title: WT HEK293T cell line - Replicate 2

data_processing:
RNA-seq sequencing reads were aligned to the human genome T2T-CHM13v2.0 with the Subread program (v2.0.6) and its align function.
RNA-seq reads were summarized to the gene-level for differential analysis using a strict RefSeq annotation with the Subread program (v2.0.6) and its featureCounts function.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: Tab-separated file containing sequence read counts for all samples together with Entrez Geneid, chromosome (Chr), Start and End genomic positions, Strand and gene Length.

extract_protocol:
Total RNA was isolated from 1 x 106 cells using RNeasy Plus Mini Kit (Qiagen) with genomic DNA removal. RNA was confirmed to be of high quality using Agilent Tapestation with RNA screentape (RIN >9.8 for these samples).
500ng was prepared for RNA-seq using Truseq RNA library preparation protocol with poly-A capture (Illumina). Libraries were sequenced on an Illumina NextSeq 2000 to produce 65bp paired-end reads.


title: MORC2 KO HEK293T cell line - Replicate 2

status: Public on May 05 2025

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: genotype

value: MORC2 knock-out

tag: knock-out sgrna


title: Raw_ID 131, Male, WT, Saline, Rep 5

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

country: USA

institute: University of Washington

description:
Library name: 131
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Reads were aligned to the Mus musculus GRCm38 ERCC reference genome assembly (ENSEMBL) using STAR aligner v.2.5.2b. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: Text count files from featureCounts

molecule: total RNA

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
RNA was extracted and prepared using rRNA depletion
PE 2x150bp cDNA libraries were constructed at Azenta using the Illumina TruSeq RNA Sample Prep Kit with ERCC spike-in

tag: tissue

value: Cerebellum

value: WT

tag: treatment

value: Saline

tag: batch


title: Raw_ID 124, Female, WT, Saline, Rep 3

description:
Library name: 124
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 20, Male, WT, Saline, Rep 4

description:
Library name: 20
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DNA from MCF-7 POU1F1 1

status: Public on May 06 2025

type: genomic

city: Santiago de Compostela

first: Leandro

middle: Avila

last: Concepcion

state: Coruña

address: Ave Barcelona

department: Department of Physiology, Center for Molecular Medicine and Chronic Diseases

country: Spain

institute: University  Santiago de Compostela

description: DNA from MCF-7 POU1F1 1

hyb_protocol: Bisulphite converted DNA (protocol EZ-DNA Methylation (D5001/Zymo Research) was amplified fragmentet and hybridized to human Infinitum MethylationEPIC V.2 BeadChip (Illumina)

scan_protocol: Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing: Genome Studio Illumina Software (v210.3)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: cell culture

label_protocol: Standard Illumina Protocol

extract_protocol: MasterPure DNA Extraction Kit (Epicentre Biotechnologies, Madison, WI, EE. UU),

value: cell culture

tag: cell type

value: breast cancer luminal A

value: overexpression of POU1F1


title: Raw_ID 16, Male, WT, Hu_ASO, Rep 2

description:
Library name: 16
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: ChIP-seq MORC2 library from MORC2 WT HEK293T cell line - Replicate 1

library_source: genomic

data_processing:
Processing of ChIP-seq reads followed closely the ENCODE data processing pipeline. Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ChIP-seq reads were aligned with the bowtie2 program following the data processing guidelines from ENCODE project [https://www.encodeproject.org/data-standards/chip-seq/].
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak and broadPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step and IgG libraries were used as negative controls during ChIP-seq peak calling.

extract_protocol:
5-10 x 106 cells per IP were cross-linked by adding 1/10 volume of fresh 11% formaldehyde solution (50mM HEPES-KOH pH 7.4, mM NaCl, 1 mM EDTA, 1 mM EGTA, 11% formaldehyde) to a 1 x 106 cell suspension for 20 minutes at room temperature with mixing. 1/12.5 volumes of 2.5 M glycine was added to quench formaldehyde and cells were washed twice in ice-cold PBS. Cross-linked cells were lysed in Lysis Buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% (v/v) glycerol, 0.5% (v/v) IGEPAL CA-630, 0.25% (v/v) Triton X-100, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) for 10 minutes at 4 °C with rocking, pelleted at 1350 x g for 5 minutes at 4°C, then Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) for 10 minutes at room temperature with rocking, pelleted again at 1350 x g for 5 minutes at 4 °C, then resuspended in Lysis Buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) Na-Deoxycholate, 0.5% (v/v) N-lauroylsarcosine, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) and transferred to Covaris miniTUBEs. Cell lysates were sonicated using a Covaris E220 focused-ultrasonicator with the following settings to shear DNA to a size of 300-500 bp suitable for high-throughput sequencing: Fill Level 10, Duty Cycle 10, PIP 175, Cycles/Burst 200 for 80 seconds. 1/10 volume of 10% (v/v) Triton X-100 was then added to the sonicated lysate and cellular debris was pelleted at 20,000 x g for 10 minutes at 4 °C. Immunoprecipitation was then performed overnight at 4 °C with rotation using ProteinG Dynabeads (50 μL per IP) pre-coupled with antibody (5 μL per IP) in 0.5% BSA/PBS for >5 h. Antibodies used were anti-MORC2 Rabbit pAb (Invitrogen #PA5-51172), H3K9me3 Rabbit pAb (Abcam #8898), Rabbit IgG pAb (Abcam #ab46540). Following immunoprecipitation, beads were collected using a magnet and washed 5 times with Wash Buffer (50 mM HEPES-KOH pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1% (v/v) IGEPAL CA-630, 0.7% (w/v) Na-Deoxycholate, then 1 time with Tris-EDTA-NaCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). DNA was then eluted from beads by incubation in Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS) at 65 °C for 30 minutes with shaking. Bead-free supernatant was reverse crosslinked by incubation at 65 °C for 6-15 h, diluted with equal volume of TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA), then digested sequentially with RNaseA (0.2 mg/mL) at 37 °C for 2h and Proteinase K (0.2 μg/mL) at 55 °C for 2 h.
Final immunoprecipitated DNA was then purified using Zymo ChIP DNA Clean & Concentrator kit and prepared for sequencing using Illumina Truseq 1⁄2 reaction library preparation kit. Libraries were sequenced on an Illumina NextSeq 2000 to produce 65bp paired-end reads.

value: Wild-type

tag: chip antibody

value: Anti-MORC2 Rabbit pAb (Invitrogen #PA5-51172)


title: ChIP-seq H3K9me3 library from MORC2 KO HEK293T cell line - Replicate 2

value: H3K9me3 Rabbit pAb (Abcam #8898)


title: MORC2 WT HEK293T cell line, Replicate 2

description:
ATAC_WT2_S18.trimmed.filt.nodup.bam
ATAC_WT_peaks.narrowPeak

data_processing:
Processing of ATAC-seq reads followed closely the ENCODE data processing pipeline. Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ATAC-seq reads were aligned with the bowtie2 program following the data processing guidelines from ENCODE project [https://www.encodeproject.org/data-standards/chip-seq/].
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step
Supplementary files format and content: ATAC-seq reads were first summarized to narrow windows of 250bp for differential analyses with the R/Bioconductor package csaw (v1.38.0). ATAC-seq reads were then summarized to promoter regions (TSS +/- 2kb ) for visualization purposes using a strict RefSeq gene annotation with the Subread program (v2.0.6) and its featureCounts function.

extract_protocol:
50,000 cells were pelleted at 500 x g for 5 minutes at 4C then lysed on ice for 3 minutes in 50 μL ATAC-RSB Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) also containing 0.1% (v/v) IGEPAL CA-630, 0.1% (v/v) Tween-20, 0.01% (w/v) Digitonin. After lysis, 1mL of ATAC-RSB containing only 0.1% (v/v) Tween-20 but no IGEPAL CA-630 or Digitonin was added, and nuclei were pelleted at 500 x g for 10 minutes at 4C. All supernatant was aspirated and discarded, and each pellet of nuclei was resuspended in 50 μL of transposition mix (25 μL 2x TD Buffer, 2.5 μL Tn5 transposase (100 nM final), 16.5 μL PBS, 0.1 μL 5% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) and incubated at 37 °C for 30 minutes exactly in a thermomixer with 1000 RPM mixing.
DNA was then purified using Zymo DNA Clean & Concentrator-5 Kit to generate 20 μL of product which was pre-amplified for 5 cycles using NEBNext 2x Master Mix (#E7649A) and indexed primers as described previously57. A 5 μL of pre-amplified DNA was then used in a 15 μL qPCR reaction using Promega GoTaq qPCR Master Mix to determine the required number of additional cycles to yield minimally amplified DNA for optimal library diversity for next-generation sequencing (determined to be 3-4 additional cycles for these libraries). Amplified DNA was then purified using NucleoMag NGS Clean-up and Size Select beads (Macherey-Nagel) using a 0.5x ratio of beads to DNA to initially clear large DNA fragments from the library and then a 1.5x ratio of beads to supernatant to adsorb DNA fragments of appropriate size for sequencing. DNA-bound beads were then washed twice with 80% EtOH and size-selected DNA was eluted in nuclease-free water. Libraries were sequenced on an Illumina NextSeq 2000 to produce 65bp paired-end reads.


title: MORC2 KO HEK293T cell line, Replicate 2


title: Raw_ID 87, Male, WT, Mo_ASO, Rep 2

description:
Library name: 87
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: TF-1, CRIPSRgate screen, 14 days, rep1

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

data_processing:
Data Filtering: Discard PhiX genome and remove low quality reads (<20)
Trimm forward read 5' end: 21 bp and 3' end: 39bp
Reverse complement reverse read and trimm 5' end: 22 bp and 3' end 6 bp
Join forward and reverse reads to one megaread
Split reads based on barcodes and trimm 3' end: 27 bp
Mageck count and normalized to reads per million
Library strategy: CRISPR screen

source_name: Bone marrow

growth_protocol: TF-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 4 mM L-Glutamine, 10 mM HEPES, 1 mM Sodium pyruvate solution, 100 U/mL Penicillin and 100 µg/mL Streptomycin, 2 ng/mL recombinant GM-CSF in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
After 14 days post induction of ZIM3-Cas9 expression cells were harvested in a 1000x library representation and genomic DNA for the three single cell clones was isolated with phenol-extraction using PhaseLock tubes, followed by ethanol precipitation.
Multiple parallel 50 µL PCR reactions, each containing 1 µL gDNA template adding up to 7 µg gDNA, were performed to maintain sgRNA representation. sgRNAs were PCR amplified using the AmpliTaq Gold Polymerase (Life technologies). In a first round of PCRs, random barcodes and sample barcodes were added to the sgRNA sequences. PCR products for each single cell clone were combined and purified using the NucleoSpin Gel and PCR clean-up kit (macherey-Nagel). Afterwards using a second round PCR, using similar cycling conditions with the exception of 10 ng input as template and 7 total cycles the standard Illumina P7 and P5 adaptors were added. The final libraries were cleaned up from a 2% agarose gel, pooled and analyzed on an P2 flow cell (400 mio reads).

