody Buffer (wash buffer with 2 mM EDTA). After staining, cells were washed twice with wash buffer, and incubated with 1.5-2.5 μL pAG-MNase (EpiCypher, 15-1016) per sample for 1 hour at 4°C with rocking, then washed with once with 150 μL wash buffer, then 150 μL low salt buffer (3.5 mM HEPES pH 7.5, 0.5 mM spermidine, 0.1% BSA, 0.05%Triton X-100, and Roche protease inhibitor) and resuspend in 50 µL low salt buffer. After 5 minutes on ice, 2 μL of 250 mM CaCl2 was added to the beads and beads were subsequentially incubated on ice for 18-25 minutes. The reactions were quenched with an equal volume 2X STOP buffer (300 mM NaCl, 20 mM EDTA, 40 mM EGTA, 0.025% SDS, 0.5% Triton X100, 0.05 mg/mL RNAse A, 0.05 mg/mL glycogen) for 30 minutes at 37°C according to the manufacturer’s protocol. Beads were placed on a magnet, and supernatant containing released fragments was removed.
DNA was extracted by a Zymo DNA Clean and Concentrator (Zymo Research, D4014), eluting in 27 μL water. Library was prepared using the NEB Ultra II DNA library prep kit (NEB, E7103S) following dx.doi.org/10.17504/protocols.io.bagaibse6, with the following modifications: the adapter was diluted 20-25 fold, PCR was performed with SYBR dye to visualize amplification, and after PCR, 20 μL of water, then 30 μL of beads (0.6X instead of 0.8X) beads were added for the initial selection to remove large small fragments, followed by the second size selection using the addition of 20 μL beads (1X instead of 1.2X) for library capture. Sequencing was performed on a NovaSeq X Plus, paired-end, 150 bp length, with 15-20 M reads for each sample.

treatment_protocol: If differentiated ("Day 4"), cells were induced to differentiate by the addition of 1.2 mM calcium for 4 days at full confluence.

tag: antibody

value: Primary keratinocytes

tag: treatment:


title: Translatome AA vehicle AML cells biol rep5

description:
RFP 5B
gene_counts_translatome.tsv


title: E9_MV411_colonies_rep3, RNA


title: ETV3 Prog 1 CnR 345

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: Translatome AA vehicle AML cells biol rep3

description:
RFP 3B
gene_counts_translatome.tsv


title: E7_MV411_colonies_rep2, RNA


title: DLX3 Day4 1 CnR 412

description: control: IgG_Day4_1_CnR_389, batch: 230818_cnr10, high stringency buffer?: No

value: Differentiated


title: Translatome AA vehicle AML cells biol rep4

description:
RFP 4B
gene_counts_translatome.tsv

value: bone marrow


title: Translatome BCAA vehicle AML cells biol rep5

description:
RFP 15
gene_counts_translatome.tsv

value: MLL-AF9 AML


title: DLX3 Day4 287

description: control: IgG_Day4_284, batch: 230803_cnr8, high stringency buffer?: Yes


title: DLX3 Prog 1 CnR 436

description: control: IgG_Prog_1_CnR_421, batch: 230818_cnr10, high stringency buffer?: No


title: Translatome AA vehicle AML cells biol rep1

description:
RFP 1B
gene_counts_translatome.tsv

value: Acute myeloid leukemia


title: DLX3 Day4 288


title: DLX3 Prog 308

description: control: IgG_Prog_322, batch: 230803_cnr8, high stringency buffer?: Yes


title: Male WT, AOM/DSS, 15 weeks, Tumor, rep 5

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

country: Sweden

institute: Karolinska Institute

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence and trimming for low-quality regions using TrimGalore, then mapped to mm10 whole genome using STAR
FeatureCounts were used to generate the raw counts and FPKM and TPM values were generated with StringTie
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including FPKM and TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: colon tumor

extract_protocol:
colon tissue was snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were treated with AOM/DSS for 15 weeks or given vehicle (saline)

value: colon tumor

value: male

value: AOM/DSS


title: DLX3 Prog 307

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: CXXC1 Day4 2 CnR 398

description: control: IgG_Day4_2_CnR_390, batch: 230818_cnr10, high stringency buffer?: No


title: CXXC1 Day4 1 CnR 397


title: Male WT, AOM/DSS, 15 weeks, Tumor, rep 4


title: D11_MV411_colonies_rep2, RNA

value: Peripheral blood

value: macrophage

value: Biphenotypic B Myelomonocytic Leukemia


title: Male WT, AOM/DSS, 15 weeks, Tumor, rep 3

value: WT


title: Male WT, AOM/DSS, 15 weeks, Tumor, rep 2


title: Male WT, AOM/DSS, 15 weeks, Tumor, rep 1


title: CXXC1 Day4 2 CnR 120

description: control: IgG_Day4_2_CnR_128, batch: 230403_cnr3, high stringency buffer?: Yes


title: CXXC1 Day4 1 CnR 119

description: control: IgG_Day4_1_CnR_127, batch: 230403_cnr3, high stringency buffer?: Yes


title: Male ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 4

value: ER[beta]KOVil


title: CXXC1 Prog 1 CnR 553

description: control: IgG_Prog_1_CnR_533, batch: 231204_cnr14, high stringency buffer?: nan


title: CXXC1 Prog 2 CnR 414

description: control: IgG_Prog_2_CnR_422, batch: 230818_cnr10, high stringency buffer?: No


title: Male ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 3


title: Male ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 2


title: Translatome  AA vehicle AML cells biol rep2

description:
RFP 2B
gene_counts_translatome.tsv


title: CXXC1 Prog 1 CnR 413


title: CXXC1 Prog 2 CnR 101

description: control: IgG_Prog_2_CnR_106, batch: 230403_cnr3, high stringency buffer?: Yes


title: Male ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 1


title: CXXC1 Prog 1 CnR 100

description: control: IgG_Prog_3_CnR_107, batch: 230403_cnr3, high stringency buffer?: Yes


title: CREB Day4 1 CnR 475

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No

value: CREB


title: Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 5

source_name: colon epithelial scrape

value: colon epithelial scrape


title: Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 3


title: Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 2


title: Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 4


title: Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 1


title: CREB Day4 1 CnR 151

description: control: IgG_Day4_2_CnR_150, batch: 230407_cnr4, high stringency buffer?: Yes


title: Male ERβKOVil, Vehicle, Scrape, rep 5

value: Vehicle


title: CREB Day4 1 CnR 471


title: CREB Prog 1 CnR 439


title: H11_MV411_colonies_rep2, RNA

value: Male

value: RNA-Seq

value: azacytidine


title: CREB Prog 316

value: Primary keratinocytes


title: Male ERβKOVil, Vehicle, Scrape, rep 4


title: Male ERβKOVil, Vehicle, Scrape, rep 3


title: CJUN Day4 2 CnR 400

value: CJUN

value: Differentiated


title: Male ERβKOVil, Vehicle, Scrape, rep 1


title: Male ERβKOVil, Vehicle, Scrape, rep 2


title: CJUN Day4 1 CnR 474


title: Female WT, AOM/DSS, 15 weeks, Tumor, rep 5

value: colon tumor

value: female


title: CJUN Day4 2 CnR 382

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: CJUN Day4 1 CnR 381

description: control: IgG_Day4_1_CnR_357, batch: 230814_cnr9, high stringency buffer?: No


title: Female WT, AOM/DSS, 15 weeks, Tumor, rep 3

value: AOM/DSS


title: CJUN Day4 1 CnR 196

description: control: IgG_Day4_1_CnR_193, batch: 230517_cnr6, high stringency buffer?: Yes


title: Female WT, AOM/DSS, 15 weeks, Tumor, rep 4


title: CJUN Day4 1 CnR 146

description: control: IgG_Day4_1_CnR_141, batch: 230407_cnr4, high stringency buffer?: Yes


title: CJUN Prog 2 CnR 443

description: control: IgG_Prog_2_CnR_438, batch: 230911_cnr11, high stringency buffer?: No