treatment_protocol: TF-1 cells expressing dox inducbile ZIM3-Cas9 were spinfected (900g) with 4µg/mL polybrene with lentivirus for the CRISPRgate library. sgRNA positive cells were measured after 2 days of transduction and selected for one week using 500 µg/mL G418 solution. ZIM3-Cas9 expression was induced using DOX and cells were cultivated for two weeks

value: Bone marrow

value: erythroleukemia


title: Raw_ID 52, Female, WT, Saline, Rep 2

description:
Library name: 52
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: WT_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of genes.

source_name: heart

extract_protocol:
RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 2µg of total RNA was used as input for Vazyme_VAHTS Universal Stranded mRNA-seq - V8 (Vazyme). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: heart

value: Wildtype


title: WT_2

description: Library name: Sample 5


title: WT HEK293T cell line - Replicate 1


title: Raw_ID 102, Male, Q112, Hu_ASO, Rep 5

description:
Library name: 102
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 107, Male, WT, Hu_ASO, Rep 5

description:
Library name: 107
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: MORC2 KO HEK293T cell line - Replicate 1


title: TF-1, CRIPSRgate screen, 14 days, rep2


title: WT_1

description: Library name: Sample 4


title: TF-1, CRIPSRgate screen, 14 days, rep3


title: Raw_ID 15, Male, Q112, Hu_ASO, Rep 3

description:
Library name: 15
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: R1KO_3

description: Library name: Sample 3


title: R1KO_2

description: Library name: Sample 2


title: Raw_ID 34, Female, Q112, Hu_ASO, Rep 2

description:
Library name: 34
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 13, Female, Q112, Hu_ASO, Rep 1

description:
Library name: 13
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: R1KO_1

description: Library name: Sample 1


title: Raw_ID 58, Male, Q112, Mo_ASO, Rep 4

description:
Library name: 58
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 116, Male, Q112, Mo_ASO, Rep 5

description:
Library name: 116
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 41, Male, Q112, Mo_ASO, Rep 3

description:
Library name: 41
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: AL12-Old-Bleo-D30

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Assembly: mm10
Supplementary files format and content: starsolo outputs

source_name: Lung

extract_protocol:
FACS sorted cells were stained with SytoxTM (Thermofisher Scientific) for dead cell exclusion. 9000 sorted viable tdTomato cells per time point were loaded into 10x Genomics Chromium.
Library preparation was conducted according to the manufacturer indications (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121).

value: Lung

tag: time

value: Day 30

value: tdTomatopos cells

value: Bleomycin


title: AL23-Old-Bleo-D60

description: 10x Genomics

value: Day 60


title: AL18-Old-Bleo-D14

description: 10x Genomics

value: Day 14


title: Raw_ID 115, Female, Q112, Mo_ASO, Rep 2

description:
Library name: 115
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

value: Cerebellum


title: Raw_ID 7, Female, WT, Saline, Rep 1

description:
Library name: 7
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

value: WT

value: Saline


title: HB67_Mo17

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Illumina reads were mapped using bowtie2 with default parameters. Mapped reads were filtered to retain MAPQ scores greater than 30 using samtools. Peaks were called using GEM3.0 with variable significance thresholds.
Assembly: B73v5 or Mo17_CAU1.0
Supplementary files format and content: narrowPeak format
Library strategy: DAP-seq

organism: Zea mays subsp. mays

source_name: seedling leaf

extract_protocol:
genomic DNA was extracted from 14 day-old leaves
genomic DNA was fragmented to 200bp and subjected to standard Illumina library construction prior to incubation with in vitro expressed transcription factor

value: seedling leaf

value: DAP-seq


title: Raw_ID 132, Male, Q112, Saline, Rep 5

description:
Library name: 132
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: AL24-Old-Saline-D14

description: 10x Genomics


title: Raw_ID 84, Female, Q112, Mo_ASO, Rep 1

description:
Library name: 84
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: GATA20_Mo17


title: Raw_ID 26, Male, Q112, Hu_ASO, Rep 4

description:
Library name: 26
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 55, Female, Q112, Saline, Rep 2

description:
Library name: 55
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 21, Male, Q112, Saline, Rep 3

description:
Library name: 21
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 45, Female, WT, Mo_ASO, Rep 1

description:
Library name: 45
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: SBP1_Mo17


title: Raw_ID 8, Female, Q112, Saline, Rep 1

description:
Library name: 8
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: SBP8_Mo17


title: PK110 Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 2

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Centre for Genomic Regulation

description:
Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 2
10x Genomics

data_processing:
Samples were profiled using the Illumina HiSeq 2000. RNA sequencing reads were mapped to the GRCm38 (mm10) reference genome using TopHat2. Reads mapping to known genes, based on Entrez gene identifiers, were then counted using the GenomicFeatures R package (Bioconductor)
Assembly: GRCm38 (mm10)
Supplementary files format and content: txt (genes, cell barcodes, counts, barcodes to samples mapping)

source_name: Embryo

extract_protocol:
RNA was extracted using TRITON(R) X-100 (Sigma-Aldrich) and SUPERaseIn RNase Inhibitor (Thermo Fisher Scientific)
Library prepared according to the polyA-capture Illumina TruSeq protocol in a HiSeq 2000 instrument (Illumina)

value: Embryo

value: Blastocyst

value: Morpholino


title: HALO-GST_Mo17

description: negative control


title: HSF10_Mo17


title: BHLH149_Mo17


title: PK109 Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 1

description:
Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 1
10x Genomics


title: PK108 Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 2

value: Morula


title: PK107 Control morpholino (even wells) and NKX1_2 morpholino (odd wells) replicate 1


title: NPC-29-7a

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
The adaptor sequences and low quality bases were trimmed from the reads using the Trim Galore tool ver. 0.6.5.
Reads were aligned to the mouse genome using the Bismark alignment software.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated by bismark_methylation_extractor
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: NPC

extract_protocol:
DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
Briefly, genomic DNA was digested using the MspI restriction enzyme and subjected to bisulfite treatment, which converts unmethylated cytosine residues to uracil. Genomic fragments were sequenced using next-generation sequencing

value: HOM

tag: age


title: NPC-J1-7a

value: wt


title: TCP3_Mo17


title: mNPC-J1-12


title: mNPC-J1-9


title: Raw_ID 53, Male, Q112, Saline, Rep 4

description:
Library name: 53
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: mESC-HOM-2

source_name: ESC


title: mESC-J1-2


title: mESC-HOM-1


title: ARF14_Mo17


title: ARF35_Mo17


title: BHLH106_Mo17


title: ARF25_Mo17


title: mESC-J1-1


title: WRKY82_B73


title: WRKY64_B73


title: GATA20_B73


title: TCP15_B73


title: YAB2_B73


title: BZIP57_Mo17


title: mouse CB-0088

source_name: cerebellum


title: mouse CB-0087


title: mouse CB-0086


title: TCP11_B73


title: mouse CB-0082


title: SBP2_B73


title: MYB94_Mo17


title: NLP14_B73


title: NAC74_B73


title: mouse CB-0076


title: NAC49_B73


title: Neuron 29-12

source_name: In vitro differentiated neuron


title: Neuron J1-12


title: BHLH149_B73


title: MYBR52_B73


title: Neuron 29-9


title: mouse CB-4721


title: mouse CB-4723


title: SBP15_B73


title: mouse CB-8568


title: MYBR111_B73


title: HB54_B73


title: mouse CB-4722


title: MADS72_B73


title: Neuron J1-9


title: HSF10_B73


title: HSF7_B73


title: mouse CB-4719


title: HB22_B73


title: HB122_B73


title: mouse CB-8566


title: mouse CB-8565


title: mouse CB-0077


title: HB102_B73


title: HB15_B73


title: NAC12_B73


title: het_cortexG2_meth

description: DNA was extracted from prefontal cortex from mouse

source_name: Cortex

extract_protocol:
NEBNext Enzymatic Methyl-Seq  Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
300ng of DNA was used for library construction using the NEBNext Enzymatic Methyl-Seq (NEB), respectively.

value: Het

value: Cortex

tag: strain

value: 12 months old


title: het_cortex1_meth


title: het_cortexG4_meth


title: BZR1_B73


title: het_cortexG3_meth


title: het_cor_w3_meth


title: hom_cortex1_meth

value: Hom


title: hom_cor_g1_meth


title: GLK20_B73


title: wt_cor_b6_meth


title: wt_cor_g5_meth


title: hom_cor_w4_meth


title: GLK48_B73


title: EREB53_B73


title: GLK21_B73


title: EREB2_B73


title: wt_cortex1_meth


title: EREB126_B73


title: EREB49_B73


title: wt_cortex_w1_meth


title: MYB138_B73


title: Riboseq DNMT1 knockdown

description: Library name: Riboseq DNMT1 knockdown

data_processing:
For Ribo-seq data processing, raw reads were processed with Cutadapt (4.9) with parameter “-a AACTGTAGGCACCATCAAT -m 25 -M 34”. Adapter sequences were removed and only reads with length between 25 and 34 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using Bowtie2 software, remaining reads as well as the reads form corresponding mRNA-seq were aligned to human reference genome (hg38) separately by using Hisat2. Then read counts were calculated using featureCounts software. Raw counts were further normalized as FPM by using DESeq2 package. Translational efficiencies were determined as the log2 transformed ratio of (normalized abundance determined by ribosome profiling)/ (normalized abundance determined by RNA-seq. For corresponding bulk RNA-seq data processing, the clean reads were mapped to the mouse genome (Hg38) using Hisat2. Then, the number of reads uniquely mapped to each gene was determined using FeatureCounts from subread2.
Assembly: GRCh38
Supplementary files format and content: gene count files generated by featureCounts
Library strategy: Ribo-Seq