title: Female WT, AOM/DSS, 15 weeks, Tumor, rep 1


title: Female WT, AOM/DSS, 15 weeks, Tumor, rep 2


title: CJUN Prog 1 CnR 442

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: CJUN Prog 2 CnR 416


title: Female ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 2


title: Female ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 4


title: Female ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 1


title: Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 5


title: CJUN Day4 1 CnR 399

description: control: IgG_Day4_1_CnR_389, batch: 230818_cnr10, high stringency buffer?: No


title: CJUN Prog 1 CnR 349

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 4


title: CJUN Prog 1 CnR 180

description: control: IgG_Prog_1_CnR_177, batch: 230517_cnr6, high stringency buffer?: Yes


title: Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 3


title: CJUN Prog 1 CnR 138

description: control: IgG_Prog_1_CnR_133, batch: 230407_cnr4, high stringency buffer?: Yes


title: ATF4 Day4 3 CnR 500

description: control: IgG_Day4_2_CnR_470, batch: 230911_cnr11, high stringency buffer?: No


title: Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 2


title: ATF4 Day4 2 CnR 410

description: control: IgG_Day4_2_CnR_390, batch: 230818_cnr10, high stringency buffer?: No


title: Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, rep 1


title: Female ERβKOVil, Vehicle, Scrape, rep 5


title: ATF4 Day4 2 CnR 110

description: control: IgG_Day4_2_CnR_128, batch: 230403_cnr3, high stringency buffer?: Yes


title: Female ERβKOVil, Vehicle, Scrape, rep 3


title: ATF4 Day4 1 CnR 365


title: ATF4 Day4 2 CnR 366


title: Female ERβKOVil, Vehicle, Scrape, rep 1


title: ATF4 Day4 1 CnR 109

description: control: IgG_Day4_1_CnR_127, batch: 230403_cnr3, high stringency buffer?: Yes


title: Female ERβKOVil, AOM/DSS, 15 weeks, Tumor, rep 3


title: ATF4 Prog 1 CnR 458


title: CJUN Prog 1 CnR 415

description: control: IgG_Prog_1_CnR_421, batch: 230818_cnr10, high stringency buffer?: No


title: KMN-4

city: shanghai

first: wenxin

last: feng

address: 1954 Huashan Road, Shanghai

institute: shanghai jiaotong university

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: Ksp-Cre; Myc OE/+; Nsd2 OE/+


title: ATF4 Prog 1 CnR 433


title: CJUN Prog 2 CnR 350

description: control: IgG_Prog_2_CnR_326, batch: 230814_cnr9, high stringency buffer?: No


title: KMN-3


title: ATF4 Prog 2 CnR 434

description: control: IgG_Prog_2_CnR_422, batch: 230818_cnr10, high stringency buffer?: No


title: KMN-2


title: KMN-1


title: KM-3

value: Ksp-Cre; Myc OE/+


title: ATF4 Prog 2 CnR 91

description: control: IgG_Prog_2_CnR_106, batch: 230403_cnr3, high stringency buffer?: Yes


title: KM-4


title: ATF4 Prog 2 CnR 334


title: KM-1


title: ATF4 Prog 1 CnR 90

description: control: IgG_Prog_3_CnR_107, batch: 230403_cnr3, high stringency buffer?: Yes


title: ATF4 Day4 1 CnR 409


title: Female ERβKOVil, Vehicle, Scrape, rep 4


title: AHR Day4 1 CnR 411

value: AHR


title: AHR Day4 282

description: control: IgG_Day4_284, batch: 230803_cnr8, high stringency buffer?: Yes


title: AHR Day4 299


title: KN_H3K36me2_CUT&Tag

data_processing:
*library strategy: CUT&Tag
CUT&Tag reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
CUT&Tag analysis was performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) as described by the manufacturers with some modifications. Briefly, nuclei were extracted from the 10,000 fresh cells, and added the ConA beads incubating at room temperature for 10 min. The mixed complexes were the incubated with antibodies with IgG antibody as a control, and the next day, followed by the secondary antibody. A diluted pA-Tn5 adapter complex was then added to the above system and incubated at room temperature for 1 h. After extensive washing, system were subsequently sheared by adding 5 × TTBL. Subsequent proteinase K and DNA extract beads were used for obtaining eluted DNA.
Finally, the sequencing libraries were established after 12 cycles of PCR amplification and sequenced using Illumina Novaseq 6000 with paired-end 2x150 as the sequencing mode.

value: Ksp-Cre; Nsd2 OE/+


title: AHR Prog 1 CnR 435


title: AHR Prog 1 CnR 169

description: control: IgG_Prog_1_CnR_167, batch: 230418_cnr5, high stringency buffer?: Yes


title: Female ERβKOVil, Vehicle, Scrape, rep 2

value: ER[beta]KOVil


title: Lymphnode Metastasis Sample 52

city: Philadelphia

first: Joshua

middle: Hunter

last: Rhoades

state: PA

address: 3800 Spruce St

department: Vet School

institute: University of Pennsylvania

description:
R6-lymphnode_S6_R1_001_r6_s52
lymph4_s52

data_processing:
library strategy: CRISPR screen
Processed with Mageck software
Supplementary files format and content: txt

source_name: Lymphnode Metastasis

extract_protocol:
DNeasy blood and tissue kit/ Qiagen DNA microkit
Takara Extaq targeted amplification

value: Metastasis

value: Colorectal adenocarcinoma

value: APC KO, TRP53 KO, KRASG12D mutant


title: Lymphnode Metastasis Sample 53

description:
R6-lymphnode_S6_R1_001_r6_s53
bignet?_s53


title: WT_H3K36me2_CUT&Tag

value: WT


title: H08_AZA_220331, RNA

data_processing:
Following demultiplexing, multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element counts from unique and ambiguously aligned reads (bam files) using TEcount with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single count table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Bismark output file: genome-wide GpC methylation reports (GpC.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Counts for individual samples are contained in column 14 onwards.

growth_protocol: AML cell line, HL-60 (ATCC #CCL-240), were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium. HL-60 cells were maintained in Iscove′s Modified Dulbecco′s media (IMDM; Sigma-Aldrich) supplemented with 4mM GlutaMAX (Thermo Fisher Scientific) and 10% Fetal Bovine Serum (FBS; Sigma-Aldrich).