source_name: ribosome-protected mRNA fragment on HeLa cells with DNMT1 knockdown

extract_protocol:
Ribosome profiling libraries were prepared on the DNMT1 knockdown HeLa cells as well the control HeLa.
A total of 107 cells were prepared for cell lysis. Then, the cell medium was discarded, and the cells were washed twice with ice-cold PBS containing 100 μg/mL cycloheximide (Adooq, 66-81-9). 100 mg tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide. Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814). Subsequently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016). EpiTM RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805) was used for rRNA depletion. Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679). Total RNA was purified using RNeasy per manufacturer’s instructions (Qiagen). For corresponding mRNAseq, mRNA were obtained by using NEBNext® rRNA Depletion Kit and libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

value: HeLa cells

value: DNMT1 knockdown


title: het_cortex_w2_meth


title: HB67_B73


title: RNAseq DNMT1 knockdown

description: Library name: RNAseq DNMT1 knockdown

data_processing:
For Ribo-seq data processing, raw reads were processed with Cutadapt (4.9) with parameter “-a AACTGTAGGCACCATCAAT -m 25 -M 34”. Adapter sequences were removed and only reads with length between 25 and 34 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using Bowtie2 software, remaining reads as well as the reads form corresponding mRNA-seq were aligned to human reference genome (hg38) separately by using Hisat2. Then read counts were calculated using featureCounts software. Raw counts were further normalized as FPM by using DESeq2 package. Translational efficiencies were determined as the log2 transformed ratio of (normalized abundance determined by ribosome profiling)/ (normalized abundance determined by RNA-seq. For corresponding bulk RNA-seq data processing, the clean reads were mapped to the mouse genome (Hg38) using Hisat2. Then, the number of reads uniquely mapped to each gene was determined using FeatureCounts from subread2.
Assembly: GRCh38
Supplementary files format and content: gene count files generated by featureCounts

source_name: corresponding rRNA depleted RNA-seq on  HeLa cell with DNMT1 knockdown


title: Riboseq mock treatment

description: Library name: Riboseq mock treatment

source_name: ribosome-protected mRNA fragment on HeLa cells with mock treatment

value: mock


title: RNAseq mock treatment

description: Library name: RNAseq mock treatment

source_name: corresponding  rRNA depleted RNA-seq  on HeLa cells with mock treatment


title: BZIP27_B73


title: HB68_B73


description: Library name: SLAM-seq_Human_NPC_with_homozygous_A570V_24h

data_processing:
For Slam-seq data processing, raw reads were trimmed of adapters and low-quality bases using TrimGalore (V0.6.7). Then only read1 were used and processed with SLAMDUNK (V0.4.3) to map reads, filter alignments, call variants on final alignments by using the hg38 analysis set reference genome.
Assembly: GRCh38
Supplementary files format and content: bed files generated by SLAMDUNK containing the T-C conversion rates

source_name: Slam-seq on human NPC cell with homozygous A570V DNMT1 mutation at 24h

extract_protocol:
Medium with 4SU was used for HeLa cells labeling for 24 hours and was later replaced with 4SU-free medium (time 0).
Total RNA was processed according to the standard Slam-seq protocol, described previously(Nat Methods 14, 1198-1204. 10.1038/nmeth.4435). Briefly, Slam-seq were performed in HeLa cells and Human NPCs at three time points of IAA treatment (0, 6 and 24 h). Basically, cells were feed with 100 uM 4sU for 24 h, fresh media containing s4U was changed every 12 h. After 24 h labelling, old media are removed and cells were washed with PBS three times before adding media without 4sU, but 10 mM UTP instead, samples were collected at 0, 6, 24 h for RNA extract and IAA treatment. All the operations were done in red light source to protect 4sU from crosslink. Then RNA was used for 3' mRNA-seq library construction and sequencing.

value: Human neural progenitor cells


title: BHLH106_B73


title: BZIP54_B73


description: Library name: SLAM-seq_Human_NPC_with_homozygous_A570V_6h

source_name: Slam-seq on human NPC cell with homozygous A570V DNMT1 mutation at 6h


title: ARR5_B73


title: HB117_B73


description: Library name: SLAM-seq_Human_NPC_with_homozygous_A570V_0h

source_name: Slam-seq on human NPC cell with homozygous A570V DNMT1 mutation at 0h


title: DD_BHLH61_BHLH168_B73

value: doubleDAP-seq


title: DD_BHLH113_BHLH168_B73

value: seedling leaf


title: DD_BHLH135_BHLH168_B73


title: SLAM-seq_Human_NPC_WT_24h

description: Library name: SLAM-seq_Human_NPC_WT_24h

source_name: Slam-seq on wild type human NPC cell at 24h


title: DD_BHLH52_BHLH168_B73


title: BZIP2_B73

value: DAP-seq


title: DD_BHLH85_BHLH168_B73


description: Library name: SLAM-seq_Human_NPC_with_heterozygous_A570V_24h

source_name: Slam-seq on human NPC cell with heterozygous A570V DNMT1 mutation at 24h


title: DD_BHLH67_BHLH125_B73


title: DD_BHLH67_BHLH168_B73


title: PB_qinMa

city: Shanghai

first: Chaoran

last: Xia

state: Shanghai

address: 800# Dong Chuan Road,  Shanghai, China

country: China

institute: Shanghai Jiaotong University

description:
Genomic DNA extracted from peripheral blood was genotyped using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.)
207875410041_R03C01

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

label: biotin

source_name: Peripheral blood, qinMa

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from Peripheral blood was performed using the Wizard Genomic DNA Purification Kit, according to the manufacturer's instructions (cat no. DP318-02; Tiangen Biotech Co., Ltd.).

tag: gender

value: female

tag: subject

value: qinMa

value: Peripheral blood


description: Library name: SLAM-seq_Human_NPC_with_heterozygous_A570V_6h

source_name: Slam-seq on human NPC cell with heterozygous A570V DNMT1 mutation at 6h


title: PB_qinFa

description:
Genomic DNA extracted from peripheral blood was genotyped using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.)
207875410041_R02C01

source_name: Peripheral blood, qinFa

value: male

value: qinFa


title: SLAM-seq_Human_NPC_WT_6h

description: Library name: SLAM-seq_Human_NPC_WT_6h

source_name: Slam-seq on wild type human NPC cell at 6h


title: RNP NEG 3 96h

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: RNP_NEG_3_96h_S1

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters unstranded --minOverlap 10)
Differential expression analysis was computed with DESeq2
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: Primary CB-derived HSPCs

extract_protocol:
miRNeasy micro kit (QIAGEN)
SMART-seq Ultra low input unstranded

value: Primary CB-derived HSPCs

value: HSPCs experiencing the RNP NEG treatment (replicate 3)


title: DD_BHLH85_BHLH125_Mo17

source_name: seedling leaf


title: DD_BHLH85_BHLH125_B73


title: SLAM-seq_Human_NPC_WT_0h

description: Library name: SLAM-seq_Human_NPC_WT_0h

source_name: Slam-seq on wild type human NPC cell at 0h


title: DD_BHLH92_BHLH168_B73


title: BHLH52_Mo17


title: BHLH113_Mo17


title: RNP NEG 2 96h

description: Library name: RNP_NEG_2_96h_S1

value: HSPCs experiencing the RNP NEG treatment (replicate 2)


title: E3_159_RNP_NEG_24h

description: Library name: E3_159_RNP_NEG_24h

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Differential expression analysis was computed with DESeq2
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

extract_protocol:
miRNeasy Micro Kit (QIAGEN)
TruSeq Stranded mRNA (Illumina)


title: PB_qin_proband

description:
Genomic DNA extracted from peripheral blood was genotyped using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.)
207875410041_R01C01

source_name: Peripheral blood, qin, proband

value: qin, proband


title: BHLH135_Mo17


title: RNP NEG 1 96h

description: Library name: RNP_NEG_1_96h_S1

value: HSPCs experiencing the RNP NEG treatment (replicate 1)


description: Library name: SLAM-seq_Human_NPC_with_heterozygous_A570V_0h

source_name: Slam-seq on human NPC cell with heterozygous A570V DNMT1 mutation at 0h


title: E2_159_RNP_NEG_24h

description: Library name: E2_159_RNP_NEG_24h


title: BHLH150_Mo17


title: A3_159_RNP_NEG_24h

description: Library name: A3_159_RNP_NEG_24h


title: MADS69_Mo17


title: OV2

city: NanChang

first: Qi

last: Xiao

address: Nanchang University, 17 yongwai Zheng jie street, NanChang 33006, Jiangxi, China

institute: Department of Transplantation，The First Affiliated Hospital， Jiangxi Medical College，Nanchang University

description: Library name: Simple5

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm counts for each sample

source_name: HUVECs

extract_protocol:
Total RNA was extracted from liver tissue using Trizol reagent (Servicebio, Wuhan, China). mRNA was then reverse-transcribed into cDNA using a reverse transcription kit (Servicebio, Wuhan, China). The SYBR Green (Biosharp, Wuhan, China) reaction system was loaded into a 96-well plate, and PCR amplification was performed according to the manufacturer’s instructions. β-Actin was used as the reference gene.
RNA was extracted from cell samples using the Trizol method and its integrity was assessed using the Agilent 2100 Bioanalyzer. mRNA was enriched via poly(A) selection, then fragmented and reverse-transcribed to synthesize cDNA. A cDNA library was constructed and high-throughput sequencing was performed on the RNA library using the Illumina sequencing platform to generate raw data

value: HUVECs

value: KLF2 overexpression


title: OV3

description: Library name: Simple6


title: ZIM2_Mo17


title: ZHD5_Mo17


title: OV1

description: Library name: Simple4


title: NC1

description: Library name: Simple1

value: wt


title: ZHD1_Mo17


title: ZHD4_Mo17


title: NC3

description: Library name: Simple3


title: NC2

description: Library name: Simple2


title: BHLH61_Mo17


title: WRKY57_Mo17


title: ZR75

city: Hong Kong

first: Ui-soon

last: Khoo

address: Queen Mary hospital

department: Pathology

country: Hong Kong

institute: University of Hong Kong

description:
Library name: Sample 3
ZR75_1

data_processing:
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low Quality is defined as: i. Reads with more than 5% unknown bases (“N”) ii. Reads having more than 50% of bases with quality value <= 11
Reads were mapped to the reference genome using STAR (default parameters) with the following exception: i. twopassMode: Basic
Differentially expression analysis was done using EBSeq
Assembly: GRCh38.p14
Supplementary files format and content: CSV file contains TPM and normalised TPM

source_name: Breast; Mammary gland

growth_protocol: All the cell lines were culture in DMEM with 10%FBS and 1%P/S at 37'C with 5% CO2

extract_protocol:
RNA was isolated using Trizol
cDNA libraries were prepared by KAPA Stranded mRNA-Seq Kit (KR0960-v3.15).

treatment_protocol: no treatment

value: Breast; Mammary gland

value: epithelial cell

value: WT

value: Control


title: MCF7BQ

description:
Library name: Sample 5
MCF7BQ_1

value: BQ OE

value: Stable BQ overexpression


title: ZR75BQ

description:
Library name: Sample 7
ZR75BQ_1


title: ZHD15_Mo17

value: seedling leaf

value: DAP-seq


title: WRKY125_Mo17


title: WRKY64_Mo17


title: R2-PLJM1-LSM12

city: Shenyang

first: Gang

last: Zhao

address: 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description:
Library name: Sample 5
FPKM.R2-PLJM1-LSM12

data_processing:
Total RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and mRNA was used to synthesize complementary DNA (cDNA).  In accordance with the manufacturer's instructions, sequencing libraries were created using the NEBNext Ultra RNA Library Prep Kit for Illumina, and index numbers were appended to each sample to assign sequences. Using the PE150 strategy, the qualified libraries were combined and sequenced on Illumina platforms. Base calling is used to convert the original fluorescence image files from the Illumina platform into short reads (raw data), which are then recorded in the FASTQ format. This format includes sequence information and matching sequencing quality information. Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
Assembly: GRCh38
Supplementary files format and content: processed data file includes counts and FPKM for each sample.

extract_protocol:
Total RNA was extracted from samples with TRIzol. The total RNA quantity and purity were analyzed by NanoDrop.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Tumor cells

value: LSM12 overexpression


title: R3-PLJM1-LSM12

description:
Library name: Sample 6
FPKM.R3-PLJM1-LSM12


title: R1-PLJM1-LSM12

description:
Library name: Sample 4
FPKM.R1-PLJM1-LSM12


title: ZHD21_Mo17


title: WRKY11_Mo17


title: WRKY53_Mo17


title: MCF7

description:
Library name: Sample 1
MCF7_1


title: THX26_Mo17


title: R2-PLJM1

description:
Library name: Sample 2
FPKM.R2-PLJM1_1

value: WT (Control)


title: THX20_Mo17


title: R1-PLJM1

description:
Library name: Sample 1
FPKM.R1-PLJM1_1


title: THX16_Mo17


title: TCP8_Mo17


title: R3-PLJM1

description:
Library name: Sample 3
FPKM.R3-PLJM1_1


description:
Library name: RNA-BS-seq α-Amanitin treatment and DNMT1 knockdown
RNA Bisulfite Sequencing in HeLa Cells  with DNMT1 knockdown and α-Amanitin treatment for 12h

data_processing:
For RNA-BS-seq data analysis, meRanTK was used to determine the methylation level for all of the sequenced cytosine sites. Firstly, the clean reads were mapped to the corresponding genomes (hg38) by meRanGs function through star alignment tools. The methylated cytosines in each sample were identified by meRanCall with FDR less than 0.01.
Assembly: GRCh38
Supplementary files format and content: all the candiate m5C site identified by meRANTK

source_name: HeLa cells

extract_protocol:
Total mRNA was extracted by the NEBNext® rRNA Depletion Kit (NEB).
1 μg of the mRNA was used for bisulfite treatment by EZ Methylation Kit (Zymo) following the protocols provided by the manufacturer. After bisulfite conversion, the purified RNA was used for library construction by NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

value: HeLa cells


title: WRKY82_Mo17


title: YAB2_Mo17


title: TCP5_Mo17


title: Human sickle HSPCs RNA - donor3 control

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova

description:
Library name: MT_TE
donor3_TE

data_processing:
Read quality was evaluated using FastQC (v. 0.11.9). Raw reads were trimmed for adapters and low-quality tails (quality < Q20) with BBDuk (v. 38.92); moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp after trimming were removed.
Trimmed reads were aligned to the human reference genome (hg38) using STAR (v. 2.7.9a). Raw gene counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.8.1) and the GENCODE v44 basic gene annotation for hg38 human reference genome.
Gene counts were normalized to counts per million mapped reads (CPM) using the edgeR R package (v. 3.36.0); only genes with a CPM greater than 1 in at least 3 samples were retained.
Assembly: hg38
Supplementary files format and content: CPM obtained using edgeR

source_name: Blood HSPCs

growth_protocol: Cells were grown in “HSPC medium” containing StemSpan (STEMCELL Technologies) supplemented with penicillin/streptomycin (Gibco), 250 nM StemRegenin1 (STEMCELL Technologies), and the following recombinant human cytokines (PeproTech): human stem cell factor (SCF) (300 ng/ml), Flt-3L (300 ng/ml), thrombopoietin (TPO) (100 ng/ml), and interleukin-3 (IL-3) (60 ng/ml).

extract_protocol:
Total RNA was isolated from edited HSPCs 48h following electroporation (ZD7001, Zymo Research). RNA quality and concentrations were assessed by capillary electrophoresis using High Sensitivity RNA reagents with the Fragment Analyzer (Agilent Technologies).
Bulk mRNA-seq libraries were prepared by the Imagine Genomic Core Facility (Paris, France) starting from 50ng of total RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit according to manufacturer’s guidelines.

treatment_protocol: 1x105 to 3x105 HSPCs per condition were transfected with 3.0 μg of the ABE-encoding mRNA and 3.2 μg of the synthetic gRNA. We used the P3 Primary Cell 4D-Nucleofector X Kit S (Lonza) and the CA137 program (Nucleofector 4D). Cells transfected only with TE buffer served as negative controls.

value: Blood HSPCs

value: biallelic sickle cell disease-causing mutations

value: Mock transfected


title: TCP4_Mo17


title: RNA-BS-seq α-Amanitin treatment

description:
Library name: RNA-BS-seq α-Amanitin treatment
RNA Bisulfite Sequencing in HeLa Cells with α-Amanitin treatment for 12h

value: α-Amanitin treatment


title: Human sickle HSPCs RNA - donor3 edited

description:
Library name: MT_cor
donor3_cor

value: Corrected


title: TCP30_Mo17


title: Human sickle HSPCs RNA - donor2 edited

description:
Library name: DM_cor
donor2_cor


title: Human sickle HSPCs RNA - donor2 control

description:
Library name: DM_TE
donor2_TE


title: TCP2_Mo17


title: TCP15_Mo17


title: SBP32_Mo17


title: TCP11_Mo17


title: SBP6_Mo17


title: Human sickle HSPCs RNA - donor1 edited

description:
Library name: AD_cor
donor1_cor


title: Human sickle HSPCs RNA - donor1 control

description:
Library name: AD_TE
donor1_TE


title: SLAM-seq_HeLa_DNMT1 knockdown_24h

description: Library name: SLAM-seq_HeLa_DNMT1 knockdown_24h

source_name: Slam-seq on HeLa cell with DNMT1 knockdown at 24h


title: SBP30_Mo17


title: SBP2_Mo17


title: SLAM-seq_HeLa_WT_24h

description: Library name: SLAM-seq_HeLa_WT_24h

source_name: Slam-seq on HeLa cell at 24h


title: SBP15_Mo17


title: SLAM-seq_HeLa_WT_0h

description: Library name: SLAM-seq_HeLa_WT_0h

source_name: Slam-seq on HeLa cell at 0h


title: eCLIP-seq DNMT1 Input 293T

description:
Library name: eCLIP-seq DNMT1 Input 293T
DNMT1 eclip-seq 293T Input

data_processing:
The processing of raw eCLIP sequencing data follows the ENCODE pipeline, as previously published in Nature Methods (13, 508–514, 2016). Briefly, PCR duplicates were removed by Clumpify of BBTools (sourceforge.net/projects/bbmap/) by making use of the random-mer sequence. Trim adaptor sequences and the random-mer sequences (first 10 bp of forward reads) off of reads using TrimGalore (V0.6.7) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trim 3′ ends of reads for low quality bases and filter reads for length using Sickle (https://github.com/najoshi/sickle) with a quality threshold of 20 and a length threshold of 18 bp. Then the processed reads were mapping to the human genome (hg38) by using Star (V2.7.0a). The resulting SAM files were compressed into BAM and sort by Samtools. Then clipper and idr was used for peaks calling. Only unique mapped reads were used for peaks calling.
Assembly: GRCh38
Supplementary files format and content: bigwig file genearted by genomecov for each sample
Supplementary files format and content: bed file containing the NSUN2 or DNMT1 binding peaks

extract_protocol:
Subsequent steps were performed as described in the eCLIP protocol. Nat Methods 13, 508–14 (2016)). We used the following antibodies for immunoprecipitation reactions: NSUN2 antibody (Abcam, ab259941),
eCLIP-seq  were performed by following the previous study(Nat Methods 13, 508–14 (2016))  Briefly, 20 million HeLa cells were washed in PBS and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation on ice, pelleted and snap frozen. Cells were then lysed in lysis buffer (50 mM Tris-HCl (pH 7.4), 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:100 Protease Inhibitor Cocktail III) and treated with Turbo DNase and RNase I to fragment RNA, and supernatants from lysates were collected for immunoprecipitation. 30 μg of DNMT1 antibody mixture (Novus Biologicals) for each sample was then pre-coupled to 400 μl of sheep anti-rabbit Dynabeads (Life Technology), added to the lysates and incubate overnight at 4°C. 2% of the sample from cell lysates (without DNMT1 antibody) was taken as input sample. After overnight incubation, the mixture was magnetically separated and washed twice with cold high salt wash buffer (50 mM Tris-HCl (pH 7.4), 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and wash buffer (20 mM Tris-HCl (pH 7.4), 10 mM MgCl2, 0.2% Tween-20). After RNA adapter ligation, IP-western, eCLIP was performed by excising the area from 180 to 240 kDa for input and IP samples. Maxima Reverse Transcriptases (Thermo Fisher Scientific) were used for reverse transcription. Then cDNA purification, DNA adapter ligation, and PCR amplification were performed according to the standard eCLIP experimental procedure. Both SPRI beads and gel-extract were used to select the size of the libraries with 175-350 bp.