extract_protocol:
At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS) and sorted into 2.5µL of RLT PLUS buffer (Qiagen) containing 2.5U SUPERas-In (Thermo Fisher Scientific) in LoBind 96-well full skirted plates (Eppendorf) using indexed sorting on a FACS Aria II (BD Biosciences). Plates were sealed and briefly centrifuged before storage at -80°C for sequencing analyses.
For scNMT-seq, matched scNOMe-seq and scRNA-seq libraries were prepared from sorted HL-60 single cells, as previously described (Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature Communications [2018]) with minor modifications described below and within the associated manuscript.
Cell lysates were incubated with magnetic Dynabeads conjugated to the Bio-dT30VN oligonucleotide (5’- AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3’). Poly-adenylated mRNA captured on the Dynabeads underwent reverse transcription and cDNA amplification (for scRNA-seq), while genomic DNA was transferred to a new multi-well plate for bisulphite conversion (for scNOMe-seq).
For reverse transcription, Dynabeads were resuspended in 10µL reaction mix containing: 100U SuperScript II reverse transcriptase (Thermofisher), 1X First-strand buffer (Thermofisher), 2.5mM DTT (Thermofisher), 1M Betaine (Sigma-Aldrich), 9mM MgCl2 (Thermofisher), 1μM Template switching oligo (5’AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 1mM dNTPs (New England Biolabs) and 5U SUPERase-In RNAse inhibitor (Thermofisher). First-strand synthesis and template switching was then performed by incubating at 42 °C for 60 min, 50 °C for 30 min and 60 °C for 10 min. Amplification of cDNA was performed by adding KAPA HiFi HotStart ReadyMix (final concentration 1x, Roche sequencing) and ISPCR primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’, final concentration 0.11μM) to the reverse transcription mix and amplifying as follows: 98 °C for 3 min, 23 repeats of (98 °C for 20s, 67 °C for 15 s, 72 °C for 6 min) and 72 °C for 5 min. Amplified cDNA was stored at -20 °C for later scRNA-seq library preparation.
Genomic DNA was purified using a 0.8x volume of AMPure XP beads (Beckman Coulter), and bisulphite converted using the Zymo EZ-96 DNA Methylation-Direct MagPrep Kit (Zymo Research) with halved reaction volumes. Converted DNA was eluted in first-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 - 5’CTACACGACGCTCTTCCGATCTNNNNNN 3’. Samples were incubated at 65 °C for 3 min and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo– (Enzymatics). The final reaction volume was 40µL, and samples were incubated as follows: 4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min. Samples were heated to 95°C for 45s and rapidly cooled before addition of 2.5µL containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 and 25U of Klenow 3’ -> 5’ exo–. The first strand synthesis step was then repeated (4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min). In total, 5 rounds of first-strand synthesis were performed with the final round having an extended incubation for strand extension (4°C 5 min, +1°C/15 s to 37°C, 37°C 90 min). Samples were then incubated with 40 U exonuclease I (New England Bio-labs) for 1 h at 37 °C before DNA was purified using a 0.65x volume of AMPure XP beads. Samples were eluted in second-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTP mix, 0.4 μM oligo2 (5’-TGCTGAACCGCTCTTCCGATCTNNNNNN-3’. Samples were incubated at 95°C for 45s and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo–. The final reaction volume was 40µL, and samples were incubated as follows: 4 °C for 5 min, +1 °C/15 s to 37 °C, 37 °C for 90 min. DNA purification was carried out using a 0.65x volume of AMPure XP bead buffer. Beads were resuspended in 1X KAPA HiFi HotStart ReadyMix with 0.2μM of i5 and i7 indexed primers from the NEBNext Multiplex Oligos for Illumina Dual Index Primer Sets (New England Biolabs, USA). Libraries were then amplified by PCR as follows: 95 °C 2 min, 12–14 repeats of (94 °C for 80 s, 65 °C for 30 s, 72 °C for 30 s), 72 °C for 3 min and 4 °C hold. Amplified libraries were purified using a 0.65x volume of AMPure XP beads and eluted in nuclease free water.
Amplified cDNA samples were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and normalised to 0.2 ng/μL with nuclease free water before proceeding with RNA-seq library preparation. The Nextera XT DNA library preparation kit (Illumina) was used according to the manufacturer’s guidelines, but with halved reaction volumes and one in five dilutions of i5 and i7 indexed primers.

treatment_protocol: HL-60 cells were treated in suspension culture, every 24h for 72h total, with 100nM decitabine (DAC; Selleckchem #S1200) or with 2000nM azacytidine (AZA; Selleckchem # S1782). Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a negative control.

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female

value: azacytidine


title: AHR Day4 1 CnR 161

description: control: IgG_Day4_1_CnR_159, batch: 230418_cnr5, high stringency buffer?: Yes