treatment_protocol: For eCLIP experiments,   20 millions Hela cells or 293T were briefly rinsed with PBS and subjected to UV-irradiation. Cells were scraped in PBS using a rubber policeman, pelleted at 200x g for 5 min and lysed by adding 2x CLIP lysis buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2 mM EDTA, 2% (v/v) NP40, 1% sodium deoxycholate, 0.5 mM DTT).


title: BZIP1_Mo17


title: eCLIP-seq DNMT1 IP 293T rep2

description:
Library name: eCLIP-seq DNMT1 IP 293T rep2
DNMT1 antibody 293T IP rep2


title: ARF27_Mo17


title: ARF10_Mo17


title: NLP14_Mo17


title: NKD2_Mo17


title: eCLIP-seq DNMT1 IP 293T rep1

description:
Library name: eCLIP-seq DNMT1 IP 293T rep1
DNMT1 antibody 293T IP rep1


title: NKD1_Mo17


title: eCLIP-seq DNMT1 Input HeLa  rep2

description:
Library name: eCLIP-seq DNMT1 Input HeLa  rep2
DNMT1 eclip-seq HeLa Input rep2


title: eCLIP-seq DNMT1 IP HeLa rep2

description:
Library name: eCLIP-seq DNMT1 IP HeLa rep2
DNMT1 antibody HeLa IP rep2


title: NFYA1_LEC1_CA5P16_Mo17


title: eCLIP-seq DNMT1 Input HeLa rep1

description:
Library name: eCLIP-seq DNMT1 Input HeLa rep1
DNMT1 eclip-seq HeLa Input rep1


title: NAC91_Mo17


title: SLAM-seq_HeLa_DNMT1 knockdown_6h

description: Library name: SLAM-seq_HeLa_DNMT1 knockdown_6h

source_name: Slam-seq on HeLa cell with DNMT1 knockdown at 6h


title: SLAM-seq_HeLa_DNMT1 knockdown_0h

description: Library name: SLAM-seq_HeLa_DNMT1 knockdown_0h

source_name: Slam-seq on HeLa cell with DNMT1 knockdown at 0h


title: eCLIP-seq NSUN2 Input rep2

description:
Library name: eCLIP-seq NSUN2 Input rep2
NSUN2 eclip-seq Input rep2


title: NAC49_Mo17


title: NAC74_Mo17


title: eCLIP-seq NSUN2 IP rep2

description:
Library name: eCLIP-seq NSUN2 IP rep2
NSUN2 antibody IP rep2


title: eCLIP-seq NSUN2 Input rep1

description:
Library name: eCLIP-seq NSUN2 Input rep1
NSUN2 eclip-seq Input rep1


title: NAC71_Mo17


title: SLAM-seq_HeLa_WT_6h

description: Library name: SLAM-seq_HeLa_WT_6h

source_name: Slam-seq on HeLa cell at 6h


title: eCLIP-seq NSUN2 IP rep1

description:
Library name: eCLIP-seq NSUN2 IP rep1
NSUN2 antibody IP rep1


title: NAC42_Mo17


title: RNA-BS-seq mock treatment rep2

description:
Library name: RNA-BS-seq mock treatment rep2
RNA Bisulfite Sequencing in HeLa Cells with mock treatment

data_processing:
For RNA-BS-seq data analysis, meRanTK was used to determine the methylation level for all of the sequenced cytosine sites. Firstly, the clean reads were mapped to the corresponding genomes (hg38) by meRanGs function through star alignment tools. The methylated cytosines in each sample were identified by meRanCall with FDR less than 0.01. Then the wand function of RADMeth was carried out to identify the differently methylated RNA cytosine sites due to NSUN2 knockdown with p-values less than 0.05 and fold change larger than 0.1.
Assembly: GRCh38
Supplementary files format and content: all the candiate m5C site identified by meRANTK
Supplementary files format and content: bed file with the total count and methylated count of all samples at NSUN2 dependent m5C sites


title: NAC3_Mo17


title: RNA-BS-seq mock treatment rep1

description:
Library name: RNA-BS-seq mock treatment rep1
RNA Bisulfite Sequencing in HeLa Cells with mock treatment


title: NAC33_Mo17


title: NAC28_Mo17


title: RNA-BS-seq  NSUN2 knockdown rep2

description:
Library name: RNA-BS-seq  NSUN2 knockdown rep2
RNA Bisulfite Sequencing in HeLa Cells with NSUN2 Knockdown


title: NAC27_Mo17


title: PBMC SubAB stimulated, rep 2

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome, using the CellRanger Pipeline v7.1.0. Unfiltered RNA UMI counts were loaded into Seurat v5.01 for quality control, data integration and downstream analyses.
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 matrices

source_name: Blood

growth_protocol: PBMCs were isolated from healthy blood donors' buffy coats (Établissement Français du Sang (EFS), Marseille, FR) by density gradient centrifugation, using Ficoll-Paque Plus (Cytiva, Marlborough, MA, USA). Briefly, the buffy coat blood was diluted 1:1 in RPMI 1640 medium and overlaid onto Ficoll-Paque Plus density gradient media, and cells separated by centrifugation (2,200 rpm for 30 min, no breaks). The mononuclear cell layer was transferred into a new tube and washed with RPMI 1640 medium at 1,900 rpm for 5 minutes. The final PBMCs pellet was resuspended at the desired concentration for downstream use.

extract_protocol:
The scRNA-seq libraries were generated using Chromium Single Cell 30 Library & Gel Bead Kit v.3 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1,000 cells/mL in PBS and 20,000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary-DNA was isolated and amplified by PCR. Following fragmentation, end repair, and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2.
scRNA-seq experiments were performed at the “Labtech SingleCell@Imagine” on PBMCs isolated from healthy blood donors' buffy coats. The scRNA-seq libraries were generated using Chromium Single Cell 30 Library & Gel Bead Kit v.3 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1,000 cells/mL in PBS and 20,000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary-DNA was isolated and amplified by PCR. Following fragmentation, end repair, and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2.

value: Blood

value: Peripheral blood mononuclear cells

value: SubAB


title: PBMC Mock treated

value: Mock


title: RNA-BS-seq  NSUN2 knockdown rep1

description:
Library name: RNA-BS-seq  NSUN2 knockdown rep1
RNA Bisulfite Sequencing in HeLa Cells with NSUN2 Knockdown


title: eCLIP-seq DNMT1 IP HeLa rep1

description:
Library name: eCLIP-seq DNMT1 IP HeLa rep1
DNMT1 antibody HeLa IP rep1


title: NAC25_Mo17

data_processing:
Illumina reads were mapped using bowtie2 with default parameters. Mapped reads were filtered to retain MAPQ scores greater than 30 using samtools. Peaks were called using GEM3.0 with variable significance thresholds.
Assembly: B73v5 or Mo17_CAU1.0
Supplementary files format and content: narrowPeak format
Library strategy: DAP-seq


title: NAC20_Mo17


title: NAC86_Mo17


title: PBMC CL307 +SubAB stimulated, rep 2

value: CL307 +SubAB


title: NAC12_Mo17


title: NAC116_Mo17


title: PBMC CL307 stimulated, rep 2


title: NAC115_Mo17


title: replicate 1 of G4P CUT&Tag in HeLa-S3

city: Changsha

first: Kewei

last: Zheng

address: Lushan Road

department: School of Biomedical Sciences

institute: Hunan University

data_processing:
The clean paired-end sequencing data were analyzed as described (Zheng et al., 2024). The human genome (version hg38) was used as a reference. Reads were aligned with bowtie2 (v.2.3.5.1) using --fast-local. Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 50 --normalizeUsing RPGC.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: cervical cancer tissue

growth_protocol: HeLa-S3 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (P/S)

extract_protocol:
The G4-CUT&Tag method was constructed following the described protocol (Zheng et al., 2024) with some modifications. Briefly, a total of 10^5 cells were washed twice with 100 µL wash buffer (20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors), and then resuspended with 100 µL wash buffer. Next, 10 µL of pre-activated concanavalin A coated magnetic beads were added to the cells and incubated on a rotator for 10 minutes at room temperature. The supernatant was removed, and the bead-bound cells were resuspended in 100 µL of dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1× protease inhibitors) containing either 250 nM of recombinant G4P or 0.7 µg/mL of recombinant anti-NCL antibody (14574, CST). After two-hours rotation at room temperature, the cells incubated with G4P were washed twice with 100 µL of dig-wash buffer and resuspended with 100 µL of dig-wash buffer containing 1 µL of anti-FLAG M2 antibody (F1804, Sigma), incubated for another one hour at room temperature. The buffer containing primary antibodies was then removed from the cells, and 100 µL of dig-wash buffer containing 1 µL of Goat anti-mouse IgG (AP124, Sigma) or 1 µL of Goat anti-rabbit IgG (AP132, Sigma) was mixed with the cells and incubated for one hour at room temperature. After washing three times with dig-wash buffer, a 1:250 dilution of pA-Tn5 adapter complex (~0.2 µM) was prepared in 100 µL of dig-wash buffer and added to the cells, which were then rotated for one hour at room temperature. After five washes with dig-wash buffer, the bead-bound cells were resuspended with 50 µL of tagmentation buffer (20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 10 mM MgCl2, 0.5 mM spermidine, 1× protease inhibitors) and incubated at 37°C for one hour. To terminate the tagmentation reaction, 2.5 µL of 0.5 M EDTA, and 1 µL of 20 mg/mL proteinase K were added and incubated at 55°C for 30 min. The DNA was then extracted using 120 µL of Ampure XP beads (Beckman Counter) for library preparation. DNA was eluted in 40 µL of 5 mM Tris−HCl (pH 8.0).
To amplify the libraries, 16 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer, and amplified using Q5 high-fidelity 2× master mix (NEB). The libraries were purified with 1.3× volume of Ampure XP beads, and eluted in 20 µL of 10 mM Tris−HCl (pH 8.0).

value: cervical cancer tissue

value: Uterine/Vaginal Epith

value: untreated


title: replicate 2 of G4P CUT&Tag in HeLa-S3


title: MYBR52_Mo17

extract_protocol:
genomic DNA was extracted from 14 day-old leaves
genomic DNA was fragmented to 200bp and subjected to standard Illumina library construction prior to incubation with in vitro expressed transcription factor

value: seedling leaf

value: DAP-seq


title: MYBR58_Mo17


title: replicate 2 of NCL CUT&Tag in HeLa-S3


title: Human beta-thalassemia HSPCs RNA - donor3 edited

treatment_protocol: 1x105 to 3x105 HSPCs per condition were transfected with 3.0 μg of the ABE-encoding mRNA and 3.2 μg of the synthetic gRNA. We used the P3 Primary Cell 4D-Nucleofector X Kit S (Lonza) and the CA137 program (Nucleofector 4D). Cells transfected only with TE buffer served as negative controls


title: MYBR111_Mo17


title: MYBR17_Mo17


title: replicate 1 of NCL CUT&Tag in HeLa-S3


title: Human beta-thalassemia HSPCs RNA - donor3 control


title: MYBR101_Mo17


title: Human beta-thalassemia HSPCs RNA - donor2 edited


title: MYB73_DED1_Mo17


title: Human beta-thalassemia HSPCs RNA - donor1 edited


title: MYB50_Mo17


title: Human beta-thalassemia HSPCs RNA - donor1 control


title: MYB138_Mo17


title: MYB40_Mo17


title: amplicon_pool

data_processing:
Reads were split based on an internal barcode
the reads were trimmed to a length of 20 bp and consolidated
They were then compared to the appropriate genomic target region and the percentage of wrong reads was calculated
hg38
Excel worksheet. Consolidated read count of the target genomic region

source_name: Bone marrow

extract_protocol:
Genomic DNA of > 1 Mio sgRNA positive and WT cells was amplified and extracted from an agarose gel and the DNA concentration was determined. For amplicon sequencing, Illumina adapters were added to the PCR product using a second PCR step, the resulting PCR amplicons were then extracted from an agarose gel. The size, concentration, and purity of the DNA amplicon was assessed using the BioAnalyzer 2100 high sensitivity DNA kit. All amplicons were pooled and sent for Illumina sequencing.
The library was generated using custom primers amplifying the target genomic region where the sgRNA targets

treatment_protocol: TF-1 cells expressing Cas9-ZIM3 were spinfected (900g) with 4µg/mL polybrene with lentivirus for the respective normal length and truncated sgRNAs targeting CD33 or CD13 or a scr sgRNA control. sgRNA positive cells were measured after 2 days of transduction and selected for one week using 500 µg/mL G418 solution. The cells were cultivated for a total of two weeks, depletion of CD13 and CD33 was monitored and then harvested

value: Bone marrow

value: erythroleukemia


title: MYB131_Mo17

source_name: seedling leaf


title: WT

data_processing:
Data filtering based on read calling and removal of illumina adapter reads
Alignment of forward and reverse reads to the genome using HISAT2
hg38
Read count file obtained by HISAT2

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) and the mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) kit.
Library was generated using the  NEBNext® Ultra™ II RNA Library Prep (NEB).

treatment_protocol: TF-1 cells expressing dCas9-ZIM3 were spinfected (900g) with 4µg/mL polybrene with lentivirus for the respective normal length and truncated sgRNAs targeting CD33. sgRNA positive cells were measured after 2 days of transduction and selected for one week using 500 µg/mL G418 solution. The cells were cultivated for a total of two weeks and then harvested


title: MADS12_Mo17


title: Control_rep2


title: Control_rep1


title: 20mer_sgRNA2_rep2


title: DOF24_Mo17


title: EREB53_Mo17


title: 20mer_sgRNA1_rep2


title: 20mer_sgRNA2_rep1


title: 20mer_sgRNA1_rep1


title: BZIP84_Mo17


title: MYB83_Mo17


title: BZIP40_Mo17


title: 15mer_sgRNA2_rep1


title: 15mer_sgRNA2_rep2


title: MADS73_Mo17


title: BHLH125_Mo17


title: Human beta-thalassemia HSPCs RNA - donor2 control

value: Blood HSPCs


title: MADS72_Mo17


title: LBD37_Mo17


title: 15mer_sgRNA1_rep2


title: LBD5_Mo17


title: MADS68_Mo17


title: BHLH99_Mo17


title: HSF7_Mo17


title: BHLH57_Mo17


title: HSF25_Mo17


title: HB68_Mo17


title: HSF24_Mo17


title: HB15_Mo17


title: 15mer_sgRNA1_rep1


title: HB122_Mo17


title: HB117_Mo17


title: GRF7_Mo17


title: MADS43_Mo17


title: GRF2_Mo17


title: HB102_Mo17


title: GRF3_Mo17


title: GRF6_Mo17


title: LBD16_Mo17


title: 8035073962-G, Exercise Response (Post), GEX, bio rep 2

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Cell Ranger ARC 1.0.0 pipeline was run on the samples following 10x Genomics guidelines. Seurat v4 and Signac v1 were used to perform data processing and analysis.
Assembly: hg38
Supplementary files format and content: rds file contains the integrated data of all samples

source_name: PBMC

extract_protocol:
Frozen human skeletal muscle samples were pulverized and the powder used for nuclei isolation. Briefly, and all on ice, RNAse inhibitor (NEB cat# MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from StemCell cat# 07820), 35% OptiPrep and 30% OptiPrep right before isolation. Each sample was homogenized in a Dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 17,792xg; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei dilution buffer for sn multiome (10x Genomics) and counted (Cellometer).
Sn multiome was performed following the Chromium Single Cell Multiome ATAC and Gene Expression Reagent Kits V1 User Guide (10x Genomics, Pleasanton, CA). Nuclei were counted (Countess counter), transposition was performed in 10 ul at 37C for 60min targeting up to 10,000 nuclei, before loading of the Chromium Chip J (PN-2000264) for GEM generation and barcoding. Following post-GEM cleanup, libraries were pre-amplified by PCR, after which the sample was split into three parts: one part for generating the snRNAseq library, one part for the snATACseq library, and the rest was kept at -20C. SnATAC and snRNA libraries were indexed for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262, and Chromium i7 Sample Index TT, Set A kit PN-3000431 respectively).
Single Cell Multiome ATAC and Gene Expression

value: PBMC

tag: Sex

value: Male

tag: group

value: Exercise Response

value: Post


title: 8035073962-G, Exercise Response (Post), GEX, bio rep 1


title: GRF9_Mo17


title: 8035073790-E, Exercise Response (Post), GEX, bio rep 2

value: Female


title: LBD19_Mo17


title: 8035073981-G, Exercise Response (Pre), GEX, bio rep 2

value: Pre


title: 8035073981-G, Exercise Response (Pre), GEX, bio rep 1


title: GLK47_Mo17


title: HB54_Mo17


title: 8035073800-E, Exercise Response (Pre), GEX, bio rep 2


title: GLK48_Mo17


title: GLK44_Mo17


title: GLK21_Mo17


title: HB22_Mo17


title: 8035073800-E, Exercise Response (Pre), GEX, bio rep 1


title: GLK20_Mo17


title: 8035074016-I, Exercise Response (Pre), GEX


title: 8035073722-I, Exercise Response (Post), GEX


title: GLK17_Mo17


title: 8035073603-L, Circadian control (Post), GEX, bio rep 2

value: Circadian control


title: GBP11_Mo17


title: GBP10_Mo17


title: GBP4_Mo17


title: 8035073603-L, Circadian control (Post), GEX, bio rep 1


title: 8035073530-L, Circadian control (Pre), GEX, bio rep 2


title: GLK56_Mo17


title: 8035073530-L, Circadian control (Pre), GEX, bio rep 1


title: EREB87_Mo17


title: 8035073790-E, Exercise Response (Post), GEX, bio rep 1


title: 8035073524-J, Exercise Response (Post), GEX


title: EREB4_Mo17


title: GLK53_Mo17


title: EREB46_Mo17


title: EREB36_Mo17


title: EREB2_Mo17


title: EREB24_Mo17


title: 8035073605-N, Circadian control (Post), GEX, bio rep 2


title: 8035074040-J, Exercise Response (Pre), GEX


title: S018_TR_1

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

description: Total RNA-Seq S018 Trabectedin - Replicate 1

data_processing:
Sequencing reads were preprocessed and filtered using fastp v0.23.1
Filtered reads were aligned to transcript annotations using Salmon v1.4.0 in default settings with seqBias and gcBias options to correct for hexamer priming and GC-content biases, respectively
Gencode v36 was used as a reference transcriptome. Read alignments were preprocessed with tximport v1.18.0 R package and expression levels were normalized as Transcript Per Million (TPM).
Assembly: hg38
Supplementary files format and content: TPM-normalized gene expression levels

source_name: cell line

growth_protocol: HT-1080 cell lines were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured respectively in Eagle’s Minimum Essential Medium (EMEM, Sigma-Aldrich, Merck KGaA, Darmstadt, Germany), McCoy’s 5a (Sigma-Aldrich), and RPMI-1640 (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine and penicillin/streptomycin. DMR cells were kindly provided by Dr. Paola Spessotto and cultured in RPMI-1640 (Sigma-Aldrich), supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine, and penicillin/streptomycin. Undifferentiated pleomorphic sarcoma primary cell lines, S018 were obtained from surgical biopsies and maintained in Knock-out DMEM (Gibco, Life Technology Italia, Monza, Italy), supplemented with 10% FBS (Gibco), 100 U/ml penicillin and 100 U/ml streptomycin (Gibco) and 25 mmol/L HEPES. All cell lines were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from sarcoma cell lines and xenografts using the Maxwell® RSC miRNA Tissue Kit (Promega Italia Srl, Pero, Milan, Italy) and the RSC Maxwell Instrument (Promega Italia, Srl) following the manufacturer’s instructions. RNA quality and concentration were checked by DS 11+ Spectrophotometer (Denovix Inc, Wilmington, DE, USA). Starting
After RNA extraction, RNA purity was checked by NanoDropTM (Thermo Fisher Scientific). RNA concentration was determined by the Qubit RNA BR (broad range) assay kit (Thermo Fisher Scientific) and the Qubit® 3.0 Fluorometer (Thermo Fisher Scientific).  RNA fragmentation was assessed by gel electrophoresis and 2100 Bioanalyzer High Sensitivity RNA assay Kit (Agilent Technologies, Inc., Santa Clara, CA, USA). The total RNA was processed for RNA-sequencing analysis with the TruSeq Stranded Total RNA gold (Illumina Italy Srl, Milan, Italy) following the manufacturer’s instruction and sequenced on the NovaSeq6000 (Illumina Italy Srl).