value: Primary keratinocytes

value: Differentiated


title: Lymphnode Metastasis Sample 63

description:
R7-lymphnode_S7_R1_001_r7_s63
lymph_s63


title: Lymphnode Metastasis Sample 62

description:
R7-lymphnode_S7_R1_001_r7_s62
small_lymph_s62


title: Liver Metastasis Sample 38

description:
R5-livermet_S5_R1_001_r5_s38
liver3.1_s38

source_name: Liver Metastasis


title: AHR Prog 302

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: Primary Tumor Sample 13

description:
R2-primary_S2_R1_001_r2_s13
primary_s13

source_name: Primary Tumor


title: Lymphnode Metastasis Sample 61

description:
R7-lymphnode_S7_R1_001_r7_s61
lymph_s61


title: H06_AZA_220331, RNA


title: H12_Neg_220331, RNA

value: control


title: ATF4 Prog 1 CnR 333

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: H10_AZA_220331, RNA


title: H03_AZA_220331, RNA


title: Primary Tumor Sample 5

description:
R1-primary_S1_R1_001_r1_s05
primary_s5

value: Tumor


title: Kidney Metastasis Sample 77

description:
kidney_membrane2_s77
R8-peritoneal_S8_R1_001_r8_s77

source_name: Kidney Metastasis


title: KM-2

value: kidney

value: Ksp-Cre; Myc OE/+


title: Peritoneal Metastasis Sample 75

description:
peritoneal_s75
R8-peritoneal_S8_R1_001_r8_s75

source_name: Peritoneal Metastasis


title: H01_Unt_220331, RNA

value: untreated


title: Lymphnode Metastasis Sample 51

description:
R6-lymphnode_S6_R1_001_r6_s51
lymph3_s51


title: Lymphnode Metastasis Sample 50

description:
R6-lymphnode_S6_R1_001_r6_s50
lymph2_s50


title: G09_AZA_220331, RNA


title: G11_AZA_220331, RNA


title: Lymphnode Metastasis Sample 49

description:
R6-lymphnode_S6_R1_001_r6_s49
lymph1_s49


title: Peritoneal Metastasis Sample 71

description:
R8-peritoneal_S8_R1_001_r8_s71
peritoneal_s71


title: H07_AZA_220331, RNA


title: H09_AZA_220331, RNA


title: Intestine Metastasis Sample 72

description:
intestine_wall_s72
R8-peritoneal_S8_R1_001_r8_s72

source_name: Intestine Metastasis


title: H04_AZA_220331, RNA


title: Primary Tumor Sample 12

description:
R2-primary_S2_R1_001_r2_s12
primary_s12


title: H05_AZA_220331, RNA


title: Primary Tumor Sample 11

description:
R2-primary_S2_R1_001_r2_s11
primary_s11


title: H11_AZA_220331, RNA


title: H02_AZA_220331, RNA


title: G06_AZA_220331, RNA


title: Kidney Metastasis Sample 76

description:
kidney_membrane1_s76
R8-peritoneal_S8_R1_001_r8_s76


title: Abdominal Metastasis Sample 65

description:
abd_lymph_s65
R7-lymphnode_S7_R1_001_r7_s65

source_name: Abdominal Metastasis


title: G07_AZA_220331, RNA

source_name: Peripheral blood


title: Primary Tumor Sample 4

description:
R1-primary_S1_R1_001_r1_s04
primary_s4


title: Peritoneal Metastasis Sample 74

description:
peritoneal3_s74
R8-peritoneal_S8_R1_001_r8_s74


title: G10_AZA_220331, RNA


title: Lymph Metastasis Sample 57

description:
lymph_s57
R6-lymphnode_S6_R1_001_r6_s57

source_name: Lymph Metastasis


title: G04_AZA_220331, RNA


title: Lymph Metastasis Sample 66

description:
lymph_s66
R7-lymphnode_S7_R1_001_r7_s66


title: Lymph Metastasis Sample 56

description:
lymph_s56
R6-lymphnode_S6_R1_001_r6_s56


title: Lymph Metastasis Sample 55

description:
lymph_s55
R6-lymphnode_S6_R1_001_r6_s55


title: Gallbladder Metastasis Sample 73

description:
galbladder_s73
R8-peritoneal_S8_R1_001_r8_s73

source_name: Gallbladder Metastasis


title: G08_AZA_220331, RNA


title: Lung Metastasis Sample 47

description:
lung_s47
R5-livermet_S5_R1_001_r5_s47

source_name: Lung Metastasis


title: Lymph Metastasis Sample 67

description:
lymph2_s67
R7-lymphnode_S7_R1_001_r7_s67


title: G03_AZA_220331, RNA


title: G05_AZA_220331, RNA