treatment_protocol: Trabectedin (PharmaMar, Madrid, Spain) and olaparib (Biosynth Carbosynth, Staad, Switzerland) were dissolved in dimethyl sulfoxide (DMSO, Sigma-Aldrich), stored at -80°C, and diluted in fresh media immediately before use at a final concentration of 0.5 nM trabectedin and 5 µM olaparib. Cells were treated for 72hr befor RNA extraction.

value: cell line

value: TR


title: S018_TR_2

description: Total RNA-Seq S018 Trabectedin - Replicate 2


title: 8035073276-N, Circadian control (Pre), GEX, bio rep 2


title: 8035073276-N, Circadian control (Pre), GEX, bio rep 1


title: EREB201_Mo17


title: S018_OL_2

description: Total RNA-Seq S018 Olaparib - Replicate 2

value: OL


title: S018_OL_1

description: Total RNA-Seq S018 Olaparib - Replicate 1


title: EREB183_Mo17


title: EREB145_Mo17


title: EREB149_Mo17


title: S018_NT_2

description: Total RNA-Seq S018 Untreated - Replicate 2

value: Untreated


title: EREB49_Mo17


title: S018_NT_1

description: Total RNA-Seq S018 Untreated - Replicate 1


title: EREB29_Mo17


title: EREB126_Mo17


title: DOF1_Mo17


title: 8035073605-N, Circadian control (Post), GEX, bio rep 1


title: S018_CB_2

description: Total RNA-Seq S018 Olaparib+Trabectedin - Replicate 2

value: CB


title: HT-1080_TR_1

description: Total RNA-Seq HT-1080 Trabectedin - Replicate 1


title: HT-1080_TR_2

description: Total RNA-Seq HT-1080 Trabectedin - Replicate 2


title: CCHH2_Mo17

value: seedling leaf


title: HT-1080_OL_2

description: Total RNA-Seq HT-1080 Olaparib - Replicate 2


title: CA2P13_CA3P1_CA5P7_Mo17

value: DAP-seq


title: BZR1_Mo17


title: HT-1080_OL_1

description: Total RNA-Seq HT-1080 Olaparib - Replicate 1


title: BZIP99_Mo17


title: HT-1080_NT_1

description: Total RNA-Seq HT-1080 Untreated - Replicate 1


title: HT-1080_CB_2

description: Total RNA-Seq HT-1080 Olaparib+Trabectedin - Replicate 2


title: HT-1080_NT_2

description: Total RNA-Seq HT-1080 Untreated - Replicate 2


title: BZIP94_Mo17


title: BZIP96_Mo17


title: BZIP92_Mo17


title: HT-1080_CB_1

description: Total RNA-Seq HT-1080 Olaparib+Trabectedin - Replicate 1


title: BZIP91_Mo17


title: DMR_OL_2

description: Total RNA-Seq DMR Olaparib - Replicate 2

value: DMR


title: BZIP90_Mo17


title: DMR_TR_2

description: Total RNA-Seq DMR Trabectedin - Replicate 2


title: DMR_TR_1

description: Total RNA-Seq DMR Trabectedin - Replicate 1


title: BZIP86_rep2_Mo17


title: BZIP87_Mo17


title: S018_CB_1

description: Total RNA-Seq S018 Olaparib+Trabectedin - Replicate 1


title: CA2P13_CA3P4_CA5P7_Mo17


title: BZIP79_Mo17


title: BZIP86_rep1_Mo17


title: DMR_OL_1

description: Total RNA-Seq DMR Olaparib - Replicate 1


title: DMR_NT_1

description: Total RNA-Seq DMR Untreated - Replicate 1


title: DMR_NT_2

description: Total RNA-Seq DMR Untreated - Replicate 2


title: BZIP68_Mo17


title: DMR_CB_1

description: Total RNA-Seq DMR Olaparib+Trabectedin - Replicate 1


title: DMR_CB_2

description: Total RNA-Seq DMR Olaparib+Trabectedin - Replicate 2


title: BZIP70_Mo17


title: BZIP72_Mo17


title: BZIP62_Mo17


title: BZIP61_Mo17


title: QGP1_3_Tg 24h

city: Indianapolis

first: Michael

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

data_processing:
Quality control: The sequencing reads were first quality checked using FastQC (v.0.11.5) for quality control.
Read mapping: The sequence data were then mapped to either the mouse reference genome mm10, the human reference genome hg38, or the rat reference genome rn6 using the RNA-seq aligner STAR (v.2.710a) with the following parameter: “--outSAMmapqUnique 60”. To evaluate the quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bam-stats (from NGSUtilsJ v.0.4.17).
Feature counting: Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs Q 10”.  Transcripts per million (TPM) were calculated using length values determined by using the “makeTxDbFromGFF” and “exonsBy” functions in the “GenomicFeatures” library and the “reduce” function in the “GenomicRanges” library in R to find the length of the union of non-overlapping exons for each gene.
Assembly: mm10, hg38, rn6
Supplementary files format and content: One processed data file is an excel file containing multiple sheets including read mapping statistics and raw reads, edgeR results per cell line, and TPMs.

growth_protocol: MIN6 β-cells (RRID: CVCL_0431) were cultured in high glucose DMEM containing 10% fetal bovine serum (FBS), 50 µM β-mercaptoethanol, 4 mM L-glutamine, 1 mM pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse intestinal L cell line GLUTag (RRID: CVCL_J406) was cultured in low glucose DMEM containing 10% FBS, 4 mM L-glutamine, 1 mM pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin. Human somatostatinoma QGP-1 (RRID: CVCL_3143) cells (Iguchi, Hayashi et al. 1990) were cultured in RPMI-1640 with 10% FBS, 1 mM pyruvate, 4 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse ghrelinoma cell line MGN3 (RRID: CVCL_C4PL) (Iwakura, Li et al. 2010) was cultured in high glucose DMEM supplemented with 10% FBS and containing 4 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. Successful culture required pre-coating flasks with diluted Matrigel (1:20) for 1 h at 37°C prior to seeding. The rat thyroid cell line PCCL3 (RRID: CVCL_6712) (Morishita, Kabil et al. 2020) was cultured in Coons F-12 supplemented with 1 mIU/mL thyrotropin, 1 µg/mL insulin, 5 µg/mL apo-transferrin, 1 nM  hydrocortisone, 5% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse pancreatic alpha cell line αTC1 clone 6 (αTC1-6) (RRID: CVCL_B036) was previously described (Hamaguchi and Leiter 1990). αTC1-6 cells were cultured in 15 mM glucose DMEM supplemented with 15 mM HEPES, 0.1 mM non-essential amino acids, 10% FBS, 0.03% BSA, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA extraction was done with the BioRad Aurum RNA miniprep kit with on-column DNAse digestion.
Total RNA samples were first evaluated for their quantity and quality using Agilent Bioanalyzer 2100. All samples had good quality with RIN (RNA Integrity Number) greater than 9. 100 nanograms of total RNA was used for library preparation with the KAPA mRNA Hyperprep Kit (KK8581) on Biomek following the manufacturer’s protocol. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity. The pooled libraries were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

treatment_protocol: GLUTag, QGP-1, PCCL3, aTC1, MGN3, PTH-C1 and MIN6 cells were plated in 6-well dishes and exposed to DMSO 0.1% or thapsigargin 100 nM (GLUTag, QGP1, MGN3 and MIN6) or 500 nM (PCCL3 and αTC1-6) for 6 and 24 hours before harvesting for RNA purification, downstream gene expression analysis and RNA sequence transcriptome. For drug treatments, all cells were treated with DMSO (0.1%) for 24 h or thapsigargin (100 nM for MIN6, MGN3, QGP1, GLUTag, PTH-C1; 500 nM for αTC1-6 and PCCL3) for 6 and 24 hours and RNA was collected for each time point at the end of the time course.

value: delta cell

tag: time point

value: thapsigargin, 100nM


title: QGP1_2_Tg 24h


title: QGP1_3_Tg 6h


title: BZIP54_Mo17


title: BZIP52_Mo17


title: EREB138_Mo17


title: QGP1_1_Tg 24h


title: QGP1_1_Tg 6h


title: QGP1_2_ DMSO


title: BZIP48_Mo17


title: BZIP39_Mo17


title: QGP1_1_ DMSO


title: BZIP34_Mo17


title: BZIP27_Mo17


title: Y_C_1_MUM2B cells, YM201636+Cisplatin, 72hours

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d).
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Homo sapiens.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Mus musculus.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies), then the concentration, quality and integrity of RNA were determined by NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: uveal melanoma cells

value: WT

value: YM201636+Cisplatin, 72hours


title: Y_C_2_MUM2B cells, YM201636+Cisplatin, 72hours


title: BZIP25_Mo17


title: BZIP2_Mo17


title: Y_C_3_MUM2B cells, YM201636+Cisplatin, 72hours


title: QGP1_3_ DMSO


title: BZIP21_Mo17


title: Cis_2_MUM2B cells, Cisplatin, 72hours


title: BZIP160_Mo17


title: Cis_1_MUM2B cells, Cisplatin, 72hours


title: Cis_3_MUM2B cells, Cisplatin, 72hours


title: BZIP58_Mo17


title: Y_2_MUM2B cells, YM201636, 72hours


title: BZIP13_Mo17


title: QGP1_2_Tg 6h


title: Y_1_MUM2B cells, YM201636, 72hours


title: BZIP12_Mo17


title: BZIP41_Mo17


title: Y_3_MUM2B cells, YM201636, 72hours


title: BZIP128_Mo17


title: S0_2_MUM2B cells, DMSO, 72hours

value: DMSO, 72hours


title: S0_1_MUM2B cells, DMSO, 72hours


title: HeLa_siRNA2, bsseq

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
meRanTK were used to determine the methylation level for all the sequenced cytosine sites
Assembly: GRCh38
Supplementary files format and content: txt files for each sample were generated by meRanTK
Library strategy: RNA-BS-Seq

source_name: HeLa

growth_protocol: HeLA cell lines were cultured at 37 °C in medium

extract_protocol:
Total mRNA of HeLa cells was extracted by the Ribo-Zero rRNA depletion kit. Then 1 μg of the mRNA were used for bisulfite treatment by EZ Methylation Kit (Zymo) following the protocols provided by the manufacturer.
After bisulfite conversion, the purified RNA was used for library construction by NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

treatment_protocol: HeLa cell lines treated with siRNA against DNMT1 by Lipofectamine RNAiMAX according to the manufacturer's instructions. Cells were harvested for subsequent analysis 3 days after transfection.

value: HeLa

value: Dnmt1 siRNA treatment

value: Dnmt1 mutation


title: BZIP124_Mo17


title: BZIP23_Mo17


title: BZIP111_Mo17


title: BZIP112_Mo17


title: HeLa_ctrl2, bsseq

value: Control


title: HeLa_ctrl1, bsseq


title: BZIP105_Mo17


title: BZIP106_Mo17


title: hom  α-Amanitin treatment 4h

description: Cells in culture were treated with 15 μg/ml of the RNA Pol II and Pol III inhibitor α-Amanitin (Santa Cruz) or equal volume of PBS (vehicle) for 0 h and 4 h. Then the cells were collected after washing with PBS twice and processed for RNAseq library construction.

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (mm10) using Hisat2
the number of reads uniquely mapped to each gene was determined using featurecount
Genome_build: mm10
Supplementary_files_format_and_content: reads count per gene

source_name: fibroblast

growth_protocol: Fibroblast cell lines were isolated from the tails of WT, Het and Hom mice littermates of the same gender and cultured at 37 °C in fibroblast medium: DMEM medium containing 10% FBS, 1X NEAA and 1% (v/v) penicillin-streptomycin as described (Ilsley et al., 2018). Cell lines were validated by DNA sequencing and routinely tested for mycoplasma (Universal Mycoplasma Detection Kit, ATCC).

extract_protocol:
Cells in culture were treated with 15 μg/ml of the RNA Pol II and Pol III inhibitor α-Amanitin (Santa Cruz) or equal volume of PBS (vehicle) for 0 h and 4 h. Then the cells were collected after washing with PBS twice and processed for RNA extraction
mRNA were used for library construction by using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

tag: agent

value: alpha-Amanitin

value: hom


title: BHLH85_Mo17


title: BHLH91_Mo17


title: BHLH17_Mo17


title: BHLH168_Mo17


title: wt  α-Amanitin treatment 4h

value: wt


title: hom  α-Amanitin treatment 0h


title: het  α-Amanitin treatment 0h

value: het


title: BAFL12_Mo17

value: seedling leaf


title: het  α-Amanitin treatment 4h


title: BAFL3_Mo17

value: DAP-seq


title: wt  α-Amanitin treatment 0h


title: BAF1_Mo17


title: S0_3_MUM2B cells, DMSO, 72hours

value: cell line

tag: cell line


title: BHLH67_BA1_Mo17

tag: genotype


title: BZIP115_Mo17


title: HK-2, 240 ug/ml DHA, rep3

city: Reykjavík

first: Þórarinn

last: Guðjónsson

address: Læknagarður -  Lg-416

country: Iceland

institute: University of Iceland

description: Library name: HRH88_240DHA3A

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke developed by BGI.
Raw reads were filtered to remove: (1) reads containing ≥25% adapter sequence (≤2 mismatches allowed), (2) reads <150 bp in length, (3) reads with ≥0.1% N bases, (4) reads with polyX stretches >50 bp, and (5) reads with ≥40% of bases having quality scores <20. Clean reads were retained using Phred+33 quality encoding
Assembly: GRCh38.p14
Supplementary files format and content: no processed data files

growth_protocol: HK-2 cells were cultured in minimal essential medium containing 10% FBS, 5mM sodium pyruvate and 1% penicillin/streptomycin at 37°C with 5% CO2

extract_protocol:
Samples were preserved in TRI Reagent and shipped on dry ice to BGI for RNA extraction. Total RNA was extracted at BGI following the manufacturer’s protocol for TRI Reagent
Total RNA was extracted and mRNA was enriched using oligo(dT) beads. The mRNA was fragmented and used for first strand cDNA synthesis with random primers. Second strand synthesis was performed using dUTP. After end repair and 3' adenylation, sequencing adapters were ligated. Libraries were PCR-amplified, quality-checked, and circularized. DNA nanoballs (DNBs) were generated and sequenced on the DNBSEQ platform (e.g., G400) using paired-end 150 bp reads.

treatment_protocol: Cells were subjected to 72 hour treatment with 60, 120 or 240 ug/ml DHA in media. Controls got just media.

value: proximal tubule epithelial cell

value: 240 ug/ml DHA


title: HK-2, 240 ug/ml DHA, rep1

description: Library name: HRH88_240DHA1A


title: HeLa_siRNA1, bsseq


title: ARF7_Mo17


title: HK-2, 120 ug/ml DHA, rep3

description: Library name: HRH88_120DHA3A

value: 120 ug/ml DHA


title: HK-2, 120 ug/ml DHA, rep2

description: Library name: HRH88_120DHA2A


title: ARF4_Mo17


title: ARF39_Mo17


title: ARR5_Mo17


title: HK-2, 60 ug/ml DHA, rep3

description: Library name: HRH88_60DHA3A

value: 60 ug/ml DHA


title: HK-2, 120 ug/ml DHA, rep1

description: Library name: HRH88_120DHA1A


title: ARF36_Mo17


title: ARF34_Mo17


title: HK-2, 60 ug/ml DHA, rep2

description: Library name: HRH88_60DHA2A


title: ARF29_Mo17


title: HK-2, 60 ug/ml DHA, rep1

description: Library name: HRH88_60DHA1A


title: ARF18_Mo17


title: HK-2, CTRL, rep3

description: Library name: HRH88_CTRL3A

value: no treatment


title: ARF16_Mo17


title: HK-2, CTRL, rep2

description: Library name: HRH88_CTRL2A


title: HK-2, 240 ug/ml DHA, rep2

description: Library name: HRH88_240DHA2A


title: ABI8_Mo17


title: ARF13_Mo17


title: ABI34_Mo17


title: HK-2, CTRL, rep1

description: Library name: HRH88_CTRL1A


title: ABI19_Mo17


title: Liver-lung, PAOI stimulation, 24 h, Rep2

city: Homburg

first: Christian

last: Herr

address: Kirrberger-Str. 100

department: Internal Medicine V

institute: Saarland University

description: Library name: LiLu_24_P2

data_processing:
STAR 7.2.3a
featureCounts 2.0.1
DESeq2
pheatmaps 1.0.12
Assembly: GRCH38
Supplementary files format and content: feature coounts

source_name: Huh-7 cell line

growth_protocol: submersed under flow

extract_protocol:
column-based extraction
STAR 7.2.3a

treatment_protocol: stimulation with heat inactivated bacteria

value: Huh-7 cell line

value: hepatocyte

value: PAOI-Stimulation


title: MADS69_B73

first: Andrea

last: Gallavotti

address: 190 Frelinghuysen Rd

institute: Rutgers University


title: Liver-lung, NTHi stimulation, 24 h, Rep3

description: Library name: LiLu_24_N3

value: NTHi-Stimulation


title: Liver-lung, PAOI stimulation, 24 h, Rep1

description: Library name: LiLu_24_P1


title: ZIM2_B73


title: Liver-lung, NTHi stimulation, 24 h, Rep2

description: Library name: LiLu_24_N2


title: Liver-Lung, control, 24 h, Rep3

description: Library name: LiLu_24_3

value: control


title: ZHD21_B73


title: Liver-Lung, control, 24 h, Rep2

description: Library name: LiLu_24_2


title: ZHD4_B73


title: ZHD5_B73


title: Liver-lung, NTHi stimulation, 24 h, Rep1

description: Library name: LiLu_24_N1


title: ZHD1_B73


title: ZHD15_B73


title: Liver-Lung, control, 24 h, Rep1

description: Library name: LiLu_24_1


title: Mtb treated with PA824, Rep 2

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

description: Library name: Mtb_PA824_Rep_2

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5).
The sequencing reads were analyzed using the commercially licensed CLC Genomics Suite
Assembly: M. tuberculosis CDC1551 genome (NCBI accession AE000516), M. abscessus  ATCC 19977 (GCA_000069185.1)
Supplementary files format and content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates
Supplementary files format and content: Dataset 1_Mab_HC2210 vs DMSO.xlsx
Supplementary files format and content: Dataset 2_Mtb_HC2210 vs DMSO and PA824 vs DMSO.xlsx

organism: Mycobacterium tuberculosis CDC1551

source_name: Bacterial Cell

growth_protocol: Mab cultures were cultured for 24 hours in T25 standing flasks in a 37C incubator (without 5% CO2). Mtb cultures were incubated in T25 standing flasks at 37C, 5% CO2 for 24 hours.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: For Mab, cultures were treated with 10 uM HC2210 or an equivalent volume of DMSO for 24 hours. For Mtb, cultures were treated with 2 uM HC2210 or PA824 or equivalent volume of DMSO for 24 hours.

value: Bacterial Cell


title: WRKY57_B73

city: Piscataway


title: WRKY53_B73


title: Mtb treated with HC2210, Rep 2

description: Library name: Mtb_HC2210_Rep_2


title: Mtb treated with PA824, Rep 1

description: Library name: Mtb_PA824_Rep_1


title: Mtb treated with HC2210, Rep 1

description: Library name: Mtb_HC2210_Rep_1


title: Liver-lung, PAOI stimulation, 24 h, Rep3

description: Library name: LiLu_24_P3


title: WRKY125_B73


title: Mtb treated with DMSO, Rep 2

description: Library name: Mtb_DMSO_Rep2


title: Mtb treated with DMSO, Rep 1

description: Library name: Mtb_DMSO_Rep_1


title: THX20_B73


title: THX26_B73


title: THX16_B73


title: WGS_2642_rep1

city: Bloomington

first: Xindan

last: Wang

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: Library name: WGS_2642_rep1

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Agrobacterium tumefaciens

source_name: Agrobacterium tumefaciens

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: Agrobacterium tumefaciens

value: bacterial

value: wild type

value: Cells grown in ATGN medium at 30°C


title: WGS_2407_rep1

description: Library name: WGS_2407_rep1


title: TCP30_B73

value: seedling leaf

value: DAP-seq


title: SBP32_B73


title: WGS_47-2_rep1

description: Library name: WGS_47-2_rep1


title: SBP1_B73


title: HiC_2642_rep1

description: Library name: HiC_2642_rep1


title: HiC_2407_rep1

description: Library name: HiC_2407_rep1


title: SBP30_rep2_B73


title: HiC_47-2_rep1

description: Library name: HiC_47-2_rep1


title: NFYA1_LEC1_CA5P16_B73


title: SBP30_rep1_B73


title: MYB50_B73