title: Lymph Metastasis Sample 64

description:
lymph_s64
R7-lymphnode_S7_R1_001_r7_s64


title: Liver Metastasis Sample 46

description:
liver1.1_s46
R5-livermet_S5_R1_001_r5_s46


title: F09_AZA_220331, RNA


title: G02_AZA_220331, RNA


title: G01_Unt_220331, RNA


title: Liver Metastasis Sample 45

description:
liver3.1_s45
R5-livermet_S5_R1_001_r5_s45


title: Lymph Metastasis Sample 54

description:
lymph_s54
R6-lymphnode_S6_R1_001_r6_s54


title: G12_Unt_220331, RNA


title: F12_Unt_220331, RNA


title: F11_AZA_220331, RNA


title: F10_AZA_220331, RNA


title: Liver Metastasis Sample 44

description:
liver2.1_s44
R5-livermet_S5_R1_001_r5_s44


title: F06_AZA_220331, RNA


title: Liver Metastasis Sample 43

description:
liver1.4_s43
R5-livermet_S5_R1_001_r5_s43


title: Liver Metastasis Sample 40

description:
liver_s40
R5-livermet_S5_R1_001_r5_s40


title: F08_AZA_220331, RNA


title: Liver Metastasis Sample 42

description:
liver1.2_s42
R5-livermet_S5_R1_001_r5_s42


title: F04_AZA_220331, RNA


title: F03_AZA_220331, RNA


title: Primary Tumor Sample 16

description:
primary_s16
R2-primary_S2_R1_001_r2_s16


title: F01_Unt_220331, RNA


title: E12_Unt_220331, RNA


title: F02_AZA_220331, RNA


title: Primary Tumor Sample 17

description:
primary_s17
R2-primary_S2_R1_001_r2_s17


title: Primary Tumor Sample 15

description:
primary_s15
R2-primary_S2_R1_001_r2_s15


title: Primary Tumor Sample 8

description:
primary_s8
R1-primary_S1_R1_001_r1_s08


title: E11_AZA_220331, RNA


title: E10_AZA_220331, RNA


title: E09_AZA_220331, RNA


title: Primary Tumor Sample 7

description:
primary_s7
R1-primary_S1_R1_001_r1_s07


title: E08_AZA_220331, RNA


title: Primary Tumor Sample 6

description:
primary_s6
R1-primary_S1_R1_001_r1_s06


title: E07_AZA_220331, RNA


title: Peritoneal Metastisis Sample 53

data_processing:
library strategy: CRISPR screen
Processed with Mageck software
Assembly: N/A
Supplementary files format and content: txt


title: F07_AZA_220331, RNA


title: Peritoneal Metastisis Sample 52

description: sample52_mouse8_smallintestinemet_i706F7


title: E06_AZA_220331, RNA


title: F05_AZA_220331, RNA


title: Liver Metastasis Sample 41

description:
liver1.1_s41
R5-livermet_S5_R1_001_r5_s41


title: Peritoneal Metastisis Sample 51


title: E05_AZA_220331, RNA


title: Peritoneal Metastisis Sample 50


title: Liver Metastasis Sample 39

description:
liver_s39
R5-livermet_S5_R1_001_r5_s39


title: Peritoneal Metastisis Sample 48

description: sample48_mouse7_smallintestinemet_i706F5


title: E03_AZA_220331, RNA


title: Liver Metastisis Sample 44


title: Liver Metastisis Sample 45


title: E01_Unt_220331, RNA


title: Liver Metastisis Sample 40


title: E02_AZA_220331, RNA


title: D12_Unt_220331, RNA


title: Liver Metastisis Sample 42


title: D11_DAC_220331, RNA

value: decitabine


title: Liver Metastisis Sample 38

value: Metastasis


title: Liver Metastisis Sample 37

value: Colorectal adenocarcinoma


title: D09_DAC_220331, RNA


title: Live Metastisis Sample 39

value: APC KO, TRP53 KO, KRASG12D mutant


title: Primary Tumor Sample 14

description:
primary_s14
R2-primary_S2_R1_001_r2_s14


title: D08_DAC_220331, RNA


title: Liver Metastisis Sample 34


title: D07_DAC_220331, RNA


title: Liver Metastisis Sample 33


title: D06_DAC_220331, RNA


title: D05_DAC_220331, RNA


title: Liver Metastisis Sample 28


title: Liver Metastisis Sample 26


title: D04_DAC_220331, RNA


title: Liver Metastisis Sample 32


title: E04_AZA_220331, RNA


title: Liver Metastisis Sample 22


title: Lymphnode Metastisis Sample 21


title: D03_DAC_220331, RNA


title: D01_Unt_220331, RNA